Repository: mwouts/jupytext (language: python)

Issue:
1.11.4: pytest is failing when `pytest-randomly` plugin is used
I'm trying to package your module as rpm packag. So I'm using typical in such case build, install and test cycle used on building package from non-root account:
- "setup.py build"
- "setup.py install --root </install/prefix>"
- "pytest with PYTHONPATH pointing to sitearch and sitelib inside </install/prefix>

May I ask for help because few units are failing:
```console
+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.11.4-3.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.11.4-3.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.11, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
Using --randomly-seed=3239909864
rootdir: /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4
plugins: forked-1.3.0, shutil-1.7.0, virtualenv-1.7.0, expect-1.1.0, flake8-1.0.7, timeout-1.4.2, betamax-0.8.1, freezegun-0.4.2, aspectlib-1.5.2, toolbox-0.5, rerunfailures-9.1.1, requests-mock-1.9.3, cov-2.12.1, pyfakefs-4.5.0, flaky-3.7.0, benchmark-3.4.1, xdist-2.3.0, pylama-7.7.1, datadir-1.3.1, regressions-2.2.0, cases-3.6.3, xprocess-0.18.1, black-0.3.12, checkdocs-2.7.1, anyio-3.3.0, Faker-8.11.0, asyncio-0.15.1, trio-0.7.0, httpbin-1.0.0, subtests-0.5.0, isort-2.0.0, hypothesis-6.14.6, mock-3.6.1, profiling-1.7.0, randomly-3.8.0
collected 2585 items

tests/test_knitr_spin.py .                                                                                                                                           [  0%]
tests/test_read_simple_matlab.py ..                                                                                                                                  [  0%]
tests/test_read_simple_rmd.py .........                                                                                                                              [  0%]
tests/test_rmd_to_ipynb.py ......                                                                                                                                    [  0%]
tests/test_changelog.py ...                                                                                                                                          [  0%]
tests/test_pre_commit_scripts.py ....s...                                                                                                                            [  1%]
tests/test_read_dotnet_try_markdown.py ...                                                                                                                           [  1%]
tests/test_read_simple_R.py ............                                                                                                                             [  1%]
tests/test_read_simple_sphinx.py ...                                                                                                                                 [  1%]
tests/test_read_write_functions.py .....                                                                                                                             [  2%]
tests/test_ipynb_to_myst.py .s........s.                                                                                                                             [  2%]
tests/test_save_multiple.py .....................................................                                                                                    [  4%]
tests/test_metadata_filter.py .................                                                                                                                      [  5%]
tests/test_read_simple_ipynb.py .                                                                                                                                    [  5%]
tests/test_ipynb_to_py.py ....................                                                                                                                       [  6%]
tests/test_read_simple_markdown.py ....................................                                                                                              [  7%]
tests/test_read_simple_java.py .                                                                                                                                     [  7%]
tests/test_config.py .................                                                                                                                               [  8%]
tests/test_preserve_empty_cells.py .......                                                                                                                           [  8%]
tests/test_doxygen.py ..........                                                                                                                                     [  8%]
tests/test_pre_commit_4_sync_execute.py s                                                                                                                            [  8%]
tests/test_isort.py .                                                                                                                                                [  8%]
tests/test_markdown_in_code_cells.py ....                                                                                                                            [  8%]
tests/test_read_simple_groovy.py .                                                                                                                                   [  9%]
tests/test_cell_id.py .                                                                                                                                              [  9%]
tests/test_formats.py ................s........                                                                                                                      [ 10%]
tests/test_unicode.py ...............................                                                                                                                [ 11%]
tests/test_write_does_not_modify_notebook.py ..............................................................................................................          [ 15%]
tests/test_cells.py ...............                                                                                                                                  [ 16%]
tests/test_read_simple_clojure.py .                                                                                                                                  [ 16%]
tests/test_header.py ..........                                                                                                                                      [ 16%]
tests/test_nbformat_version.py .......                                                                                                                               [ 16%]
tests/test_jupytext_errors.py ..                                                                                                                                     [ 16%]
tests/test_pre_commit_0_ipynb_to_py.py s                                                                                                                             [ 16%]
tests/test_mirror.py ........s.......s.........ss...s.....................s..........s.....................................s............s.........s........s........ [ 22%]
................s................ss......s.......s............s.........s.............s.......s.............................................s....................... [ 28%]
.............s..s......s..s......s...............s....s...............................s..............s..                                                             [ 32%]
tests/test_execute.py ....s...                                                                                                                                       [ 33%]
tests/test_read_simple_percent.py ......................                                                                                                             [ 33%]
tests/test_jupytext_read.py ..                                                                                                                                       [ 34%]
tests/test_read_folding_markers.py .....                                                                                                                             [ 34%]
tests/test_read_simple_nomarker.py ..                                                                                                                                [ 34%]
tests/test_pre_commit_mode.py ............                                                                                                                           [ 34%]
tests/test_pre_commit_5_reformat_markdown.py s                                                                                                                       [ 34%]
tests/test_read_simple_julia.py .                                                                                                                                    [ 34%]
tests/test_using_cli.py .                                                                                                                                            [ 34%]
tests/test_cell_metadata.py ..........................F.............FF.F....F..F..F..F..                                                                             [ 37%]
tests/test_pep8.py ...................................................................................................................                               [ 41%]
tests/test_ipynb_to_R.py ....                                                                                                                                        [ 41%]
tests/test_read_simple_rust.py ...                                                                                                                                   [ 41%]
tests/test_read_simple_csharp.py .......                                                                                                                             [ 42%]
tests/test_read_all_py.py ..........................................................................................................                                 [ 46%]
tests/test_load_multiple.py ..                                                                                                                                       [ 46%]
tests/test_paired_paths.py ......................                                                                                                                    [ 47%]
tests/test_hide_remove_input_outputs_rmarkdown.py ........                                                                                                           [ 47%]
tests/test_read_simple_pandoc.py sssss                                                                                                                               [ 47%]
tests/test_active_cells.py .....................                                                                                                                     [ 48%]
. .                                                                                                                                                                  [ 48%]
tests/test_active_cells.py .......                                                                                                                                   [ 48%]
tests/test_auto_ext.py .....................................x........................s........................                                                       [ 52%]
tests/test_escape_magics.py ................................................................................                                                         [ 55%]
tests/test_stringparser.py ....                                                                                                                                      [ 55%]
tests/test_read_simple_scheme.py .                                                                                                                                   [ 55%]
tests/test_pytest.py ..                                                                                                                                              [ 55%]
tests/test_ipynb_to_rmd.py ........................                                                                                                                  [ 56%]
tests/test_custom_cell_magics.py .                                                                                                                                   [ 56%]
tests/test_cli_config.py ...........                                                                                                                                 [ 56%]
tests/test_black.py ....s........                                                                                                                                    [ 57%]
tests/test_jupytext_nbconvert_round_trip.py .......................                                                                                                  [ 58%]
tests/test_metadata_filters_from_config.py .                                                                                                                         [ 58%]
tests/test_compare.py .....................                                                                                                                          [ 59%]
tests/test_read_incomplete_rmd.py ...                                                                                                                                [ 59%]
