[MAINT] using tox to test in different environments

.github/workflows/README.md

@@ -16,7 +16,7 @@ Automatically comments on a newly open pull request to provide some guidelines,
 
 ### black.yml
 
-Runs black code formatter on the codebase both in pull requests and on main. Configurations can be found in [pyproject.toml](/pyproject.toml).
+Runs black code formatter on the codebase both in pull requests and on main. Configurations can be found in [pyproject.toml](../../pyproject.toml).
 
 ## Building the development documentation
 
@@ -76,7 +76,7 @@ Runs only if the workflow in `build-docs.yml` completes successfully. Triggers t
 
 ### [.circleci/config.yml](/.circleci/config.yml)
 
-Artifacts hosting and deployment of development docs use CircleCI. See [.circleci/README.md](/.circleci/README.md) for details.
+Artifacts hosting and deployment of development docs use CircleCI. See [.circleci/README.md](../../.circleci/README.md) for details.
 On a pull request, only the "host" job is run. Then the artifacts can be accessed from the `host_and_deploy_doc` workflow seen under the checks list. Click on "Details" and then on the "host_docs" link on the page that opens. From there you can click on the artifacts tab to see all the html files. If you click on any of them you can then normally navigate the pages from there.
 With a merge on main, both "host" and "deploy" jobs are run.
 
@@ -92,34 +92,35 @@ It works by calling pytest with an environment variable that will trigger a pyte
 
 ### codespell.yml
 
-Checks for spelling errors. Configured in [pyproject.toml](/pyproject.toml). More information here: https://github.com/codespell-project/actions-codespell
+Checks for spelling errors. Configured in [pyproject.toml](../../pyproject.toml). More information here: https://github.com/codespell-project/actions-codespell
 
 ## PEP8 check
 
 ### flake8.yml
 
-Uses flake8 tool to verify code is PEP8 compliant. Configured in [.flake8](/.flake8)
+Uses flake8 tool to verify code is PEP8 compliant. Configured in [.flake8](../../.flake8)
 
 ## f strings
 
 ### f_strings.yml
 
-Checks for f strings in the codebase with [flynt](https://pypi.org/project/flynt/).
-Configured in [pyproject.toml](/pyproject.toml)
+Checks for f strings in the codebase with [flynt](https:/pypi.org/project/flynt/).
+Configured in [pyproject.toml](../../pyproject.toml)
 Flynt will check if it automatically convert "format" or "%" strings to "f strings".
 This workflow will fail if it finds any potential target to be converted.
 
 ## Sort imports automatically
 
 ### isort.yml
 
-Sorts Python imports alphabetically and by section. Configured in [pyproject.toml](/pyproject.toml)
+Sorts Python imports alphabetically and by section. Configured in [pyproject.toml](../../pyproject.toml)
 
 ## Running unit tests
 
-### testing.yml
+### test_with_tox.yml
 
 Runs pytest in several environments including several Python and dependencies versions as well as on different systems.
+All environments are defined in [tox.ini](../../tox.ini).
 
 ## Test installation
 

.github/workflows/build-docs.yml

@@ -17,8 +17,8 @@ on:
 
 jobs:
 
-  # Make citation metadata from CITATION.cff is valid.
-  # as it is used in the documentation build.
+    # Make citation metadata from CITATION.cff is valid.
+    # as it is used in the documentation build.
     validate_cff:
         if: github.repository == 'nilearn/nilearn'
         runs-on: ubuntu-latest
@@ -30,11 +30,11 @@ jobs:
             with:
                 args: --validate
 
