Merge remote-tracking branch 'gallantlab/main'

.codecov.yml

@@ -0,0 +1,33 @@
+# For more configuration details:
+# https://docs.codecov.io/docs/codecov-yaml
+
+# Check if this file is valid by running in bash:
+# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate
+
+# Coverage configuration
+# ----------------------
+coverage:
+  status:
+    project:
+      default:
+        threshold: 1%  # complain if change in codecoverage is greater than 1%
+    patch: false
+  range: 70..90     # First number represents red, and second represents green
+  # (default is 70..100)
+  round: down       # up, down, or nearest
+  precision: 2      # Number of decimal places, between 0 and 5
+
+
+# Ignoring Paths
+# --------------
+# which folders/files to ignore
+# ignore:
+#   - */tests/.*
+#  - setup.py
+
+# Pull request comments:
+# ----------------------
+# Diff is the Coverage Diff of the pull request.
+# Files are the files impacted by the pull request
+comment: false
+#  layout: diff, files  # accepted in any order: reach, diff, flags, and/or files

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/build_docs.yml

@@ -0,0 +1,45 @@
+name: Build docs
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y inkscape
+        pip install --upgrade pip
+        pip install wheel numpy "cython<3.0" pillow
+        pip install -q ipython Sphinx sphinx-gallery numpydoc
+        pip install -e . --no-build-isolation
+        python -c 'import cortex; print(cortex.__full_version__)'
+
+    - name: Build documents
+      run: |
+        cd docs && make html && cd ..
+        touch docs/_build/html/.nojekyll
+
+    - name: Publish to gh-pages if tagged
+      if: startsWith(github.ref, 'refs/tags')
+      uses: JamesIves/github-pages-deploy-action@v4.4.3
+      with:
+        branch: gh-pages
+        folder: docs/_build/html

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/install_from_wheel.yml

@@ -0,0 +1,50 @@
+name: Install from wheel
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  install-from-wheel:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y inkscape
+        pip install --upgrade pip
+        pip install wheel numpy "cython<3.0"
+
+    - name: Create the wheel
+      run: python setup.py bdist_wheel
+
+    - name: Install from the wheel
+      run: |
+        pip install $(ls dist/*.whl) --no-build-isolation
+
+    - name: Test installation of the filestore
+      run: |
+        # change directory to avoid conflict with cortex directory
+        cd ..
+        python -c 'import cortex; print(cortex.db.filestore)'
+        python -c 'from cortex.webgl.view import cmapdir; print(cmapdir)'

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,28 @@
+name: Build and publish to PyPI if tagged
+on: push
+jobs:
+  build-n-publish:
+    name: Build and publish to PyPI if tagged
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+    - name: Build a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --outdir dist/
+    - name: Publish distribution to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -0,0 +1,49 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9, "3.10"]
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions/cache@v3
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y inkscape
+        pip install --upgrade pip
+        pip install wheel numpy "cython<3.0"
+        # force using latest nibabel
+        pip install -U nibabel
+        pip install -e . --no-build-isolation
+        python -c 'import cortex; print(cortex.__full_version__)'
+
+    - name: Test with pytest
+      run: |
+        pip install -q pytest pytest-cov codecov
+        pytest --cov=./
+
+    - name: Run codecov
+      run: |
+        codecov

.gitignore

@@ -25,6 +25,7 @@ lib64
 # NOTE: the filestore really should never be in the git repo... Needs work.
 filestore/db/*/cache
 filestore/db/*/surface-info
+filestore
 
 # Installer logs
 pip-log.txt
@@ -42,15 +43,22 @@ nosetests.xml
 .project
 .pydevproject
 
-# OS X bullshit
+# OS X 
 .DS_store
 
 # vim temp files
 *~
 
-# vscode
+# vscode and other IDEs
 .vscode
+.idea
 
 *.nfs*
 
 .ipynb_checkpoints/
+
+# docs build
+docs/_build
+docs/auto_examples
+docs/generated
+docs/colormaps.rst