Merge remote-tracking branch 'upstream/main' into skip

* upstream/main: (366 commits) BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115) Add API entry list and map (mne-tools#10999) Add legacy decorator (mne-tools#11097) [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095) Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104) MRG: Fixes for mne-tools#11090 (mne-tools#11108) add test for edf units param (mne-tools#11105) BUG: Improve logic for bti (mne-tools#11102) add spectrum class (mne-tools#10184) ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099) ENH: Add temperature and galvanic (mne-tools#11090) Add error message when conversion of EEG locs to head space fails (mne-tools#11080) DOC: removed unnecessary line in PSF example (mne-tools#11085) FIX: Update helmet during ICP (mne-tools#11084) Fix various typos (mne-tools#11086) DOC: Rel BUG: don't assume that channel info contains particular keys (mne-tools#11074) [BUG] Fix plot_topomap with sphere="eeglab" (mne-tools#11081) Add `vmin` and `vmax` specification to `mne.Evoked.animate_topomap` (mne-tools#11073) Add _on_missing functionality to UpdateChannelsMixin (mne-tools#11077) ...
larsoner · Aug 29, 2022 · 99fa0c1 · 99fa0c1
2 parents e61a759 + d587b89
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -11,22 +11,14 @@
 
 version: 2.1
 
-_xvfb: &xvfb
-  name: Start Xvfb virtual framebuffer
-  command: |
-    echo "export DISPLAY=:99" >> $BASH_ENV
-    /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1280x1024x24 -ac +extension GLX +render -noreset -nolisten tcp -nolisten unix
-
 jobs:
     build_docs:
       parameters:
         scheduled:
           type: string
           default: "false"
       docker:
-        # Use 18.04 rather than 20.04 because MESA 20.0.8 on 18.04 has working
-        # transparency but 21.0.3 on 20.04 does not!
-        - image: cimg/base:stable-18.04
+        - image: cimg/base:current-22.04
       steps:
         - restore_cache:
             keys:
@@ -95,23 +87,20 @@ jobs:
             name: Set BASH_ENV
             command: |
               set -e
-              sudo apt update -qq
-              sudo apt install -qq libosmesa6 libglx-mesa0 libopengl0 libglx0 libdbus-1-3 \
-                libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 \
-                libxcb-render-util0 libxcb-shape0 libxcb-xfixes0 libxcb-xinerama0 \
-                graphviz optipng \
-                python3.8-venv python3-venv \
-                xvfb libxft2 ffmpeg
-              python3.8 -m venv ~/python_env
+              ./tools/setup_xvfb.sh
+              sudo apt install -qq graphviz optipng python3.10-venv python3-venv libxft2 ffmpeg
+              python3.10 -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 MNE_FULL_DATE=true" >> $BASH_ENV
               source tools/get_minimal_commands.sh
               echo "export MNE_3D_BACKEND=pyvistaqt" >> $BASH_ENV
+              echo "export MNE_3D_OPTION_MULTI_SAMPLES=1" >> $BASH_ENV
               echo "export MNE_BROWSER_BACKEND=qt" >> $BASH_ENV
               echo "export MNE_BROWSER_PRECOMPUTE=false" >> $BASH_ENV
               echo "export PATH=~/.local/bin/:$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
@@ -124,9 +113,6 @@ jobs:
             command: |
               neuromag2ft --version
 
-        - run:
-            <<: *xvfb
-
         - run:
             name: Install fonts needed for diagrams
             command: |
@@ -141,7 +127,7 @@ jobs:
               - pip-cache
         - restore_cache:
             keys:
-              - user-install-bin-cache
+              - user-install-bin-cache-310
 
         # Hack in uninstalls of libraries as necessary if pip doesn't do the right thing in upgrading for us...
         - run:
@@ -154,14 +140,14 @@ jobs:
             paths:
               - ~/.cache/pip
         - save_cache:
-            key: user-install-bin-cache
+            key: user-install-bin-cache-310
             paths:
-              - ~/.local/lib/python3.8/site-packages
+              - ~/.local/lib/python3.10/site-packages
               - ~/.local/bin
 
         - run:
-            name: Check PyQt5
-            command: LD_DEBUG=libs python -c "from PyQt5.QtWidgets import QApplication, QWidget; app = QApplication([])"
+            name: Check Qt
+            command: LD_DEBUG=libs python -c "from PySide6.QtWidgets import QApplication, QWidget; app = QApplication([])"
 
         # Load tiny cache so that ~/.mne does not need to be created below
         - restore_cache:
@@ -522,7 +508,7 @@ workflows:
             branches:
               only:
                 - main
-                - maint/0.24
+                - maint/1.1
 
   main:
     jobs:

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,4 +1,4 @@
-blank_issues_enabled: false
+blank_issues_enabled: true
 contact_links:
   - name: Forum
     url: https://mne.discourse.group

diff --git a/.github/ISSUE_TEMPLATE/documentation.md b/.github/ISSUE_TEMPLATE/documentation.md
@@ -10,6 +10,6 @@ assignees: ''
 For example: "add 'foo' to the glossary" or "add my favorite visualization to
 the ERP tutorial".*
 