-  # Steps to build the documentation.
+    # Steps to build the documentation.
     build_docs:
         needs: validate_cff
-    # This prevents this workflow from running on a fork.
-    # To test this workflow on a fork, uncomment the following line.
+        # This prevents this workflow from running on a fork.
+        # To test this workflow on a fork, uncomment the following line.
         if: github.repository == 'nilearn/nilearn'
         runs-on: ubuntu-latest
         timeout-minutes: 360
@@ -45,18 +45,19 @@ jobs:
         defaults:
             run:
                 shell: bash -el {0}
+
         steps:
         -   name: Source caching
             uses: actions/cache@v3
             with:
                 path: .git
                 key: source-cache-${{ runner.os }}-${{ github.run_id }}
-                restore-keys: |
-                    source-cache-${{ runner.os }}
+                restore-keys: source-cache-${{ runner.os }}
+
         -   name: Checkout nilearn
             uses: actions/checkout@v4
             with:
-          # If pull request, checkout HEAD commit with all commit history
+        # If pull request, checkout HEAD commit with all commit history
                 ref: ${{ github.event.pull_request.head.sha }}
                 fetch-depth: 0
         -   name: Complete checkout
@@ -77,23 +78,36 @@ jobs:
                     git pull --ff-only upstream "refs/pull/$(cat merge.txt)";
                 fi
 
-      # Set up environment
+        # Set up environment
         -   name: Install apt packages
             run: |
-                ./build_tools/github/build_docs_apt_dependencies.sh
-        -   name: Setup conda
-            uses: conda-incubator/setup-miniconda@v2
+                sudo -E apt-get -yq update
+                sudo -E apt-get -yq --no-install-suggests --no-install-recommends install \
+                    dvipng texlive-latex-base texlive-latex-extra
+        -   name: Setup python
+            uses: actions/setup-python@v4
             with:
-                auto-activate-base: true
-                activate-environment: ''
-                miniconda-version: latest
-                channels: conda-forge
-        -   name: Install packages in conda env
+                python-version: '3.12'
+        # Install the local version of the library, along with both standard and testing-related dependencies
+        # The `doc` dependency group is included because the build_docs job uses this script.
+        # See pyproject.toml for dependency group options
+        -   name: Install packages
             run: |
-                ./build_tools/github/build_docs_dependencies.sh
+                python -m pip install --user --upgrade pip setuptools
+                python -m pip install .[plotting,doc]
 
