Fix codecov (#115)

* Fix codecov * Fix readme and citation * Fix readme and citation * fix coverage settings * remove codecov.yml * Fix for pydata sphinx theme * Revert "remove codecov.yml" This reverts commit cef1b92. * better coverage configuration * Fix format? Co-authored-by: mscheltienne <[email protected]> Co-authored-by: Mathieu Scheltienne <[email protected]>
mne-tools · Aug 31, 2022 · 34a896e · 34a896e
1 parent 2a20183
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diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -2,7 +2,7 @@ on:
   push:
     branches: [main]
     paths:
-      - 'paper/*'
+      - "paper/*"
 
 jobs:
   paper:

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -5,13 +5,13 @@ concurrency:
 on:
   pull_request:
     paths:
-      - '**.py'
+      - "**.py"
   push:
     branches: [main, maint/0.2, maint/0.3]
     tags:
-      - 'v*.*.*'
+      - "v*.*.*"
     paths:
-      - '**.py'
+      - "**.py"
   workflow_dispatch:
 
 jobs:
@@ -24,8 +24,8 @@ jobs:
       - name: Setup Python 3.9
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
-          architecture: 'x64'
+          python-version: "3.9"
+          architecture: "x64"
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
@@ -45,15 +45,15 @@ jobs:
         with:
           check_filenames: true
           check_hidden: true
-          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
+          skip: "./.git,./build,./.mypy_cache,./.pytest_cache"
           ignore_words_file: ./.codespellignore
       - name: Run pydocstyle
         run: pydocstyle .
       - name: Run mypy
         uses: jpetrucciani/mypy-check@master
         with:
-          path: './mne_icalabel'
-          mypy_flags: '--config-file pyproject.toml'
+          path: "./mne_icalabel"
+          mypy_flags: "--config-file pyproject.toml"
 
   build:
     timeout-minutes: 10
@@ -74,7 +74,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel
@@ -110,7 +110,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.7, "3.10"]  # oldest and newest supported versions
+        python-version: [3.7, "3.10"] # oldest and newest supported versions
         mne: [stable, main]
     name: pytest ${{ matrix.os }} - py${{ matrix.python-version }} - MNE ${{ matrix.mne }}
     runs-on: ${{ matrix.os }}-latest
@@ -121,12 +121,12 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
-          path: main  # clone repository in a sub-directory
+          path: main # clone repository in a sub-directory
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install Qt dependencies
         if: "matrix.os == 'ubuntu'"
         run: |
@@ -156,7 +156,7 @@ jobs:
         run: |
           python -c "import mne; mne.datasets.testing.data_path()"
           python -c "import mne_icalabel; mne_icalabel.datasets.icalabel.data_path()"
-      - name: Run pytest  # headless via Xvfb on linux
+      - name: Run pytest # headless via Xvfb on linux
         uses: GabrielBB/[email protected]
         with:
           run: pytest main/mne_icalabel --cov=main/mne_icalabel --cov-report=xml --cov-config=main/pyproject.toml
@@ -165,8 +165,10 @@ jobs:
         uses: codecov/codecov-action@v3
         with:
           files: ./coverage.xml
-          fail_ci_if_error: true
-          verbose: true
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)
 
   # release is ran when a release is made on Github
   release:
@@ -181,7 +183,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.9
-          architecture: 'x64'
+          architecture: "x64"
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel

diff --git a/CITATION.cff b/CITATION.cff
@@ -46,4 +46,43 @@ keywords:
 message: >-
   Please cite this software using the metadata from
   'preferred-citation' in the CITATION.cff file.
+preferred-citation:
+  title: >-
+    MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python
+  journal: Journal of Open Source Software
+  type: article
+  year: 2022
+  volume: 7
+  issue: 76
+  start: 4484
+  doi: 10.21105/joss.04484
+  authors:
+    - given-names: Adam
+      family-names: Li
+      affiliation: 'Department of Computer Science, Columbia University, New York, NY, USA'
+      orcid: 'https://orcid.org/0000-0001-8421-365X'
+    - given-names: Richard
+      family-names: Höchenberger
+      affiliation: 'Institute of Neuroscience and Medicine (INM-3), Research Center Jülich, Germany'
+      orcid: 'https://orcid.org/0000-0002-0380-4798'
+    - given-names: Thomas
+      family-names: Donoghue
+      affiliation: 'Department of Biomedical Engineering, Columbia University'
+      orcid: 'https://orcid.org/0000-0001-5911-0472'
+    - given-names: Mathieu
+      family-names: Scheltienne
+      affiliation: 'Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland'
+      orcid: 'https://orcid.org/0000-0001-8316-7436'
+    - given-names: Jacob
+      family-names: Feitelberg
+      affiliation: 'Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA'
+      orcid: 'https://orcid.org/0000-0002-4551-0245'
+    - given-names: Anand
+      family-names: Saini
+      affiliation: 'Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland'
+      orcid: 'https://orcid.org/0000-0003-3595-5969'
+identifiers:
+  - description: "Code archive on Zenodo"
+    type: doi
+    value: 10.5281/zenodo.7017165
 ...
diff --git a/README.md b/README.md
@@ -78,3 +78,26 @@ If you are interested in contributing, please read the
 For any usage questions, please post to the
 [MNE Forum](https://mne.discourse.group). Be sure to add the `mne-icalabel` tag to
 your question.
+
+# Citing
+
+If you use the ``ICLabel`` model, please consider citing our paper:
+
+    Li et al., (2022). MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python. Journal of Open Source Software, 7(76), 4484, https://doi.org/10.21105/joss.04484
+
+with the corresponding BibTex:
+
+    @article{Li2022,
+        doi       = {10.21105/joss.04484},
+        url       = {https://doi.org/10.21105/joss.04484},
+        year      = {2022},
+        publisher = {The Open Journal},
+        volume    = {7},
+        number    = {76},
+        pages     = {4484},
+        author    = {Adam Li and Jacob Feitelberg and Anand Prakash Saini and Richard Höchenberger and Mathieu Scheltienne},
+        title     = {MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python},
+        journal   = {Journal of Open Source Software}
+    }
+
+Future versions of the software are aimed at improved models and may have different papers associated with it.
diff --git a/doc/index.rst b/doc/index.rst
@@ -15,6 +15,9 @@ that build upon the ICLabel model.
 
 We encourage you to use the package for your research and also build on top
 with relevant Pull Requests. See our examples for walk-throughs of how to use the package.
+Also, see our `contributing guide <https://github.com/mne-tools/mne-icalabel/blob/main/CONTRIBUTING.md>`_.
+
+We are licensed under BSD-3 (see `License <https://github.com/mne-tools/mne-icalabel/blob/main/LICENSE>`_).
 
 Contents
 --------
@@ -28,19 +31,6 @@ Contents
    api
    auto_examples/index
 
-.. toctree::
-   :hidden:
-   :caption: Development
-
-   License <https://raw.githubusercontent.com/mne-tools/mne-icalabel/main/LICENSE>
-   Contributing <https://github.com/mne-tools/mne-icalabel/blob/main/CONTRIBUTING.md>
-
-License
--------
-
-**mne-icalabel** is licensed under `BSD 3.0 <https://opensource.org/licenses/BSD-3-Clause>`_.
-A full copy of the license can be found `on GitHub <https://raw.githubusercontent.com/mne-tools/mne-icalabel/main/LICENSE>`_.
-
 Indices and tables
 ------------------
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -167,13 +167,10 @@ filterwarnings = []
 [tool.coverage.run]
 branch = true
 cover_pylib = false
-source = [
-    'mne_icalabel',
-]
 omit = [
     '**/__init__.py',
-    'mne_icalabel/commands/*',
-    'mne_icalabel/_version.py',
+    '**/mne_icalabel/_version.py',
+    '**/mne_icalabel/commands/*',
     '**/tests/**',
 ]
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ on: @@
       push:
         branches: [main]
         paths:
-          - 'paper/*'
+          - "paper/*"
     jobs:
       paper:
@@ Expand Down @@