From 665f9a58c2c475bd3219f802376aa00cfd5a9df9 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 14 Nov 2025 10:57:44 -0600 Subject: [PATCH 01/57] placeholders --- .github/workflows/spec_zero.yml | 6 ++++++ .github/workflows/tests.yml | 3 +++ tools/github_actions_dependencies.sh | 2 ++ tools/github_actions_env_vars.sh | 2 ++ 4 files changed, 13 insertions(+) diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index 6a45f2876b6..73a1c6174f3 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -60,3 +60,9 @@ jobs: PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}).

*Adjustments may need to be made to shims in \`mne/fixes.py\` in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed") echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY if: steps.status.outputs.dirty == 'true' + # TODO add one or more steps here to (re)create the lockfile based on the pins + # found in pyproject.toml. For now, any dependency that has a >= pin should + # become an == pin, and all other pins should be unchanged. Don't forget to + # pin Python version based on the `requires-python` field. Ideally, this step + # should only run if the pins in pyproject.toml have changed (e.g., see how + # we use "dirty" above to make the "Create PR" step conditional). diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 507bf4ebfb1..45b31234f68 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -152,7 +152,10 @@ jobs: python=${{ env.PYTHON_VERSION }} -v if: ${{ !startswith(matrix.kind, 'pip') }} + # TODO this ↑↑↑ will include matrix.kind == 'old' but we no longer want it to timeout-minutes: 20 + # TODO add a step here to install uv or pixi using their provided action + # it should only happen for matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index f9a60080f4b..50dc24d5af9 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -27,6 +27,8 @@ if [ ! -z "$CONDA_ENV" ]; then GROUP="test_extra" EXTRAS="[hdf5]" fi +# TODO add a conditional branch here, that uses uv/pixi to recreate the "old" env +# from its lockfile, activate the env, and exit the bash script elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" diff --git a/tools/github_actions_env_vars.sh b/tools/github_actions_env_vars.sh index 9f424ae5f48..28326994b24 100755 --- a/tools/github_actions_env_vars.sh +++ b/tools/github_actions_env_vars.sh @@ -15,6 +15,8 @@ if [[ "$MNE_CI_KIND" == "pip"* ]]; then fi else # conda-like echo "Setting conda env vars for $MNE_CI_KIND" + # TODO pull this ↓↓↓ conditional branch out of its parent "else" clause, and + # adjust so it no longer sets a CONDA_ENV environment variable if [[ "$MNE_CI_KIND" == "old" ]]; then echo "CONDA_ENV=tools/environment_old.yml" | tee -a $GITHUB_ENV echo "MNE_IGNORE_WARNINGS_IN_TESTS=true" | tee -a $GITHUB_ENV From 5422e7a4b6984b18142a81f1e25666aa5c92cf69 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 19 Dec 2025 10:02:18 -0600 Subject: [PATCH 02/57] use resolution:lowest-direct; pin 2 unpinned deps to ensure resolution --- .github/workflows/spec_zero.yml | 11 +-- environment.yml | 4 +- pyproject.toml | 6 +- tools/pylock.ci-old.toml | 157 ++++++++++++++++++++++++++++++++ 4 files changed, 167 insertions(+), 11 deletions(-) create mode 100644 tools/pylock.ci-old.toml diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index 73a1c6174f3..73e43fadc8a 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -43,7 +43,10 @@ jobs: python-version: '3.12' - run: pip install packaging requests tomlkit - run: python tools/dev/spec_zero_update_versions.py - - run: | + - name: Create lockfile for old CI + run: uv pip compile pyproject.toml --python-version 3.10 --resolution lowest-direct --output-file tools/pylock.ci-old.toml + - name: check if files changed + run: | git diff && git status --porcelain if [[ $(git status --porcelain) ]]; then echo "dirty=true" >> $GITHUB_OUTPUT @@ -60,9 +63,3 @@ jobs: PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}).

*Adjustments may need to be made to shims in \`mne/fixes.py\` in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed") echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY if: steps.status.outputs.dirty == 'true' - # TODO add one or more steps here to (re)create the lockfile based on the pins - # found in pyproject.toml. For now, any dependency that has a >= pin should - # become an == pin, and all other pins should be unchanged. Don't forget to - # pin Python version based on the `requires-python` field. Ideally, this step - # should only run if the pins in pyproject.toml have changed (e.g., see how - # we use "dirty" above to make the "Create PR" step conditional). diff --git a/environment.yml b/environment.yml index b72d39925e4..a0b00f1bde2 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ dependencies: - antio >=0.5.0 - curryreader >=0.1.2 - darkdetect - - decorator + - decorator >=3.4 - defusedxml - dipy - edfio >=0.4.10 @@ -21,7 +21,7 @@ dependencies: - ipympl - ipython !=8.7.0 - ipywidgets - - jinja2 + - jinja2 >=2.1 - joblib - jupyter - lazy_loader >=0.3 diff --git a/pyproject.toml b/pyproject.toml index 4bcb69b0655..6d671b307de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -90,8 +90,8 @@ classifiers = [ "Topic :: Software Development", ] dependencies = [ - "decorator", - "jinja2", + "decorator >= 3.4", + "jinja2 >= 2.1", "lazy_loader >= 0.3", "matplotlib >= 3.8", # released 2023-09-15, will become 3.9 on 2026-05-15 "numpy >= 1.26, < 3", # released 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"ec21cddfe7724fc7cb4ba4bea7aa8e2ef36f607a4bab81aa6ce42a13dc3f03dd" } }] From ff35f5672297ce58d1c8a1a5c3eae638198c94f8 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 19 Dec 2025 13:18:19 -0600 Subject: [PATCH 03/57] install uv (and not micromamba) in old CI job Co-authored-by: Carina Forster --- .github/workflows/tests.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 45b31234f68..6e2da1ae4ff 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -151,11 +151,10 @@ jobs: create-args: >- python=${{ env.PYTHON_VERSION }} -v - if: ${{ !startswith(matrix.kind, 'pip') }} - # TODO this ↑↑↑ will include matrix.kind == 'old' but we no longer want it to + if: matrix.kind == 'conda' || matrix.kind == 'mamba' timeout-minutes: 20 - # TODO add a step here to install uv or pixi using their provided action - # it should only happen for matrix.kind == 'old' + - uses: astral-sh/setup-uv@v1 + if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh From 9fc848717e30dcf34ba51b412866de35b9530007 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 19 Dec 2025 13:45:04 -0600 Subject: [PATCH 04/57] don't set CONDA_ENV for old CI anymore --- tools/github_actions_env_vars.sh | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/tools/github_actions_env_vars.sh b/tools/github_actions_env_vars.sh index 28326994b24..08a232ad6b3 100755 --- a/tools/github_actions_env_vars.sh +++ b/tools/github_actions_env_vars.sh @@ -13,15 +13,12 @@ if [[ "$MNE_CI_KIND" == "pip"* ]]; then else echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV fi +elif [[ "$MNE_CI_KIND" == "old" ]]; then + echo "MNE_IGNORE_WARNINGS_IN_TESTS=true" | tee -a $GITHUB_ENV + echo "MNE_SKIP_NETWORK_TESTS=1" | tee -a $GITHUB_ENV + echo "MNE_QT_BACKEND=PyQt5" | tee -a $GITHUB_ENV else # conda-like echo "Setting conda env vars for $MNE_CI_KIND" - # TODO pull this ↓↓↓ conditional branch out of its parent "else" clause, and - # adjust so it no longer sets a CONDA_ENV environment variable - if [[ "$MNE_CI_KIND" == "old" ]]; then - echo "CONDA_ENV=tools/environment_old.yml" | tee -a $GITHUB_ENV - echo "MNE_IGNORE_WARNINGS_IN_TESTS=true" | tee -a $GITHUB_ENV - echo "MNE_SKIP_NETWORK_TESTS=1" | tee -a $GITHUB_ENV - echo "MNE_QT_BACKEND=PyQt5" | tee -a $GITHUB_ENV elif [[ "$MNE_CI_KIND" == "minimal" ]]; then echo "CONDA_ENV=tools/environment_minimal.yml" | tee -a $GITHUB_ENV echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV From 7e0af0cca0da2aeeb1304bb6970c6c0197148127 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 19 Dec 2025 13:57:04 -0600 Subject: [PATCH 05/57] restore from lockfile when setting up old CI --- pyproject.toml | 3 ++- tools/github_actions_dependencies.sh | 9 +++++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6d671b307de..b4ab26cf5f9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -118,7 +118,8 @@ name = "mne" readme = {content-type = "text/x-rst", file = "README.rst"} requires-python = ">= 3.10" # ↑↑↑↑↑↑↑↑↑↑↑ when this changes, bump the `--python-version` in the `uv pip compile ...