Autogenerate environment.yml file from pyproject.toml (#12914)

Co-authored-by: Eric Larson <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/tests.yml

@@ -106,6 +106,7 @@ jobs:
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
             mamba
+            nomkl
         if: ${{ !startswith(matrix.kind, 'pip') }}
       # Make sure we have the right Python
       - run: python -c "import platform; assert platform.machine() == 'arm64', platform.machine()"

.pre-commit-config.yaml

@@ -64,10 +64,17 @@ repos:
         files: pyproject.toml
 
   # dependencies
+  - repo: local
+    hooks:
+      - id: update-env-file
+        name: Copy dependency changes from pyproject.toml to environment.yml
+        language: python
+        entry: ./tools/hooks/update_environment_file.py
+        files: pyproject.toml
   - repo: local
     hooks:
       - id: dependency-sync
-        name: Sync dependency list between pyproject.toml and README.rst
+        name: Copy core dependencies from pyproject.toml to README.rst
         language: python
         entry: ./tools/hooks/sync_dependencies.py
         files: pyproject.toml

environment.yml

@@ -1,67 +1,61 @@
+# THIS FILE IS AUTO-GENERATED BY tools/hooks/update_environment_file.py AND WILL BE OVERWRITTEN
 name: mne
 channels:
   - conda-forge
 dependencies:
   - python >=3.10
-  - pip
-  - numpy
-  - scipy
-  - openblas
-  - matplotlib
-  - tqdm
-  - pooch>=1.5
+  - antio >=0.4.0
+  - darkdetect
   - decorator
-  - h5io
-  - packaging
-  - numba
-  - pandas
-  - pyarrow
-  - xlrd
-  - scikit-learn
+  - defusedxml
+  - dipy
+  - edfio >=0.2.1
+  - eeglabio
+  - h5io >=0.2.4
   - h5py
-  - jinja2
-  - pillow
-  - statsmodels
-  - jupyter
-  - ipython !=8.7.0
-  - joblib
-  - psutil
-  - numexpr
-  - imageio
-  - spyder-kernels >=1.10.0
   - imageio >=2.6.1
   - imageio-ffmpeg >=0.4.1
-  - vtk >=9.2
-  - traitlets
-  - pyvista >=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0
-  - pyvistaqt >=0.4
-  - qdarkstyle !=3.2.2
-  - darkdetect
-  - dipy
+  - ipyevents
+  - ipympl
+  - ipython !=8.7.0
+  - ipywidgets
+  - jinja2
+  - joblib
+  - jupyter
+  - lazy_loader >=0.3
+  - matplotlib >=3.6
+  - mffpy >=0.5.7
+  - mne-qt-browser
   - nibabel
-  - openmeeg >=2.5.5
   - nilearn
+  - numba
+  - numpy >=1.23,<3
+  - openmeeg >=2.5.5
+  - packaging
+  - pandas
+  - pillow
+  - pip
+  - pooch >=1.5
+  - pyarrow
+  - pybv
+  - pymatreader
+  - PySide6 !=6.8.0,!=6.8.0.1
+  - python-neo
   - python-picard
+  - pyvista >=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0
+  - pyvistaqt >=0.4
+  - qdarkstyle !=3.2.2
   - qtpy
-  - pyside6 !=6.8.0,!=6.8.0.1
-  - mne-base
-  - seaborn-base
-  - mffpy >=0.5.7
-  - ipyevents
-  - ipywidgets
-  - ipympl
+  - scikit-learn
+  - scipy >=1.9
+  - sip
+  - snirf
+  - statsmodels
+  - threadpoolctl
+  - tqdm
+  - traitlets
   - trame
   - trame-vtk
   - trame-vuetify
-  - jupyter_client
-  - nbformat
-  - nbclient
-  - mne-qt-browser
-  - pymatreader
-  - eeglabio
-  - edfio >=0.2.1
-  - pybv
-  - mamba
-  - lazy_loader
-  - defusedxml
-  - python-neo
+  - vtk >=9.2
+  - xlrd

