Merge pull request #47 from YosefLab/workflow

Update test.yml and readthedocs.yml

Author: deto

.github/workflows/test.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: hotspot
 
 on:
@@ -9,30 +6,50 @@ on:
   pull_request:
     branches: [master]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build:
-    runs-on: ubuntu-latest
-    timeout-minutes: 20
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest]
+        python: ["3.10", "3.11", "3.12"]
+
+    name: Integration
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip
-      uses: actions/cache@v2
-      with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-v1-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-v1-
-    - name: Install dependencies
-      run: |
-        pip install .[test]
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+
+      - name: Install dependencies
+        run: |
+          pip install ".[test]"
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --color=yes

.readthedocs.yml

@@ -1,12 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  image: latest
+  os: ubuntu-20.04
+  tools:
+    python: "3.11"
 sphinx:
   configuration: docs/source/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
 python:
-  version: 3.8
   install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - docs
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

docs/source/conf.py

@@ -44,7 +44,7 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
     'sphinx.ext.napoleon',
-    'nbsphinx',
+    'myst_nb',
 ]
 
 #autodoc settings
@@ -64,6 +64,7 @@
 napoleon_use_ivar = False
 napoleon_use_param = True
 napoleon_use_rtype = True
+nb_execution_mode = "off"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -90,7 +91,6 @@
 
 # nbsphinx specific settings
 exclude_patterns = ["_build", "**.ipynb_checkpoints"]
-nbsphinx_execute = "never"
 
 
 # -- Options for HTML output -------------------------------------------------

pyproject.toml

@@ -47,15 +47,15 @@ python = ">=3.7,<4.0"
 pynndescent = ">=0.5"
 anndata = ">=0.7"
 sphinx-book-theme = {version= ">=0.2.0", optional = true}
-nbsphinx = {version = "*", optional = true}
+myst-nb = {version = "*", optional = true}
 sphinx = {version = ">=4.1", optional = true}
 ipython = {version = "*", optional = true}
 scanpy = {version = "*", optional = true}
 
 
 [tool.poetry.extras]
 test = ["pytest", "scanpy"]
-docs=["sphinx-book-theme", "nbsphinx", "sphinx", "ipython"]
+docs=["sphinx-book-theme", "myst-nb", "sphinx", "ipython"]
 
 [tool.poetry.dev-dependencies]