Merge pull request #203 from knaaptime/infrastructure

infrastructure

.github/workflows/build_docs.yml

@@ -13,7 +13,7 @@
      strategy:
        matrix:
          os: ['ubuntu-latest']
-         environment-file: [.ci/39.yml]
+         environment-file: [ci/311.yml]
          experimental: [false]
      defaults:
        run:

.github/workflows/unittests.yml

@@ -1,4 +1,5 @@
- name: Unit Tests
+ name: Continuous Integration
+
  on:
    push:
      branches:
@@ -8,52 +9,87 @@
      - '*'
    schedule:
      - cron: '59 23 * * *'
+   workflow_dispatch:
+    inputs:
+      version:
+        description: Manual CI Run
+        default: test
+        required: false
 
  jobs:
-   unittests:
-     name: CI (${{ matrix.os }}-${{ matrix.environment-file }})
+   tests:
+     name: ${{ matrix.os }}, ${{ matrix.environment-file }}
      runs-on: ${{ matrix.os }}
-     continue-on-error: false
-     timeout-minutes: 45
+     timeout-minutes: 30
      strategy:
        matrix:
-         os: [ubuntu-latest, macos-latest, windows-latest]
-         environment-file: [ .ci/39.yml, .ci/310.yml, .ci/311.yml]
+         os: [ubuntu-latest]
+         environment-file: [
+            ci/310.yml,
+            ci/311.yml,
+            ci/312.yml,
+         ]
+         include:
+           - environment-file: ci/312.yml
+             os: macos-latest
+           - environment-file: ci/312.yml
+             os: macos-14 # Apple Silicon
+           - environment-file: ci/312.yml
+             os: windows-latest
        fail-fast: false
 
+     defaults:
+       run:
+         shell: bash -l {0}
+
      steps:
        - name: checkout repo
-         uses: actions/checkout@v2
+         uses: actions/checkout@v4
+         with:
+           fetch-depth: 0 # Fetch all history for all branches and tags.
 
        - name: setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
+         uses: mamba-org/setup-micromamba@v1
          with:
            environment-file: ${{ matrix.environment-file }}
            micromamba-version: 'latest'
-
-       - name: reinstall tobler - bash
-         shell: bash -l {0}
-         run: pip install -e . --no-deps --force-reinstall
-         if: matrix.os != 'windows-latest'
-
-       - name: reinstall tobler - powershell
-         shell: powershell
-         run: pip install -e . --no-deps --force-reinstall
-         if: matrix.os == 'windows-latest'
+
+       - name: environment info
+         run: |
+           micromamba info
+           micromamba list
        
-       - name: run pytest - bash
-         shell: bash -l {0}
-         run: pytest -v tobler --cov=tobler --cov-report=xml
-         if: matrix.os != 'windows-latest'
+       - name: spatial versions
+         run: 'python -c "import geopandas; geopandas.show_versions();"'
+
+       - name: install package
+         run: 'pip install . --no-deps'
 
-       - name: run pytest - powershell
-         shell: powershell
-         run: pytest -v tobler --cov=tobler --cov-report=xml
-         if: matrix.os == 'windows-latest'
+       - name: run tests
+         run: |
+           pytest tobler \
+           -v \
+           -r a \
+           -n auto \
+           --color yes \
+           --cov tobler \
+           --cov-append \
+           --cov-report term-missing \
+           --cov-report xml
        
        - name: codecov
-         uses: codecov/codecov-action@v1
+         uses: codecov/codecov-action@v3
          with:
            token: ${{ secrets.CODECOV_TOKEN }}
            file: ./coverage.xml
            name: tobler-codecov
+
+       - name: Generate and publish the report
+         if: |
+           failure()
+           && steps.status.outcome == 'failure'
+           && github.event_name == 'schedule'
+           && github.repository_owner == 'pysal'
+         uses: xarray-contrib/issue-from-pytest-log@v1
+         with:
+           log-path: pytest-log.jsonl

.ci/310.yml → ci/310.yml

@@ -5,7 +5,6 @@ dependencies:
   - python=3.10
   - dask
   - dask-geopandas
-  - distributed
   - jupyterlab
   - numpy
   - geopandas
@@ -19,10 +18,11 @@ dependencies:
   - libpysal
   - tqdm
   - codecov
-  - quilt3
   - pytest
   - pytest-mpl
   - pytest-cov
+  - pytest-xdist
+  - coverage
   - twine
   - pip
   - h3-py

.ci/311.yml → ci/311.yml

@@ -6,7 +6,6 @@ dependencies:
   - jupyterlab
   - dask
   - dask-geopandas
-  - distributed
   - numpy
   - geopandas
   - pandas
@@ -20,11 +19,20 @@ dependencies:
   - tqdm
   - codecov
   - pytest
-  - quilt3
   - pytest-mpl
   - pytest-cov
+  - pytest-xdist
+  - coverage
   - twine
   - pip
   - h3-py
   - joblib
   - astropy
+  - mapclassify
+  - sphinx>=1.4.3
+  - sphinxcontrib-bibtex==1.0.0
+  - sphinx_bootstrap_theme
+  - numpydoc
+  - nbsphinx
+  - joblib
+  - astropy

.ci/39.yml → ci/312.yml

@@ -2,10 +2,9 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.12
   - dask
   - dask-geopandas
-  - distributed
   - numpy
   - geopandas
   - pandas
@@ -17,15 +16,15 @@ dependencies:
   - libpysal
   - tqdm
   - codecov
+  - pytest-xdist
+  - coverage
   - pytest
-  - quilt3
   - pytest-mpl
   - pytest-cov
   - twine
   - pip
   - h3-py
   - mapclassify
-  - descartes
   - sphinx>=1.4.3
   - sphinxcontrib-bibtex==1.0.0
   - sphinx_bootstrap_theme

codecov.yml

@@ -0,0 +1,20 @@
+codecov:
+  notify:
+    after_n_builds: 7
+coverage:
+  range: 50..95
+  round: nearest
+  precision: 1
+  status:
+    project:
+      default:
+        threshold: 15%
+    patch:
+      default:
+        threshold: 20%
+        target: 60%
+comment:
+  layout: "reach, diff, files"
+  behavior: once
+  after_n_builds: 7
+  require_changes: true

environment.yml

@@ -4,7 +4,6 @@ channels:
 dependencies:
   - dask-geopandas
   - dask
-  - distributed
   - jupyterlab
   - numpy
   - geopandas >=0.13

pyproject.toml

@@ -64,6 +64,7 @@ tests = [
     "pytest",
     "pytest-mpl",
     "pytest-cov",
+    "pytest-xdist",
     "watermark",
     "h3",
     "astropy"