add ci/requirements/environment.yml

Author: simonbesnard1

.github/workflows/ci.yaml

@@ -6,7 +6,7 @@ on:
   pull_request:
     branches:
       - "main"
-  workflow_dispatch: # allows you to trigger manually
+  workflow_dispatch: # Allows manual trigger
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -17,7 +17,7 @@ env:
 
 jobs:
   detect-ci-trigger:
-    name: detect ci trigger
+    name: Detect CI Trigger
     runs-on: ubuntu-latest
     if: |
       github.repository == 'simonbesnard1/gedidb'
@@ -32,96 +32,28 @@ jobs:
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
+
   test:
-    name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.env }}
-    runs-on: ${{ matrix.os }}
+    name: "Ubuntu-latest Python 3.10"
+    runs-on: ubuntu-latest
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
-    env:
-      ZARR_V3_EXPERIMENTAL_API: 1
-    defaults:
-      run:
-        shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        # Bookend python versions
-        python-version: ["3.10", "3.13"]
-        env: [""]
-        include:
-          # Minimum python version:
-          - env: "bare-minimum"
-            python-version: "3.10"
-            os: ubuntu-latest
-          - env: "min-all-deps"
-            python-version: "3.10"
-            os: ubuntu-latest
-          # Latest python version:
-          - env: "all-but-numba"
-            python-version: "3.13"
-            os: ubuntu-latest
-          - env: "all-but-dask"
-            python-version: "3.12"
-            os: ubuntu-latest
-          - env: "flaky"
-            python-version: "3.13"
-            os: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout Code
+        uses: actions/checkout@v4
         with:
-          fetch-depth: 0 # Fetch all history for all branches and tags.
-      - name: Set environment variables
-        run: |
-          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-
-          if [[ ${{ matrix.os }} == windows* ]] ;
-          then
-            if [[ ${{ matrix.python-version }} != "3.14" ]]; then
-              echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
-            else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.14.yml" >> $GITHUB_ENV
-            fi
-          elif [[ "${{ matrix.env }}" != "" ]] ;
-          then
-            if [[ "${{ matrix.env }}" == "flaky" ]] ;
-            then
-              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
-              echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
-            else
-              echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
-            fi
-            if [[ "${{ matrix.env }}" == "min-all-deps" ]] ;
-            then
-              # Don't raise on warnings
-              echo "PYTEST_ADDOPTS=-W default" >> $GITHUB_ENV
-            fi
-          else
-            if [[ ${{ matrix.python-version }} != "3.14" ]]; then
-              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
-            else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-3.14.yml" >> $GITHUB_ENV
-            fi
-          fi
-
-          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
+          fetch-depth: 0
 
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v2
         with:
-          environment-file: ${{ env.CONDA_ENV_FILE }}
+          environment-file: ci/requirements/environment.yml
           environment-name: gedidb-tests
           cache-environment: true
-          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          cache-environment-key: "ubuntu-latest-py3.10-${{ hashFiles('ci/requirements/environment.yml') }}"
           create-args: >-
-            python=${{matrix.python-version}}
-
-      # We only want to install this on one run, because otherwise we'll have
-      # duplicate annotations.
-      - name: Install error reporter
-        if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.12'
-        run: |
-          python -m pip install pytest-github-actions-annotate-failures
+            python=3.10
 
       - name: Install gedidb
         run: |
@@ -144,17 +76,15 @@ jobs:
           save-always: true
 
       - name: Run tests
-        run: python -m pytest -n 4
-          --timeout 180
-          --cov=gedidb
-          --cov-report=xml
-          --junitxml=pytest.xml
+        run: |
+          python -m pytest -n 4 --timeout 180 \
+          --cov=gedidb --cov-report=xml --junitxml=pytest.xml
 
       - name: Upload test results
         if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: Test results for ${{ runner.os }}-${{ matrix.python-version }} ${{ matrix.env }}
+          name: Test results
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
@@ -166,15 +96,4 @@ jobs:
           flags: unittests
           env_vars: RUNNER_OS,PYTHON_VERSION
           name: codecov-umbrella
-          fail_ci_if_error: false
-
-  event_file:
-    name: "Event File"
-    runs-on: ubuntu-latest
-    if: github.repository == 'simonbesnard1/gedidb'
-    steps:
-      - name: Upload
-        uses: actions/upload-artifact@v4
-        with:
-          name: Event File
-          path: ${{ github.event_path }}
+          fail_ci_if_error: false

ci/requirements/environment.yml

@@ -0,0 +1,52 @@
+name: gedidb-tests
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - aiobotocore
+  - array-api-strict
+  - boto3
+  - bottleneck
+  - cartopy
+  - cftime
+  - dask
+  - distributed
+  - flox
+  - fsspec
+  - geopandas
+  - h5netcdf
+  - h5py
+  - hdf5
+  - hypothesis
+  - lxml # Optional dep of pydap
+  - matplotlib-base
+  - nc-time-axis
+  - netcdf4
+  - numba
+  - numbagg
+  - numexpr
+  - numpy>=2
+  - opt_einsum
+  - packaging
+  - pandas
+  - pip
+  - pooch
+  - pre-commit
+  - pyarrow # pandas raises a deprecation warning without this, breaking doctests
+  - pydap
+  - pydap-server
+  - pytest
+  - pytest-cov
+  - pytest-env
+  - pytest-xdist
+  - pytest-timeout
+  - requests
+  - retry
+  - scipy
+  - sparse
+  - tiledb
+  - toolz
+  - typing_extensions
+  - xarray
+  - pip:
+      - jax # no way to get cpu-only jaxlib from conda if gpu is present