-      # Restore data from cache, or set up caching if data not found or
-      # [force download] is defined in commit message
+        # Check if we are doing a full or partial build
+        -   name: Find build type
+            run: ./build_tools/github/build_type.sh
+            env:
+                COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
+        -   name: Verify build type
+            run: |
+                echo "PATTERN = $(cat pattern.txt)"
+                echo "BUILD = $(cat build.txt)"
+
+        # Restore data from cache, or set up caching if data not found or
+        # [force download] is defined in commit message
         -   name: Determine restore data
             run: |
                 commit_msg=$(git log -2 --format=oneline);
@@ -105,6 +119,12 @@ jobs:
                   echo "Data cache will be used if available.";
                   echo "true" | tee restore.txt;
                 fi
+
+                if [[ "$(cat build.txt)" == "ci-html-noplot" ]]; then
+                  echo "Data cache will not be used for partial builds.";
+                  echo "false" | tee restore.txt;
+                fi
+
         -   name: Get cache key
             id: cache-key
             run: |
@@ -134,173 +154,145 @@ jobs:
             uses: actions/cache@v3
         # ~45 MB
             with:
-                path: |
-                    nilearn_data/adhd
+                path: nilearn_data/adhd
                 key: v1-adhd-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~32 MB
             with:
-                path: |
-                    nilearn_data/allen_rsn_2011
+                path: nilearn_data/allen_rsn_2011
                 key: v1-allen_rsn_2011-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~66 MB
             with:
-                path: |
-                    nilearn_data/brainomics_localizer
+                path: nilearn_data/brainomics_localizer
                 key: v1-brainomics_localizer-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~373 MB
             with:
-                path: |
-                    nilearn_data/development_fmri
+                path: nilearn_data/development_fmri
                 key: v1-development_fmri-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~832 MB
             with:
-                path: |
-                    nilearn_data/ds000030
+                path: nilearn_data/ds000030
                 key: v1-ds000030-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~82 MB
             with:
-                path: |
-                    nilearn_data/fiac_nilearn.glm
+                path: nilearn_data/fiac_nilearn.glm
                 key: v1-fiac_nilearn.glm-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~750 MB
             with:
-                path: |
-                    nilearn_data/fMRI-language-localizer-demo-dataset
+                path: nilearn_data/fMRI-language-localizer-demo-dataset
                 key: v1-fMRI-language-localizer-demo-dataset-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~30 MB
             with:
-                path: |
-                    nilearn_data/fsl
+                path: nilearn_data/fsl
                 key: v1-fsl-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~302 MB
             with:
-                path: |
-                    nilearn_data/haxby2001
+                path: nilearn_data/haxby2001
                 key: v1-haxby2001-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~63 MB
             with:
-                path: |
-                    nilearn_data/icbm152_2009
+                path: nilearn_data/icbm152_2009
                 key: v1-icbm152_2009-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~105 MB
             with:
-                path: |
-                    nilearn_data/jimura_poldrack_2012_zmaps
+                path: nilearn_data/jimura_poldrack_2012_zmaps
                 key: v1-jimura_poldrack_2012_zmaps-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~35 MB
             with:
-                path: |
-                    nilearn_data/localizer_first_level
+                path: nilearn_data/localizer_first_level
                 key: v1-localizer_first_level-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~181 MB
             with:
-                path: |
-                    nilearn_data/miyawaki2008
+                path: nilearn_data/miyawaki2008
                 key: v1-miyawaki2008-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~85 MB
             with:
-                path: |
-                    nilearn_data/nki_enhanced_surface
+                path: nilearn_data/nki_enhanced_surface
                 key: v1-nki_enhanced_surface-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~913 MB
             with:
-                path: |
-                    nilearn_data/oasis1
+                path: nilearn_data/oasis1
                 key: v1-oasis1-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~171 MB
             with:
-                path: |
-                    nilearn_data/smith_2009
+                path: nilearn_data/smith_2009
                 key: v1-smith_2009-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~230 MB
             with:
-                path: |
-                    nilearn_data/spm_auditory
+                path: nilearn_data/spm_auditory
                 key: v1-spm_auditory-${{ hashFiles('week_num') }}
         -   name: Data caching
             if: steps.cache-key.outputs.restore == 'true'
             uses: actions/cache@v3
         # ~227 MB
             with:
-                path: |
-                    nilearn_data/spm_multimodal_fmri
+                path: nilearn_data/spm_multimodal_fmri
                 key: v1-spm_multimodal_fmri-${{ hashFiles('week_num') }}
 
-      # Update the authors file and the names file
-      # in case a contributor has been added to citation.cff
-      # but did not run the maint_tools/citation_cff_maint.py script.
+        # Update the authors file and the names file
+        # in case a contributor has been added to citation.cff
+        # but did not run the maint_tools/citation_cff_maint.py script.
         -   name: update AUTHORS.rst and doc/changes/names.rst
             run: python maint_tools/citation_cff_maint.py
 
-      # Run the doc build. If no data is restored in previous steps, the data
-      # will be downloaded during the build (this only applies for full builds;
-      # no data is downloaded for partial builds).
-        -   name: Find build type
-            run: |
-                ./build_tools/github/build_type.sh
-            env:
-                COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
-        -   name: Verify build type
-            run: |
-                echo "PATTERN = $(cat pattern.txt)"
-                echo "BUILD = $(cat build.txt)"
-      # Set up and launch a virtual browser needed for one example to run
-      # without stalling the job. The example launches an html in the browser.
+        # Set up and launch a virtual browser needed for one example to run
+        # without stalling the job. The example launches an html in the browser.
         -   name: Set up display server for virtual browser
             run: |
                 Xvfb -ac :99 -screen 0 1280x1024x16 > /dev/null 2>&1 &
+
+        # Run the doc build. If no data is restored in previous steps, the data
+        # will be downloaded during the build (this only applies for full builds;
+        # no data is downloaded for partial builds).
         -   name: Build docs
             run: |
-                source activate testenv
-                echo "Conda active env = $CONDA_DEFAULT_ENV";
                 cd doc;
                 set -o pipefail;
                 PATTERN=$(cat ../pattern.txt) make $(cat ../build.txt) 2>&1 | tee log.txt;