tests/test_cm_config.py ............                                                                                                                                 [ 59%]
tests/test_contentsmanager.py .s..s.............................................................s......s......s..................................................... [ 65%]
.....................................s....................................s............s...................s.......s..s...s.....................................s... [ 71%]
..........................................................s....ss...s.......................s................................................s.............s........ [ 77%]
....                                                                                                                                                                 [ 77%]
tests/test_pre_commit_2_sync_nbstripout.py s                                                                                                                         [ 77%]
tests/test_pre_commit_3_sync_black_nbstripout.py s                                                                                                                   [ 77%]
tests/test_trust_notebook.py ................................................                                                                                        [ 79%]
tests/test_read_simple_hydrogen.py .......                                                                                                                           [ 80%]
tests/test_combine.py ..................................................                                                                                             [ 81%]
tests/test_cli.py ...............s.s.....................s......................................s..........s......................s.......s............s............ [ 87%]
...ss........s................s...................................s.s.........s....s.......s.s........................s.....................s...................s... [ 93%]
........s.........s.................s.......s....................................................s........                                                           [ 98%]
tests/test_read_simple_python.py ................................................                                                                                    [ 99%]
tests/test_pre_commit_1_sync.py s                                                                                                                                    [100%]

================================================================================= FAILURES =================================================================================
____________________________________________________ test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4] ____________________________________________________

options = 'r plot_1, echo=TRUE', language_and_metadata = ('R', {'echo': True})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'echo': True, 'name': 'plot_1'}), expected = ('R', {'echo': True}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,7 @@
E            [
E             "R",
E             {
E           -  "echo": true
E           +  "echo": true,
E           +  "name": "plot_1"
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
_________________________________________ test_parse_rmd_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] _________________________________________

options = 'r chunk_name, include=FALSE, active="Rmd"', language_and_metadata = ('R', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'active': 'Rmd', 'name': 'chunk_name', 'tags': ['remove_cell']}), expected = ('R', {'active': 'Rmd'}), actual_name = 'actual', expected_name = 'expected'
return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,10 @@
E            [
E             "R",
E             {
E           -  "active": "Rmd"
E           +  "active": "Rmd",
E           +  "name": "chunk_name",
E           +  "tags": [
E           +   "remove_cell"
E           +  ]
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
_________________________________________________________ test_build_options[r echo=FALSE-language_and_metadata3] __________________________________________________________

options = 'r echo=FALSE', language_and_metadata = ('R', {})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r', expected = 'r echo=FALSE', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r echo=FALSE
E           +r

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
______________________________________________ test_build_options[python include=FALSE, active="Rmd"-language_and_metadata8] _______________________________________________

options = 'python include=FALSE, active="Rmd"', language_and_metadata = ('python', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'python active="Rmd"', expected = 'python include=FALSE, active="Rmd"', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -python include=FALSE, active="Rmd"
E           +python active="Rmd"

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
_________________________________ test_build_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] __________________________________

options = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', language_and_metadata = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'python tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', expected = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', actual_name = 'actual'
expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}
E           +python tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
______________________________________________________ test_build_options[r plot_1, echo=TRUE-language_and_metadata4] ______________________________________________________

options = 'r plot_1, echo=TRUE', language_and_metadata = ('R', {'echo': True})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r echo=TRUE', expected = 'r plot_1, echo=TRUE', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r plot_1, echo=TRUE
E           +r echo=TRUE

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
__________________________________________ test_parse_rmd_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] ___________________________________________

options = 'r plot_1, dpi=72, fig.path="fig_path/"', language_and_metadata = ('R', {'dpi': 72, 'fig.path': 'fig_path/'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'dpi': 72, 'fig.path': 'fig_path/', 'name': 'plot_1'}), expected = ('R', {'dpi': 72, 'fig.path': 'fig_path/'}), actual_name = 'actual'
expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -2,6 +2,7 @@
E             "R",
E             {
E              "dpi": 72,
E           -  "fig.path": "fig_path/"
E           +  "fig.path": "fig_path/",
E           +  "name": "plot_1"
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
_______________________________________________________ test_parse_rmd_options[r echo=FALSE-language_and_metadata3] ________________________________________________________

options = 'r echo=FALSE', language_and_metadata = ('R', {})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'tags': ['remove_input']}), expected = ('R', {}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,4 +1,8 @@
E            [
E             "R",
E           - {}
E           + {
E           +  "tags": [
E           +   "remove_input"
E           +  ]
E           + }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/compare.py:47: AssertionError
============================================================================= warnings summary =============================================================================
jupytext/cell_reader.py:20
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.9.0 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
    warnings.warn(

tests/test_pre_commit_scripts.py::test_manual_call_of_pre_commit_hook
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/jupytext/cli.py:332: DeprecationWarning: The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)
    warnings.warn(

tests/test_execute.py::test_execute_sync
  /usr/lib/python3.8/site-packages/nbconvert/exporters/html.py:110: DeprecationWarning: 'contextfilter' is renamed to 'pass_context', the old name will be removed in Jinja 3.1.
    def markdown2html(self, context, source):

tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
  /usr/lib/python3.8/site-packages/traitlets/config/configurable.py:82: DeprecationWarning: Passing unrecognized arguments to super(JupytextConfiguration).__init__(not_a_jupytext_option=True).
  object.__init__() takes exactly one argument (the instance to initialize)
  This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.
    super(Configurable, self).__init__(**kwargs)

tests/test_contentsmanager.py: 48 warnings
  /usr/lib/python3.8/site-packages/send2trash/plat_gio.py:18: PyGIDeprecationWarning: GObject.GError is deprecated; use GLib.GError instead
    except GObject.GError as e:

tests/test_cli.py::test_cli_expect_errors
  [warning] The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)

tests/test_cli.py::test_format_prefix_suffix
  [warning] You have passed a file name to the '--to' option, when a format description was expected. Maybe you want to use the '-o' option instead?

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] tests/test_pre_commit_scripts.py:335: pandoc>=2.11 is not available
SKIPPED [1] tests/test_ipynb_to_myst.py:171: myst is available
SKIPPED [1] tests/test_ipynb_to_myst.py:162: myst is available
SKIPPED [1] tests/test_pre_commit_4_sync_execute.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_formats.py:324: pandoc>=2.11 is not available
SKIPPED [1] tests/test_pre_commit_0_ipynb_to_py.py:16: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_mirror.py:208: sphinx_gallery is not available
SKIPPED [11] tests/test_mirror.py:151: sphinx_gallery is not available
SKIPPED [17] tests/test_mirror.py:131: pandoc>=2.11 is not available
SKIPPED [1] tests/test_mirror.py:202: sphinx_gallery is not available
SKIPPED [1] tests/test_execute.py:150: irkernel is not installed
SKIPPED [1] tests/test_pre_commit_5_reformat_markdown.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_read_simple_pandoc.py:35: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:13: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:82: Pandoc is installed
SKIPPED [1] tests/test_read_simple_pandoc.py:64: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:50: pandoc>=2.11 is not available
SKIPPED [1] tests/test_auto_ext.py:36: No file_extension in language_info
SKIPPED [1] tests/test_black.py:68: autopep8 not found
SKIPPED [17] tests/test_contentsmanager.py:180: pandoc>=2.11 is not available
SKIPPED [1] tests/test_contentsmanager.py:1188: sphinx_gallery is not available
SKIPPED [2] tests/test_contentsmanager.py:1765: jupyterfs is not available
SKIPPED [1] tests/test_pre_commit_2_sync_nbstripout.py:14: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_3_sync_black_nbstripout.py:13: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_cli.py:1075: pandoc>=2.11 is not available
SKIPPED [15] tests/test_cli.py:557: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:795: sphinx_gallery is not available
SKIPPED [3] tests/test_cli.py:991: pandoc>=2.11 is not available
SKIPPED [5] tests/test_cli.py:1005: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1188: Please run 'python -m ipykernel install --name python_kernel --user'
SKIPPED [1] tests/test_pre_commit_1_sync.py:17: Jupytext folder is not a git repository #814
XFAIL tests/test_auto_ext.py::test_auto_from_kernelspecs_works[/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.4/tests/notebooks/ipynb_sage/sage_print_hello.ipynb]
  reason: Sage notebooks have Python in their language_info metadata, see #727
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r echo=FALSE-language_and_metadata3] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[python include=FALSE, active="Rmd"-language_and_metadata8] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r plot_1, echo=TRUE-language_and_metadata4] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r echo=FALSE-language_and_metadata3] - AssertionError:
============================================== 8 failed, 2480 passed, 94 skipped, 1 xfailed, 57 warnings in 160.49s (0:02:40) ==============================================
pytest-xprocess reminder::Be sure to terminate the started process by running 'pytest --xkill' if you have not explicitly done so in your fixture with 'xprocess.getinfo(<process_name>).terminate()'.
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c/test_safe_get_no_perms0
<class 'OSError'>: [Errno 39] Directory not empty: 'test_safe_get_no_perms0'
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c/test_safe_delete_no_perms0
<class 'OSError'>: [Errno 39] Directory not empty: 'test_safe_delete_no_perms0'
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c/test_safe_set_no_perms0
<class 'OSError'>: [Errno 39] Directory not empty: 'test_safe_set_no_perms0'
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c/test_rmtree_errorhandler_rerai0
<class 'OSError'>: [Errno 39] Directory not empty: 'test_rmtree_errorhandler_rerai0'
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c/test_rmtree_errorhandler_reado0
<class 'OSError'>: [Errno 39] Directory not empty: 'test_rmtree_errorhandler_reado0'
[warning] (rm_rf) error removing /tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c
<class 'OSError'>: [Errno 39] Directory not empty: '/tmp/pytest-of-tkloczko/garbage-cacdfa54-1a74-4a90-aec3-6475cd47892c'
```



