[MAINT] Update to new Python and dev tools (#55)

* Update to new Python and dev tools Ran black Renamed docs/ -> doc/ Setup pyproject.toml Updated min Python version to 3.8 - 3.11 Updated GH actions and circleCI workflows --------- Signed-off-by: Adam Li <[email protected]> Co-authored-by: Eric Larson <[email protected]>
mne-tools · Sep 21, 2023 · 3de8c9d · 3de8c9d
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,146 +2,135 @@
 version: 2.1
 
 jobs:
-  docs-build:
+  build_doc:
     docker:
-      - image: circleci/python:3.8.5-buster
-    environment:
-      CODECOV_TOKEN: "895aebcc-753e-49f2-b964-b70d38d471c4"
+      - image: cimg/base:stable-20.04
     steps:
-      - checkout
-
-      # make sure pandoc is on the system
-      - run: sudo apt update && sudo apt install -y pandoc optipng
-
-      # restore cache from last build. Unless __init__.py has changed since then
       - restore_cache:
+          name: Restore .git
           keys:
-            - data-cache-0-{{ checksum "./mne_hfo/__init__.py" }}
-
-      # Also restore pip cache to speed up installations
-      - restore_cache: # ensure this step occurs *before* installing dependencies
-          keys:
-            # when lock file changes, use increasingly general patterns to restore cache
-            - pip-packages-v1-{{ .Branch }}-{{ checksum "Pipfile.lock" }}
-            - pip-packages-v1-{{ .Branch }}-
-            - pip-packages-v1-
-
-      - run:
-          name: Setup Python environment via Pipenv
-          command: |
-            sudo pip install --upgrade pip
-            sudo pip install pipenv
-            pipenv install --skip-lock --dev
-            pipenv run pip install --upgrade --progress-bar off https://github.com/mne-tools/mne-python/zipball/main
-
-      - run:
-          name: Run style check
-          command: |
-            pipenv run make pep
-
-      - run:
-          name: Build the documentation
-          command: |
-            pipenv run make build-doc
-
-      - persist_to_workspace:
-          root: docs/_build
-          paths: html
-
-      - store_artifacts:
-          path: docs/_build/html/
-          destination: dev
-
-      - save_cache:
-          key: pip-packages-v1-{{ .Branch }}-{{ checksum "Pipfile.lock" }}
-          paths:
-            - "~/.local/share/virtualenvs/venv"
-
-  docs-build-test:
-    docker:
-      - image: circleci/python:3.8.1-buster
-    environment:
-      CODECOV_TOKEN: "895aebcc-753e-49f2-b964-b70d38d471c4"
-    steps:
-      - restore_cache:
-            keys:
-              - source-cache-hfo
-
+            - source-cache-hfo
       - checkout
-
       - run:
           name: Complete checkout
           command: |
             if ! git remote -v | grep upstream; then
-              git remote add upstream git://github.com/mne-tools/mne-hfo.git
+              git remote add upstream https://github.com/mne-tools/mne-hfo.git
             fi
+            git remote set-url upstream https://github.com/mne-tools/mne-hfo.git
             git fetch upstream
-
       - save_cache:
+          name: Save .git
           key: source-cache-hfo
           paths:
             - ".git"
-
-      # make sure pandoc is on the system
-      - run: sudo apt update && sudo apt install -y pandoc
-
-      # Load pip cache
+      - run:
+          name: Check-skip
+          command: |
+            set -e
+            export COMMIT_MESSAGE=$(git log --format=oneline -n 1);
+            if [[ -v CIRCLE_PULL_REQUEST ]] && ([[ "$COMMIT_MESSAGE" == *"[skip circle]"* ]] || [[ "$COMMIT_MESSAGE" == *"[circle skip]"* ]]); then
+              echo "Skip detected, exiting job ${CIRCLE_JOB} for PR ${CIRCLE_PULL_REQUEST}."
+              circleci-agent step halt;
+            fi
+      - run:
+          name: Merge with upstream
+          command: |
+            echo $(git log -1 --pretty=%B) | tee gitlog.txt
+            echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+            if [[ $(cat merge.txt) != "" ]]; then
+              echo "Merging $(cat merge.txt)";
+              git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+            fi
+      - run:
+          name: Set BASH_ENV
+          command: |
+            set -e
+            curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/setup_xvfb.sh -o setup_xvfb.sh
+            chmod +x setup_xvfb.sh
+            ./setup_xvfb.sh
+            sudo apt install -qq graphviz optipng python3.9-venv python3-venv libxft2
+            python3.9 -m venv ~/python_env
+            echo "set -e" >> $BASH_ENV
+            echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+            echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
+            echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
+            echo "export DISPLAY=:99" >> $BASH_ENV
+            echo "source ~/python_env/bin/activate" >> $BASH_ENV
+            mkdir -p ~/.local/bin
+            ln -s ~/python_env/bin/python ~/.local/bin/python
+            echo "BASH_ENV:"
+            cat $BASH_ENV
+      - run:
+          name: Setup pandoc
+          command: sudo apt update && sudo apt install -y pandoc optipng
       - restore_cache:
+          name: Restore pip cache
           keys:
             - pip-cache
       - restore_cache:
+          name: Restore install-bin-cache
           keys:
             - user-install-bin-cache
-
       - run:
-          name: Setup Python environment
+          name: Get Python running and install dependencies
           command: |
-            python -m pip install --upgrade --progress-bar off --only-binary matplotlib -r requirements.txt
-            python -m pip install --upgrade --progress-bar off -r requirements_testing.txt
-            python -m pip install --upgrade --progress-bar off https://github.com/mne-tools/mne-python/zipball/main
-            python -m pip install --progress-bar off https://github.com/sphinx-gallery/sphinx-gallery/zipball/master
-            sudo python -m pip install -e .
-
+            python -m pip install --progress-bar off --upgrade pip setuptools wheel
+            python -m pip install --progress-bar off .
+            python -m pip install --progress-bar off .[doc]
+            python -m pip install --progress-bar off git+https://github.com/mne-tools/mne-python
       - save_cache:
+          name: Save pip cache
           key: pip-cache
           paths:
             - ~/.cache/pip
-
       - save_cache:
+          name: Save install-bin-cache
           key: user-install-bin-cache
           paths:
-            - ~/.local/lib/python3.8/site-packages
+            - ~/.local/lib/python3.9/site-packages
             - ~/.local/bin
-
-      # Look at what we have and fail early if there is some library conflict
+      - run:
+          name: Check pip package versions
+          command: pip freeze
+      - run:
+          name: Display MNE infos
+          command: QT_DEBUG_PLUGINS=1 mne sys_info -pd
       - run:
           name: Check installation
           command: |
-              which python
-              python -c "import mne; mne.sys_info()"
               LIBGL_DEBUG=verbose python -c "import matplotlib.pyplot as plt; plt.figure()"
               python -c "import mne; mne.set_config('MNE_LOGGING_LEVEL', 'info')"
               python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"
-
+              python -c "import numpy; numpy.show_config()"
       - run:
-          name: Build the documentation
+          name: Build documentation
           command: |
-            make build-doc
-
-      - persist_to_workspace:
-          root: docs/_build
-          paths: html
-
+            cd doc
+            make html
+      # Save the example test results
+      - store_test_results:
+          path: doc/_build/test-results
       - store_artifacts:
-          path: docs/_build/html/
+          path: doc/_build/test-results
+          destination: test-results
+      # Save the SG RST
+      - store_artifacts:
+          path: doc/auto_examples.zip
+      - store_artifacts:
+          path: doc/generated.zip
+      # Save the outputs
+      - store_artifacts:
+          path: doc/_build/html/
           destination: dev
-
-#      - run:
-#          name: Check links
-#          command: |
-#            pipenv run make -C doc clean
-#            pipenv run make -C docs linkcheck
-#            pipenv run make -C doc linkcheck-grep
+      # - store_artifacts:
+      #     path: doc/_build/html_stable/
+      #     destination: stable
+      - persist_to_workspace:
+          root: doc/_build
+          paths:
+            - html
+            # - html_stable
 
