Repository: mne-tools/mne-nirs (language: python)

Issue:
Use MNE-BIDS official repo and update docs
With https://github.com/mne-tools/mne-bids/pull/406 merged we can change from using my fork for testing. And we can remove the confusing extra instructions from the documentation


Discussion / hints:

Fix patch:
diff --git a/Dockerfile b/Dockerfile
index f0f982b17..fb8e7f408 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,17 +1,19 @@
 ARG mne_python_v=main
 ARG nilearn_v=main
+ARG mne_bids_v=main
 ARG mne_nirs_v=main
 
 FROM ghcr.io/mne-tools/mne-python-plot:${mne_python_v}
 
 ARG nilearn_v
+ARG mne_bids_v
 ARG mne_nirs_v
 
 USER root
 
 RUN pip install statsmodels lets-plot dabest fooof h5io
 RUN pip install https://github.com/nilearn/nilearn/archive/${nilearn_v}.zip
-RUN pip install https://codeload.github.com/rob-luke/mne-bids/zip/nirs
+RUN pip install https://github.com/mne-tools/mne-bids/archive/${mne_bids_v}.zip
 RUN pip install https://github.com/mne-tools/mne-nirs/archive/${mne_nirs_v}.zip
 
 # Copy examples
diff --git a/examples/general/plot_12_group_glm.py b/examples/general/plot_12_group_glm.py
index 0ec1cc0fb..8aab41c3f 100644
--- a/examples/general/plot_12_group_glm.py
+++ b/examples/general/plot_12_group_glm.py
@@ -45,12 +45,9 @@
    This tutorial uses data in the BIDS format.
    The BIDS specification for NIRS data is still under development. See:
    `fNIRS BIDS proposal <https://github.com/bids-standard/bids-specification/pull/802>`_.
-   As such, to run this tutorial you must use the fNIRS development branch of MNE-BIDS.
+   As such, to run this tutorial you must use the MNE-BIDS 0.10 or later.
 
-   To install the fNIRS development branch of MNE-BIDS run:
-   `pip install -U https://codeload.github.com/rob-luke/mne-bids/zip/nirs`.
-
-   MNE-Python. allows you to process fNIRS data that is not in BIDS format too.
+   MNE-Python allows you to process fNIRS data that is not in BIDS format too.
    Simply modify the ``read_raw_`` function to match your data type.
    See :ref:`data importing tutorial <tut-importing-fnirs-data>` to learn how
    to use your data with MNE-Python.
diff --git a/examples/general/plot_13_fir_glm.py b/examples/general/plot_13_fir_glm.py
index 42830e740..81b080ea1 100644
--- a/examples/general/plot_13_fir_glm.py
+++ b/examples/general/plot_13_fir_glm.py
@@ -45,12 +45,9 @@
    This tutorial uses data in the BIDS format.
    The BIDS specification for NIRS data is still under development. See:
    `fNIRS BIDS proposal <https://github.com/bids-standard/bids-specification/pull/802>`_.
-   As such, to run this tutorial you must use the fNIRS development branch of MNE-BIDS.
+   As such, to run this tutorial you must use the MNE-BIDS 0.10 or later.
 
-   To install the fNIRS development branch of MNE-BIDS run:
-   `pip install -U https://codeload.github.com/rob-luke/mne-bids/zip/nirs`.
-
-   MNE-Python. allows you to process fNIRS data that is not in BIDS format too.
+   MNE-Python allows you to process fNIRS data that is not in BIDS format too.
    Simply modify the ``read_raw_`` function to match your data type.
    See :ref:`data importing tutorial <tut-importing-fnirs-data>` to learn how
    to use your data with MNE-Python.
diff --git a/examples/general/plot_16_waveform_group.py b/examples/general/plot_16_waveform_group.py
index 885ea6476..0dc566ff5 100644
--- a/examples/general/plot_16_waveform_group.py
+++ b/examples/general/plot_16_waveform_group.py
@@ -47,12 +47,9 @@
    This tutorial uses data in the BIDS format.
    The BIDS specification for NIRS data is still under development. See:
    `fNIRS BIDS proposal <https://github.com/bids-standard/bids-specification/pull/802>`_.
-   As such, to run this tutorial you must use the fNIRS development branch of MNE-BIDS.
+   As such, to run this tutorial you must use the MNE-BIDS 0.10 or later.
 
