Update deps and doc cleaning (#315)

* update poetry deps and start cleaning docs * update example with new seaborn version * rename page * update code link button in doc * update docs for datasets * correct error with np type, add warning for the dataset * reduce computation time for documentation * fix plot issue * update doc workflow * fix download path location * switch to pre-commit.ci * correct spelling * fix pre commit config * switch to python 3.8 and latest ubuntu * add coverage requirements * correct typo * update actions * try xml report for codecov, add coveralls * remove coveralls
NeuroTechX · Dec 31, 2022 · 6b41ad1 · 6b41ad1
1 parent 978ad05
commit 6b41ad1
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Showing 25 changed files with 636 additions and 1,302 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -1,7 +1,6 @@
 [run]
 branch = True
 source = moabb
-include = */moabb/*
 omit =
     */docs/*
     */pipelines/*

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -14,30 +14,30 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-18.04]
+        os: [ubuntu-latest]
         python-version: ["3.9"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Create local data folder
         run: |
           mkdir ~/mne_data
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install Poetry
-        uses: snok/install-poetry@v1.1.6
+        uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
 
       - name: Cache datasets and docs
         id: cached-dataset-docs
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
           path: |
@@ -68,26 +68,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04]
+        os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Create local data folder
         run: |
           mkdir ~/mne_data
 
       - name: Cache datasets and docs
         id: cached-dataset-docs
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
           path: |
             ~/mne_data
             docs/build
 
       - name: Checkout moabb.github.io
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: "NeuroTechX/moabb.github.io"
           path: moabb-ghio
@@ -111,26 +111,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04]
+        os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Create local data folder
         run: |
           mkdir ~/mne_data
 
       - name: Cache datasets and docs
         id: cached-dataset-docs
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
           path: |
             ~/mne_data
             docs/build
 
       - name: Checkout gh pages
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: gh-pages
           path: moabb-ghpages

diff --git a/.github/workflows/test-devel.yml b/.github/workflows/test-devel.yml
@@ -13,16 +13,16 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-18.04, windows-latest, macOS-latest]
-        python-version: ["3.7"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+        python-version: ["3.8"]
     defaults:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -35,7 +35,7 @@ jobs:
       - name: Load cached venv
         if: runner.os != 'Windows'
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: .venv
           key:
@@ -55,34 +55,18 @@ jobs:
         run: |
           source $VENV
           poetry run coverage run -m unittest moabb.tests
+          poetry run coverage xml
 
       - name: Run pipelines
         run: |
           source $VENV
           poetry run python -m moabb.run --pipelines=./moabb/tests/test_pipelines/ --verbose
 
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         if: success()
         with:
           verbose: true
           directory: /home/runner/work/moabb/moabb
-          files: ./.coverage
-
-  lint:
-    name: lint ${{ matrix.os }}, py-${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: true
-      matrix:
-        os: [ubuntu-18.04]
-        python-version: ["3.8"]
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Setup Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - uses: pre-commit/action@v3.0.0
+          files: ./.coverage,coverage.xml
+          env_vars: OS,PYTHON
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,16 +13,16 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-18.04, windows-latest, macOS-latest]
-        python-version: ["3.7", "3.8", "3.9"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+        python-version: ["3.8", "3.9"]
     defaults:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -35,7 +35,7 @@ jobs:
       - name: Load cached venv
         if: runner.os != 'Windows'
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: .venv
           key:
@@ -54,17 +54,19 @@ jobs:
       - name: Run tests
         run: |
           source $VENV
-          poetry run python -m unittest moabb.tests
+          poetry run coverage run -m unittest moabb.tests
+          poetry run coverage xml
 
       - name: Run pipelines
         run: |
           source $VENV
           poetry run python -m moabb.run --pipelines=./moabb/tests/test_pipelines/ --verbose
 
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         if: success()
         with:
           verbose: true
           directory: /home/runner/work/moabb/moabb
-          files: ./.coverage
+          files: ./.coverage,coverage.xml
+          env_vars: OS,PYTHON
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,5 +1,16 @@
 default_language_version:
   python: python3
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+  autofix_prs: true
+  autoupdate_branch: "develop"
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
+  autoupdate_schedule: quarterly
+  skip: []
+  submodules: false
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.4.0
@@ -22,7 +33,7 @@ repos:
     hooks:
       - id: isort
 