Discussion / hints:
Hi @kloczek , thank you for reporting this.

I must say that at the moment I am puzzled by your observation. The tests seem to be run with completely unadequate parameters! Take for instance this one:
```
____________________________________________________ test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4] ____________________________________________________

options = 'r plot_1, echo=TRUE', language_and_metadata = ('R', {'echo': True})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)
```
I would expect that `options, language_and_metadata` should match 
https://github.com/mwouts/jupytext/blob/4692a828072d5b287a99c48b6dc501abfdd557c1/tests/test_cell_metadata.py#L28
but this is clearly not the case.

May I ask which version of `pytest` you are using? Do you think I could reproduce this on a standard Ubuntu machine? Thanks
Above output was with pytest 6.2.4.
Just tested 1.11.5 with latest pytest 6.2.6
```console
+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.11.5-2.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.11.5-2.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.11, pytest-6.2.5, py-1.10.0, pluggy-0.13.1
benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
Using --randomly-seed=1120978200
rootdir: /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5
plugins: forked-1.3.0, shutil-1.7.0, virtualenv-1.7.0, expect-1.1.0, flake8-1.0.7, timeout-1.4.2, betamax-0.8.1, freezegun-0.4.2, aspectlib-1.5.2, toolbox-0.5, rerunfailures-9.1.1, requests-mock-1.9.3, cov-2.12.1, flaky-3.7.0, benchmark-3.4.1, xdist-2.3.0, pylama-7.7.1, datadir-1.3.1, regressions-2.2.0, cases-3.6.3, xprocess-0.18.1, black-0.3.12, anyio-3.3.0, asyncio-0.15.1, trio-0.7.0, subtests-0.5.0, isort-2.0.0, hypothesis-6.14.6, mock-3.6.1, profiling-1.7.0, randomly-3.8.0, Faker-8.12.1, nose2pytest-1.0.8, pyfakefs-4.5.1, tornado-0.8.1
collected 2582 items

tests/test_header.py ..........                                                                                                                                      [  0%]
tests/test_pre_commit_2_sync_nbstripout.py s                                                                                                                         [  0%]
tests/test_read_simple_matlab.py ..                                                                                                                                  [  0%]
tests/test_black.py ...........s.                                                                                                                                    [  1%]
tests/test_escape_magics.py ................................................................................                                                         [  4%]
tests/test_execute.py ....s...                                                                                                                                       [  4%]
tests/test_using_cli.py .                                                                                                                                            [  4%]
tests/test_pre_commit_mode.py ............                                                                                                                           [  4%]
tests/test_cell_id.py .                                                                                                                                              [  4%]
tests/test_cm_config.py ............                                                                                                                                 [  5%]
tests/test_preserve_empty_cells.py .......                                                                                                                           [  5%]
tests/test_read_simple_groovy.py .                                                                                                                                   [  5%]
tests/test_read_simple_rmd.py .........                                                                                                                              [  6%]
tests/test_ipynb_to_py.py ....................                                                                                                                       [  6%]
tests/test_save_multiple.py .....................................................                                                                                    [  8%]
tests/test_metadata_filter.py .................                                                                                                                      [  9%]
tests/test_jupytext_errors.py ..                                                                                                                                     [  9%]
tests/test_ipynb_to_R.py ....                                                                                                                                        [  9%]
tests/test_read_simple_sphinx.py ...                                                                                                                                 [  9%]
tests/test_read_simple_ipynb.py .                                                                                                                                    [  9%]
tests/test_cell_metadata.py ........................F...........F.F..F...F.....F...FF...                                                                             [ 12%]
tests/test_metadata_filters_from_config.py .                                                                                                                         [ 12%]
tests/test_pep8.py ...................................................................................................................                               [ 16%]
tests/test_stringparser.py ....                                                                                                                                      [ 16%]
tests/test_pytest.py ..                                                                                                                                              [ 17%]
tests/test_read_simple_hydrogen.py .......                                                                                                                           [ 17%]
tests/test_unicode.py ...............................                                                                                                                [ 18%]
tests/test_read_all_py.py ..........................................................................................................                                 [ 22%]
tests/test_read_simple_rust.py ...                                                                                                                                   [ 22%]
tests/test_cli.py ............................s..............................ss................ss.....................s..........ss.....s..s........................ [ 28%]
.....................s.......................s..........s.........s........................s.....s...............s......s....................s.s.................... [ 34%]
.................................s.............................s.......s.........s..............s..s......                                                           [ 38%]
tests/test_compare.py .....................                                                                                                                          [ 39%]
tests/test_paired_paths.py ......................                                                                                                                    [ 40%]
tests/test_formats.py .........s...............                                                                                                                      [ 41%]
tests/test_read_simple_scheme.py .                                                                                                                                   [ 41%]
tests/test_jupytext_read.py ..                                                                                                                                       [ 41%]
tests/test_nbformat_version.py .......                                                                                                                               [ 41%]
tests/test_pre_commit_scripts.py .....s..                                                                                                                            [ 42%]
tests/test_config.py .................                                                                                                                               [ 42%]
tests/test_read_simple_pandoc.py sssss                                                                                                                               [ 42%]
tests/test_load_multiple.py ..                                                                                                                                       [ 43%]
tests/test_pre_commit_4_sync_execute.py s                                                                                                                            [ 43%]
tests/test_read_simple_python.py ................................................                                                                                    [ 44%]
tests/test_read_simple_markdown.py ....................................                                                                                              [ 46%]
tests/test_pre_commit_1_sync.py s                                                                                                                                    [ 46%]
tests/test_pre_commit_3_sync_black_nbstripout.py s                                                                                                                   [ 46%]
tests/test_read_simple_clojure.py .                                                                                                                                  [ 46%]
tests/test_read_simple_R.py ............                                                                                                                             [ 46%]
tests/test_combine.py ..................................................                                                                                             [ 48%]
tests/test_read_incomplete_rmd.py ...                                                                                                                                [ 48%]
tests/test_read_simple_percent.py ......................                                                                                                             [ 49%]
tests/test_ipynb_to_myst.py .....s.....s                                                                                                                             [ 50%]
tests/test_cells.py ...............                                                                                                                                  [ 50%]
tests/test_read_simple_nomarker.py ..                                                                                                                                [ 50%]
tests/test_rmd_to_ipynb.py ......                                                                                                                                    [ 51%]
tests/test_pre_commit_5_reformat_markdown.py s                                                                                                                       [ 51%]
tests/test_read_simple_java.py .                                                                                                                                     [ 51%]
tests/test_custom_cell_magics.py .                                                                                                                                   [ 51%]
tests/test_read_simple_julia.py .                                                                                                                                    [ 51%]
tests/test_markdown_in_code_cells.py ....                                                                                                                            [ 51%]
tests/test_read_simple_csharp.py .......                                                                                                                             [ 51%]
tests/test_doxygen.py ..........                                                                                                                                     [ 52%]
tests/test_mirror.py ..............s.....s...s.....s......s............................................s..............s....s..............s.................s.s..... [ 57%]
.s...................s.....s.......................................s...............ss...s..............s....................s.......................s............... [ 64%]
.........s...........................................s......ss.............s...ss....s...........s......                                                             [ 68%]
tests/test_read_folding_markers.py .....                                                                                                                             [ 68%]
tests/test_read_write_functions.py .....                                                                                                                             [ 68%]
tests/test_pre_commit_0_ipynb_to_py.py s                                                                                                                             [ 68%]
tests/test_knitr_spin.py .                                                                                                                                           [ 68%]
tests/test_read_dotnet_try_markdown.py ...                                                                                                                           [ 68%]
tests/test_ipynb_to_rmd.py ........................                                                                                                                  [ 69%]
tests/test_jupytext_nbconvert_round_trip.py .......................                                                                                                  [ 70%]
tests/test_auto_ext.py ................................................x.....................................s                                                       [ 73%]
tests/test_contentsmanager.py ...................s..............s.......................................................s........s.................................. [ 79%]
.......s...................................................s............................................s........s...s................s............................. [ 85%]
.....................s...s.......................s................s.......................s...........s...s.....................s.....s..............s.............. [ 91%]
....                                                                                                                                                                 [ 91%]
tests/test_write_does_not_modify_notebook.py ..............................................................................................................          [ 96%]
tests/test_trust_notebook.py ................................................                                                                                        [ 98%]
tests/test_isort.py .                                                                                                                                                [ 98%]
tests/test_changelog.py ...                                                                                                                                          [ 98%]
tests/test_active_cells.py ............................                                                                                                              [ 99%]
tests/test_cli_config.py ...........                                                                                                                                 [ 99%]
tests/test_hide_remove_input_outputs_rmarkdown.py ........                                                                                                           [100%]

================================================================================= FAILURES =================================================================================
____________________________________________ test_build_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] _____________________________________________

options = 'r plot_1, dpi=72, fig.path="fig_path/"', language_and_metadata = ('R', {'dpi': 72, 'fig.path': 'fig_path/'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r dpi=72, fig.path="fig_path/"', expected = 'r plot_1, dpi=72, fig.path="fig_path/"', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r plot_1, dpi=72, fig.path="fig_path/"
E           +r dpi=72, fig.path="fig_path/"

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
___________________________________________ test_build_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2] ___________________________________________

options = 'r plot_1, bool=TRUE, fig.path="fig_path/"', language_and_metadata = ('R', {'bool': True, 'fig.path': 'fig_path/'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r bool=TRUE, fig.path="fig_path/"', expected = 'r plot_1, bool=TRUE, fig.path="fig_path/"', actual_name = 'actual', expected_name = 'expected'
return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r plot_1, bool=TRUE, fig.path="fig_path/"
E           +r bool=TRUE, fig.path="fig_path/"

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
_________________________________________ test_parse_rmd_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2] _________________________________________

options = 'r plot_1, bool=TRUE, fig.path="fig_path/"', language_and_metadata = ('R', {'bool': True, 'fig.path': 'fig_path/'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'bool': True, 'fig.path': 'fig_path/', 'name': 'plot_1'}), expected = ('R', {'bool': True, 'fig.path': 'fig_path/'}), actual_name = 'actual'
expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -2,6 +2,7 @@
E             "R",
E             {
E              "bool": true,
E           -  "fig.path": "fig_path/"
E           +  "fig.path": "fig_path/",
E           +  "name": "plot_1"
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
____________________________________________ test_parse_rmd_options[python include=FALSE, active="Rmd"-language_and_metadata8] _____________________________________________

options = 'python include=FALSE, active="Rmd"', language_and_metadata = ('python', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('python', {'active': 'Rmd', 'tags': ['remove_cell']}), expected = ('python', {'active': 'Rmd'}), actual_name = 'actual', expected_name = 'expected'
return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,9 @@
E            [
E             "python",
E             {
E           -  "active": "Rmd"
E           +  "active": "Rmd",
E           +  "tags": [
E           +   "remove_cell"
E           +  ]
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
____________________________________________________ test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4] ____________________________________________________

options = 'r plot_1, echo=TRUE', language_and_metadata = ('R', {'echo': True})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'echo': True, 'name': 'plot_1'}), expected = ('R', {'echo': True}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,7 @@
E            [
E             "R",
E             {
E           -  "echo": true
E           +  "echo": true,
E           +  "name": "plot_1"
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
_________________________________________________________ test_build_options[r echo=FALSE-language_and_metadata3] __________________________________________________________

options = 'r echo=FALSE', language_and_metadata = ('R', {})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r', expected = 'r echo=FALSE', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r echo=FALSE
E           +r

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
_______________________________ test_parse_rmd_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] ________________________________

options = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', language_and_metadata = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'name': 'noname', 'tags': ['a', 'b', 'c']})
expected = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -2,6 +2,7 @@
E             "python",
E             {
E              "echo": "#R_CODE#{sum(a+c(1,2))>1}",
E           +  "name": "noname",
E              "tags": [
E               "a",
E               "b",

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
_________________________________ test_build_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] __________________________________

options = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', language_and_metadata = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'python tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', expected = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', actual_name = 'actual'
expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}
E           +python tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}

/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/compare.py:47: AssertionError
============================================================================= warnings summary =============================================================================
jupytext/cell_reader.py:20
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.9.0 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
    warnings.warn(

tests/test_execute.py::test_execute
  /usr/lib/python3.8/site-packages/nbconvert/exporters/html.py:110: DeprecationWarning: 'contextfilter' is renamed to 'pass_context', the old name will be removed in Jinja 3.1.
    def markdown2html(self, context, source):

tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
  /usr/lib/python3.8/site-packages/traitlets/config/configurable.py:82: DeprecationWarning: Passing unrecognized arguments to super(JupytextConfiguration).__init__(not_a_jupytext_option=True).
  object.__init__() takes exactly one argument (the instance to initialize)
  This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.
    super(Configurable, self).__init__(**kwargs)

tests/test_cli.py::test_cli_expect_errors
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/cli.py:332: DeprecationWarning: The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)
    warnings.warn(

tests/test_cli.py::test_format_prefix_suffix
  [warning] You have passed a file name to the '--to' option, when a format description was expected. Maybe you want to use the '-o' option instead?

tests/test_pre_commit_scripts.py::test_manual_call_of_pre_commit_hook
  [warning] The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)

tests/test_contentsmanager.py: 48 warnings
  [warning] GObject.GError is deprecated; use GLib.GError instead

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] tests/test_pre_commit_2_sync_nbstripout.py:14: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_black.py:68: autopep8 not found
SKIPPED [1] tests/test_execute.py:150: irkernel is not installed
SKIPPED [5] tests/test_cli.py:1005: pandoc>=2.11 is not available
SKIPPED [15] tests/test_cli.py:557: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:795: sphinx_gallery is not available
SKIPPED [1] tests/test_cli.py:1075: pandoc>=2.11 is not available
SKIPPED [3] tests/test_cli.py:991: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1188: Please run 'python -m ipykernel install --name python_kernel --user'
SKIPPED [1] tests/test_formats.py:324: pandoc>=2.11 is not available
SKIPPED [1] tests/test_pre_commit_scripts.py:335: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:50: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:13: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:35: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:64: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:82: Pandoc is installed
SKIPPED [1] tests/test_pre_commit_4_sync_execute.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_1_sync.py:17: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_3_sync_black_nbstripout.py:13: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_ipynb_to_myst.py:171: myst is available
SKIPPED [1] tests/test_ipynb_to_myst.py:162: myst is available
SKIPPED [1] tests/test_pre_commit_5_reformat_markdown.py:15: Jupytext folder is not a git repository #814
SKIPPED [11] tests/test_mirror.py:151: sphinx_gallery is not available
SKIPPED [17] tests/test_mirror.py:131: pandoc>=2.11 is not available
SKIPPED [1] tests/test_mirror.py:202: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:208: sphinx_gallery is not available
SKIPPED [1] tests/test_pre_commit_0_ipynb_to_py.py:16: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_auto_ext.py:36: No file_extension in language_info
SKIPPED [17] tests/test_contentsmanager.py:180: pandoc>=2.11 is not available
SKIPPED [1] tests/test_contentsmanager.py:1188: sphinx_gallery is not available
SKIPPED [2] tests/test_contentsmanager.py:1765: jupyterfs is not available
XFAIL tests/test_auto_ext.py::test_auto_from_kernelspecs_works[/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/notebooks/ipynb_sage/sage_print_hello.ipynb]
  reason: Sage notebooks have Python in their language_info metadata, see #727
FAILED tests/test_cell_metadata.py::test_build_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[python include=FALSE, active="Rmd"-language_and_metadata8] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r echo=FALSE-language_and_metadata3] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] - AssertionError:
============================================== 8 failed, 2479 passed, 94 skipped, 1 xfailed, 57 warnings in 149.35s (0:02:29) ==============================================
pytest-xprocess reminder::Be sure to terminate the started process by running 'pytest --xkill' if you have not explicitly done so in your fixture with 'xprocess.getinfo(<pr
```