` -# ↑↑↑↑↑↑↑↑↑↑↑ command in `.github/workflows/spec_zero.yaml` (astral-sh/uv/#16333) +# command in `.github/workflows/spec_zero.yaml` (astral-sh/uv/#16333), and also the +# `--python` version in the `uv venv` command in `tools/github_actions_dependencies.sh` scripts = {mne = "mne.commands.utils:main"} [project.optional-dependencies] diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 50dc24d5af9..5741635787d 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -27,8 +27,13 @@ if [ ! -z "$CONDA_ENV" ]; then GROUP="test_extra" EXTRAS="[hdf5]" fi -# TODO add a conditional branch here, that uses uv/pixi to recreate the "old" env -# from its lockfile, activate the env, and exit the bash script +elif [[ ${MNE_CI_KIND} == "old" ]]; then + GROUP="test" + EXTRAS="" + STD_ARGS="--progress-bar off" + uv venv --python 3.10 + uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml + source .venv/bin/activate elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" From c5fb37cd7b8aaf7750a89ddac82baacabb107fd2 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 19 Dec 2025 15:19:10 -0600 Subject: [PATCH 06/57] elif --- tools/github_actions_env_vars.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_env_vars.sh b/tools/github_actions_env_vars.sh index 08a232ad6b3..ca95fca4d2c 100755 --- a/tools/github_actions_env_vars.sh +++ b/tools/github_actions_env_vars.sh @@ -19,7 +19,7 @@ elif [[ "$MNE_CI_KIND" == "old" ]]; then echo "MNE_QT_BACKEND=PyQt5" | tee -a $GITHUB_ENV else # conda-like echo "Setting conda env vars for $MNE_CI_KIND" - elif [[ "$MNE_CI_KIND" == "minimal" ]]; then + if [[ "$MNE_CI_KIND" == "minimal" ]]; then echo "CONDA_ENV=tools/environment_minimal.yml" | tee -a $GITHUB_ENV echo "MNE_QT_BACKEND=PySide6" | tee -a $GITHUB_ENV else # conda, mamba (use warning level for completeness) From 7a342c63d0564c0998a4d8d79a39c66ecc308f3f Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 26 Dec 2025 17:33:52 -0600 Subject: [PATCH 07/57] update actions --- .github/workflows/spec_zero.yml | 4 +++- tools/github_actions_dependencies.sh | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index 79a4013f2ed..fac86fd4769 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -47,7 +47,9 @@ jobs: - run: pip install packaging requests tomlkit - run: python tools/dev/spec_zero_update_versions.py - name: Create lockfile for old CI - run: uv pip compile pyproject.toml --python-version 3.10 --resolution lowest-direct --output-file tools/pylock.ci-old.toml + # uv pip compile requires setting the python version explicitly in the command :( + # run: uv pip compile --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --resolution lowest-direct --format pylock.toml --output-file tools/pylock.old-ci.toml + run: uv export --format pylock.toml --group test --resolution lowest-direct --output-file tools/pylock.old-ci.toml - name: check if files changed run: | git diff && git status --porcelain diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 5741635787d..636cadd04e1 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -28,7 +28,7 @@ if [ ! -z "$CONDA_ENV" ]; then EXTRAS="[hdf5]" fi elif [[ ${MNE_CI_KIND} == "old" ]]; then - GROUP="test" + GROUP="" # group "test" already included when pylock file generated EXTRAS="" STD_ARGS="--progress-bar off" uv venv --python 3.10 From 21eae2ac4e2b0711baa7ef6087c0df9dd53f7462 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Fri, 26 Dec 2025 17:34:29 -0600 Subject: [PATCH 08/57] update dep pins to get uv export to actually work --- environment.yml | 20 ++++++++++---------- pyproject.toml | 40 ++++++++++++++++++++-------------------- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/environment.yml b/environment.yml index 7dd63efa1a8..7ccf9b81ca3 100644 --- a/environment.yml +++ b/environment.yml @@ -7,32 +7,32 @@ dependencies: - antio >=0.5.0 - curryreader >=0.1.2 - darkdetect - - decorator >=3.4 + - decorator >=3.5 - defusedxml - - dipy + - dipy >=0.8 - edfio >=0.4.10 - eeglabio - filelock >=3.18.0 - h5io >=0.2.4 - - h5py + - h5py >=2.4 - imageio >=2.6.1 - imageio-ffmpeg >=0.4.1 - ipyevents - ipympl - - ipython !=8.7.0 + - ipython >=2.0,!=8.7.0 - ipywidgets - - jinja2 >=2.1 - - joblib + - jinja2 >=2.7 + - joblib >=0.8 - jupyter - lazy_loader >=0.3 - mamba - matplotlib >=3.8 - mffpy >=0.5.7 - mne-qt-browser - - nibabel + - nibabel >=2.0 - nilearn - nomkl - - numba + - numba >=0.35 - numpy >=1.26,<3 - openmeeg >=2.5.7 - packaging @@ -45,7 +45,7 @@ dependencies: - pymatreader - PySide6 !=6.9.1 - python-neo - - python-picard + - python-picard >=0.4 - pyvista >=0.43 - pyvistaqt >=0.11 - qdarkstyle !=3.2.2 @@ -54,7 +54,7 @@ dependencies: - scipy >=1.11 - sip - snirf - - statsmodels + - statsmodels >=0.6 - threadpoolctl - tqdm - traitlets diff --git a/pyproject.toml b/pyproject.toml index 4fabdcf0127..1d29dff8ae8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,21 +1,21 @@ [build-system] build-backend = "hatchling.build" -requires = ["hatch-vcs", "hatchling"] +requires = ["hatch-vcs", "hatchling >= 1.27"] [dependency-groups] -dev = ["pip >= 25.1", "rcssmin", {include-group = "doc"}, {include-group = "test_extra"}] +dev = ["pip >= 25.1", "rcssmin >= 1.1", {include-group = "doc"}, {include-group = "test_extra"}] # Dependencies for building the documentation doc = [ "graphviz", "intersphinx_registry >= 0.2405.27", "ipython != 8.7.0", # also in "full-no-qt" and "test" - "memory_profiler", + "memory_profiler >= 0.16", "mne-bids", "mne-connectivity", "mne-gui-addons", "neo", - "numpydoc", - "openneuro-py", + "numpydoc >= 0.5", + "openneuro-py >= 2020.1", "psutil", "pydata_sphinx_theme >= 0.15.2", "pygments >= 2.13", @@ -24,7 +24,7 @@ doc = [ "pyxdf", "pyzmq != 24.0.0", "scikit-learn", - "seaborn != 0.11.2", + "seaborn >= 0.5, != 0.11.2", "selenium >= 4.27.1", "sphinx >= 6", "sphinx-design", @@ -37,12 +37,12 @@ doc = [ test = [ "codespell", "ipython != 8.7.0", # for testing notebook backend; also in "full-no-qt" and "doc" - "mypy", + "mypy >= 0.14", "numpydoc", "pre-commit", "pytest >= 8.0", "pytest-cov", - "pytest-qt", + "pytest-qt >= 1.1", "pytest-rerunfailures", "pytest-timeout", "ruff", @@ -50,7 +50,7 @@ test = [ "tomli; python_version<'3.11'", "twine", "vulture", - "wheel", + "wheel >= 0.21", ] # 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 @@ -64,7 +64,7 @@ test_extra = [ "nbclient", "nbformat", "neo", - "nitime", + "nitime >= 0.7", "pybv", "snirf", "sphinx-gallery", @@ -90,8 +90,8 @@ classifiers = [ "Topic :: Software Development", ] dependencies = [ - "decorator >= 3.4", - "jinja2 >= 2.1", + "decorator >= 3.5", + "jinja2 >= 2.7", "lazy_loader >= 0.3", "matplotlib >= 3.8", # released 2023-09-15, will become 3.9 on 2026-05-15 "numpy >= 1.26, < 3", # released 2023-09-16, will become 2.0 on 2026-06-16 @@ -136,34 +136,34 @@ full-no-qt = [ "curryreader >= 0.1.2", "darkdetect", "defusedxml", - "dipy", + "dipy >= 0.8", "edfio >= 0.4.10", "eeglabio", "filelock >= 3.18.0", - "h5py", + "h5py >= 2.4", "imageio >= 2.6.1", "imageio-ffmpeg >= 0.4.1", "ipyevents", "ipympl", - "ipython != 8.7.0", # for notebook backend; also in "doc" and "test" + "ipython >= 2.0, != 8.7.0", # for notebook backend; also in "doc" and "test" "ipywidgets", - "joblib", + "joblib >= 0.8", "jupyter", "mffpy >= 0.5.7", "mne-qt-browser", "mne[hdf5]", "neo", "nest-asyncio2", - "nibabel", + "nibabel >= 2.0", "nilearn", - "numba", + "numba >= 0.35", "openmeeg >= 2.5.7", "pandas >= 2.1", # released 2023-08-30, will become 2.2 on 2026-01-19 "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'", - "python-picard", + "python-picard >= 0.4", "pyvista >= 0.43", # released 2023-12-07, will become 0.44 on 2026-07-07 "pyvistaqt >= 0.11", # released 2023-06-30, no newer version available "qdarkstyle != 3.2.2", @@ -171,7 +171,7 @@ full-no-qt = [ "scikit-learn >= 1.3", # released 2023-06-30, will become 1.4 on 2026-01-17 "sip", "snirf", - "statsmodels", + "statsmodels >= 0.6", "threadpoolctl", "traitlets", "trame", From 3a5bfe40305f672397aae93c5510107de14bf5c4 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 12:47:33 +0000 Subject: [PATCH 09/57] Pin to newer uv version --- .github/workflows/tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c1626f8ca72..fc271c639cd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -153,7 +153,9 @@ jobs: -v if: matrix.kind == 'conda' || matrix.kind == 'mamba' timeout-minutes: 20 - - uses: astral-sh/setup-uv@v1 + - uses: astral-sh/setup-uv@v7 + with: + version: ">=0.9.x" if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) From b2122721ab84657f15070ca1c86fda19e42cb6e2 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 12:55:50 +0000 Subject: [PATCH 10/57] Update ver tag --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a7008e16724..09f88766f63 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -155,7 +155,7 @@ jobs: timeout-minutes: 20 - uses: astral-sh/setup-uv@v7 with: - version: ">=0.9.x" + version: ">=0.9" if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) From 2f5dbc9fc1f2ee36f9d161fb45bc98940e41f991 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 13:33:02 +0000 Subject: [PATCH 11/57] Fix lock file name --- .github/workflows/spec_zero.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index fac86fd4769..dcf06b34b55 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -48,8 +48,8 @@ jobs: - run: python tools/dev/spec_zero_update_versions.py - name: Create lockfile for old CI # uv pip compile requires setting the python version explicitly in the command :( - # run: uv pip compile --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --resolution lowest-direct --format pylock.toml --output-file tools/pylock.old-ci.toml - run: uv export --format pylock.toml --group test --resolution lowest-direct --output-file tools/pylock.old-ci.toml + # run: uv pip compile --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml + run: uv export --format pylock.toml --group test --resolution lowest-direct --output-file tools/pylock.ci-old.toml - name: check if files changed run: | git diff && git status --porcelain From 7688ec8499798c94850fe782979b027f0b5ef5cf Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 13:34:28 +0000 Subject: [PATCH 12/57] Add pip to venv --- tools/github_actions_dependencies.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 5f1f010b9b9..0784565bf3c 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -33,6 +33,7 @@ elif [[ ${MNE_CI_KIND} == "old" ]]; then STD_ARGS="--progress-bar off" uv venv --python 3.10 uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml + uv pip install pip source .venv/bin/activate elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" From 85c20e9759d049649adbec39b3cbedcacef51b28 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 13:41:46 +0000 Subject: [PATCH 13/57] Avoid empty groups arg --- tools/github_actions_dependencies.sh | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 0784565bf3c..96328729586 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -49,8 +49,15 @@ echo "" # until quantities releases... STD_ARGS="$STD_ARGS git+https://github.com/python-quantities/python-quantities" +# Make sure we only pass non-empty groups argument +if [ -z "$GROUP" ]; then + GROUP_ARG="" +else + GROUP_ARG="--group=$GROUP" +fi + echo "::group::Installing test dependencies using pip" set -x -python -m pip install $STD_ARGS $INSTALL_ARGS .$EXTRAS --group=$GROUP +python -m pip install $STD_ARGS $INSTALL_ARGS .$EXTRAS $GROUP_ARG set +x echo "::endgroup::" From 3d34c081d01c6027413047d7114e0529b69b2b23 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 24 Jan 2026 15:19:28 +0000 Subject: [PATCH 14/57] Update deps from spec0 --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1d29dff8ae8..7a279363d7b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -97,7 +97,7 @@ dependencies = [ "numpy >= 1.26, < 3", # released 2023-09-16, will become 2.0 on 2026-06-16 "packaging", "pooch >= 1.5", - "scipy >= 1.11", # released 2023-06-28, will become 1.12 on 2026-01-19 + "scipy >= 1.12", # released 2024-01-20, will become 1.13 on 2026-04-02 "tqdm", ] description = "MNE-Python project for MEG and EEG data analysis." @@ -158,7 +158,7 @@ full-no-qt = [ "nilearn", "numba >= 0.35", "openmeeg >= 2.5.7", - "pandas >= 2.1", # released 2023-08-30, will become 2.2 on 2026-01-19 + "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 "pillow", # for `Brain.save_image` and `mne.Report` "pyarrow", # only needed to avoid a deprecation warning in pandas "pybv", @@ -168,7 +168,7 @@ full-no-qt = [ "pyvistaqt >= 0.11", # released 2023-06-30, no newer version available "qdarkstyle != 3.2.2", "qtpy", - "scikit-learn >= 1.3", # released 2023-06-30, will become 1.4 on 2026-01-17 + "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 "sip", "snirf", "statsmodels >= 0.6", From e98514b29b878993d33dc7ed089159b78729d4b3 Mon Sep 17 00:00:00 2001 From: "Thomas S. 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{ url = "https://files.pythonhosted.org/packages/73/ae/b48f95715333080afb75a4504487cbe142cae1268afc482d06692d605ae6/yarl-1.22.0-py3-none-any.whl", upload-time = 2025-10-06T14:12:53Z, size = 46814, hashes = { sha256 = "1380560bdba02b6b6c90de54133c81c9f2a453dee9912fe58c1dcced1edb7cff" } }, -] From be03ca52547f116834ff9ebce1bca48e5804f5d2 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 21:31:06 +0000 Subject: [PATCH 19/57] Add extra dep pins --- pyproject.toml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7a279363d7b..9653438324b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,16 +36,17 @@ doc = [ ] test = [ "codespell", - "ipython != 8.7.0", # for testing notebook backend; also in "full-no-qt" and "doc" + "ipython >= 8.20", # for testing notebook backend; also in "full-no-qt" and "doc" "mypy >= 0.14", - "numpydoc", + "numpydoc >= 1.6", + "pillow >= 10.2", "pre-commit", "pytest >= 8.0", "pytest-cov", "pytest-qt >= 1.1", "pytest-rerunfailures", "pytest-timeout", - "ruff", + "ruff >= 0.1", "toml-sort", "tomli; python_version<'3.11'", "twine", From 32da34e54d36ff81c14c03c6cd19fb28157aa5e3 Mon Sep 17 00:00:00 2001 From: "Thomas S. 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Binns" Date: Sun, 25 Jan 2026 21:39:09 +0000 Subject: [PATCH 21/57] Re-delete quantities in action --- tools/github_actions_dependencies.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 96328729586..12284e6674a 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -46,8 +46,6 @@ else EXTRAS="" fi echo "" -# until quantities releases... -STD_ARGS="$STD_ARGS git+https://github.com/python-quantities/python-quantities" # Make sure we only pass non-empty groups argument if [ -z "$GROUP" ]; then From fc3bf72efefda74a90aafb2024f5c9a8a8be708f Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 21:57:09 +0000 Subject: [PATCH 22/57] Move up venv activation --- tools/github_actions_dependencies.