-   To install the fNIRS development branch of MNE-BIDS run:
-   `pip install -U https://codeload.github.com/rob-luke/mne-bids/zip/nirs`.
-
-   MNE-Python. allows you to process fNIRS data that is not in BIDS format too.
+   MNE-Python allows you to process fNIRS data that is not in BIDS format too.
    Simply modify the ``read_raw_`` function to match your data type.
    See :ref:`data importing tutorial <tut-importing-fnirs-data>` to learn how
    to use your data with MNE-Python.
diff --git a/examples/general/plot_50_decoding.py b/examples/general/plot_50_decoding.py
index f608c08c7..179760942 100644
--- a/examples/general/plot_50_decoding.py
+++ b/examples/general/plot_50_decoding.py
@@ -25,13 +25,9 @@
    This tutorial uses data in the BIDS format.
    The BIDS specification for NIRS data is still under development. See:
    `fNIRS BIDS proposal <https://github.com/bids-standard/bids-specification/pull/802>`_.
-   As such, to run this tutorial you must use the fNIRS development
-   branch of MNE-BIDS.
+   As such, to run this tutorial you must use the MNE-BIDS 0.10 or later.
 
-   To install the fNIRS development branch of MNE-BIDS run:
-   `pip install -U https://codeload.github.com/rob-luke/mne-bids/zip/nirs`.
-
-   MNE-Python. allows you to process fNIRS data that is not in BIDS format too.
+   MNE-Python allows you to process fNIRS data that is not in BIDS format too.
    Simply modify the ``read_raw_`` function to match your data type.
    See :ref:`data importing tutorial <tut-importing-fnirs-data>` to learn how
    to use your data with MNE-Python.
diff --git a/examples/general/plot_80_save_read_glm.py b/examples/general/plot_80_save_read_glm.py
index 0c2533935..38c172ade 100644
--- a/examples/general/plot_80_save_read_glm.py
+++ b/examples/general/plot_80_save_read_glm.py
@@ -29,10 +29,7 @@
 
    The BIDS specification for NIRS data is still under development. See:
    `fNIRS BIDS proposal <https://github.com/bids-standard/bids-specification/pull/802>`_.
-   As such, you must use the development branch of MNE-BIDS.
-
-   To install the fNIRS development branch of MNE-BIDS run:
-   `pip install https://codeload.github.com/rob-luke/mne-bids/zip/nirs`
+   As such, to run this tutorial you must use the MNE-BIDS 0.10 or later.
 
 .. contents:: Page contents
    :local:
diff --git a/requirements_doc.txt b/requirements_doc.txt
index 4faf76f79..f95a15706 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -13,7 +13,7 @@ matplotlib
 pillow
 numpy
 h5py
-https://codeload.github.com/rob-luke/mne-bids/zip/nirs
+https://github.com/mne-tools/mne-bids/archive/main.zip
 lets-plot
 memory_profiler
 Ipython


Test patch:
diff --git a/requirements_testing.txt b/requirements_testing.txt
index 1e4a80d55..4122710f5 100644
--- a/requirements_testing.txt
+++ b/requirements_testing.txt
@@ -14,7 +14,7 @@ wheel
 
 # mne-nirs specific requirements
 # redundancy with docs as all doc notebooks are tested
-https://codeload.github.com/rob-luke/mne-bids/zip/nirs
+https://github.com/mne-tools/mne-bids/archive/main.zip
 lets-plot
 seaborn
 fooof