mne/utils/config.py

@@ -771,10 +771,12 @@ def sys_info(
         use_mod_names += (
             "# Testing",
             "pytest",
-            "nbclient",
             "statsmodels",
             "numpydoc",
             "flake8",
+            "jupyter_client",
+            "nbclient",
+            "nbformat",
             "pydocstyle",
             "nitime",
             "imageio",

pyproject.toml

@@ -22,12 +22,12 @@ classifiers = [
 dependencies = [
   "decorator",
   "jinja2",
-  "lazy_loader>=0.3",
-  "matplotlib>=3.6",
-  "numpy>=1.23,<3",
+  "lazy_loader >= 0.3",
+  "matplotlib >= 3.6",
+  "numpy >= 1.23,<3",
   "packaging",
-  "pooch>=1.5",
-  "scipy>=1.9",
+  "pooch >= 1.5",
+  "scipy >= 1.9",
   "tqdm",
 ]
 description = "MNE-Python project for MEG and EEG data analysis."
@@ -45,7 +45,7 @@ license = {text = "BSD-3-Clause"}
 maintainers = [{email = "[email protected]", name = "Dan McCloy"}]
 name = "mne"
 readme = {content-type = "text/x-rst", file = "README.rst"}
-requires-python = ">=3.10"
+requires-python = ">= 3.10"
 scripts = {mne = "mne.commands.utils:main"}
 
