Move requirements to pyproject.toml (mne-tools#12178)

Co-authored-by: Eric Larson <[email protected]>

.circleci/config.yml

@@ -43,8 +43,8 @@ jobs:
             brew install [email protected]
             which python
             which pip
-            pip install --upgrade pip setuptools wheel
-            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve . -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt PyQt6
+            pip install --upgrade pip
+            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve .[full,test_extra]
             # 3D too slow on Apple's software renderer, and numba causes us problems
             pip uninstall -y vtk pyvista pyvistaqt numba
             mkdir -p test-results

.github/workflows/tests.yml

@@ -59,9 +59,6 @@ jobs:
           - os: ubuntu-latest
             python: '3.10'
             kind: conda
-          - os: ubuntu-latest
-            python: '3.10'
-            kind: notebook
           - os: ubuntu-latest
             python: '3.11'
             kind: pip-pre
@@ -87,7 +84,6 @@ jobs:
         with:
           qt: true
           pyvista: false
-        if: matrix.kind != 'notebook'
       # Python (if pip)
       - uses: actions/setup-python@v4
         with:
@@ -103,19 +99,13 @@ jobs:
           miniforge-variant: Mambaforge
           use-mamba: ${{ matrix.kind != 'conda' }}
         if: ${{ !startswith(matrix.kind, 'pip') }}
-      - name: 'Install OSMesa VTK variant'
-        run: |
-          # TODO: As of 2023/02/28, notebook tests need a pinned mesalib
-          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4" "numpy=1.24.4" "numba=0.57.1"
-          mamba list
-        if: matrix.kind == 'notebook'
       - run: ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: ./tools/get_minimal_commands.sh
         if: ${{ startswith(matrix.os, 'ubuntu') }}
       - run: ./tools/github_actions_install.sh
       - run: ./tools/github_actions_infos.sh
-      # Check Qt on non-notebook
+      # Check Qt
       - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
         if: ${{ env.MNE_QT_BACKEND != '' }}
       - name: Run tests with no testing data

MANIFEST.in

@@ -1,12 +1,6 @@
 include *.rst
 include LICENSE.txt
 include SECURITY.md
-include requirements.txt
-include requirements_base.txt
-include requirements_hdf5.txt
-include requirements_testing.txt
-include requirements_testing_extra.txt
-include requirements_doc.txt
 include mne/__init__.py
 
 recursive-include examples *.py

Makefile

@@ -24,8 +24,8 @@ clean-cache:
 
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache
 
-wheel_quiet:
-	$(PYTHON) setup.py -q sdist bdist_wheel
+wheel:
+	$(PYTHON) -m build
 
 sample_data:
 	@python -c "import mne; mne.datasets.sample.data_path(verbose=True);"
@@ -57,7 +57,7 @@ codespell:  # running manually
 check-manifest:
 	check-manifest -q --ignore .circleci/config.yml,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store,mne/_version.py
 
-check-readme: clean wheel_quiet
+check-readme: clean wheel
 	twine check dist/*
 
 nesting:

azure-pipelines.yml

@@ -51,8 +51,8 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -eo pipefail
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
-              python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
+              python -m pip install --progress-bar off --upgrade pip build
+              python -m pip install --progress-bar off -ve .[hdf5,test]
               python -m pip uninstall -yq pytest-qt  # don't want to set up display, etc. for this
               pre-commit install --install-hooks
             displayName: Install dependencies
@@ -107,8 +107,8 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -e
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1" qtpy nibabel
+              python -m pip install --progress-bar off --upgrade pip
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1" qtpy nibabel sphinx-gallery
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -166,11 +166,10 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -e
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
+              python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
-              python -m pip install --progress-bar off --upgrade -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt
-              python -m pip install -e .
+              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

doc/changes/v0.24.rst

@@ -191,7 +191,7 @@ Enhancements
 
 - All functions for reading and writing files should now automatically handle ``~`` (the tilde character) and expand it to the user's home directory. Should you come across any function that doesn't do it, please do let us know! (:gh:`9613`, :gh:`9845` by `Richard Höchenberger`_)
 
-- All functions accepting a FreeSurfer subjects directory via a ``subjects_dir`` parameter can now consume :py:class:`pathlib.Path` objects too (used to be only strings) (:gh:`9613` by `Richard Höchenberger`_)
+- All functions accepting a FreeSurfer subjects directory via a ``subjects_dir`` parameter can now consume :class:`pathlib.Path` objects too (used to be only strings) (:gh:`9613` by `Richard Höchenberger`_)
 