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 12284e6674a..3bd218af95a 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -32,9 +32,9 @@ elif [[ ${MNE_CI_KIND} == "old" ]]; then EXTRAS="" STD_ARGS="--progress-bar off" uv venv --python 3.10 + source .venv/bin/activate uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml uv pip install pip - source .venv/bin/activate elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" From 04e60e6715086deefe7e07b0da29442aecffdb65 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 22:16:52 +0000 Subject: [PATCH 23/57] Try have source activated --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 09f88766f63..889b0cba4b3 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -160,7 +160,7 @@ jobs: - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh - if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' + if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' - run: bash ./tools/github_actions_infos.sh # Check Qt - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND From c2485d1a42f4af41e0a14a2f4742165ca23a47ba Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 22:22:18 +0000 Subject: [PATCH 24/57] Try have source activated --- .github/workflows/tests.yml | 2 +- tools/github_actions_infos.sh | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 889b0cba4b3..09f88766f63 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -160,7 +160,7 @@ jobs: - run: bash ./tools/github_actions_dependencies.sh # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh - if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' + if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' - run: bash ./tools/github_actions_infos.sh # Check Qt - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND diff --git a/tools/github_actions_infos.sh b/tools/github_actions_infos.sh index 95d18cdd2ba..9b1577909f7 100755 --- a/tools/github_actions_infos.sh +++ b/tools/github_actions_infos.sh @@ -1,5 +1,9 @@ #!/bin/bash -ef +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi + which mne mne sys_info -pd python -c "import numpy; numpy.show_config()" From 4cfe9662af1af02edd2f80df672c8077401904bc Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 22:27:46 +0000 Subject: [PATCH 25/57] Activate env in bash scripts --- tools/github_actions_download.sh | 4 ++++ tools/github_actions_test.sh | 3 +++ 2 files changed, 7 insertions(+) diff --git a/tools/github_actions_download.sh b/tools/github_actions_download.sh index 7543275b58e..4793077efb9 100755 --- a/tools/github_actions_download.sh +++ b/tools/github_actions_download.sh @@ -1,5 +1,9 @@ #!/bin/bash -ef +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi + if [ "${DEPS}" != "minimal" ]; then python -c 'import mne; mne.datasets.testing.data_path(verbose=True)'; python -c "import mne; mne.datasets.misc.data_path(verbose=True)"; diff --git a/tools/github_actions_test.sh b/tools/github_actions_test.sh index 202b041bc79..e6013253046 100755 --- a/tools/github_actions_test.sh +++ b/tools/github_actions_test.sh @@ -2,6 +2,9 @@ set -eo pipefail +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi if [[ "${CI_OS_NAME}" == "ubuntu"* ]]; then CONDITION="not (ultraslowtest or pgtest)" else # macOS or Windows From 8b9438337ba0bb3f7e3a7f8c16845ec6955470ca Mon Sep 17 00:00:00 2001 From: "Thomas S. 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Binns" Date: Sun, 25 Jan 2026 23:00:43 +0000 Subject: [PATCH 27/57] Add explicit PyQt5 to old test --- tools/github_actions_dependencies.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 3bd218af95a..3ed92b3f83a 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -34,7 +34,7 @@ elif [[ ${MNE_CI_KIND} == "old" ]]; then uv venv --python 3.10 source .venv/bin/activate uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml - uv pip install pip + uv pip install pip PyQt5 elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" From 2371c904430053e315633677d80b7ac3332a6fcb Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 23:21:13 +0000 Subject: [PATCH 28/57] Add dep pin --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 484df4bbdae..6eb6020a040 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ test = [ "pytest-cov >= 4.1", "pytest-qt >= 4.3", "pytest-rerunfailures", - "pytest-timeout", + "pytest-timeout >= 2.2", "ruff >= 0.1", "toml-sort", "tomli; python_version<'3.11'", From a4c102ff824676df85860eba43611b5138204d1d Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sun, 25 Jan 2026 23:26:50 +0000 Subject: [PATCH 29/57] Add dep pin --- tools/pylock.ci-old.toml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tools/pylock.ci-old.toml b/tools/pylock.ci-old.toml index a7cbbe2dc0d..8d54b73e786 100644 --- a/tools/pylock.ci-old.toml +++ b/tools/pylock.ci-old.toml @@ -399,8 +399,9 @@ sdist = { url = "https://files.pythonhosted.org/packages/47/9f/4b1dea735b5e419e0 [[packages]] name = "pytest-timeout" -version = "0.1" -sdist = { url = "https://files.pythonhosted.org/packages/fd/c9/bbbddea660ec7c8253ae48bd4d6a8386e7001a519a9fabd88055d13b74a5/pytest-timeout-0.1.tar.gz", upload-time = 2012-02-27T00:06:13Z, size = 4562, hashes = { sha256 = "6f25f0579aab685af1ed3626a45701bc36a5ba481a31f112d1abfc81abf9aa32" } } +version = "2.2.0" +sdist = { url = "https://files.pythonhosted.org/packages/2a/b0/8e3182e9ed65ad5b247f9d13769f214fc52b0d3522c3e1c8dbfa2f879e5a/pytest-timeout-2.2.0.tar.gz", upload-time = 2023-10-08T10:14:25Z, size = 16391, hashes = { sha256 = "3b0b95dabf3cb50bac9ef5ca912fa0cfc286526af17afc806824df20c2f72c90" } } +wheels = [{ url = "https://files.pythonhosted.org/packages/e2/3e/abfdb7319d71a179bb8f5980e211d93e7db03f0c0091794dbcd652d642da/pytest_timeout-2.2.0-py3-none-any.whl", upload-time = 2023-10-08T10:14:23Z, size = 13142, hashes = { sha256 = "bde531e096466f49398a59f2dde76fa78429a09a12411466f88a07213e220de2" } }] [[packages]] name = "python-dateutil" From 63c304396871725367bd22b760a1158ef46f672c Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Mon, 26 Jan 2026 19:38:57 +0000 Subject: [PATCH 30/57] Use env var for Qt backend --- tools/github_actions_dependencies.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 3ed92b3f83a..6be2ba1d589 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -34,7 +34,7 @@ elif [[ ${MNE_CI_KIND} == "old" ]]; then uv venv --python 3.10 source .venv/bin/activate uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml - uv pip install pip PyQt5 + uv pip install pip ${MNE_QT_BACKEND} elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" From a501a75bae54fd69b4d08232307e50c81d936dbe Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Mon, 26 Jan 2026 19:39:27 +0000 Subject: [PATCH 31/57] Add h5py to test deps --- pyproject.toml | 1 + tools/pylock.ci-old.toml | 6 ++++++ 2 files changed, 7 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 6eb6020a040..8118b1a197a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,6 +36,7 @@ doc = [ ] test = [ "codespell", + "h5py >= 3.10", "ipython >= 8.20", # for testing notebook backend; also in "full-no-qt" and "doc" "mypy >= 0.14", "numpydoc >= 1.6", diff --git a/tools/pylock.ci-old.toml b/tools/pylock.ci-old.toml index 8d54b73e786..d9e49af0fc9 100644 --- a/tools/pylock.ci-old.toml +++ b/tools/pylock.ci-old.toml @@ -151,6 +151,12 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/c7/4e/ce75a57ff3aebf6fc1f4e9d508b8e5810618a33d900ad6c19eb30b290b97/fonttools-4.61.1-py3-none-any.whl", upload-time = 2025-12-12T17:31:21Z, size = 1148996, hashes = { sha256 = "17d2bf5d541add43822bcf0c43d7d847b160c9bb01d15d5007d84e2217aaa371" } }, ] +[[packages]] +name = "h5py" +version = "3.10.0" +sdist = { url = "https://files.pythonhosted.org/packages/37/fc/0b1825077a1c4c79a13984c59997e4b36702962df0bca420698f77b70b10/h5py-3.10.0.tar.gz", upload-time = 2023-10-09T14:45:56Z, size = 403716, hashes = { sha256 = "d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049" } } +wheels = [{ url = "https://files.pythonhosted.org/packages/3b/d3/ecb4b3d2ec2c84132987e5f12ab1408f455bec1d90cd5bc408ebf37800f5/h5py-3.