Aftter deselecting above failing units I have another set fails.
Because I'm usomg `pytest-randomly` it may be showinmg that there are some dependencies beteeen units and changing to random order produces some random results.
Will try to repeat whole test with disabled randomisation.
```console
+ /usr/bin/pytest -ra --deselect 'tests/test_cell_metadata.py::test_build_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6]' --deselect 'tests/test_cell_metadata.py::test_build_options[r echo=FALSE-language_and_metadata3]' --deselect 'tests/test_cell_metadata.py::test_build_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2]' --deselect 'tests/test_cell_metadata.py::test_build_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1]' --deselect 'tests/test_cell_metadata.py::test_parse_rmd_options[python include=FALSE, active="Rmd"-language_and_metadata8]' --deselect 'tests/test_cell_metadata.py::test_parse_rmd_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6]' --deselect 'tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, bool=TRUE, fig.path="fig_path/"-language_and_metadata2]' --deselect 'tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, echo=TRUE-language_and_metadata4]'
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.11, pytest-6.2.5, py-1.10.0, pluggy-0.13.1
benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
Using --randomly-seed=1386331291
rootdir: /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5
plugins: forked-1.3.0, shutil-1.7.0, virtualenv-1.7.0, expect-1.1.0, flake8-1.0.7, timeout-1.4.2, betamax-0.8.1, freezegun-0.4.2, aspectlib-1.5.2, toolbox-0.5, rerunfailures-9.1.1, requests-mock-1.9.3, cov-2.12.1, flaky-3.7.0, benchmark-3.4.1, xdist-2.3.0, pylama-7.7.1, datadir-1.3.1, regressions-2.2.0, cases-3.6.3, xprocess-0.18.1, black-0.3.12, anyio-3.3.0, asyncio-0.15.1, trio-0.7.0, subtests-0.5.0, isort-2.0.0, hypothesis-6.14.6, mock-3.6.1, profiling-1.7.0, randomly-3.8.0, Faker-8.12.1, nose2pytest-1.0.8, pyfakefs-4.5.1, tornado-0.8.1
collected 2582 items / 8 deselected / 2574 selected

tests/test_pre_commit_0_ipynb_to_py.py s                                                                                                                             [  0%]
tests/test_pytest.py ..                                                                                                                                              [  0%]
tests/test_custom_cell_magics.py .                                                                                                                                   [  0%]
tests/test_markdown_in_code_cells.py ....                                                                                                                            [  0%]
tests/test_ipynb_to_py.py ....................                                                                                                                       [  1%]
tests/test_read_simple_csharp.py .......                                                                                                                             [  1%]
tests/test_contentsmanager.py ...............s...............................................................s...........s.s...s.................s.................. [  6%]
..........s.....s...........................................................................s.s...........s......................s.................................. [ 12%]
......s...s........s....s.s................s..........................................................s............................................s................ [ 19%]
....                                                                                                                                                                 [ 19%]
tests/test_trust_notebook.py ................................................                                                                                        [ 21%]
tests/test_cell_metadata.py ..................................F.....F...........                                                                                     [ 23%]
tests/test_read_simple_nomarker.py ..                                                                                                                                [ 23%]
tests/test_read_simple_python.py ................................................                                                                                    [ 25%]
tests/test_read_write_functions.py .....                                                                                                                             [ 25%]
tests/test_cell_id.py .                                                                                                                                              [ 25%]
tests/test_header.py ..........                                                                                                                                      [ 25%]
tests/test_read_simple_hydrogen.py .......                                                                                                                           [ 26%]
tests/test_jupytext_errors.py ..                                                                                                                                     [ 26%]
tests/test_pre_commit_5_reformat_markdown.py s                                                                                                                       [ 26%]
tests/test_write_does_not_modify_notebook.py ..............................................................................................................          [ 30%]
tests/test_read_simple_matlab.py ..                                                                                                                                  [ 30%]
tests/test_read_simple_rmd.py .........                                                                                                                              [ 31%]
tests/test_cells.py ...............                                                                                                                                  [ 31%]
tests/test_read_simple_scheme.py .                                                                                                                                   [ 31%]
tests/test_nbformat_version.py .......                                                                                                                               [ 31%]
tests/test_cli_config.py ...........                                                                                                                                 [ 32%]
tests/test_formats.py ......s..................                                                                                                                      [ 33%]
tests/test_read_simple_julia.py .                                                                                                                                    [ 33%]
tests/test_read_simple_percent.py ......................                                                                                                             [ 34%]
tests/test_cli.py ..................ss.s....s.s.........s..s.........s...............................s................s...s..........s...............s.............. [ 39%]
......s.s............................s.s.............................s............................................................s................................. [ 46%]
...................................s...s....s.......s.......s......s......s...............................                                                           [ 50%]
tests/test_read_simple_markdown.py ....................................                                                                                              [ 51%]
tests/test_pre_commit_3_sync_black_nbstripout.py s                                                                                                                   [ 51%]
tests/test_read_all_py.py ..........................................................................................................                                 [ 55%]
tests/test_active_cells.py ............................                                                                                                              [ 56%]
tests/test_using_cli.py .                                                                                                                                            [ 57%]
tests/test_jupytext_nbconvert_round_trip.py .......................                                                                                                  [ 57%]
tests/test_compare.py .....................                                                                                                                          [ 58%]
tests/test_metadata_filter.py .................                                                                                                                      [ 59%]
tests/test_stringparser.py ....                                                                                                                                      [ 59%]
tests/test_isort.py .                                                                                                                                                [ 59%]
tests/test_auto_ext.py ...............................s..........x............................................                                                       [ 62%]
tests/test_metadata_filters_from_config.py .                                                                                                                         [ 63%]
tests/test_read_dotnet_try_markdown.py ...                                                                                                                           [ 63%]
tests/test_read_simple_clojure.py .                                                                                                                                  [ 63%]
tests/test_pre_commit_1_sync.py s                                                                                                                                    [ 63%]
tests/test_read_folding_markers.py .....                                                                                                                             [ 63%]
tests/test_pre_commit_scripts.py .....s..                                                                                                                            [ 63%]
tests/test_unicode.py ...............................                                                                                                                [ 64%]
tests/test_pre_commit_2_sync_nbstripout.py s                                                                                                                         [ 64%]
tests/test_doxygen.py ..........                                                                                                                                     [ 65%]
tests/test_ipynb_to_rmd.py ........................                                                                                                                  [ 66%]
tests/test_read_simple_ipynb.py .                                                                                                                                    [ 66%]
tests/test_ipynb_to_myst.py ..........ss                                                                                                                             [ 66%]
tests/test_escape_magics.py ................................................................................                                                         [ 69%]
tests/test_hide_remove_input_outputs_rmarkdown.py ........                                                                                                           [ 70%]
tests/test_save_multiple.py .....................................................                                                                                    [ 72%]
tests/test_rmd_to_ipynb.py ......                                                                                                                                    [ 72%]
tests/test_read_simple_groovy.py .                                                                                                                                   [ 72%]
tests/test_execute.py ......s.                                                                                                                                       [ 72%]
tests/test_read_simple_rust.py ...                                                                                                                                   [ 72%]
tests/test_pre_commit_4_sync_execute.py s                                                                                                                            [ 72%]
tests/test_changelog.py ...                                                                                                                                          [ 73%]
tests/test_pre_commit_mode.py ............                                                                                                                           [ 73%]
tests/test_combine.py ..................................................                                                                                             [ 75%]
tests/test_read_simple_R.py ............                                                                                                                             [ 75%]
tests/test_read_simple_pandoc.py sssss                                                                                                                               [ 76%]
tests/test_load_multiple.py ..                                                                                                                                       [ 76%]
tests/test_read_simple_java.py .                                                                                                                                     [ 76%]
tests/test_config.py .................                                                                                                                               [ 76%]
tests/test_ipynb_to_R.py ....                                                                                                                                        [ 77%]
tests/test_black.py
 ...........s.                                                                                                                                    [ 77%]
tests/test_cm_config.py ............                                                                                                                                 [ 78%]
tests/test_knitr_spin.py .                                                                                                                                           [ 78%]
tests/test_preserve_empty_cells.py .......                                                                                                                           [ 78%]
tests/test_paired_paths.py ......................                                                                                                                    [ 79%]
tests/test_jupytext_read.py ..                                                                                                                                       [ 79%]
tests/test_mirror.py .........................s...........s...s............................................s............s......s............s....ss................. [ 84%]
.s..........................s....s.s.s......s...s......ss..s............s...........................s.............s.......s......s...s........................s..... [ 91%]
........s..............................s...................s.....................s......................                                                             [ 95%]
tests/test_read_incomplete_rmd.py ...                                                                                                                                [ 95%]
tests/test_read_simple_sphinx.py ...                                                                                                                                 [ 95%]
tests/test_pep8.py ...................................................................................................................                               [100%]

================================================================================= FAILURES =================================================================================
_______________________________________________________ test_parse_rmd_options[r echo=FALSE-language_and_metadata3] ________________________________________________________

options = 'r echo=FALSE', language_and_metadata = ('R', {})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'tags': ['remove_input']}), expected = ('R', {}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,4 +1,8 @@
E            [
E             "R",
E           - {}
E           + {
E           +  "tags": [
E           +   "remove_input"
E           +  ]
E           + }
E            ]

jupytext/compare.py:47: AssertionError
______________________________________________ test_build_options[python include=FALSE, active="Rmd"-language_and_metadata8] _______________________________________________

options = 'python include=FALSE, active="Rmd"', language_and_metadata = ('python', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'python active="Rmd"', expected = 'python include=FALSE, active="Rmd"', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -python include=FALSE, active="Rmd"
E           +python active="Rmd"

jupytext/compare.py:47: AssertionError
============================================================================= warnings summary =============================================================================
jupytext/cell_reader.py:20
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.9.0 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
    warnings.warn(

tests/test_contentsmanager.py: 48 warnings
  /usr/lib/python3.8/site-packages/send2trash/plat_gio.py:18: PyGIDeprecationWarning: GObject.GError is deprecated; use GLib.GError instead
    except GObject.GError as e:

tests/test_cli.py::test_format_prefix_suffix
  [warning] You have passed a file name to the '--to' option, when a format description was expected. Maybe you want to use the '-o' option instead?

tests/test_cli.py::test_utf8_out_331
  [warning] 'contextfilter' is renamed to 'pass_context', the old name will be removed in Jinja 3.1.

tests/test_cli.py::test_cli_expect_errors
tests/test_pre_commit_scripts.py::test_manual_call_of_pre_commit_hook
  [warning] The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)

tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
  [warning] Passing unrecognized arguments to super(JupytextConfiguration).__init__(not_a_jupytext_option=True).
  object.__init__() takes exactly one argument (the instance to initialize)
  This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] tests/test_pre_commit_0_ipynb_to_py.py:16: Jupytext folder is not a git repository #814
SKIPPED [17] tests/test_contentsmanager.py:180: pandoc>=2.11 is not available
SKIPPED [2] tests/test_contentsmanager.py:1765: jupyterfs is not available
SKIPPED [1] tests/test_contentsmanager.py:1188: sphinx_gallery is not available
SKIPPED [1] tests/test_pre_commit_5_reformat_markdown.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_formats.py:324: pandoc>=2.11 is not available
SKIPPED [15] tests/test_cli.py:557: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1075: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:795: sphinx_gallery is not available
SKIPPED [5] tests/test_cli.py:1005: pandoc>=2.11 is not available
SKIPPED [3] tests/test_cli.py:991: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1188: Please run 'python -m ipykernel install --name python_kernel --user'
SKIPPED [1] tests/test_pre_commit_3_sync_black_nbstripout.py:13: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_auto_ext.py:36: No file_extension in language_info
SKIPPED [1] tests/test_pre_commit_1_sync.py:17: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_scripts.py:335: pandoc>=2.11 is not available
SKIPPED [1] tests/test_pre_commit_2_sync_nbstripout.py:14: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_ipynb_to_myst.py:162: myst is available
SKIPPED [1] tests/test_ipynb_to_myst.py:171: myst is available
SKIPPED [1] tests/test_execute.py:150: irkernel is not installed
SKIPPED [1] tests/test_pre_commit_4_sync_execute.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_read_simple_pandoc.py:50: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:35: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:13: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:64: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:82: Pandoc is installed
SKIPPED [1] tests/test_black.py:68: autopep8 not found
SKIPPED [17] tests/test_mirror.py:131: pandoc>=2.11 is not available
SKIPPED [11] tests/test_mirror.py:151: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:208: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:202: sphinx_gallery is not available
XFAIL tests/test_auto_ext.py::test_auto_from_kernelspecs_works[/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/notebooks/ipynb_sage/sage_print_hello.ipynb]
  reason: Sage notebooks have Python in their language_info metadata, see #727
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r echo=FALSE-language_and_metadata3] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[python include=FALSE, active="Rmd"-language_and_metadata8] - AssertionError:
======================================= 2 failed, 2477 passed, 94 skipped, 8 deselected, 1 xfailed, 57 warnings in 229.48s (0:03:49) =======================================
```

