diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 2fb0e964..0b999e55 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -39,22 +39,30 @@ jobs: - name: Nvidia SMI sanity check run: nvidia-smi - - uses: mamba-org/setup-micromamba@v2 + - name: Install Python + uses: actions/setup-python@v5 with: - environment-file: ci/environment.yml - init-shell: >- - bash - cache-environment: true - post-cleanup: 'all' + python-version: "3.12" + + - name: Install UV + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + cache-dependency-glob: pyproject.toml + + - name: Set UV Timeout + env: + UV_HTTP_TIMEOUT: 120 + run: echo "UV_HTTP_TIMEOUT is set to $UV_HTTP_TIMEOUT" - name: Install rapids-singlecell - run: pip install -e .[test] + run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com --index-strategy=unsafe-best-match - name: Pip list run: pip list - name: Run test - run: pytest + run: pytest --setup-show -vv -s - name: Remove 'run-gpu-ci' Label if: always() diff --git a/.gitignore b/.gitignore index 59b337df..667392bd 100644 --- a/.gitignore +++ b/.gitignore @@ -4,7 +4,6 @@ __pycache__/ /*cache/ .ipynb_checkpoints/ /data/ -.vscode/ # Distribution / packaging /dist/ diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..c8e93a10 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,22 @@ +{ + "[python][toml][json][jsonc]": { + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.organizeImports": "explicit", + "source.fixAll": "explicit", + }, + }, + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff", + }, + "[toml]": { + "editor.defaultFormatter": "tamasfe.even-better-toml", + }, + "[json][jsonc]": { + "editor.defaultFormatter": "biomejs.biome", + }, + "python.analysis.typeCheckingMode": "basic", + "python.testing.pytestArgs": ["-vv", "--color=yes"], + "python.testing.pytestEnabled": true, + "python.terminal.activateEnvironment": true, +} diff --git a/biome.jsonc b/biome.jsonc new file mode 100644 index 00000000..55827f80 --- /dev/null +++ b/biome.jsonc @@ -0,0 +1,18 @@ +{ + "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json", + "formatter": { "useEditorconfig": true }, + "overrides": [ + { + "include": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"], + "json": { + "formatter": { + "trailingCommas": "all", + }, + "parser": { + "allowComments": true, + "allowTrailingCommas": true, + }, + }, + }, + ], +}