 [project.optional-dependencies]
@@ -55,97 +55,99 @@ dev = ["mne[doc,test]", "rcssmin"]
 # Dependencies for building the documentation
 doc = [
   "graphviz",
-  "intersphinx_registry>=0.2405.27",
-  "ipython!=8.7.0",
+  "intersphinx_registry >= 0.2405.27",
+  "ipython != 8.7.0",  # also in "full-no-qt" and "test"
   "memory_profiler",
   "mne-bids",
   "mne-connectivity",
   "mne-gui-addons",
   "neo",
   "numpydoc",
   "psutil",
-  "pydata_sphinx_theme>=0.15.2",
-  "pygments>=2.13",
+  "pydata_sphinx_theme >= 0.15.2",
+  "pygments >= 2.13",
   "pytest",
   "pyxdf",
-  "pyzmq!=24.0.0",
-  "seaborn!=0.11.2",
+  "pyzmq != 24.0.0",
+  "seaborn != 0.11.2",
   "selenium",
+  "sphinx >= 6",
   "sphinx-design",
-  "sphinx-gallery>=0.16",
-  "sphinx>=6",
+  "sphinx-gallery >= 0.16",
   "sphinx_copybutton",
-  "sphinxcontrib-bibtex>=2.5",
+  "sphinxcontrib-bibtex >= 2.5",
   "sphinxcontrib-towncrier",
   "sphinxcontrib-youtube",
   # https://github.com/sphinx-contrib/sphinxcontrib-towncrier/issues/92
-  "towncrier<24.7",
+  "towncrier < 24.7",
 ]
-full = ["mne[full-no-qt]", "PyQt6!=6.6.0", "PyQt6-Qt6!=6.6.0,!=6.7.0"]
+full = ["mne[full-no-qt]", "PyQt6 != 6.6.0", "PyQt6-Qt6 != 6.6.0, != 6.7.0"]
 # Dependencies for full MNE-Python functionality (other than raw/epochs export)
 # We first define a variant without any Qt bindings. The "complete" variant, mne[full],
 # makes an opinionated choice and installs PyQt6.
 # We also offter two more variants: mne[full-qt6] (which is equivalent to mne[full]),
 # and mne[full-pyside6], which will install PySide6 instead of PyQt6.
 full-no-qt = [
-  "antio>=0.4.0",
+  "antio >= 0.4.0",
   "darkdetect",
   "defusedxml",
   "dipy",
-  "edfio>=0.2.1",
+  "edfio >= 0.2.1",
   "eeglabio",
   "h5py",
-  "imageio-ffmpeg>=0.4.1",
-  "imageio>=2.6.1",
+  "imageio >= 2.6.1",
+  "imageio-ffmpeg >= 0.4.1",
   "ipyevents",
   "ipympl",
+  "ipython != 8.7.0",  # for notebook backend; also in "doc" and "test"
   "ipywidgets",
   "joblib",
   "jupyter",
-  "mffpy>=0.5.7",
+  "mffpy >= 0.5.7",
   "mne-qt-browser",
   "mne[hdf5]",
   "neo",
   "nibabel",
   "nilearn",
   "numba",
-  "openmeeg>=2.5.5",
+  "openmeeg >= 2.5.5",
   "pandas",
+  "pillow",  # for `Brain.save_image` and `mne.Report`
   "pyarrow",  # only needed to avoid a deprecation warning in pandas
   "pybv",
-  "pyobjc-framework-Cocoa>=5.2.0; platform_system=='Darwin'",
+  "pyobjc-framework-Cocoa >= 5.2.0; platform_system == 'Darwin'",
   "python-picard",
-  "pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0",
-  "pyvistaqt>=0.4",
-  "qdarkstyle!=3.2.2",
+  "pyvista >= 0.32, != 0.35.2, != 0.38.0, != 0.38.1, != 0.38.2, != 0.38.3, != 0.38.4, != 0.38.5, != 0.38.6, != 0.42.0",
+  "pyvistaqt >= 0.4",
+  "qdarkstyle != 3.2.2",
   "qtpy",
   "scikit-learn",
   "sip",
   "snirf",
-  # duplicated in test_extra:
   "statsmodels",
   "threadpoolctl",
   "traitlets",
   "trame",
   "trame-vtk",
   "trame-vuetify",
-  "vtk",
+  "vtk >= 9.2",
   "xlrd",
 ]
 full-pyqt6 = ["mne[full]"]
-full-pyside6 = ["mne[full-no-qt]", "PySide6!=6.7.0,!=6.8.0,!=6.8.0.1"]
+full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1"]
 # Dependencies for MNE-Python functions that use HDF5 I/O
-hdf5 = ["h5io>=0.2.4", "pymatreader"]
+hdf5 = ["h5io >= 0.2.4", "pymatreader"]
 # Dependencies for running the test infrastructure
 test = [
   "codespell",
+  "ipython != 8.7.0",  # for testing notebook backend; also in "full-no-qt" and "doc"
   "mypy",
   "numpydoc",
   "pre-commit",
+  "pytest >= 8.0",
   "pytest-cov",
   "pytest-qt",
   "pytest-timeout",
-  "pytest>=8.0.0rc2",
   "ruff",
   "toml-sort",
   "tomli; python_version<'3.11'",
@@ -154,14 +156,17 @@ test = [
   "wheel",
 ]
 # Dependencies for being able to run additional tests (rare/CIs/advanced devs)
+# Changes here should be reflected in the mne/utils/config.py dev dependencies section
 test_extra = [
-  "edfio>=0.2.1",
+  "edfio >= 0.2.1",
   "eeglabio",
-  "imageio-ffmpeg>=0.4.1",
-  "imageio>=2.6.1",
+  "imageio >= 2.6.1",
+  "imageio-ffmpeg >= 0.4.1",
+  "jupyter_client",
   "mne-bids",
   "mne[test]",
   "nbclient",
+  "nbformat",
   "neo",
   "nitime",
   "pybv",

tools/azure_dependencies.sh

@@ -9,7 +9,7 @@ if [ "${TEST_MODE}" == "pip" ]; then
 	python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy" -e .[test,full] "numpy<2"
 elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	${SCRIPT_DIR}/install_pre_requirements.sh
-	python -m pip install $STD_ARGS --pre -e .[test]
+	python -m pip install $STD_ARGS --pre -e .[test_extra]
 else
 	echo "Unknown run type ${TEST_MODE}"
 	exit 1