Repository: alan-turing-institute/empiarreader (language: python)

Issue:
Fix poetry dependencies



Discussion / hints:

Fix patch:
diff --git a/poetry.lock b/poetry.lock
index 57012c4..e4e1bb6 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,40 +1,196 @@
+# This file is automatically @generated by Poetry 1.5.0 and should not be changed by hand.
+
+[[package]]
+name = "aiohttp"
+version = "3.8.3"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
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+charset-normalizer = ">=2.0,<3.0"
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+
+[[package]]
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+]
 
 [[package]]
 name = "fsspec"
-version = "2022.2.0"
+version = "2022.8.2"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "fsspec-2022.8.2-py3-none-any.whl", hash = "sha256:6374804a2c0d24f225a67d009ee1eabb4046ad00c793c3f6df97e426c890a1d9"},
+    {file = "fsspec-2022.8.2.tar.gz", hash = "sha256:7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18"},
+]
 
 [package.extras]
 abfs = ["adlfs"]
 adl = ["adlfs"]
 arrow = ["pyarrow (>=1)"]
 dask = ["dask", "distributed"]
-dropbox = ["dropboxdrivefs", "requests", "dropbox"]
+dropbox = ["dropbox", "dropboxdrivefs", "requests"]
 entrypoints = ["importlib-metadata"]
 fuse = ["fusepy"]
 gcs = ["gcsfs"]
@@ -124,21 +558,79 @@ github = ["requests"]
 gs = ["gcsfs"]
 gui = ["panel"]
 hdfs = ["pyarrow (>=1)"]
-http = ["requests", "aiohttp"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
 libarchive = ["libarchive-c"]
 oci = ["ocifs"]
 s3 = ["s3fs"]
 sftp = ["paramiko"]
 smb = ["smbprotocol"]
 ssh = ["paramiko"]
+tqdm = ["tqdm"]
+
+[[package]]
+name = "idna"
+version = "3.4"
+description = "Internationalized Domain Names in Applications (IDNA)"
+optional = false
+python-versions = ">=3.5"
+files = [
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+    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+]
+
+[[package]]
+name = "imageio"
+version = "2.22.1"
+description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "imageio-2.22.1-py3-none-any.whl", hash = "sha256:a8e7be75ebc3920e8c9a7dcc8e47b54331125fc0932d050df4af9a6f5904d472"},
+    {file = "imageio-2.22.1.tar.gz", hash = "sha256:465ec35f919d538906d3023b61ccec766d8e7575fe55fcbd7669ece55afb97ca"},
+]
+
+[package.dependencies]
+numpy = "*"
+pillow = ">=8.3.2"
+
+[package.extras]
+all-plugins = ["astropy", "av", "imageio-ffmpeg", "opencv-python", "psutil", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"]
+build = ["wheel"]
+dev = ["black", "flake8", "fsspec[github]", "invoke", "pytest", "pytest-cov"]
+docs = ["numpydoc", "pydata-sphinx-theme", "sphinx"]
+ffmpeg = ["imageio-ffmpeg", "psutil"]
+fits = ["astropy"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "opencv-python", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx", "tifffile", "wheel"]
+gdal = ["gdal"]
+itk = ["itk"]
+linting = ["black", "flake8"]
+opencv = ["opencv-python"]
+pyav = ["av"]
+test = ["fsspec[github]", "invoke", "pytest", "pytest-cov"]
+tifffile = ["tifffile"]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
 
 [[package]]
 name = "intake"
-version = "0.6.5"
+version = "0.6.6"
 description = "Data load and catalog system"
-category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+    {file = "intake-0.6.6.tar.gz", hash = "sha256:99b31484dbaca0047098cb7bbfb72cea8d6fcb004dea9a5fe145731b1c65a2ca"},
+]
 
 [package.dependencies]
 appdirs = "*"
@@ -146,22 +638,47 @@ dask = "*"
 entrypoints = "*"
 fsspec = ">=2021.7.0"
 jinja2 = "*"
+msgpack = "*"
 pyyaml = "*"
 
