use a lockfile for "old" CI job #13490

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drammock wants to merge 52 commits into mne-tools:main from drammock:old-ci

.github/workflows/spec_zero.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -46,7 +46,11 @@ 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
+            # 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
+          - name: check if files changed
+            run: |
               git diff && git status --porcelain
               if [[ $(git status --porcelain) ]]; then
                 echo "dirty=true" >> $GITHUB_OUTPUT
@@ Expand Down @@

.github/workflows/tests.yml

            
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    @@ -151,11 +151,13 @@ jobs:
  
              create-args: >-

                python=${{ env.PYTHON_VERSION }}

                -v

            if: ${{ !startswith(matrix.kind, 'pip') }}

            if: matrix.kind == 'conda' || matrix.kind == 'mamba'

            timeout-minutes: 20

          - run: bash ./tools/github_actions_dependencies.sh

          - run: python ./tools/github_actions_check_old.py

          - uses: astral-sh/setup-uv@v7

            with:

              version: ">=0.9"

            if: matrix.kind == 'old'

          - 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'

environment.yml

            
                      Original file line number
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    @@ -7,32 +7,32 @@ dependencies:
  
      - antio >=0.5.0

      - curryreader >=0.1.2

      - darkdetect

      - decorator

      - decorator >=5.1

      - 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

      - joblib

      - jinja2 >=3.1

      - 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

    @@ -54,9 +54,9 @@ dependencies:
  
      - scipy >=1.12

      - sip

      - snirf

      - statsmodels

      - statsmodels >=0.6

      - threadpoolctl

      - tqdm

      - tqdm >=4.66

      - traitlets

      - trame

      - trame-vtk

pyproject.toml

            
                      Original file line number
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    @@ -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",

    @@ -36,21 +36,22 @@ doc = [
  
    ]

    test = [

      "codespell",

      "ipython != 8.7.0",  # for testing notebook backend; also in "full-no-qt" and "doc"

      "mypy",

      "numpydoc",

      "ipython >= 8.20",  # for testing notebook backend; also in "full-no-qt" and "doc"

      "mypy >= 0.14",

      "numpydoc >= 1.6",

      "pillow >= 10.2",

      "pre-commit",

      "pytest >= 8.0",

      "pytest-cov",

      "pytest-qt",

      "pytest-cov >= 4.1",

      "pytest-qt >= 4.3",

      "pytest-rerunfailures",

      "pytest-timeout",

      "ruff",

      "pytest-timeout >= 2.2",

      "ruff >= 0.1",

      "toml-sort",

      "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 +65,7 @@ test_extra = [
  
      "nbclient",

      "nbformat",

      "neo",

      "nitime",

      "nitime >= 0.7",

      "pybv",

      "snirf",

      "sphinx-gallery",

    @@ -90,15 +91,15 @@ classifiers = [
  
      "Topic :: Software Development",

    ]

    dependencies = [

      "decorator",

      "jinja2",

      "decorator >= 5.1",

      "jinja2 >= 3.1",

      "lazy_loader >= 0.3",

      "matplotlib >= 3.8",  # released 2023-09-15, will become 3.9 on 2026-05-15

      "numpy >= 1.26, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16

      "packaging",

      "pooch >= 1.5",

      "scipy >= 1.12",  # released 2024-01-20, will become 1.13 on 2026-04-02

      "tqdm",

      "tqdm >= 4.66",

    ]

    description = "MNE-Python project for MEG and EEG data analysis."

    dynamic = ["version"]

    @@ -117,6 +118,9 @@ maintainers = [{email = "dan@mccloy.info", name = "Dan McCloy"}]
  
    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), 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]

    @@ -133,42 +137,42 @@ 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 >= 2.2",  # 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",

      "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",

      "qtpy",

      "scikit-learn >= 1.4",  # released 2024-01-18, will become 1.5 on 2026-05-21

      "sip",

      "snirf",

      "statsmodels",

      "statsmodels >= 0.6",

      "threadpoolctl",

      "traitlets",

      "trame",

tools/check_qt_import.sh

-Original file line number
+Diff line change
@@ -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
@@ Expand Down @@

tools/github_actions_dependencies.sh

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -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

    @@ -16,15 +16,28 @@ 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"

    		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]"

    	fi

    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]"

    @@ -36,13 +49,25 @@ else
  
    	EXTRAS=""

    fi

    echo ""

    # until quantities releases...

    if [[ "${MNE_CI_KIND}" != "old" ]]; then

    	STD_ARGS="$STD_ARGS git+https://github.com/python-quantities/python-quantities"

    fi

    echo "::group::Installing test dependencies using pip"

    # Make sure we only pass non-empty groups argument

    if [ -z "$GROUP" ]; then

    	GROUP_ARG=""

    else

    	GROUP_ARG="--group=$GROUP"

    fi

    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=$GROUP

    python -m pip install $STD_ARGS $INSTALL_ARGS .$EXTRAS $GROUP_ARG

    set +x

    echo "::endgroup::"

tools/github_actions_download.sh

-Original file line number
+Diff line change
@@ -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)";
@@ Expand Down @@

tools/github_actions_env_vars.sh

-Original file line number
+Diff line change
@@ Expand Up / @@ -13,14 +13,13 @@ 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 $MNE_CI_KIND"
-        if [[ "$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
+        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)
@@ Expand Down @@

tools/github_actions_infos.sh

-Original file line number
+Diff line change
@@ -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()"

tools/github_actions_test.sh

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand Down @@

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