-#### Proposed documentation ehancement
+#### Proposed documentation enhancement
 *Describe your proposed enhancement in detail. If you are requesting a new
 glossary term, please include a proposed definition.*
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -9,5 +9,5 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           artifact-path: 0/dev/index.html
-          circleci-jobs: build_docs_pr,build_docs_nightly
+          circleci-jobs: build_docs,build_docs_main
           job-title: Check the rendered docs here!
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -0,0 +1,72 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '44 14 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'javascript', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
diff --git a/.github/workflows/codespell_and_flake.yml b/.github/workflows/codespell_and_flake.yml
@@ -15,14 +15,14 @@ on:
 
 jobs:
   style:
-    timeout-minutes: 90
+    name: 'codespell and flake'
     runs-on: ubuntu-20.04
     env:
       CODESPELL_DIRS: 'mne/ doc/ tutorials/ examples/'
       CODESPELL_SKIPS: 'doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,*.bib,*.css'
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: '3.9'
           architecture: 'x64'
@@ -34,11 +34,11 @@ jobs:
         name: 'Setup flake8 annotations'
       - run: make flake
         name: 'Run flake8'
-      - uses: GuillaumeFavelier/actions-codespell@feat/quiet_level
+      - uses: codespell-project/actions-codespell@v1.0
         with:
           path: ${{ env.CODESPELL_DIRS }}
           skip: ${{ env.CODESPELL_SKIPS }}
-          quiet_level: '3'
           builtin: 'clear,rare,informal,names'
           ignore_words_file: 'ignore_words.txt'
+          uri_ignore_words_list: 'bu'
         name: 'Run codespell'
diff --git a/.github/workflows/compat_minimal.yml b/.github/workflows/compat_minimal.yml
@@ -13,8 +13,7 @@ on:
 jobs:
   # Minimal (runs with and without testing data)
   job:
-    timeout-minutes: 90
-    name: 'py3.7'
+    name: 'minimal 3.7'
     runs-on: ubuntu-20.04
     defaults:
       run:
@@ -31,7 +30,7 @@ jobs:
       PYTHONUNBUFFERED: '1'
       PYTHON_VERSION: '3.7'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - run: ./tools/setup_xvfb.sh
@@ -57,7 +56,7 @@ jobs:
       - shell: bash -el {0}
         run: MNE_SKIP_TESTING_DATASET_TESTS=true pytest -m "not (ultraslowtest or pgtest)" --tb=short --cov=mne --cov-report xml -vv -rfE mne/
         name: Run tests with no testing data
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
@@ -71,6 +70,6 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/github_actions_test.sh
         name: 'Run tests'
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: success()
         name: 'Upload coverage to CodeCov'
diff --git a/.github/workflows/compat_old.yml b/.github/workflows/compat_old.yml
@@ -12,8 +12,7 @@ on:
 
 jobs:
   job:
-    timeout-minutes: 90
-    name: 'py3.7'
+    name: 'old 3.7'
     runs-on: ubuntu-18.04
     defaults:
       run:
@@ -25,8 +24,9 @@ jobs:
       OPENBLAS_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
       PYTHON_VERSION: '3.7'
+      MNE_IGNORE_WARNINGS_IN_TESTS: 'true'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: conda-incubator/setup-miniconda@v2
@@ -47,7 +47,7 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/get_testing_version.sh
         name: 'Get testing version'
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
@@ -61,6 +61,6 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/github_actions_test.sh
         name: 'Run tests'
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: success()
         name: 'Upload coverage to CodeCov'
diff --git a/.github/workflows/linux_conda.yml b/.github/workflows/linux_conda.yml
@@ -11,10 +11,9 @@ on:
       - '*'
 
 jobs:
-  py39:
-    timeout-minutes: 90
+  py310:
     runs-on: ubuntu-20.04
-    name: py3.9
+    name: 'linux conda 3.10'
     defaults:
       run:
         shell: bash
@@ -24,9 +23,9 @@ jobs:
       MNE_LOGGING_LEVEL: 'warning'
       MKL_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.10'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: conda-incubator/setup-miniconda@v2
@@ -46,13 +45,17 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/github_actions_install.sh
         name: 'Install MNE'
+      - shell: bash -el {0}
+        run: |
+          QT_QPA_PLATFORM=xcb LIBGL_DEBUG=verbose LD_DEBUG=libs python -c "import pyvistaqt; pyvistaqt.BackgroundPlotter(show=True)"
+        name: 'Check Qt GL'
       - shell: bash -el {0}
         run: ./tools/github_actions_infos.sh
         name: 'Show infos'
       - shell: bash -el {0}
         run: ./tools/get_testing_version.sh
         name: 'Get testing version'
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
@@ -66,7 +69,7 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/github_actions_test.sh
         name: 'Run tests'
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: success()
         name: 'Upload coverage to CodeCov'
 
@@ -80,7 +83,7 @@ jobs:
       CONDA_ENV: 'server_environment.yml'
       PYTHON_VERSION: '3.8'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: 'mne'
@@ -98,7 +101,7 @@ jobs:
       - shell: bash -el {0}
         run: ./tools/get_testing_version.sh
         name: 'Get testing version'
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           key: ${{ env.TESTING_VERSION }}
           path: ~/mne_data
@@ -109,6 +112,6 @@ jobs:
       - shell: bash -el {0}
         run: pytest --tb=short -m "not pgtest" --cov=mne --cov-report=xml --cov-report=html -vv mne/viz
         name: 'Run viz tests'
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: success()
         name: 'Upload coverage to CodeCov'