 [package.extras]
-complete = ["bokeh", "dask", "hvplot", "msgpack-numpy", "msgpack-python", "panel (>=0.7.0)", "pyarrow", "python-snappy", "requests", "tornado"]
-dataframe = ["dask", "msgpack-numpy", "pyarrow"]
-plot = ["hvplot", "panel (>=0.7.0)", "bokeh"]
+complete = ["bokeh", "dask[dataframe]", "hvplot", "msgpack-numpy", "msgpack-python", "panel (>=0.7.0)", "pyarrow", "python-snappy", "requests", "tornado"]
+dataframe = ["dask[dataframe]", "msgpack-numpy", "pyarrow"]
+plot = ["bokeh", "hvplot", "panel (>=0.7.0)"]
 remote = ["requests"]
-server = ["tornado", "python-snappy", "msgpack-python"]
+server = ["msgpack-python", "python-snappy", "tornado"]
+
+[[package]]
+name = "intake-xarray"
+version = "0.6.1"
+description = "xarray plugins for Intake"
+optional = false
+python-versions = "*"
+files = [
+    {file = "intake-xarray-0.6.1.tar.gz", hash = "sha256:63dc2a8b937d8f956255d8f8641f08ea654b2d9e88687ec3d1ccc66462fabf9e"},
+    {file = "intake_xarray-0.6.1-py3-none-any.whl", hash = "sha256:b38b09019eb04eda9939c66bb45ec458ab760af82d72a5c8b2a4dba7960b7f84"},
+]
+
+[package.dependencies]
+dask = ">=2.2"
+fsspec = ">2022"
+intake = ">=0.6.6"
+msgpack = "*"
+netcdf4 = "*"
+requests = "*"
+xarray = ">=02022"
+zarr = "*"
 
 [[package]]
-name = "jinja2"
-version = "3.0.3"
+name = "Jinja2"
+version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
+    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -169,63 +686,633 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
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+version = "1.4.4"
+description = "A fast implementation of the Cassowary constraint solver"
+optional = false
+python-versions = ">=3.7"
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+tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
 
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 name = "pluggy"
 version = "0.13.1"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -234,211 +1321,120 @@ dev = ["pre-commit", "tox"]
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-category = "dev"
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-description = "Python parsing module"
-category = "main"
+version = "3.0.9"
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 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.8"
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 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
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-version = "5.4.3"
+version = "6.2.5"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
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 [package.dependencies]
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+pluggy = ">=0.12,<2.0"
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 [package.extras]
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-
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+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
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-name = "toolz"
-version = "0.11.2"
-description = "List processing tools and functional utilities"
-category = "main"
-optional = false
-python-versions = ">=3.5"
+[package.dependencies]
+six = ">=1.5"
 
 [[package]]
-name = "wcwidth"
-version = "0.2.5"
-description = "Measures the displayed width of unicode strings in a terminal"
-category = "dev"
+name = "pytz"
+version = "2022.4"
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-description = "Makes working with XML feel like you are working with JSON"
-category = "main"
+name = "PyWavelets"
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+
+[[package]]
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+description = "An implementation of chunked, compressed, N-dimensional arrays for Python."
+optional = false
+python-versions = ">=3.8, <4"
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 ]
+
+[package.dependencies]
+asciitree = "*"
+fasteners = "*"
+numcodecs = ">=0.10.0"
+numpy = ">=1.7"
+
+[package.extras]
+jupyter = ["ipytree", "notebook"]
+
+[metadata]
+lock-version = "2.0"
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+content-hash = "59fdda76d1b9ad91d2c38be9612b947b704965f08735cf68f25b0ed6004ce7fe"
diff --git a/pyproject.toml b/pyproject.toml
index 2eed9a5..e1cf8cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,9 +8,18 @@ authors = ["mooniean <bcostagomes@turing.ac.uk>", "ots22 <ostrickson@turing.ac.u
 python = "^3.8"
 intake = "^0.6.5"
 bs4 = "^0.0.1"
+matplotlib = "^3.6.1"
+requests = "^2.28.1"
+scikit-image = "^0.19.3"
+xarray = "^2022.9.0"
+mrcfile = "^1.4.3"
+starfile = "^0.4.11"
+intake-xarray = "^0.6.1"
+aiohttp = "^3.8.3"
+setuptools = "^67.7.2"
 
 [tool.poetry.dev-dependencies]
-pytest = "^5.2"
+pytest = "^6.2.5"
 