Yep pytest is OK with disabled `pytest-randomly`
```console
+ /usr/bin/pytest -ra -p no:randomly
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.11, pytest-6.2.5, py-1.10.0, pluggy-0.13.1
benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5
plugins: forked-1.3.0, shutil-1.7.0, virtualenv-1.7.0, expect-1.1.0, flake8-1.0.7, timeout-1.4.2, betamax-0.8.1, freezegun-0.4.2, aspectlib-1.5.2, toolbox-0.5, rerunfailures-9.1.1, requests-mock-1.9.3, cov-2.12.1, flaky-3.7.0, benchmark-3.4.1, xdist-2.3.0, pylama-7.7.1, datadir-1.3.1, regressions-2.2.0, cases-3.6.3, xprocess-0.18.1, black-0.3.12, anyio-3.3.0, asyncio-0.15.1, trio-0.7.0, subtests-0.5.0, isort-2.0.0, hypothesis-6.14.6, mock-3.6.1, profiling-1.7.0, Faker-8.12.1, nose2pytest-1.0.8, pyfakefs-4.5.1, tornado-0.8.1
collected 2582 items

tests/test_active_cells.py ............................                                                                                                              [  1%]
tests/test_auto_ext.py .............................................................x.s.......................                                                       [  4%]
tests/test_black.py ...s.........                                                                                                                                    [  4%]
tests/test_cell_id.py .                                                                                                                                              [  4%]
tests/test_cell_metadata.py ............................................................                                                                             [  7%]
tests/test_cells.py ...............                                                                                                                                  [  7%]
tests/test_changelog.py ...                                                                                                                                          [  8%]
tests/test_cli.py .................................................................................................................................................. [ 13%]
........................................................sssssssssssssss............................................................................................. [ 20%]
s........................................................................ssssssss...s....s................                                                           [ 24%]
tests/test_cli_config.py ...........                                                                                                                                 [ 24%]
tests/test_cm_config.py ............                                                                                                                                 [ 25%]
tests/test_combine.py ..................................................                                                                                             [ 26%]
tests/test_compare.py .....................                                                                                                                          [ 27%]
tests/test_config.py .................                                                                                                                               [ 28%]
tests/test_contentsmanager.py ...................................................sssssssssssssssss.................................................................. [ 33%]
.................................................................................................................................................................... [ 39%]
................................................................................................................................s................................... [ 46%]
..ss                                                                                                                                                                 [ 46%]
tests/test_custom_cell_magics.py .                                                                                                                                   [ 46%]
tests/test_doxygen.py ..........                                                                                                                                     [ 46%]
tests/test_escape_magics.py ................................................................................                                                         [ 50%]
tests/test_execute.py ......s.                                                                                                                                       [ 50%]
tests/test_formats.py ......................s..                                                                                                                      [ 51%]
tests/test_header.py ..........                                                                                                                                      [ 51%]
tests/test_hide_remove_input_outputs_rmarkdown.py ........                                                                                                           [ 51%]
tests/test_ipynb_to_R.py ....                                                                                                                                        [ 52%]
tests/test_ipynb_to_myst.py .......ss...                                                                                                                             [ 52%]
tests/test_ipynb_to_py.py ....................                                                                                                                       [ 53%]
tests/test_ipynb_to_rmd.py ........................                                                                                                                  [ 54%]
tests/test_isort.py .                                                                                                                                                [ 54%]
tests/test_jupytext_errors.py ..                                                                                                                                     [ 54%]
tests/test_jupytext_nbconvert_round_trip.py .......................                                                                                                  [ 55%]
tests/test_jupytext_read.py ..                                                                                                                                       [ 55%]
tests/test_knitr_spin.py .                                                                                                                                           [ 55%]
tests/test_load_multiple.py ..                                                                                                                                       [ 55%]
tests/test_markdown_in_code_cells.py ....                                                                                                                            [ 55%]
tests/test_metadata_filter.py .................                                                                                                                      [ 56%]
tests/test_metadata_filters_from_config.py .                                                                                                                         [ 56%]
tests/test_mirror.py ............................................................................................................................................... [ 61%]
..................................................................................sssssssssssssssss..........................................sssssssssss............ [ 68%]
...ss...................................................................................................                                                             [ 72%]
tests/test_nbformat_version.py .......                                                                                                                               [ 72%]
tests/test_paired_paths.py ......................                                                                                                                    [ 73%]
tests/test_pep8.py ...................................................................................................................                               [ 77%]
tests/test_pre_commit_0_ipynb_to_py.py s                                                                                                                             [ 77%]
tests/test_pre_commit_1_sync.py s                                                                                                                                    [ 77%]
tests/test_pre_commit_2_sync_nbstripout.py s                                                                                                                         [ 77%]
tests/test_pre_commit_3_sync_black_nbstripout.py s                                                                                                                   [ 78%]
tests/test_pre_commit_4_sync_execute.py s                                                                                                                            [ 78%]
tests/test_pre_commit_5_reformat_markdown.py s                                                                                                                       [ 78%]
tests/test_pre_commit_mode.py ............                                                                                                                           [ 78%]
tests/test_pre_commit_scripts.py .......s                                                                                                                            [ 78%]
tests/test_preserve_empty_cells.py .......                                                                                                                           [ 79%]
tests/test_pytest.py ..                                                                                                                                              [ 79%]
tests/test_read_all_py.py ..........................................................................................................                                 [ 83%]
tests/test_read_dotnet_try_markdown.py ...                                                                                                                           [ 83%]
tests/test_read_folding_markers.py .....                                                                                                                             [ 83%]
tests/test_read_incomplete_rmd.py ...                                                                                                                                [ 83%]
tests/test_read_simple_R.py ............                                                                                                                             [ 84%]
tests/test_read_simple_clojure.py .                                                                                                                                  [ 84%]
tests/test_read_simple_csharp.py .......                                                                                                                             [ 84%]
tests/test_read_simple_groovy.py .                                                                                                                                   [ 84%]
tests/test_read_simple_hydrogen.py .......                                                                                                                           [ 84%]
tests/test_read_simple_ipynb.py .                                                                                                                                    [ 84%]
tests/test_read_simple_java.py .                                                                                                                                     [ 84%]
tests/test_read_simple_julia.py .                                                                                                                                    [ 84%]
tests/test_read_simple_markdown.py ....................................                                                                                              [ 86%]
tests/test_read_simple_matlab.py ..                                                                                                                                  [ 86%]
tests/test_read_simple_nomarker.py ..                                                                                                                                [ 86%]
tests/test_read_simple_pandoc.py sssss                                                                                                                               [ 86%]
tests/test_read_simple_percent.py ......................                                                                                                             [ 87%]
tests/test_read_simple_python.py ................................................                                                                                    [ 89%]
tests/test_read_simple_rmd.py .........                                                                                                                              [ 89%]
tests/test_read_simple_rust.py ...                                                                                                                                   [ 89%]
tests/test_read_simple_scheme.py .                                                                                                                                   [ 89%]
tests/test_read_simple_sphinx.py ...                                                                                                                                 [ 90%]
tests/test_read_write_functions.py .....                                                                                                                             [ 90%]
tests/test_rmd_to_ipynb.py ......                                                                                                                                    [ 90%]
tests/test_save_multiple.py .....................................................                                                                                    [ 92%]
tests/test_stringparser.py ....                                                                                                                                      [ 92%]
tests/test_trust_notebook.py ................................................                                                                                        [ 94%]
tests/test_unicode.py ...............................                                                                                                                [ 95%]
tests/test_using_cli.py .                                                                                                                                            [ 95%]
tests/test_write_does_not_modify_notebook.py ..............................................................................................................          [100%]

============================================================================= warnings summary =============================================================================
jupytext/cell_reader.py:20
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.9.0 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
    warnings.warn(

tests/test_cli.py::test_utf8_out_331
  /usr/lib/python3.8/site-packages/nbconvert/exporters/html.py:110: DeprecationWarning: 'contextfilter' is renamed to 'pass_context', the old name will be removed in Jinja 3.1.
    def markdown2html(self, context, source):

tests/test_cli.py::test_cli_expect_errors
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/jupytext/cli.py:332: DeprecationWarning: The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)
    warnings.warn(

tests/test_cli.py::test_format_prefix_suffix
  [warning] You have passed a file name to the '--to' option, when a format description was expected. Maybe you want to use the '-o' option instead?

tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
  [warning] Passing unrecognized arguments to super(JupytextConfiguration).__init__(not_a_jupytext_option=True).
  object.__init__() takes exactly one argument (the instance to initialize)
  This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.

tests/test_contentsmanager.py: 48 warnings
  [warning] GObject.GError is deprecated; use GLib.GError instead

tests/test_pre_commit_scripts.py::test_manual_call_of_pre_commit_hook
  [warning] The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] tests/test_auto_ext.py:36: No file_extension in language_info
SKIPPED [1] tests/test_black.py:68: autopep8 not found
SKIPPED [15] tests/test_cli.py:557: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:795: sphinx_gallery is not available
SKIPPED [3] tests/test_cli.py:991: pandoc>=2.11 is not available
SKIPPED [5] tests/test_cli.py:1005: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1075: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1188: Please run 'python -m ipykernel install --name python_kernel --user'
SKIPPED [17] tests/test_contentsmanager.py:180: pandoc>=2.11 is not available
SKIPPED [1] tests/test_contentsmanager.py:1188: sphinx_gallery is not available
SKIPPED [2] tests/test_contentsmanager.py:1765: jupyterfs is not available
SKIPPED [1] tests/test_execute.py:150: irkernel is not installed
SKIPPED [1] tests/test_formats.py:324: pandoc>=2.11 is not available
SKIPPED [1] tests/test_ipynb_to_myst.py:162: myst is available
SKIPPED [1] tests/test_ipynb_to_myst.py:171: myst is available
SKIPPED [17] tests/test_mirror.py:131: pandoc>=2.11 is not available
SKIPPED [11] tests/test_mirror.py:151: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:202: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:208: sphinx_gallery is not available
SKIPPED [1] tests/test_pre_commit_0_ipynb_to_py.py:16: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_1_sync.py:17: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_2_sync_nbstripout.py:14: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_3_sync_black_nbstripout.py:13: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_4_sync_execute.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_5_reformat_markdown.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_scripts.py:335: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:13: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:35: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:50: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:64: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:82: Pandoc is installed
XFAIL tests/test_auto_ext.py::test_auto_from_kernelspecs_works[/home/tkloczko/rpmbuild/BUILD/jupytext-1.11.5/tests/notebooks/ipynb_sage/sage_print_hello.ipynb]
  reason: Sage notebooks have Python in their language_info metadata, see #727
=================================================== 2487 passed, 94 skipped, 1 xfailed, 57 warnings in 156.47s (0:02:36) ===================================================
pytest-xprocess reminder::Be sure to terminate the started process by running 'pytest --xkill' if you have not explicitly done so in your fixture with 'xprocess.getinfo(<process_name>).terminate()'.
```
If you want to fix that kind of issues you need to use  https://github.com/mrbean-bremen/pytest-find-dependencies/ 
In other words there are still two minor issues:
- test suite has some dependencies between units (it is important to not have such dependencies if you want to execute exact unit or set of units)
- there are still some pytest warnings
Hi @kloczek , yes last time I took a note about warnings at #823, but I've had no time to make progress there (and I am still willing to)

