Merge remote-tracking branch 'origin/main' into dmrpp_root_group_fix

.github/workflows/upstream.yml

@@ -0,0 +1,60 @@
+name: upstream
+
+on:
+  push:
+    branches: [ "main" ]
+    paths-ignore:
+    - 'docs/**'
+  pull_request:
+    branches: [ "main" ]
+    paths-ignore:
+    - 'docs/**'
+  schedule:
+    - cron: "0 0 * * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+
+  test:
+    name: ${{ matrix.python-version }}-build
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ci/upstream.yml
+          cache-environment: true
+          create-args: >-
+            python=${{matrix.python-version}}
+
+      - name: Install virtualizarr
+        run: |
+           python -m pip install -e . --no-deps
+      - name: Conda list information
+        run: |
+          conda env list
+          conda list
+
+      - name: Running Tests
+        run: |
+          python -m pytest ./virtualizarr --cov=./ --cov-report=xml --verbose
+
+      - name: Upload code coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

.pre-commit-config.yaml

@@ -3,15 +3,15 @@ ci:
   autoupdate_schedule: monthly
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.6.3"
+    rev: "v0.6.9"
     hooks:
       # Run the linter.
       - id: ruff

ci/upstream.yml

@@ -0,0 +1,30 @@
+name: virtualizarr-min-deps
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - h5netcdf
+  - h5py
+  - hdf5
+  - netcdf4
+  - numpy>=2.0.0
+  - packaging
+  - ujson
+  - universal_pathlib
+  # Testing
+  - codecov
+  - pre-commit
+  - mypy
+  - ruff
+  - pandas-stubs
+  - pytest-mypy
+  - pytest-cov
+  - pytest
+  - pooch
+  - fsspec
+  - pip
+  - pip:
+    - zarr==3.0.0b1  # beta release of zarr-python v3
+    - git+https://github.com/pydata/xarray@zarr-v3  # zarr-v3 compatibility branch
+    - git+https://github.com/zarr-developers/numcodecs@zarr3-codecs  # zarr-v3 compatibility branch
+    # - git+https://github.com/fsspec/kerchunk@main  # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516)