 [build-system]
 requires = ["poetry-core @ git+https://github.com/python-poetry/poetry-core.git@master"]
diff --git a/src/intake_cryoem/__init__.py b/src/intake_cryoem/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/intake_cryoem/empiar.py b/src/intake_cryoem/empiar.py
similarity index 100%
rename from intake_cryoem/empiar.py
rename to src/intake_cryoem/empiar.py
diff --git a/intake_cryoem/mrcsource.py b/src/intake_cryoem/mrcsource.py
similarity index 100%
rename from intake_cryoem/mrcsource.py
rename to src/intake_cryoem/mrcsource.py
diff --git a/intake_cryoem/starsource.py b/src/intake_cryoem/starsource.py
similarity index 100%
rename from intake_cryoem/starsource.py
rename to src/intake_cryoem/starsource.py


Test patch:
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures/tmp.mrc b/tests/fixtures/tmp.mrc
new file mode 100644
index 0000000..13597e6
Binary files /dev/null and b/tests/fixtures/tmp.mrc differ
diff --git a/tests/fixtures/tmp.star b/tests/fixtures/tmp.star
new file mode 100644
index 0000000..2c34ccb
--- /dev/null
+++ b/tests/fixtures/tmp.star
@@ -0,0 +1,12 @@
+# Created by the starfile Python package (version 0.4.11) at 16:15:43 on 19/05/2023
+
+data_
+
+loop_
+_a #1
+_b #2
+1	4
+2	5
+3	6
+
+
diff --git a/tests/test_empiar_cache.py b/tests/test_empiar_cache.py
new file mode 100644
index 0000000..5210006
--- /dev/null
+++ b/tests/test_empiar_cache.py
@@ -0,0 +1,150 @@
+from unittest.mock import patch
+from intake.config import conf
+
+from intake_cryoem.empiar import EmpiarCatalog, EmpiarSource
+
+import os
+import pytest
+
+
+# stolen from test_empiar_retrieval.test_empiar 
+# and adapting to test caching and renamed cache
+def test_empiar_cache():
+    conf['cache_download_progress'] = True
+    conf['cache_dir'] = os.path.join(os.getcwd(), 'test_cache_dir')
+    for attr in dir(conf):
+        print('conf attr {} is {}'.format(attr, getattr(conf,attr)))
+    print('\n\n')
+
+
+    # now get all conf dict entries
+    for k,v in conf.items():
+        print('Key: {} is: {}'.format(k,v))
+    print('\n\n')
+
+    cat = EmpiarCatalog(10340)
+    print(cat)
+    print(list(cat))
+    print('\n\n')
+
+    ##############################
+    # now looking at the EmpiarCatalog.fetch_entry_data
+    print('EmpiarCatalog.fetch_entry_data:{}'.format(cat.fetch_entry_data(10340)))
+
+    # I think cat(alogue) is a list of imagesets
+    # So EmpiarCatalogue() starts by grabbing the name of the imagesets by reading them
+    # from the online path (EmpiarCatalogue.fetch_entrydata()). 
+    # This list ??? should be accessible via EmpiarCatalogue.imagesets
+    
+    # Now checking after initialisation of EmpiarCatalogue what actually is 
+    # present in it:
+    print('\n\nDir of EmpiarCatalogue.entry_data: {}'.format(dir(cat)))
+    for thing in dir(cat):
+        print('Cat thing {} is {}'.format(thing, getattr(cat,thing)))
+    print('\n\n')
+
+    # print the args
+    for i, entry in enumerate(cat._entries):
+        print('Entry {} has {} and is {}'.format(i, entry, type(entry)))
+        #for j, arg in enumerate(entry.args):
+        #    print('Entry {} has arg {} of {}'.format(i, j, arg))
+    
+    print('\n\n')
+
+    # partition = cat.read_partition(0)
+    # print('Partition: {}'.format(partition))
+
+
+    # I don't think you re actually using the cache yet as you seem to only have grabbed metadata
+    # Try grabbing an actual data file and see what happens... do you use cache?
+    ds = cat["Unaligned movies for Case 1"]
+    """
+    ds = EmpiarSource(
+        10340,
+        directory="data/Micrographs/Case1",
+        filename_regexp="FoilHole_21756216_Data_21768957_21768958_20181221_2054-115048.mrc",