I am a bit surprised that the tests above show dependencies between units. What I think I saw in the first error above was something different, like an incorrect parameterization - I have prepared input and outputs as a list of tuple, but these inputs+outputs don't seem to be presented in pairs to the test function. Do you have a clue of what is happening there? Thanks!
That is fine. This issue is not critical but kind of minior.
Feel free to close as duplicate :)
Just tested 1.13.3 and still with `pytest-randomly` sometimes pytaest is failing.
Looks like to solve that issue https://github.com/mrbean-bremen/pytest-find-dependencies/ can be used
<details>

```console
+ PYTHONPATH=/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.13.3-2.fc35.x86_64/usr/lib64/python3.8/site-packages:/home/tkloczko/rpmbuild/BUILDROOT/python-jupytext-1.13.3-2.fc35.x86_64/usr/lib/python3.8/site-packages
+ /usr/bin/pytest -ra
=========================================================================== test session starts ============================================================================
platform linux -- Python 3.8.12, pytest-6.2.5, py-1.10.0, pluggy-0.13.1
benchmark: 3.4.1 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
Using --randomly-seed=2734066668
rootdir: /home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3
plugins: shutil-1.7.0, virtualenv-1.7.0, mock-3.6.1, cov-2.12.1, anyio-3.3.4, forked-1.3.0, xdist-2.3.0, flaky-3.7.0, tornasync-0.6.0.post2, console-scripts-1.2.0, trio-0.7.0, timeout-2.0.1, asyncio-0.16.0, freezegun-0.4.2, flake8-1.0.7, pyfakefs-4.5.3, hypothesis-6.29.3, benchmark-3.4.1, profiling-1.7.0, datadir-1.3.1, regressions-2.2.0, randomly-3.8.0
collected 2678 items

tests/test_read_simple_clojure.py .                                                                                                                                  [  0%]
tests/test_knitr_spin.py .                                                                                                                                           [  0%]
tests/test_ipynb_to_rmd.py ........................                                                                                                                  [  0%]
tests/test_black.py ......s......                                                                                                                                    [  1%]
tests/test_read_simple_python.py ................................................                                                                                    [  3%]
tests/test_ipynb_to_myst.py .s...s......                                                                                                                             [  3%]
tests/test_ipynb_to_R.py ....                                                                                                                                        [  3%]
tests/test_read_write_functions.py .....                                                                                                                             [  4%]
tests/test_read_incomplete_rmd.py ...                                                                                                                                [  4%]
tests/test_read_simple_quarto.py s                                                                                                                                   [  4%]
tests/test_read_simple_matlab.py ..                                                                                                                                  [  4%]
tests/test_read_simple_groovy.py .                                                                                                                                   [  4%]
tests/test_cli_config.py ...........                                                                                                                                 [  4%]
tests/test_config.py ..................                                                                                                                              [  5%]
tests/test_pre_commit_3_sync_black_nbstripout.py s                                                                                                                   [  5%]
tests/test_cells.py ................                                                                                                                                 [  6%]
tests/test_rmd_to_ipynb.py ......                                                                                                                                    [  6%]
tests/test_pre_commit_scripts.py .......s                                                                                                                            [  6%]
tests/test_isort.py s                                                                                                                                                [  6%]
tests/test_using_cli.py .                                                                                                                                            [  6%]
tests/test_pre_commit_4_sync_execute.py s                                                                                                                            [  6%]
tests/test_cell_metadata.py .....................................F..F..FFFF......F......                                                                             [  8%]
tests/test_read_simple_rust.py ...                                                                                                                                   [  8%]
tests/test_read_simple_percent.py ......................                                                                                                             [  9%]
tests/test_execute.py ......s.                                                                                                                                       [ 10%]
tests/test_load_multiple.py ..                                                                                                                                       [ 10%]
tests/test_hide_remove_input_outputs_rmarkdown.py ........                                                                                                           [ 10%]
tests/test_pre_commit_5_reformat_markdown.py s                                                                                                                       [ 10%]
tests/test_combine.py ...................................................                                                                                            [ 12%]
tests/test_trust_notebook.py .................................................                                                                                       [ 14%]
tests/test_stringparser.py ....                                                                                                                                      [ 14%]
tests/test_cell_markers.py ..                                                                                                                                        [ 14%]
tests/test_read_simple_julia.py .                                                                                                                                    [ 14%]
tests/test_compare.py .....................                                                                                                                          [ 15%]
tests/test_read_simple_scheme.py .                                                                                                                                   [ 15%]
tests/test_metadata_filter.py .................                                                                                                                      [ 15%]
tests/test_cm_config.py .............                                                                                                                                [ 16%]
tests/test_read_simple_java.py .                                                                                                                                     [ 16%]
tests/test_read_simple_R.py ............                                                                                                                             [ 16%]
tests/test_markdown_in_code_cells.py ....                                                                                                                            [ 17%]
tests/test_metadata_filters_from_config.py .                                                                                                                         [ 17%]
tests/test_cell_id.py .                                                                                                                                              [ 17%]
tests/test_read_simple_markdown.py ....................................                                                                                              [ 18%]
tests/test_read_simple_rmd.py ..........                                                                                                                             [ 18%]
tests/test_read_folding_markers.py .....                                                                                                                             [ 19%]
tests/test_read_simple_ocaml.py ..                                                                                                                                   [ 19%]
tests/test_read_simple_pandoc.py .ssss                                                                                                                               [ 19%]
tests/test_active_cells.py ............................                                                                                                              [ 20%]
tests/test_cli.py ......s.s......s.............s.s.........s..s.............ss...................................................................................... [ 25%]
.s...................sss............s.................s...............................s..........s............................s................s.................... [ 31%]
..............................s.........s........s.s.....s...............s...................s..............                                                         [ 35%]
tests/test_read_all_py.py ................................................................................................................                           [ 40%]
tests/test_jupytext_errors.py ..                                                                                                                                     [ 40%]
tests/test_doxygen.py ..........                                                                                                                                     [ 40%]
tests/test_write_does_not_modify_notebook.py ..............................................................................................................          [ 44%]
tests/test_preserve_empty_cells.py .......                                                                                                                           [ 44%]
tests/test_auto_ext.py ...........................x......................s.....................................                                                      [ 48%]
tests/test_jupytext_read.py ..                                                                                                                                       [ 48%]
tests/test_read_simple_csharp.py .......                                                                                                                             [ 48%]
tests/test_header.py ..........                                                                                                                                      [ 48%]
tests/test_pre_commit_mode.py ............                                                                                                                           [ 49%]
tests/test_paired_paths.py ......................                                                                                                                    [ 50%]
tests/test_pep8.py .........................................................................................................................                         [ 54%]
tests/test_jupytext_nbconvert_round_trip.py .......................                                                                                                  [ 55%]
tests/test_save_multiple.py .....................................................                                                                                    [ 57%]
tests/test_read_empty_text_notebook.py s..................................                                                                                           [ 58%]
tests/test_ipynb_to_py.py ....................                                                                                                                       [ 59%]
tests/test_pre_commit_2_sync_nbstripout.py s                                                                                                                         [ 59%]
tests/test_read_simple_hydrogen.py .......                                                                                                                           [ 59%]
tests/test_pre_commit_0_ipynb_to_py.py s                                                                                                                             [ 60%]
tests/test_read_simple_nomarker.py ..                                                                                                                                [ 60%]
tests/test_read_simple_ipynb.py .                                                                                                                                    [ 60%]
tests/test_pytest.py ..                                                                                                                                              [ 60%]
tests/test_escape_magics.py ................................................................................                                                         [ 63%]
tests/test_pre_commit_1_sync.py s                                                                                                                                    [ 63%]
tests/test_nbformat_version.py .......                                                                                                                               [ 63%]
tests/test_read_dotnet_try_markdown.py ...                                                                                                                           [ 63%]
tests/test_formats.py ..............s.............                                                                                                                   [ 64%]
tests/test_mirror.py ........s......s...................................s........s....................s......s.s..........s...s...s..s....................s..s...... [ 69%]
...s...................s........................s......s...........s...................s.......s...s....ss..............s..........s......s...........s........s.... [ 76%]
.............s...........................................................s.s.......s........s...s..s........s..s......                                               [ 80%]
tests/test_raw_strings.py .........                                                                                                                                  [ 80%]
tests/test_read_simple_sphinx.py ...                                                                                                                                 [ 80%]
tests/test_changelog.py ...                                                                                                                                          [ 81%]
tests/test_custom_cell_magics.py .                                                                                                                                   [ 81%]
tests/test_unicode.py ...............................                                                                                                                [ 82%]