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2023-10-09T14:44:00Z, size = 4800680, hashes = { sha256 = "f42e6c30698b520f0295d70157c4e202a9e402406f50dc08f5a7bc416b24e52d" } }] + [[packages]] name = "hmako" version = "1.16" From df7f3fab71e1bb604b25ab4f878450979566cda8 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:08:57 +0000 Subject: [PATCH 32/57] Remove h5py from test deps --- pyproject.toml | 1 - tools/pylock.ci-old.toml | 6 ------ 2 files changed, 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8118b1a197a..6eb6020a040 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,6 @@ doc = [ ] test = [ "codespell", - "h5py >= 3.10", "ipython >= 8.20", # for testing notebook backend; also in "full-no-qt" and "doc" "mypy >= 0.14", "numpydoc >= 1.6", diff --git a/tools/pylock.ci-old.toml b/tools/pylock.ci-old.toml index d9e49af0fc9..8d54b73e786 100644 --- a/tools/pylock.ci-old.toml +++ b/tools/pylock.ci-old.toml @@ -151,12 +151,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/c7/4e/ce75a57ff3aebf6fc1f4e9d508b8e5810618a33d900ad6c19eb30b290b97/fonttools-4.61.1-py3-none-any.whl", upload-time = 2025-12-12T17:31:21Z, size = 1148996, hashes = { sha256 = "17d2bf5d541add43822bcf0c43d7d847b160c9bb01d15d5007d84e2217aaa371" } }, ] -[[packages]] -name = "h5py" -version = "3.10.0" -sdist = { url = "https://files.pythonhosted.org/packages/37/fc/0b1825077a1c4c79a13984c59997e4b36702962df0bca420698f77b70b10/h5py-3.10.0.tar.gz", upload-time = 2023-10-09T14:45:56Z, size = 403716, hashes = { sha256 = "d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049" } } -wheels = [{ url = "https://files.pythonhosted.org/packages/3b/d3/ecb4b3d2ec2c84132987e5f12ab1408f455bec1d90cd5bc408ebf37800f5/h5py-3.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2023-10-09T14:44:00Z, size = 4800680, hashes = { sha256 = "f42e6c30698b520f0295d70157c4e202a9e402406f50dc08f5a7bc416b24e52d" } }] - [[packages]] name = "hmako" version = "1.16" From 6f19fe41e49b40ad598b14fd183196832b7f9820 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:10:29 +0000 Subject: [PATCH 33/57] Remove environment_old.yml ver checks --- .github/workflows/tests.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 76ecf872aec..09f88766f63 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -158,8 +158,6 @@ jobs: version: ">=0.9" if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh - - run: python ./tools/github_actions_check_old.py - if: matrix.kind == 'old' # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' From 01f8d63b8b6e4ac729b60f251967e307aea1a8a3 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:18:41 +0000 Subject: [PATCH 34/57] Upgrade pip version for minimal --- tools/github_actions_dependencies.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 3e38c628273..3f0127f3c80 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -24,6 +24,7 @@ if [ ! -z "$CONDA_ENV" ]; then else GROUP="test_extra" EXTRAS="[hdf5]" + STD_ARGS="$STD_ARGS pip" # upgrade pip version fi elif [[ ${MNE_CI_KIND} == "old" ]]; then GROUP="" # group "test" already included when pylock file generated From 87dac63c3fa6b8d4f20626eb1fcc0b7870d735c2 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:38:35 +0000 Subject: [PATCH 35/57] Clean up old & minimal installation --- tools/github_actions_dependencies.sh | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 3f0127f3c80..532451d78df 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -7,7 +7,7 @@ STD_ARGS="--progress-bar off --upgrade" INSTALL_ARGS="-e" if [ ! -z "$CONDA_ENV" ]; then echo "Uninstalling MNE for CONDA_ENV=${CONDA_ENV}" - # This will fail if mne-base is not in the env (like in our minimial/old envs, so ||true them): + # This will fail if mne-base is not in the env (like in our minimal env, so ||true them): echo "::group::Uninstalling MNE" conda remove -c conda-forge --force -yq mne-base || true python -m pip uninstall -y mne || true @@ -16,24 +16,24 @@ if [ ! -z "$CONDA_ENV" ]; then if [[ "${RUNNER_OS}" != "Windows" ]] && [[ "${CONDA_ENV}" != "environment_"* ]]; then INSTALL_ARGS="" fi - # If on minimal or old, just install testing deps - if [[ "${CONDA_ENV}" == *'environment_'* ]]; then + # If on minimal, just install testing deps + if [[ "${MNE_CI_KIND}" == "minimal" ]]; then GROUP="test" EXTRAS="" - STD_ARGS="--progress-bar off" else GROUP="test_extra" EXTRAS="[hdf5]" - STD_ARGS="$STD_ARGS pip" # upgrade pip version fi -elif [[ ${MNE_CI_KIND} == "old" ]]; then +elif [[ "${MNE_CI_KIND}" == "old" ]]; then GROUP="" # group "test" already included when pylock file generated EXTRAS="" STD_ARGS="--progress-bar off" + echo "::group::Syncing old environment dependencies from lockfile using uv" uv venv --python 3.10 source .venv/bin/activate uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml uv pip install pip ${MNE_QT_BACKEND} + echo "::endgroup::" elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" EXTRAS="[full-pyside6]" @@ -58,7 +58,11 @@ else GROUP_ARG="--group=$GROUP" fi -echo "::group::Installing test dependencies using pip" +if [[ "${MNE_CI_KIND}" != "old" ]]; then + echo "::group::Installing test dependencies using pip" +else + echo "::group::Installing MNE in development mode using pip" +fi set -x python -m pip install $STD_ARGS $INSTALL_ARGS .$EXTRAS $GROUP_ARG set +x From 2c6d1e48299818b9bef5923c725eb48204136517 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:42:35 +0000 Subject: [PATCH 36/57] Upgrade pip version for minimal --- tools/github_actions_dependencies.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 532451d78df..73c0c7cf236 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -20,6 +20,7 @@ if [ ! -z "$CONDA_ENV" ]; then if [[ "${MNE_CI_KIND}" == "minimal" ]]; then GROUP="test" EXTRAS="" + STD_ARGS="$STD_ARGS pip" # upgrade pip version to support --group else GROUP="test_extra" EXTRAS="[hdf5]" From 8395a682e2ed875e8cd986df70b7b4a1cb109d77 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:46:39 +0000 Subject: [PATCH 37/57] Upgrade pip version for minimal --- tools/github_actions_dependencies.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 73c0c7cf236..38541480f89 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -20,7 +20,8 @@ if [ ! -z "$CONDA_ENV" ]; then if [[ "${MNE_CI_KIND}" == "minimal" ]]; then GROUP="test" EXTRAS="" - STD_ARGS="$STD_ARGS pip" # upgrade pip version to support --group + STD_ARGS="--progress-bar off" + python -m pip install --upgrade $STD_ARGS pip # upgrade pip to support --group else GROUP="test_extra" EXTRAS="[hdf5]" From 29da1d27797098dd15f6d3299ec43f88ef52f3fe Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 12:52:48 +0000 Subject: [PATCH 38/57] Add Qt to minimal env --- tools/github_actions_dependencies.