Refactoring over ci.

mne-tools · Jun 9, 2021 · 903ca53 · 903ca53
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -0,0 +1,173 @@
+version: 2
+jobs:
+    build_docs:
+      docker:
+        - image: circleci/python:3.8.5-buster
+      steps:
+        - restore_cache:
+            keys:
+              - source-cache-realtime
+        - checkout
+        - run:
+            name: Complete checkout
+            command: |
+              if ! git remote -v | grep upstream; then
+                git remote add upstream git://github.com/mne-tools/mne-connectivity.git
+              fi
+              git fetch upstream
+        - save_cache:
+            key: source-cache-realtime
+            paths:
+              - ".git"
+        - run:
+            name: Set BASH_ENV
+            command: |
+              set -e
+              echo "set -e" >> $BASH_ENV
+              echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV
+              echo "export XDG_RUNTIME_DIR=/tmp/runtime-circleci" >> $BASH_ENV
+              wget -q -O tools/get_minimal_commands.sh https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/get_minimal_commands.sh
+              source tools/get_minimal_commands.sh
+              echo "source ${PWD}/tools/get_minimal_commands.sh" >> $BASH_ENV
+              echo "export PATH=~/.local/bin/:$PATH" >> $BASH_ENV
+              echo "BASH_ENV:"
+              cat $BASH_ENV
+              mkdir -p ~/mne_data
+
+        - 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
+
+        - restore_cache:
+            keys:
+              - pip-cache
+
+        - run:
+            name: Get Python running
+            command: |
+              pip install --user --upgrade --progress-bar off pip numpy
+              pip install --user --upgrade --progress-bar off -r requirements.txt
+              pip install --user --upgrade --progress-bar off "sphinxcontrib-bibtex==2.0.0" "https://api.github.com/repos/mne-tools/mne-python/zipball/main" "https://api.github.com/repos/rtfd/sphinx_rtd_theme/zipball/master" "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler
+
+        - save_cache:
+            key: pip-cache
+            paths:
+              - ~/.cache/pip
+
+        # Look at what we have and fail early if there is some library conflict
+        - 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)"
+
+        # Load our data
+        - restore_cache:
+            keys:
+              - data-cache
+
+        - run:
+            name: Get data
+            command: |
+              python setup.py develop --user
+              mkdir -p ~/mne_data
+              python -c "import mne; print(mne.datasets.sample.data_path(update_path=True))";
+
+        # Build docs
+        - run:
+            name: make html
+            command: |
+              cd doc;
+              make html;
+
+        # Save the JUnit file
+        - store_test_results:
+            path: doc/_build/test-results
+        - store_artifacts:
+            path: doc/_build/test-results
+            destination: test-results
+
+        # Save the outputs
+        - store_artifacts:
+            path: doc/_build/html/
+            destination: dev
+        - persist_to_workspace:
+            root: doc/_build
+            paths:
+              - html
+
+        # Keep these separate, maybe better in terms of size limitations (?)
+        - save_cache:
+            key: data-cache
+            paths:
+              - ~/.mne
+              - ~/mne_data/MNE-sample-data
+
+    deploy:
+      docker:
+        - image: circleci/python:3.6-jessie
+      steps:
+        - attach_workspace:
+            at: /tmp/build
+        - restore_cache:
+            keys:
+              - website-cache
+        - run:
+            name: Fetch docs
+            command: |
+              set -e
+              mkdir -p ~/.ssh
+              echo -e "Host *\nStrictHostKeyChecking no" > ~/.ssh/config
+              chmod og= ~/.ssh/config
+              if [ ! -d ~/mne-tools.github.io ]; then
+                git clone git@github.com:/mne-tools/mne-tools.github.io.git ~/mne-tools.github.io --depth=1
+              fi
+        - run:
+            name: Deploy docs
+            command: |
+              set -e;
+              if [ "${CIRCLE_BRANCH}" == "master" ]; then
+                git config --global user.email "circle@mne.com";
+                git config --global user.name "Circle CI";
+                cd ~/mne-tools.github.io;
+                git checkout master
+                git remote -v
+                git fetch origin
+                git reset --hard origin/master
+                git clean -xdf
+                echo "Deploying dev docs for ${CIRCLE_BRANCH}.";
+                rm -Rf mne-realtime;
+                cp -a /tmp/build/html mne-realtime;
+                git add -A;
+                git commit -m "CircleCI update of mne-realtime docs (${CIRCLE_BUILD_NUM}).";
+                git push origin master;
+              else
+                echo "No deployment (build: ${CIRCLE_BRANCH}).";
+              fi
+        - save_cache:
+            key: website-cache
+            paths:
+              - ~/mne-tools.github.io
+
+workflows:
+  version: 2
+
+  default:
+    jobs:
+      - build_docs
+      - deploy:
+          requires:
+            - build_docs
+          filters:
+            branches:
+              only:
+                - master
diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,21 @@
+# Configuration for coverage.py
+
+[run]
+branch = True
+source = mne_realtime
+include = */mne_realtime/*
+omit =
+    */setup.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+    if self.verbose:
+show_missing = True
diff --git a/.github/workflows/circle_artifacts.yml b/.github/workflows/circle_artifacts.yml
@@ -0,0 +1,12 @@
+on: [status]
+jobs:
+  circleci_artifacts_redirector_job:
+    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 }}
+          artifact-path: 0/dev/index.html
+          circleci-jobs: build_docs
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -0,0 +1,45 @@
+name: 'linux / pip'
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  job:
+    name: 'py3.9'
+    runs-on: ubuntu-20.04
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+        name: 'Setup python'
+      - shell: bash -el {0}
+        run: |
+          wget -q -O tools/get_minimal_commands.sh https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/get_minimal_commands.sh
+          source ./tools/get_minimal_commands.sh
+        name: 'Install neuromag2ft'
+      - shell: bash -el {0}
+        run: neuromag2ft --version
+        name: 'Test neuromag2ft'
+      - shell: bash -el {0}
+        run: ./tools/pip_dependencies.sh
+        name: 'Install MNE-Realtime'
+      - shell: bash -el {0}
+        run: mne sys_info
+        name: Print config
+      - shell: bash -el {0}
+        run: python -c "import mne; print(mne.datasets.testing.data_path(verbose=True))"
+        name: 'Get test data'
+      - shell: bash -el {0}
+        run: pytest mne_realtime
+        name: 'Run tests'
+      - uses: codecov/codecov-action@v1
+        if: success()
+        name: 'Upload coverage to CodeCov'
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -0,0 +1,40 @@
+name: 'macos / conda'
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  job:
+    name: 'py3.6'
+    runs-on: macos-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: '3.7'
+          auto-update-conda: true
+          environment-file: 'environment.yml'
+          activate-environment: 'mne_realtime'
+        name: 'Setup conda'
+      - shell: bash -el {0}
+        run: ./tools/pip_dependencies.sh
+        name: 'Install MNE-Realtime'
+      - shell: bash -el {0}
+        run: mne sys_info
+        name: Print config
+      - shell: bash -el {0}
+        run: python -c "import mne; print(mne.datasets.testing.data_path(verbose=True))"
+        name: 'Get test data'
+      - shell: bash -el {0}
+        run: pytest mne_realtime
+        name: 'Run tests'
+      - uses: codecov/codecov-action@v1
+        if: success()
+        name: 'Upload coverage to CodeCov'
diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,8 @@ __pycache__/
 # C extensions
 *.so
 