tests/test_contentsmanager.py ...s.........................s.......s.............................s........................s..................s...................... [ 87%]
.........s......................s...s......s.....................s.................................s.........s.......................................s.s.........s.. [ 93%]
.........................s.s.........................s.............................s.................s...s..........s.......s.........s.........s.................s. [ 99%]
.............                                                                                                                                                        [100%]

================================================================================= FAILURES =================================================================================
____________________________________________ test_parse_rmd_options[python include=FALSE, active="Rmd"-language_and_metadata8] _____________________________________________

options = 'python include=FALSE, active="Rmd"', language_and_metadata = ('python', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('python', {'active': 'Rmd', 'tags': ['remove_cell']}), expected = ('python', {'active': 'Rmd'}), actual_name = 'actual', expected_name = 'expected'
return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,9 @@
E            [
E             "python",
E             {
E           -  "active": "Rmd"
E           +  "active": "Rmd",
E           +  "tags": [
E           +   "remove_cell"
E           +  ]
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
___________________________________________ test_build_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] ___________________________________________

options = 'r chunk_name, include=FALSE, active="Rmd"', language_and_metadata = ('R', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r active="Rmd"', expected = 'r chunk_name, include=FALSE, active="Rmd"', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r chunk_name, include=FALSE, active="Rmd"
E           +r active="Rmd"

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
__________________________________________ test_parse_rmd_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] ___________________________________________

options = 'r plot_1, dpi=72, fig.path="fig_path/"', language_and_metadata = ('R', {'dpi': 72, 'fig.path': 'fig_path/'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'dpi': 72, 'fig.path': 'fig_path/', 'name': 'plot_1'}), expected = ('R', {'dpi': 72, 'fig.path': 'fig_path/'}), actual_name = 'actual'
expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -2,6 +2,7 @@
E             "R",
E             {
E              "dpi": 72,
E           -  "fig.path": "fig_path/"
E           +  "fig.path": "fig_path/",
E           +  "name": "plot_1"
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
_________________________________________ test_parse_rmd_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] _________________________________________

options = 'r chunk_name, include=FALSE, active="Rmd"', language_and_metadata = ('R', {'active': 'Rmd'})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('R', {'active': 'Rmd', 'name': 'chunk_name', 'tags': ['remove_cell']}), expected = ('R', {'active': 'Rmd'}), actual_name = 'actual', expected_name = 'expected'
return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1,6 +1,10 @@
E            [
E             "R",
E             {
E           -  "active": "Rmd"
E           +  "active": "Rmd",
E           +  "name": "chunk_name",
E           +  "tags": [
E           +   "remove_cell"
E           +  ]
E             }
E            ]

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
_______________________________ test_parse_rmd_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] ________________________________

options = 'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}', language_and_metadata = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_parse_rmd_options(options, language_and_metadata):
>       compare(rmd_options_to_metadata(options), language_and_metadata)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'name': 'noname', 'tags': ['a', 'b', 'c']})
expected = ('python', {'echo': '#R_CODE#{sum(a+c(1,2))>1}', 'tags': ['a', 'b', 'c']}), actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -2,6 +2,7 @@
E             "python",
E             {
E              "echo": "#R_CODE#{sum(a+c(1,2))>1}",
E           +  "name": "noname",
E              "tags": [
E               "a",
E               "b",

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
_________________________________________________________ test_build_options[r echo=FALSE-language_and_metadata3] __________________________________________________________

options = 'r echo=FALSE', language_and_metadata = ('R', {})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r', expected = 'r echo=FALSE', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r echo=FALSE
E           +r

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
______________________________________________________ test_build_options[r plot_1, echo=TRUE-language_and_metadata4] ______________________________________________________

options = 'r plot_1, echo=TRUE', language_and_metadata = ('R', {'echo': True})

    @pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
    def test_build_options(options, language_and_metadata):
>       compare(metadata_to_rmd_options(*language_and_metadata), options)

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/test_cell_metadata.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

actual = 'r echo=TRUE', expected = 'r plot_1, echo=TRUE', actual_name = 'actual', expected_name = 'expected', return_diff = False

    def compare(
        actual, expected, actual_name="actual", expected_name="expected", return_diff=False
    ):
        """Compare two strings, lists or dict-like objects"""
        if actual != expected:
            diff = difflib.unified_diff(
                _multilines(expected),
                _multilines(actual),
                expected_name,
                actual_name,
                lineterm="",
            )
            if expected_name == "" and actual_name == "":
                diff = list(diff)[2:]
            diff = "\n".join(diff)
            if return_diff:
                return diff
>           raise AssertionError("\n" + diff)
E           AssertionError:
E           --- expected
E           +++ actual
E           @@ -1 +1 @@
E           -r plot_1, echo=TRUE
E           +r echo=TRUE

/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/compare.py:47: AssertionError
============================================================================= warnings summary =============================================================================
jupytext/cell_reader.py:20
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/cell_reader.py:20: UserWarning: Sphinx Gallery in version 0.10.1 is not supported by Jupytext. Please use sphinx-gallery<=0.7.0 instead. If that is an issue, feel free to report it at https://github.com/mwouts/jupytext/issues, or even better, prepare a PR to handle the new signature of sphinx_gallery.notebook.rst2md.
    warnings.warn(

../../../../../usr/lib/python3.8/site-packages/jsonschema/validators.py:190: 67 warnings
tests/test_read_simple_clojure.py: 6 warnings
tests/test_knitr_spin.py: 23 warnings
tests/test_ipynb_to_rmd.py: 167 warnings
tests/test_black.py: 46 warnings
tests/test_read_simple_python.py: 194 warnings
tests/test_ipynb_to_myst.py: 20 warnings
tests/test_ipynb_to_R.py: 24 warnings
tests/test_read_write_functions.py: 10 warnings
tests/test_read_incomplete_rmd.py: 10 warnings
tests/test_read_simple_matlab.py: 2 warnings
tests/test_read_simple_groovy.py: 6 warnings
tests/test_cli_config.py: 20 warnings
tests/test_cells.py: 12 warnings
tests/test_rmd_to_ipynb.py: 58 warnings
tests/test_pre_commit_scripts.py: 7 warnings
tests/test_using_cli.py: 44 warnings
tests/test_read_simple_rust.py: 19 warnings
tests/test_read_simple_percent.py: 63 warnings
tests/test_execute.py: 34 warnings
tests/test_load_multiple.py: 2 warnings
tests/test_hide_remove_input_outputs_rmarkdown.py: 16 warnings
tests/test_combine.py: 41 warnings
tests/test_trust_notebook.py: 697 warnings
tests/test_cell_markers.py: 2 warnings
tests/test_read_simple_julia.py: 5 warnings
tests/test_compare.py: 64 warnings
tests/test_read_simple_scheme.py: 12 warnings
tests/test_metadata_filter.py: 9 warnings
tests/test_cm_config.py: 8 warnings
tests/test_read_simple_java.py: 6 warnings
tests/test_read_simple_R.py: 50 warnings
tests/test_markdown_in_code_cells.py: 7 warnings
tests/test_metadata_filters_from_config.py: 3 warnings
tests/test_cell_id.py: 2 warnings
tests/test_read_simple_markdown.py: 103 warnings
tests/test_read_simple_rmd.py: 37 warnings
tests/test_read_folding_markers.py: 16 warnings
tests/test_read_simple_ocaml.py: 2 warnings
tests/test_active_cells.py: 32 warnings
tests/test_cli.py: 206 warnings
  /usr/lib/python3.8/site-packages/jsonschema/validators.py:190: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
    warnings.warn(

tests/test_pre_commit_scripts.py::test_manual_call_of_pre_commit_hook
  /home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/jupytext/cli.py:341: DeprecationWarning: The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)
    warnings.warn(

tests/test_using_cli.py::test_jupytext_commands_in_the_documentation_work
  /usr/lib/python3.8/site-packages/nbconvert/exporters/html.py:110: DeprecationWarning: 'contextfilter' is renamed to 'pass_context', the old name will be removed in Jinja 3.1.
    def markdown2html(self, context, source):

tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[.jupytext.py-c.not_a_jupytext_option = True]
tests/test_cm_config.py::test_incorrect_config_message[pyproject.toml-[tool.jupytext]\nnot_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[pyproject.toml-[tool.jupytext]\nnot_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
tests/test_cm_config.py::test_incorrect_config_message[jupytext.toml-not_a_jupytext_option = true]
  /usr/lib/python3.8/site-packages/traitlets/config/configurable.py:85: DeprecationWarning: Passing unrecognized arguments to super(JupytextConfiguration).__init__(not_a_jupytext_option=True).
  object.__init__() takes exactly one argument (the instance to initialize)
  This is deprecated in traitlets 4.2.This error will be raised in a future release of traitlets.
    super(Configurable, self).__init__(**kwargs)

tests/test_cli.py::test_format_prefix_suffix
  [warning] You have passed a file name to the '--to' option, when a format description was expected. Maybe you want to use the '-o' option instead?

tests/test_cli.py: 2821 warnings
tests/test_read_all_py.py: 2504 warnings
tests/test_doxygen.py: 3 warnings
tests/test_write_does_not_modify_notebook.py: 200 warnings
tests/test_preserve_empty_cells.py: 47 warnings
tests/test_auto_ext.py: 195 warnings
tests/test_jupytext_read.py: 2 warnings
tests/test_read_simple_csharp.py: 8 warnings
tests/test_header.py: 7 warnings
tests/test_pre_commit_mode.py: 27 warnings
tests/test_paired_paths.py: 3 warnings
tests/test_pep8.py: 1273 warnings
tests/test_jupytext_nbconvert_round_trip.py: 53 warnings
tests/test_save_multiple.py: 512 warnings
tests/test_ipynb_to_py.py: 119 warnings
tests/test_read_simple_hydrogen.py: 21 warnings
tests/test_read_simple_nomarker.py: 14 warnings
tests/test_pytest.py: 5 warnings
tests/test_escape_magics.py: 67 warnings
tests/test_nbformat_version.py: 5 warnings
tests/test_read_dotnet_try_markdown.py: 3 warnings
tests/test_formats.py: 4 warnings
tests/test_mirror.py: 4393 warnings
tests/test_raw_strings.py: 8 warnings
tests/test_read_simple_sphinx.py: 19 warnings
tests/test_custom_cell_magics.py: 3 warnings
tests/test_unicode.py: 46 warnings
tests/test_contentsmanager.py: 3594 warnings
  [warning] Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.

tests/test_cli.py::test_cli_expect_errors
  [warning] The --pre-commit argument is deprecated. Please consider switching to the pre-commit.com framework (let us know at https://github.com/mwouts/jupytext/issues if that is an issue for you)

tests/test_contentsmanager.py: 48 warnings
  [warning] GObject.GError is deprecated; use GLib.GError instead

-- Docs: https://docs.pytest.org/en/stable/warnings.html
========================================================================= short test summary info ==========================================================================
SKIPPED [1] tests/test_black.py:68: autopep8 not found
SKIPPED [1] tests/test_ipynb_to_myst.py:162: myst is available
SKIPPED [1] tests/test_ipynb_to_myst.py:171: myst is available
SKIPPED [1] tests/test_read_simple_quarto.py:9: quarto>=0.2 is not available
SKIPPED [1] tests/test_pre_commit_3_sync_black_nbstripout.py:13: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_scripts.py:335: pandoc>=2.11 is not available
SKIPPED [1] tests/test_isort.py:8: isort not found
SKIPPED [1] tests/test_pre_commit_4_sync_execute.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_execute.py:150: irkernel is not installed
SKIPPED [1] tests/test_pre_commit_5_reformat_markdown.py:15: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_read_simple_pandoc.py:35: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:50: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:13: pandoc>=2.11 is not available
SKIPPED [1] tests/test_read_simple_pandoc.py:64: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:796: sphinx_gallery is not available
SKIPPED [5] tests/test_cli.py:1010: pandoc>=2.11 is not available
SKIPPED [15] tests/test_cli.py:558: pandoc>=2.11 is not available
SKIPPED [3] tests/test_cli.py:996: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1080: pandoc>=2.11 is not available
SKIPPED [1] tests/test_cli.py:1220: Please run 'python -m ipykernel install --name python_kernel --user'
SKIPPED [1] tests/test_auto_ext.py:36: No file_extension in language_info
SKIPPED [1] tests/test_read_empty_text_notebook.py:14: quarto is not available
SKIPPED [1] tests/test_pre_commit_2_sync_nbstripout.py:14: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_0_ipynb_to_py.py:16: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_pre_commit_1_sync.py:17: Jupytext folder is not a git repository #814
SKIPPED [1] tests/test_formats.py:350: pandoc>=2.11 is not available
SKIPPED [17] tests/test_mirror.py:132: pandoc>=2.11 is not available
SKIPPED [1] tests/test_mirror.py:225: sphinx_gallery is not available
SKIPPED [7] tests/test_mirror.py:141: quarto>=0.2 is not available
SKIPPED [11] tests/test_mirror.py:168: sphinx_gallery is not available
SKIPPED [1] tests/test_mirror.py:219: sphinx_gallery is not available
SKIPPED [17] tests/test_contentsmanager.py:181: pandoc>=2.11 is not available
SKIPPED [7] tests/test_contentsmanager.py:204: quarto>=0.2 is not available
SKIPPED [2] tests/test_contentsmanager.py:1867: jupyterfs is not available
SKIPPED [1] tests/test_contentsmanager.py:1290: sphinx_gallery is not available
XFAIL tests/test_auto_ext.py::test_auto_from_kernelspecs_works[/home/tkloczko/rpmbuild/BUILD/jupytext-1.13.3/tests/notebooks/ipynb_sage/sage_print_hello.ipynb]
  reason: Sage notebooks have Python in their language_info metadata, see #727
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[python include=FALSE, active="Rmd"-language_and_metadata8] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r plot_1, dpi=72, fig.path="fig_path/"-language_and_metadata1] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[r chunk_name, include=FALSE, active="Rmd"-language_and_metadata9] - AssertionError:
FAILED tests/test_cell_metadata.py::test_parse_rmd_options[python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}-language_and_metadata6] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r echo=FALSE-language_and_metadata3] - AssertionError:
FAILED tests/test_cell_metadata.py::test_build_options[r plot_1, echo=TRUE-language_and_metadata4] - AssertionError:
============================================ 7 failed, 2560 passed, 110 skipped, 1 xfailed, 18167 warnings in 333.95s (0:05:33) ============================================
```
</details>