 - Add support for colormap normalization in :meth:`mne.time_frequency.AverageTFR.plot` (:gh:`9851` by `Clemens Brunner`_)
 

doc/development/contributing.rst

@@ -304,11 +304,11 @@ be reflected the next time you open a Python interpreter and ``import mne``
 Finally, we'll add a few dependencies that are not needed for running
 MNE-Python, but are needed for locally running our test suite::
 
-    $ pip install -r requirements_testing.txt
+    $ pip install -e .[test]
 
 And for building our documentation::
 
-    $ pip install -r requirements_doc.txt
+    $ pip install -e .[doc]
     $ conda install graphviz
 
 .. note::
@@ -329,9 +329,15 @@ To build documentation, you will also require `optipng`_:
 - On Windows, unzip :file:`optipng.exe` from the `optipng for Windows`_ archive
   into the :file:`doc/` folder. This step is optional for Windows users.
 
-You can also choose to install some optional linters for reStructuredText::
+There are additional optional dependencies needed to run various tests, such as
+scikit-learn for decoding tests, or nibabel for MRI tests. If you want to run all the
+tests, consider using our MNE installers (which provide these dependencies) or pay
+attention to the skips that ``pytest`` reports and install the relevant libraries.
+For example, this traceback::
 
-    $ conda install -c conda-forge sphinx-autobuild doc8
+    SKIPPED [2] mne/io/eyelink/tests/test_eyelink.py:14: could not import 'pandas': No module named 'pandas'
+
+indicates that ``pandas`` needs to be installed in order to run the Eyelink tests.
 
 
 .. _basic-git:

doc/links.inc

@@ -114,7 +114,6 @@
 
 .. installation links
 
-.. _requirements file:  https://raw.githubusercontent.com/mne-tools/mne-python/main/requirements.txt
 .. _NVIDIA CUDA GPU processing: https://developer.nvidia.com/cuda-zone
 .. _NVIDIA proprietary drivers: https://www.geforce.com/drivers
 

mne/epochs.py

@@ -1902,6 +1902,8 @@ def get_data(
 
             .. versionchanged:: 1.7
                The default changed from ``False`` to ``True``.
+
+            .. versionadded:: 1.6
         %(verbose)s
 
         Returns

mne/viz/_brain/tests/test_brain.py

@@ -8,7 +8,7 @@
 # License: Simplified BSD
 
 import os
-import sys
+import platform
 from pathlib import Path
 from shutil import copyfile
 
@@ -662,15 +662,20 @@ def test_single_hemi(hemi, renderer_interactive_pyvistaqt, brain_gc):
 
 @testing.requires_testing_data
 @pytest.mark.slowtest
-def test_brain_save_movie(tmp_path, renderer, brain_gc):
+@pytest.mark.parametrize("interactive_state", (False, True))
+def test_brain_save_movie(tmp_path, renderer, brain_gc, interactive_state):
     """Test saving a movie of a Brain instance."""
-    from imageio_ffmpeg import count_frames_and_secs
+    imageio_ffmpeg = pytest.importorskip("imageio_ffmpeg")
+    # TODO: Figure out why this fails -- some imageio_ffmpeg error
+    if os.getenv("MNE_CI_KIND", "") == "conda" and platform.system() == "Linux":
+        pytest.skip("Test broken for unknown reason on conda linux")
 
     brain = _create_testing_brain(
         hemi="lh", time_viewer=False, cortex=["r", "b"]
     )  # custom binarized
     filename = tmp_path / "brain_test.mov"
-    for interactive_state in (False, True):
+
+    try:
         # for coverage, we set interactivity
         if interactive_state:
             brain._renderer.plotter.enable()
@@ -688,11 +693,12 @@ def test_brain_save_movie(tmp_path, renderer, brain_gc):
             filename, time_dilation=1.0, tmin=tmin, tmax=tmax, interpolation="nearest"
         )
         assert filename.is_file()
-        _, nsecs = count_frames_and_secs(filename)
+        _, nsecs = imageio_ffmpeg.count_frames_and_secs(filename)
         assert_allclose(duration, nsecs, atol=0.2)
 
         os.remove(filename)
-    brain.close()
+    finally:
+        brain.close()
 
 
 _TINY_SIZE = (350, 300)
@@ -1093,7 +1099,7 @@ def test_brain_traces(renderer_interactive_pyvistaqt, hemi, src, tmp_path, brain
 # TODO: don't skip on Windows, see
 # https://github.com/mne-tools/mne-python/pull/10935
 # for some reason there is a dependency issue with ipympl even using pyvista
-@pytest.mark.skipif(sys.platform == "win32", reason="ipympl issue on Windows")
+@pytest.mark.skipif(platform.system() == "Windows", reason="ipympl issue on Windows")
 @testing.requires_testing_data
 def test_brain_scraper(renderer_interactive_pyvistaqt, brain_gc, tmp_path):
     """Test a simple scraping example."""