+    )
+    """
+
+    # now because empiar entry 10340 doesn't play nice, swap to 10943
+    ds = EmpiarSource(
+        10943,
+        directory="data/MotionCorr/job003/Tiff/EER/Images-Disc1/GridSquare_11149061/Data",
+        filename_regexp=".*EER\\.mrc",
+    )
+
+    ds.read_partition(0)
+    
+    return
+
+    assert "Unaligned movies for Case 1" in cat.keys()
+
+    ds = cat["Unaligned movies for Case 1"]
+
+    assert isinstance(ds, EmpiarSource)
+
+    assert ds.directory == "data/Movies/Case1"
+
+    # Note: ds.read() is expensive
+
+
+def test_empiar_download():
+    conf['cache_download_progress'] = True
+    conf['cache_dir'] = os.path.join(os.getcwd(), 'test_cache_dir')
+    # Grab the metadata from MEPIAR entry 10340
+    cat = EmpiarCatalog(10340)
+    print('Cat start')
+    print(cat)
+    print(list(cat))
+    print('\n\n')
+    # Grab the first entry (an EmpiarSource)
+    ds = cat[list(cat)[0]]
+    print('ds start')
+    print('ds type {}'.format(type(ds)))
+    print(ds)
+    #print(list(ds))
+    assert isinstance(ds, EmpiarSource)
+    assert ds.directory == "data/Movies/Case1"
+    print('Imageset EMPIAR index: {}'.format(ds.empiar_index))
+    print('Imageset directory: {}'.format(ds.directory))
+    print('Imageset metadata: {}'.format(ds.imageset_metadata))
+    print('Imageset driver: {}'.format(ds._driver))
+    print('Imageset image urls: {}'.format(ds._image_urls))
+    print('Imageset datasource: {}'.format(ds._datasource))
+    
+    # ds read breaks it http err
+    #read_data = ds.read()
+    #print(type(read_data))
+    #print('Read data: {}'.format(read_data))
+
+    # new
+    """
+    ds = EmpiarSource(
+        10340,
+        directory="data/Micrographs/Case1",
+        filename_regexp="FoilHole_21756216_Data_21768957_21768958_20181221_2054-115048.mrc",
+    )
+    part = ds.read_partition(0)
+    print("Partition start:")
+    print(part)
+    print("Filename: {}".format(part.filenmae))
+
+    """
+    ds = EmpiarSource(
+        10943,
+        directory="data/MotionCorr/job003/Tiff/EER/Images-Disc1/GridSquare_11149061/Data",
+        filename_regexp=".*EER\\.mrc",
+    )
+    
+    # Downloads data from first mrc file
+    part = ds.read_partition(0)
+
+    assert part.filename == "https://ftp.ebi.ac.uk/empiar/world_availability/10943/data/MotionCorr/job003/Tiff/EER/Images-Disc1/GridSquare_11149061/Data/FoilHole_11161627_Data_11149751_11149753_20210911_222712_EER.mrc"
+
+    assert part[0][0] == pytest.approx(2.9199, 1.0e-4)
+    
+
+
+if __name__ == '__main__':
+    # test_empiar_cache()
+    test_empiar_download()
\ No newline at end of file
diff --git a/tests/test_load_mrc.py b/tests/test_load_mrc.py
index 68036c9..6138d57 100644
--- a/tests/test_load_mrc.py
+++ b/tests/test_load_mrc.py
@@ -6,10 +6,10 @@
 def test_load_mrc():
     data = np.arange(9, dtype="float32").reshape((3, 3))
 
-    with mrcfile.new("tmp.mrc", overwrite=True) as example_mrc:
+    with mrcfile.new("tests/fixtures/tmp.mrc", overwrite=True) as example_mrc:
         example_mrc.set_data(data)
 
-    ds = intake.open_mrc("tmp.mrc")
+    ds = intake.open_mrc("tests/fixtures/tmp.mrc")
 
     data_read = ds.read()
     
diff --git a/tests/test_load_star.py b/tests/test_load_star.py
index f21e67d..0570199 100644
--- a/tests/test_load_star.py
+++ b/tests/test_load_star.py
@@ -6,9 +6,9 @@
 def test_load_star():
     df = pd.DataFrame({"a": [1, 2, 3], "b": [4, 5, 6]})
 
-    starfile.write(df, "tmp.star", overwrite=True)
+    starfile.write(df, "tests/fixtures/tmp.star", overwrite=True)
 
-    ds = intake.open_star("tmp.star")
+    ds = intake.open_star("tests/fixtures/tmp.star")
 
     ds_read = ds.read()
     df_read = (