Merge remote-tracking branch 'upstream/master' into importBOXY

* upstream/master:
  MRG, MAINT: Try conda-forge (mne-tools#8046)
  MRG, MAINT: deduplicate definition of FIFF constants (mne-tools#8537)
  ENH: Add realign_raw (mne-tools#8540)
  CI: Use 20.04 (mne-tools#8541)
  fix example (mne-tools#8539)
  MRG, VIZ, FIX: plot_sensors title and interactivity (mne-tools#8536)
  MRG, MAINT: Test 3.9 (mne-tools#8533)

Author: larsoner

.github/workflows/main.yml .github/workflows/circle_artifacts.yml.github/workflows/main.yml renamed to .github/workflows/circle_artifacts.yml

@@ -1,7 +1,7 @@
 on: [status]
 jobs:
   circleci_artifacts_redirector_job:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step

.github/workflows/codespell_and_flake.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   style:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
-    runs-on: ubuntu-latest
+    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'

.github/workflows/compat_minimal.yml

@@ -12,7 +12,7 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.7'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash

.github/workflows/compat_old.yml

@@ -12,7 +12,7 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.6'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     defaults:
       run:
         shell: bash

.github/workflows/linux_conda.yml

@@ -12,24 +12,22 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.8'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash
     env:
       CONDA_ENV: 'environment.yml'
       DISPLAY: ':99.0'
       MNE_LOGGING_LEVEL: 'warning'
-      OPENBLAS_NUM_THREADS: '1'
+      MKL_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
       PYTHON_VERSION: '3.8'
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - run: |
-          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libopengl0
-          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: conda-incubator/setup-miniconda@v2
         with:

.github/workflows/linux_pip.yml

@@ -11,8 +11,8 @@ jobs:
   # PIP + non-default stim channel + log level info
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
-    name: 'py3.8'
-    runs-on: ubuntu-latest
+    name: 'py3.9'
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash
@@ -22,14 +22,12 @@ jobs:
       MNE_STIM_CHANNEL: 'STI101'
       OPENBLAS_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
-      PYTHON_VERSION: '3.8'
+      PYTHON_VERSION: '3.9'
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - run: |
-          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libopengl0
-          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: actions/setup-python@v2
         with:

README.rst

@@ -1,11 +1,14 @@
 .. -*- mode: rst -*-
 
-|Travis|_ |Azure|_ |Circle|_ |Codecov|_ |PyPI|_ |conda-forge|_ |Zenodo|_
+|GH-Linux|_ |GH-macOS|_ |Azure|_ |Circle|_ |Codecov|_ |PyPI|_ |conda-forge|_ |Zenodo|_
 
 |MNE|_
 
-.. |Travis| image:: https://api.travis-ci.org/mne-tools/mne-python.svg?branch=master
-.. _Travis: https://travis-ci.org/mne-tools/mne-python/branches
+.. |GH-Linux| image:: https://github.com/mne-tools/mne-python/workflows/linux%20/%20conda/badge.svg?branch=master
+.. _GH-Linux: https://github.com/mne-tools/mne-python/actions?query=branch:master+event:push
+
+.. |GH-macOS| image:: https://github.com/mne-tools/mne-python/workflows/macos%20/%20conda/badge.svg?branch=master
+.. _GH-macOS: https://github.com/mne-tools/mne-python/actions?query=branch:master+event:push
 
 .. |Azure| image:: https://dev.azure.com/mne-tools/mne-python/_apis/build/status/mne-tools.mne-python?branchName=master
 .. _Azure: https://dev.azure.com/mne-tools/mne-python/_build/latest?definitionId=1&branchName=master

azure-pipelines.yml

@@ -174,7 +174,6 @@ stages:
       OPENBLAS_NUM_THREADS: 1
       PYTHONUNBUFFERED: 1
       PYTHONIOENCODING: 'utf-8'
-      MKL_NUM_THREADS: 1
       AZURE_CI_WINDOWS: 'true'
       PYTHON_ARCH: 'x64'
     strategy:

doc/changes/latest.inc

@@ -35,6 +35,8 @@ Enhancements
 
 - Add ``proj`` argument to :func:`mne.make_fixed_length_epochs` (:gh:`8351` by `Eric Larson`_)
 
+- Add :func:`mne.preprocessing.realign_raw` to realign simultaneous raw recordings in the presence of clock drift (:gh:`8539` by `Eric Larson`_)
+
 - Reduce memory usage of volume source spaces (:gh:`8379` by `Eric Larson`_)
 
 - Speed up heavy use of :meth:`mne.SourceMorph.apply` for volumetric source spaces by use of the method :meth:`mne.SourceMorph.compute_vol_morph_mat` (:gh:`8366` by `Eric Larson`_)

doc/python_reference.rst

@@ -381,6 +381,7 @@ Projections:
    oversampled_temporal_projection
    peak_finder
    read_ica
+   realign_raw
    regress_artifact
    corrmap
    read_ica_eeglab