Merge remote-tracking branch 'upstream/main' into cola5

* upstream/main: (32 commits) MAINT: Update download buttons [skip azp] [skip actions] [skip cirrus] Fix canvas.draw() in callback (mne-tools#11697) Remove recursion in plot_ica_components and use context manager for plt.ion/plt.ioff (mne-tools#11696) Update affiliation (mne-tools#11695) BUG: Fix bug with fwd restriction (mne-tools#11694) MRG: Suggest using "conda rename" in MNE updating instructions (mne-tools#11692) FIX: Regex [ci skip] MAINT: Apply deprecations [circle deploy] (mne-tools#11687) MAINT: Release 1.4.0 (mne-tools#11686) Trap music (mne-tools#11679) Fix call to plot_tfr_topomap from interactive AverageTFR.plot_topo function (mne-tools#11683) silence spectrum plot warning in examples/tutorials [circle full] (mne-tools#11682) Spectrum plot picks (mne-tools#11680) Update website conf (mne-tools#11675) BUG: Fix bug with MF LCMV rank (mne-tools#11664) ENH: Change known_config_types to dict (mne-tools#11166) MAINT: Improve README (mne-tools#11673) MAINT: Add to git-blame-ignore-revs [circle front] MAINT: Run black on codebase MAINT: Use black ...
larsoner · May 18, 2023 · 954a990 · 954a990
2 parents 9d143ae + d8cbed2
commit 954a990
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -19,9 +19,9 @@ jobs:
           default: "false"
       docker:
         - image: cimg/base:current-22.04
-      # medium 2 vCPUs, 4GB mem; medium+ 3vCPUs 6GB mem; large 4 vCPUs 8GB mem
-      # https://circleci.com/docs/configuration-reference#resourceclass
-      resource_class: medium+
+      # large 4 vCPUs 15GB mem
+      # https://discuss.circleci.com/t/changes-to-remote-docker-reporting-pricing/47759
+      resource_class: large
       steps:
         - restore_cache:
             keys:
@@ -88,30 +88,8 @@ jobs:
 
         - run:
             name: Set BASH_ENV
-            command: |
-              set -e
-              set -o pipefail
-              ./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
-              echo "BASH_ENV:"
-              cat $BASH_ENV
-              mkdir -p ~/mne_data
-              touch pattern.txt
+            command: ./tools/circleci_bash_env.sh
+
         - run:
             name: check neuromag2ft
             command: |
@@ -247,7 +225,7 @@ jobs:
         - run:
             name: make test-doc
             command: |
-              if [[ $(cat gitlog.txt) == *"[circle front]"* ]] || [[ $(cat build.txt) == "html_dev-memory" ]] || [[ $(cat build.txt) == "html_stable-memory" ]]; then
+              if [[ $(cat gitlog.txt) == *"[circle front]"* ]] || [[ $(cat build.txt) == "html-memory" ]] ; then
                 make test-doc;
                 mkdir -p doc/_build/test-results/test-doc;
                 cp junit-results.xml doc/_build/test-results/test-doc/junit.xml;
@@ -276,7 +254,7 @@ jobs:
         - run:
             name: Reduce artifact upload time
             command: |
-              if grep -q html_dev-pattern-memory build.txt || grep -q html_dev-noplot build.txt; then
+              if grep -q html-pattern-memory build.txt || grep -q html-noplot build.txt; then
                 zip -rm doc/_build/html/_downloads.zip doc/_build/html/_downloads
               fi
               for NAME in generated auto_tutorials auto_examples; do
@@ -299,15 +277,11 @@ jobs:
         # Save the HTML
         - store_artifacts:
             path: doc/_build/html/
-            destination: dev
-        - store_artifacts:
-            path: doc/_build/html_stable/
-            destination: stable
+            destination: html
         - persist_to_workspace:
             root: doc/_build
             paths:
               - html
-              - html_stable
 
         # Keep these separate, maybe better in terms of size limitations (?)
         - save_cache:
@@ -402,18 +376,12 @@ jobs:
           type: string
           default: "false"
       docker:
-        - image: circleci/python:3.9.2-buster
+        - image: cimg/base:current-22.04
       steps:
         - restore_cache:
             keys:
               - source-cache
         - checkout
-        - run:
-            name: Set BASH_ENV
-            command: |
-              set -e
-              echo "set -e" >> $BASH_ENV
-              echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
         - run:
             name: Check-skip
             command: |
@@ -422,6 +390,9 @@ jobs:
                 echo "Skip detected, exiting job ${CIRCLE_JOB}."
                 circleci-agent step halt;
               fi
+        - run:
+            name: Set BASH_ENV
+            command: ./tools/circleci_bash_env.sh
         - restore_cache:
             keys:
               - pip-cache
@@ -465,7 +436,7 @@ jobs:
         - run:
             name: Check docs
             command: |
-              if [ ! -f /tmp/build/html/index.html ] && [ ! -f /tmp/build/html_stable/index.html ]; then
+              if [ ! -f /tmp/build/html/index.html ] ; then
                 echo "No files found to upload (build: ${CIRCLE_BRANCH}).";
                 circleci-agent step halt;
               fi;
@@ -498,7 +469,7 @@ jobs:
               else
                 echo "Deploying stable docs for ${CIRCLE_BRANCH}.";
                 rm -Rf stable;
-                cp -a /tmp/build/html_stable stable;
+                cp -a /tmp/build/html stable;
                 git add -A;
                 git commit -m "CircleCI update of stable docs (${CIRCLE_BUILD_NUM}).";
               fi;
@@ -523,7 +494,7 @@ workflows:
             branches:
               only:
                 - main
-                - maint/1.3
+                - /maint\/.*/
 
   main:
     jobs:

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1 @@
+e81ec528a42ac687f3d961ed5cf8e25f236925b0  # black
diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -10,6 +10,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           api-token: ${{ secrets.CIRCLECI_TOKEN }}
-          artifact-path: 0/dev/index.html
+          artifact-path: 0/html/index.html
           circleci-jobs: build_docs,build_docs_main
           job-title: Check the rendered docs here!
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -23,6 +23,7 @@ jobs:
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
+    - uses: psf/black@stable
     - uses: pre-commit/[email protected]
 
   pytest:

diff --git a/.mailmap b/.mailmap
@@ -19,6 +19,8 @@ Andrew Quinn <[email protected]> AJQuinn <[email protected]
 Anna Padee <[email protected]> apadee <[email protected]>
 Anne-Sophie Dubarry <[email protected]> annesodub <[email protected]>
 Archit Singhal <[email protected]> archit singhal <[email protected]>
+Arne Pelzer <[email protected]> aplzr <[email protected]>
+Arne Pelzer <[email protected]> pzr <[email protected]>
 Ashley Drew <[email protected]> ashdrew <[email protected]>
 Asish Panda <[email protected]> kaichogami <[email protected]>
 Basile Pinsard <[email protected]>
@@ -66,6 +68,7 @@ Denis A. Engemann <[email protected]> Denis Engemann <dengemann@pool-186-
 Dmitrii Altukhov <[email protected]> dmalt <[email protected]>
 Dominik Krzemiński <[email protected]> dokato <[email protected]>
 Dominik Welke <[email protected]> dominikwelke <[email protected]>
+Dominik Welke <[email protected]> dominikwelke <[email protected]>
 Eberhard Eich <[email protected]> ebeich <[email protected]>
 Eduard Ort <[email protected]> Eduard Ort <[email protected]>
 Eduard Ort <[email protected]> eort <[email protected]>
@@ -112,11 +115,13 @@ Hamid Maymandi <[email protected]> Hamid <46011104+Ha
 Hongjiang Ye <[email protected]> YE Hongjiang <[email protected]>
 Hubert Banville <[email protected]> hubertjb <[email protected]>
 Hüseyin Orkun Elmas <[email protected]> Hüseyin <[email protected]>
+Hyonyoung Shin <[email protected]> mcvain <[email protected]>
 Ingoo Lee <[email protected]> dlsrnsi <[email protected]>
 Jaakko Leppakangas <[email protected]> Jaakko Leppakangas <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
 Jaakko Leppakangas <[email protected]> jaeilepp <[email protected]>
 Jair Montoya <[email protected]> jmontoyam <[email protected]>
+Jan Ebert <[email protected]> janEbert <[email protected]>
 Jan Sosulski <[email protected]> jsosulski <[email protected]>
 Jean-Baptiste Schiratti <[email protected]> Jean-Baptiste SCHIRATTI <[email protected]>
 Jean-Remi King <[email protected]> Jean-Rémi KING <[email protected]>
@@ -222,6 +227,7 @@ Nicolas Gensollen <[email protected]> Gensollen <nicolas.gensollen@gma
 Nicolas Legrand <[email protected]> Legrand Nicolas <[email protected]>
 Nicolas Legrand <[email protected]> LegrandNico <[email protected]>
 Nicolas Legrand <[email protected]> Nicolas Legrand <[email protected]>
+Niels Focke <[email protected]> nmri-nfocke <[email protected]>
 Niklas Wilming <[email protected]> Niklas Wilming <[email protected]>
 Nikolai Chapochnikov <[email protected]> chapochn <[email protected]>
 Nikolai Chapochnikov <[email protected]> Nikolai M Chapochnikov <[email protected]>
@@ -284,6 +290,8 @@ Timon Merk <[email protected]> timonmerk <38216460+tim
 Timothy Gates <[email protected]> Tim Gates <[email protected]>
 Tod Flak <[email protected]> todflak <[email protected]>
 Tom Ma <[email protected]> myd7349 <[email protected]>
+Tom Stone <[email protected]> tomdstone <[email protected]>
+Tom Stone <[email protected]> Stone <[email protected]>
 Tristan Stenner <[email protected]> Tristan Stenner <[email protected]>
 Tziona NessAiver <[email protected]> TzionaN <[email protected]>
 Valerii Chirkov <[email protected]> Valerii <[email protected]>

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,9 +1,9 @@
 repos:
-# - repo: https://github.com/psf/black
-#   rev: 23.1.0
-#   hooks:
-#     - id: black
-#       args: [--quiet]
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+      args: [--quiet]
 
 # Ruff mne
 - repo: https://github.com/charliermarsh/ruff-pre-commit
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		e81ec528a42ac687f3d961ed5cf8e25f236925b0 # black