Hi @kloczek , sorry I still haven't find the time to fix this - I hope to unpile this issue in the coming weeks.
No ruch .. for now I'm testing with `-p no:randomly` :)


Fix patch:
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index 28e8b32da..b3505f831 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -6,6 +6,7 @@ Jupytext ChangeLog
 
 **Fixed**
 - The parsing of notebooks that don't have a YAML header (like `docs/formats.md`) was improved.
+- The test suite works with `pytest-randomly` ([#838](https://github.com/mwouts/jupytext/issues/838))
 
 
 1.13.3 (2021-12-04)
diff --git a/environment-ci.yml b/environment-ci.yml
index 83280df42..473dc204e 100644
--- a/environment-ci.yml
+++ b/environment-ci.yml
@@ -15,6 +15,7 @@ dependencies:
   - mdit-py-plugins
   - pip
   - pytest
+  - pytest-randomly
   - pytest-cov
   - coverage
   - flake8
diff --git a/environment.yml b/environment.yml
index 671b6b998..d07a0e15f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,6 +16,7 @@ dependencies:
   - jupyter_contrib_nbextensions
   - pytest
   - pytest-xdist
+  - pytest-randomly
   - pytest-cov
   - pre-commit
   - gitpython
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 4da5d171c..c76d44bdd 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -3,6 +3,7 @@ flake8
 isort
 black
 pytest>=3.6
+pytest-randomly
 pytest-cov
 notebook
 jupyter_client


Test patch:
diff --git a/tests/test_cell_metadata.py b/tests/test_cell_metadata.py
index 9de96729f..99c3b8154 100644
--- a/tests/test_cell_metadata.py
+++ b/tests/test_cell_metadata.py
@@ -14,25 +14,29 @@
 from jupytext.compare import compare
 from jupytext.metadata_filter import filter_metadata
 
-SAMPLES = [
-    ("r", ("R", {})),
-    (
-        'r plot_1, dpi=72, fig.path="fig_path/"',
-        ("R", {"name": "plot_1", "dpi": 72, "fig.path": "fig_path/"}),
-    ),
-    (
-        'r plot_1, bool=TRUE, fig.path="fig_path/"',
-        ("R", {"name": "plot_1", "bool": True, "fig.path": "fig_path/"}),
-    ),
-    ("r echo=FALSE", ("R", {"tags": ["remove_input"]})),
-    ("r plot_1, echo=TRUE", ("R", {"name": "plot_1", "echo": True})),
-    (
-        "python echo=if a==5 then TRUE else FALSE",
-        ("python", {"echo": "#R_CODE#if a==5 then TRUE else FALSE"}),
-    ),
-    (
-        'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}',
+
+def r_options_language_metadata():
+    for r_options, language, metadata in [
+        ("r", "R", {}),
+        (
+            'r plot_1, dpi=72, fig.path="fig_path/"',
+            "R",
+            {"name": "plot_1", "dpi": 72, "fig.path": "fig_path/"},
+        ),
         (
+            'r plot_1, bool=TRUE, fig.path="fig_path/"',
+            "R",
+            {"name": "plot_1", "bool": True, "fig.path": "fig_path/"},
+        ),
+        ("r echo=FALSE", "R", {"tags": ["remove_input"]}),
+        ("r plot_1, echo=TRUE", "R", {"name": "plot_1", "echo": True}),
+        (
+            "python echo=if a==5 then TRUE else FALSE",
+            "python",
+            {"echo": "#R_CODE#if a==5 then TRUE else FALSE"},
+        ),
+        (
+            'python noname, tags=c("a", "b", "c"), echo={sum(a+c(1,2))>1}',
             "python",
             {
                 "name": "noname",
@@ -40,32 +44,34 @@
                 "echo": "#R_CODE#{sum(a+c(1,2))>1}",
             },
         ),
-    ),
-    ('python active="ipynb,py"', ("python", {"active": "ipynb,py"})),
-    (
-        'python include=FALSE, active="Rmd"',
-        ("python", {"active": "Rmd", "tags": ["remove_cell"]}),
-    ),
-    (
-        'r chunk_name, include=FALSE, active="Rmd"',
-        ("R", {"name": "chunk_name", "active": "Rmd", "tags": ["remove_cell"]}),
-    ),
-    ('python tags=c("parameters")', ("python", {"tags": ["parameters"]})),
-]
+        ('python active="ipynb,py"', "python", {"active": "ipynb,py"}),
+        (
+            'python include=FALSE, active="Rmd"',
+            "python",
+            {"active": "Rmd", "tags": ["remove_cell"]},
+        ),
+        (
+            'r chunk_name, include=FALSE, active="Rmd"',
+            "R",
+            {"name": "chunk_name", "active": "Rmd", "tags": ["remove_cell"]},
+        ),
+        ('python tags=c("parameters")', "python", {"tags": ["parameters"]}),
+    ]:
+        yield r_options, language, metadata
 
 
-@pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
-def test_parse_rmd_options(options, language_and_metadata):
-    compare(rmd_options_to_metadata(options), language_and_metadata)
+@pytest.mark.parametrize("options,language, metadata", r_options_language_metadata())
+def test_parse_rmd_options(options, language, metadata):
+    compare(rmd_options_to_metadata(options), (language, metadata))
 
 
-@pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
-def test_build_options(options, language_and_metadata):
-    compare(metadata_to_rmd_options(*language_and_metadata), options)
+@pytest.mark.parametrize("options,language, metadata", r_options_language_metadata())
+def test_build_options(options, language, metadata):
+    compare(metadata_to_rmd_options(*(language, metadata)), options)
 
 
-@pytest.mark.parametrize("options,language_and_metadata", SAMPLES)
-def test_build_options_random_order(options, language_and_metadata):
+@pytest.mark.parametrize("options,language, metadata", r_options_language_metadata())
+def test_build_options_random_order(options, language, metadata):
     # Older python has no respect for order...
     # assert to_chunk_options(metadata) == options
 
@@ -73,7 +79,7 @@ def split_and_strip(opt):
         set([o.strip() for o in opt.split(",")])
 
     assert split_and_strip(
-        metadata_to_rmd_options(*language_and_metadata)
+        metadata_to_rmd_options(*(language, metadata))
     ) == split_and_strip(options)