   docs-deploy:
     # will only be run on master branch
@@ -172,22 +161,10 @@ jobs:
 workflows:
   commit:
     jobs:
-      - docs-build
+      - build_doc
       - docs-deploy:
           requires:
-            - docs-build
-          filters:
-            branches:
-              only: master
-
-  scheduled:
-    jobs:
-      - docs-build
-
-    triggers:
-      - schedule:
-          cron: "0 4 * * *"
+            - build_doc
           filters:
             branches:
-              only:
-                - master
+              only: main
diff --git a/.codespellignore b/.codespellignore
@@ -0,0 +1,5 @@
+raison
+ue
+f0
+fo
+Yse
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,26 @@
+[flake8]
+max-line-length = 100
+
+ignore =
+    # these rules don't play well with black
+    # whitespace before ':'
+    E203
+    # line break before binary operator
+    W503
+    E241,E305,W504,W605,E731
+
+exclude =
+    .git
+    .github
+    .venv
+    .mypy_cache
+    .pytest_cache
+    .circleci
+    paper
+    setup.py
+    doc
+
+per-file-ignores =
+    # __init__.py files are allowed to have unused imports
+    */__init__.py:F401
+    */**/__init__.py:F401
diff --git a/.github/workflows/cffconvert.yml b/.github/workflows/cffconvert.yml
@@ -0,0 +1,22 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+  pull_request:
+    paths:
+      - CITATION.cff        
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v4
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"
diff --git a/.github/workflows/main.yml → .github/workflows/circle_artifacts.yml b/.github/workflows/main.yml → .github/workflows/circle_artifacts.yml
@@ -1,13 +1,16 @@
 on: [status]
 jobs:
   circleci_artifacts_redirector_job:
+    if: "${{ startsWith(github.event.context, 'ci/circleci: build_doc') }}"
     runs-on: ubuntu-20.04
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step
         uses: larsoner/circleci-artifacts-redirector-action@master
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+          api-token: ${{ secrets.CIRCLECI_TOKEN }}
           artifact-path: 0/dev/index.html
-          circleci-jobs: docs-build
+          circleci-jobs: build_doc
+          job-title: Check the rendered docs here!