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index 38541480f89..ed3be3e94ee 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -20,8 +20,10 @@ if [ ! -z "$CONDA_ENV" ]; then if [[ "${MNE_CI_KIND}" == "minimal" ]]; then GROUP="test" EXTRAS="" - STD_ARGS="--progress-bar off" - python -m pip install --upgrade $STD_ARGS pip # upgrade pip to support --group + STD_ARGS="--progress-bar off ${MNE_QT_BACKEND}" + echo "::group::Upgrading pip installation" + python -m pip install --upgrade pip # upgrade pip to support --group + echo "::endgroup::" else GROUP="test_extra" EXTRAS="[hdf5]" From f8ea7a7579228afc7cb578ba6377a8224d305b13 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 13:09:24 +0000 Subject: [PATCH 39/57] Call shell scripts with source --- .github/workflows/tests.yml | 8 ++++---- tools/github_actions_download.sh | 4 ---- tools/github_actions_infos.sh | 4 ---- tools/github_actions_test.sh | 3 --- 4 files changed, 4 insertions(+), 15 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 09f88766f63..17b8495a092 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -161,9 +161,9 @@ jobs: # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' - - run: bash ./tools/github_actions_infos.sh + - run: source ./tools/github_actions_infos.sh # Check Qt - - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND + - run: source ./tools/check_qt_import.sh $MNE_QT_BACKEND if: env.MNE_QT_BACKEND != '' - name: Run tests with no testing data run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/ @@ -173,8 +173,8 @@ jobs: with: key: ${{ env.TESTING_VERSION }} path: ~/mne_data - - run: bash ./tools/github_actions_download.sh - - run: bash ./tools/github_actions_test.sh # for some reason on macOS we need to run "bash X" in order for a failed test run to show up + - run: source ./tools/github_actions_download.sh + - run: source ./tools/github_actions_test.sh # for some reason on macOS we need to run "bash X" in order for a failed test run to show up - uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/tools/github_actions_download.sh b/tools/github_actions_download.sh index 4793077efb9..7543275b58e 100755 --- a/tools/github_actions_download.sh +++ b/tools/github_actions_download.sh @@ -1,9 +1,5 @@ #!/bin/bash -ef -if [[ ${MNE_CI_KIND} == "old" ]]; then - source .venv/bin/activate -fi - if [ "${DEPS}" != "minimal" ]; then python -c 'import mne; mne.datasets.testing.data_path(verbose=True)'; python -c "import mne; mne.datasets.misc.data_path(verbose=True)"; diff --git a/tools/github_actions_infos.sh b/tools/github_actions_infos.sh index 9b1577909f7..95d18cdd2ba 100755 --- a/tools/github_actions_infos.sh +++ b/tools/github_actions_infos.sh @@ -1,9 +1,5 @@ #!/bin/bash -ef -if [[ ${MNE_CI_KIND} == "old" ]]; then - source .venv/bin/activate -fi - which mne mne sys_info -pd python -c "import numpy; numpy.show_config()" diff --git a/tools/github_actions_test.sh b/tools/github_actions_test.sh index e6013253046..202b041bc79 100755 --- a/tools/github_actions_test.sh +++ b/tools/github_actions_test.sh @@ -2,9 +2,6 @@ set -eo pipefail -if [[ ${MNE_CI_KIND} == "old" ]]; then - source .venv/bin/activate -fi if [[ "${CI_OS_NAME}" == "ubuntu"* ]]; then CONDITION="not (ultraslowtest or pgtest)" else # macOS or Windows From 7e72395d549a7f7f8baaca05847da3d35546dd5f Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 13:14:50 +0000 Subject: [PATCH 40/57] Activate uv venv --- .github/workflows/tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 17b8495a092..a2daed30877 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -161,6 +161,8 @@ jobs: # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' + - run: source .venv/bin/activate + if: matrix.kind == 'old' - run: source ./tools/github_actions_infos.sh # Check Qt - run: source ./tools/check_qt_import.sh $MNE_QT_BACKEND From d0f6581d1746a69a3ada5898e50a461cad3b4097 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 13:24:10 +0000 Subject: [PATCH 41/57] Try calling from bash after venv activation --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a2daed30877..8e69334052a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -163,9 +163,9 @@ jobs: if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' - run: source .venv/bin/activate if: matrix.kind == 'old' - - run: source ./tools/github_actions_infos.sh + - run: bash ./tools/github_actions_infos.sh # Check Qt - - run: source ./tools/check_qt_import.sh $MNE_QT_BACKEND + - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND if: env.MNE_QT_BACKEND != '' - name: Run tests with no testing data run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/ @@ -175,8 +175,8 @@ jobs: with: key: ${{ env.TESTING_VERSION }} path: ~/mne_data - - run: source ./tools/github_actions_download.sh - - run: source ./tools/github_actions_test.sh # for some reason on macOS we need to run "bash X" in order for a failed test run to show up + - run: bash ./tools/github_actions_download.sh + - run: bash ./tools/github_actions_test.sh # for some reason on macOS we need to run "bash X" in order for a failed test run to show up - uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} From 6cbd9c5af7381c226ce543ef9f500138bc2c78d2 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 13:40:51 +0000 Subject: [PATCH 42/57] Restore venv activations within scripts --- .github/workflows/tests.yml | 2 -- tools/check_qt_import.sh | 4 ++++ tools/github_actions_download.sh | 4 ++++ tools/github_actions_infos.sh | 4 ++++ tools/github_actions_test.sh | 3 +++ 5 files changed, 15 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 8e69334052a..09f88766f63 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -161,8 +161,6 @@ jobs: # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' - - run: source .venv/bin/activate - if: matrix.kind == 'old' - run: bash ./tools/github_actions_infos.sh # Check Qt - run: bash ./tools/check_qt_import.sh $MNE_QT_BACKEND diff --git a/tools/check_qt_import.sh b/tools/check_qt_import.sh index dde00f497e7..3457a8b651d 100755 --- a/tools/check_qt_import.sh +++ b/tools/check_qt_import.sh @@ -1,5 +1,9 @@ #!/bin/bash -ef +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi + if [[ "$1" == "" ]]; then echo "Qt library must be provided as first argument" exit 1 diff --git a/tools/github_actions_download.sh b/tools/github_actions_download.sh index 7543275b58e..4793077efb9 100755 --- a/tools/github_actions_download.sh +++ b/tools/github_actions_download.sh @@ -1,5 +1,9 @@ #!/bin/bash -ef +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi + if [ "${DEPS}" != "minimal" ]; then python -c 'import mne; mne.datasets.testing.data_path(verbose=True)'; python -c "import mne; mne.datasets.misc.data_path(verbose=True)"; diff --git a/tools/github_actions_infos.sh b/tools/github_actions_infos.sh index 95d18cdd2ba..9b1577909f7 100755 --- a/tools/github_actions_infos.sh +++ b/tools/github_actions_infos.sh @@ -1,5 +1,9 @@ #!/bin/bash -ef +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi + which mne mne sys_info -pd python -c "import numpy; numpy.show_config()" diff --git a/tools/github_actions_test.sh b/tools/github_actions_test.sh index 202b041bc79..e6013253046 100755 --- a/tools/github_actions_test.sh +++ b/tools/github_actions_test.sh @@ -2,6 +2,9 @@ set -eo pipefail +if [[ ${MNE_CI_KIND} == "old" ]]; then + source .venv/bin/activate +fi if [[ "${CI_OS_NAME}" == "ubuntu"* ]]; then CONDITION="not (ultraslowtest or pgtest)" else # macOS or Windows From c86482d38ef42a94829ee51f59183586f4dba35d Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 16:11:07 +0000 Subject: [PATCH 43/57] Bump min dep vers --- pyproject.toml | 4 +-- tools/pylock.ci-old.toml | 72 ++++++++++++++++++---------------------- 2 files changed, 35 insertions(+), 41 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6eb6020a040..29e94326c8b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -91,8 +91,8 @@ classifiers = [ "Topic :: Software Development", ] dependencies = [ - "decorator >= 3.5", - "jinja2 >= 2.7", + "decorator >= 5.1", + "jinja2 >= 2.10", "lazy_loader >= 0.3", "matplotlib >= 3.8", # released 2023-09-15, will become 3.9 on 2026-05-15 "numpy >= 1.26, < 3", # released 2023-09-16, will become 2.0 on 2026-06-16 diff --git a/tools/pylock.ci-old.toml b/tools/pylock.ci-old.toml index 