+.DS_Store
+
 # Distribution / packaging
 .Python
 build/

diff --git a/doc/api.rst b/doc/api.rst
@@ -1,28 +1,21 @@
 :orphan:
 
 ################
-mne-realtime API
+mne-connectivity API
 ################
 
-:py:mod:`mne_realtime`:
+:py:mod:`mne_connectivity`:
 
-.. automodule:: mne_realtime
+.. automodule:: mne_connectivity
    :no-members:
    :no-inherited-members:
 
-MNE-Realtime
-============
+MNE-Connectivity
+================
 
-.. currentmodule:: mne_realtime
+.. currentmodule:: mne_connectivity
 
 .. autosummary::
    :toctree: generated/
 
    FieldTripClient
-   LSLClient
-   MockLSLStream
-   MockRtClient
-   RtEpochs
-   RtClient
-   StimServer
-   StimClient
diff --git a/doc/authors.rst b/doc/authors.rst
@@ -0,0 +1 @@
+.. _Adam Li: https://github.com/adam2392
diff --git a/doc/conf.py b/doc/conf.py
@@ -26,7 +26,7 @@
 from sphinx_gallery.sorting import FileNameSortKey
 from numpydoc import docscrape
 import mne  # noqa
-from mne_realtime import __version__
+from mne_connectivity import __version__
 
 # -- General configuration ------------------------------------------------
 
@@ -76,9 +76,9 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'MNE-Realtime'
+project = u'MNE-Connectivity'
 td = date.today()
-copyright = u'2012-%s, MNE Developers. Last updated on %s' % (td.year,
+copyright = u'2021-%s, MNE Developers. Last updated on %s' % (td.year,
                                                               td.isoformat())
 
 nitpicky = True
@@ -129,7 +129,7 @@
 html_style = 'css/project-template.css'
 
 # A list of ignored prefixes for module index sorting.
-modindex_common_prefix = ['mne_realtime.']
+modindex_common_prefix = ['mne_connectivity.']
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
 #keep_warnings = False
@@ -218,7 +218,7 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mne-realtime-doc'
+htmlhelp_basename = 'mne-connectivity-doc'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -411,7 +411,7 @@ def reset_warnings(gallery_conf, fname):
     'Montage': 'mne.channels.Montage', 'Forward': 'mne.Forward',
     'DigMontage': 'mne.channels.DigMontage',
     # mne_realtime
-    'RtEpochs': 'mne_realtime.RtEpochs',
+    # 'RtEpochs': 'mne_realtime.RtEpochs',
 }
 numpydoc_xref_ignore = {
     # words
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,6 +6,8 @@ __pycache__/ @@
     # C extensions
     *.so
+    .DS_Store
     # Distribution / packaging
     .Python
     build/
@@ Expand Down @@