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 3.8.4
     hooks:
       - id: flake8

diff --git a/docs/source/README.md b/docs/source/README.md
@@ -5,7 +5,7 @@
 ![banner](images/M.png)
 
 <p align=center>
-n  Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.
+  Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.
 </p>
 
 ## Disclaimer

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -36,7 +36,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "moabb"
-copyright = "2018-2021, Alexandre Barachant, Sylvain Chevallier"
+copyright = "2018-2023 MOABB contributors"
 author = "Alexandre Barachant, Vinay Jayaram, Sylvain Chevallier"
 
 # The short X.Y version
@@ -69,35 +69,40 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.linkcode",
     "sphinx.ext.mathjax",
-    "sphinx.ext.viewcode",
+    # "sphinx.ext.viewcode",
     "sphinx_gallery.gen_gallery",
     "gh_substitutions",
-    #  "m2r2",
+    "m2r2",
     "numpydoc",
 ]
 
 
 def linkcode_resolve(domain, info):  # noqa: C901
     """Determine the URL corresponding to a Python object.
+
     Parameters
     ----------
     domain : str
         Only useful when 'py'.
     info : dict
         With keys "module" and "fullname".
+
     Returns
     -------
     url : str
         The code URL.
+
     Notes
     -----
     This has been adapted to deal with our "verbose" decorator.
     Adapted from SciPy (doc/source/conf.py).
     """
-    import mne
+    repo = "https://github.com/NeuroTechX/moabb"
 
     if domain != "py":
         return None
+    if not info["module"]:
+        return None
 
     modname = info["module"]
     fullname = info["fullname"]
@@ -112,9 +117,6 @@ def linkcode_resolve(domain, info):  # noqa: C901
             obj = getattr(obj, part)
         except Exception:
             return None
-    # deal with our decorators properly
-    while hasattr(obj, "__wrapped__"):
-        obj = obj.__wrapped__
 
     try:
         fn = inspect.getsourcefile(obj)
@@ -127,7 +129,7 @@ def linkcode_resolve(domain, info):  # noqa: C901
             fn = None
     if not fn:
         return None
-    fn = op.relpath(fn, start=op.dirname(mne.__file__))
+    fn = op.relpath(fn, start=op.dirname(moabb.__file__))
     fn = "/".join(op.normpath(fn).split(os.sep))  # in case on Windows
 
     try:
@@ -140,15 +142,11 @@ def linkcode_resolve(domain, info):  # noqa: C901
     else:
         linespec = ""
 
-    if "dev" in moabb.__version__:
-        kind = "master"
-    else:
-        kind = "maint/%s" % (".".join(mne.__version__.split(".")[:2]))
-    return "http://github.com/NeuroTechX/moabb/blob/%s/moabb/%s%s" % (  # noqa
-        kind,
-        fn,
-        linespec,
-    )
+    # if "dev" in moabb.__version__:
+    #     kind = "develop"
+    # else:
+    #     kind = "master"
+    return f"{repo}/blob/develop/moabb/{fn}{linespec}"
 
 
 napoleon_google_docstring = False
@@ -194,7 +192,7 @@ def linkcode_resolve(domain, info):  # noqa: C901
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -222,9 +220,9 @@ def linkcode_resolve(domain, info):  # noqa: C901
 # theme further.
 html_theme_options = {
     # Navigation bar title. (Default: ``project`` value)
-    # 'navbar_title': "Demo",
+    "navbar_title": "MOABB",
     # Tab name for entire site. (Default: "Site")
-    # 'navbar_site_name': "Site",
+    "navbar_site_name": "MOABB",
     # A list of tuples containing pages or urls to link to.
     # Valid tuples should be in the following forms:
     #    (name, page)                 # a link to a page
@@ -347,7 +345,7 @@ def linkcode_resolve(domain, info):  # noqa: C901
         "moabb Documentation",
         author,
         "moabb",
-        "One line description of project.",
+        "Mother of all BCI benchmarks.",
         "Miscellaneous",
     ),
 ]

diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst
@@ -40,7 +40,7 @@ ERP Datasets
     :toctree: generated/
     :template: class.rst
 
-    bi2012a
+    bi2012
     bi2013a
     bi2014a
     bi2014b