8d54b73e786..b79882300ba 100644 --- a/tools/pylock.ci-old.toml +++ b/tools/pylock.ci-old.toml @@ -107,9 +107,9 @@ wheels = [{ url = "https://files.pythonhosted.org/packages/98/a7/4fe7da308224102 [[packages]] name = "decorator" 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Binns" Date: Sat, 31 Jan 2026 17:42:37 +0000 Subject: [PATCH 47/57] Token commit --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d97dd5caba8..2643732921b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ test = [ "wheel >= 0.21", ] # 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 +# Changes here should be reflected in the mne/utils/config.py dev dependencies sectio test_extra = [ "edfio >= 0.4.10", "eeglabio", From 5ee1418073056ec3231d4b6af29607f4504fda8b Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Sat, 31 Jan 2026 17:42:45 +0000 Subject: [PATCH 48/57] Token commit --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2643732921b..d97dd5caba8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ test = [ "wheel >= 0.21", ] # 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 sectio +# Changes here should be reflected in the mne/utils/config.py dev dependencies section test_extra = [ "edfio >= 0.4.10", "eeglabio", From fd6f8e301a464ed16312a8671e486c1c89fc627b Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 20:41:25 +0000 Subject: [PATCH 49/57] Move auto-bumped opt deps to new group --- pyproject.toml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d97dd5caba8..af50de29c91 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -132,7 +132,12 @@ full = ["mne[full-no-qt]", "PyQt6 != 6.6.0", "PyQt6-Qt6 != 6.6.0, != 6.7.0"] # 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. +ver-auto-bumped = [ + "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 + "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 +] full-no-qt = [ + "mne[ver-auto-bumped]", "antio >= 0.5.0", "curryreader >= 0.1.2", "darkdetect", @@ -159,7 +164,6 @@ full-no-qt = [ "nilearn", "numba >= 0.35", "openmeeg >= 2.5.7", - "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 "pillow", # for `Brain.save_image` and `mne.Report` "pyarrow", # only needed to avoid a deprecation warning in pandas "pybv", @@ -169,7 +173,6 @@ full-no-qt = [ "pyvistaqt >= 0.11", # released 2023-06-30, no newer version available "qdarkstyle != 3.2.2", "qtpy", - "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 "sip", "snirf", "statsmodels >= 0.6", From 77a341c32f03eafe97ed934f2f5c565a21c7e1b1 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 20:42:00 +0000 Subject: [PATCH 50/57] Update lock file compilation for opt deps --- .github/workflows/spec_zero.yml | 2 +- tools/pylock.ci-old.toml | 55 ++++++++++++++++++++++++++++----- 2 files changed, 48 insertions(+), 9 deletions(-) diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index 85b02d47953..1e33da52edf 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -48,7 +48,7 @@ jobs: - run: python tools/dev/spec_zero_update_versions.py - name: Create lockfile for old CI # uv pip compile requires setting the python version explicitly in the command :( - run: uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml + run: uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --extra ver-auto-bumped --resolution 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["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. -ver-auto-bumped = [ - "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 - "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 -] full-no-qt = [ - "mne[ver-auto-bumped]", "antio >= 0.5.0", "curryreader >= 0.1.2", "darkdetect", @@ -158,6 +148,7 @@ full-no-qt = [ "mffpy >= 0.5.7", "mne-qt-browser", "mne[hdf5]", + "mne[ver-auto-bumped]", "neo", "nest-asyncio2", "nibabel >= 2.0", @@ -188,6 +179,15 @@ full-pyqt6 = ["mne[full]"] full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1, != 6.9.1"] # Dependencies for MNE-Python functions that use HDF5 I/O hdf5 = ["h5io >= 0.2.4", "pymatreader"] +# 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. +ver-auto-bumped = [ + "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 + "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 +] [project.urls] "Bug Tracker" = "https://github.com/mne-tools/mne-python/issues/" From 8a7d96c629405aea61cf42ffe1e8ed750f40707a Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 20:44:43 +0000 Subject: [PATCH 52/57] Undo some pre-commit changes --- pyproject.toml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index fe7e4061600..902d563f3b8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -127,6 +127,11 @@ scripts = {mne = "mne.commands.utils:main"} # Leave this one here for backward-compat data = [] 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 >= 0.5.0", "curryreader >= 0.1.2", @@ -179,11 +184,6 @@ full-pyqt6 = ["mne[full]"] full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1, != 6.9.1"] # Dependencies for MNE-Python functions that use HDF5 I/O hdf5 = ["h5io >= 0.2.4", "pymatreader"] -# 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. ver-auto-bumped = [ "pandas >= 2.2", # released 2024-01-20, will become 2.3 on 2027-06-05 "scikit-learn >= 1.4", # released 2024-01-18, will become 1.5 on 2026-05-21 From f3e58ea3e43af8df292fcff4fc3eeb669513f05a Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 22:25:38 +0000 Subject: [PATCH 53/57] Add check that lockfile compiles correctly --- .github/workflows/spec_zero.yml | 4 +- tools/check_old_lockfile.py | 73 +++++++++++++++++++++++++++++++++ 2 files changed, 76 insertions(+), 1 deletion(-) create mode 100644 tools/check_old_lockfile.py diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml index 1e33da52edf..b8e16078969 100644 --- a/.github/workflows/spec_zero.yml +++ b/.github/workflows/spec_zero.yml @@ -48,7 +48,9 @@ jobs: - run: python tools/dev/spec_zero_update_versions.py - name: Create lockfile for old CI # uv pip compile requires setting the python version explicitly in the command :( - run: uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --extra ver-auto-bumped --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml + run: | + uv pip compile pyproject.toml --python "3.10" --python-platform "x86_64-unknown-linux-gnu" --group test --extra ver-auto-bumped --resolution lowest-direct --format pylock.toml --output-file tools/pylock.ci-old.toml + python tools/check_old_lockfile.py - name: check if files changed run: | git diff && git status --porcelain diff --git a/tools/check_old_lockfile.py b/tools/check_old_lockfile.py new file mode 100644 index 00000000000..b961caed9b0 --- /dev/null +++ b/tools/check_old_lockfile.py @@ -0,0 +1,73 @@ +#!/usr/bin/env python + +# Authors: The MNE-Python contributors. +# License: BSD-3-Clause +# Copyright the MNE-Python contributors. + +from pathlib import Path + +from packaging.version import Version +from tomlkit.toml_file import TOMLFile + +project_root = Path(__file__).parent.parent + +# Get dependencies to check from pyproject.toml +pyproject = TOMLFile(project_root / "pyproject.toml") +pyproject_data = pyproject.read() +project_info = pyproject_data["project"] +check_deps = ( + project_info["dependencies"] + + project_info["optional-dependencies"]["ver-auto-bumped"] +) +n_want_deps = 11 # should be updated when we add more core deps or auto-bumped pins! +assert len(check_deps) == n_want_deps, ( + f"Number of dependencies being checked ({len(check_deps)=}) is not as " + f"expected {n_want_deps=}" +) + +# Get 'old' lockfile pins for dependencies +lockfile = TOMLFile(project_root / "tools/pylock.ci-old.toml") +lockfile_data = lockfile.read() +lockfile_packages = {pkg["name"]: pkg["version"] for pkg in lockfile_data["packages"]} + +# Check that the versions in the lockfile match the minimum versions in pyproject.toml +package_name_mapping = {"lazy_loader": "lazy-loader"} +bad_missing = [] +bad_version = [] +for dep in check_deps: + components = dep.split(">=") + if len(components) == 1: + continue + package = components[0].strip() + package = package_name_mapping.get(package, package) + pyproject_version = components[1].split(",")[0].strip() + + if package not in lockfile_packages.keys(): + bad_missing.append(package) + continue + lockfile_version = lockfile_packages[package] + + if Version(lockfile_version) != Version(pyproject_version): + bad_version.append( + f"`pyproject.toml` expects {package} == {pyproject_version}, but " + f"`pylock.ci-old.toml` has {lockfile_version}" + ) + +if bad_missing: + bad_missing = ( + "The following package(s) are missing from the `pylock.ci-old.toml` lockfile: " + + ", ".join(bad_missing) + ) +else: + bad_missing = "" + +if bad_version: + bad_version = ( + "The following package(s) have incorrect versions in the `pylock.ci-old.toml` " + "lockfile:\n" + "\n".join(bad_version) + ) +else: + bad_version = "" + +if bad_missing or bad_version: + raise RuntimeError("\n\n".join([bad_missing, bad_version])) From 709bbe9fcd5b66d73f8a173c27b564a44e644411 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 22:26:19 +0000 Subject: [PATCH 54/57] Add/update check that env dep vers are expected --- .github/workflows/tests.yml | 2 + tools/github_actions_check_old.py | 91 ++++++++++++++++++++++--------- 2 files changed, 67 insertions(+), 26 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 09f88766f63..76ecf872aec 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -158,6 +158,8 @@ jobs: version: ">=0.9" if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh + - run: python ./tools/github_actions_check_old.py + if: matrix.kind == 'old' # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old' diff --git a/tools/github_actions_check_old.py b/tools/github_actions_check_old.py index d1dc5550beb..8fa80440d83 100644 --- a/tools/github_actions_check_old.py +++ b/tools/github_actions_check_old.py @@ -4,32 +4,71 @@ # License: BSD-3-Clause # Copyright the MNE-Python contributors. + import importlib -import re -import sys +from importlib import metadata from pathlib import Path -want_parts = 7 # should be updated when we add more pins! -regex = re.compile(r"^ - ([a-zA-Z\-]+) =([0-9.]+)$", re.MULTILINE) -this_root = Path(__file__).parent -env_old_text = (this_root / "environment_old.yml").read_text("utf-8") -parts = regex.findall(env_old_text) -assert len(parts) == want_parts, f"{len(parts)=} != {want_parts=}" -bad = list() -mod_name_map = { - "scikit-learn": "sklearn", -} -for mod_name, want_ver in parts: - if mod_name == "python": - got_ver = ".".join(map(str, sys.version_info[:2])) - else: - try: - mod = importlib.import_module(mod_name_map.get(mod_name, mod_name)) - except Exception as exc: - bad.append(f"{mod_name}: not importable ({type(exc).__name__}: {exc})") - continue - got_ver = mod.__version__.lstrip("v") # pooch prepends v - if ".".join(got_ver.split(".")[:2]) != want_ver: - bad.append(f"{mod_name}: {got_ver} != {want_ver}") -if bad: - raise RuntimeError("At least one module is the wrong version:\n" + "\n".join(bad)) +from packaging.version import Version +from tomlkit.toml_file import TOMLFile + +project_root = Path(__file__).parent.parent + +# Get dependencies to check from pyproject.toml +pyproject = TOMLFile(project_root / "pyproject.toml") +pyproject_data = pyproject.read() +project_info = pyproject_data["project"] +check_deps = ( + project_info["dependencies"] + + project_info["optional-dependencies"]["ver-auto-bumped"] +) +n_want_deps = 11 # should be updated when we add more core deps or auto-bumped pins! +assert len(check_deps) == n_want_deps, ( + f"Number of dependencies being checked ({len(check_deps)=}) is not as " + f"expected {n_want_deps=}" +) + +# Check that the versions in the env match the minimum versions in pyproject.toml +package_name_mapping = {"scikit-learn": "sklearn"} +bad_missing = [] +bad_version = [] +for dep in check_deps: + components = dep.split(">=") + if len(components) == 1: + continue + package_name = components[0].strip() + package_import_name = package_name_mapping.get(package_name, package_name) + pyproject_version = components[1].split(",")[0].strip() + + try: + mod = importlib.import_module(package_import_name) + except Exception as exc: + bad_missing.append(f"{package_name}: ({type(exc).__name__}: {exc})") + continue + # Not all packages have a __version__ attribute, so use importlib.metadata instead + # Also requires the true package name, not the import variant (if different) + env_ver = metadata.version(package_name) + + if Version(env_ver) != Version(pyproject_version): + bad_version.append( + f"{package_name}: is {env_ver}; {pyproject_version} expected from " + "`pyproject.toml`" + ) + +if bad_missing: + bad_missing = "The following package(s) could not be imported:\n" + "\n".join( + bad_missing + ) +else: + bad_missing = "" + +if bad_version: + bad_version = ( + "The following package(s) have incorrect versions in the environment:\n" + + "\n".join(bad_version) + ) +else: + bad_version = "" + +if bad_missing or bad_version: + raise RuntimeError("\n\n".join([bad_missing, bad_version])) From d714cc307536b25e331f78f0d984bd14398ebacc Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 22:33:04 +0000 Subject: [PATCH 55/57] Add tomlkit to old install --- tools/github_actions_dependencies.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/github_actions_dependencies.sh b/tools/github_actions_dependencies.sh index ed3be3e94ee..8dc964045e4 100755 --- a/tools/github_actions_dependencies.sh +++ b/tools/github_actions_dependencies.sh @@ -36,7 +36,7 @@ elif [[ "${MNE_CI_KIND}" == "old" ]]; then uv venv --python 3.10 source .venv/bin/activate uv pip sync ${SCRIPT_DIR}/pylock.ci-old.toml - uv pip install pip ${MNE_QT_BACKEND} + uv pip install pip tomlkit ${MNE_QT_BACKEND} echo "::endgroup::" elif [[ "${MNE_CI_KIND}" == "pip" ]]; then GROUP="test_extra" From e03450fbc5d87a053b010126965658a97f34e520 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 22:40:16 +0000 Subject: [PATCH 56/57] Try fix env activation --- tools/check_old_lockfile.py | 2 -- tools/github_actions_check_old.py | 2 -- 2 files changed, 4 deletions(-) diff --git a/tools/check_old_lockfile.py b/tools/check_old_lockfile.py index b961caed9b0..d557d12c18c 100644 --- a/tools/check_old_lockfile.py +++ b/tools/check_old_lockfile.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - # Authors: The MNE-Python contributors. # License: BSD-3-Clause # Copyright the MNE-Python contributors. diff --git a/tools/github_actions_check_old.py b/tools/github_actions_check_old.py index 8fa80440d83..6173e629c16 100644 --- a/tools/github_actions_check_old.py +++ b/tools/github_actions_check_old.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - # Authors: The MNE-Python contributors. # License: BSD-3-Clause # Copyright the MNE-Python contributors. From 65a273abdd62444cf6dfaa900b76d88ecd7eb503 Mon Sep 17 00:00:00 2001 From: "Thomas S. Binns" Date: Thu, 5 Feb 2026 22:46:40 +0000 Subject: [PATCH 57/57] Try fix env activation --- .github/workflows/tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 76ecf872aec..d71a2820c77 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -158,7 +158,9 @@ jobs: version: ">=0.9" if: matrix.kind == 'old' - run: bash ./tools/github_actions_dependencies.sh - - run: python ./tools/github_actions_check_old.py + - run: | + source .venv/bin/activate + python ./tools/github_actions_check_old.py if: matrix.kind == 'old' # Minimal commands on Linux (macOS stalls) - run: bash ./tools/get_minimal_commands.sh