From 3cfdc0bcb26796ed1bc0126adc472d0db4a9be2e Mon Sep 17 00:00:00 2001 From: Intron7 Date: Mon, 5 May 2025 15:52:50 +0200 Subject: [PATCH 1/4] update biome --- .gitignore | 1 - .pre-commit-config.yaml | 2 +- .vscode/settings.json | 22 ++++++++++++++++++++++ biome.jsonc | 18 ++++++++++++++++++ 4 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 biome.jsonc 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/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6fd9b2fe..89218b30 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: id: ruff args: ["--preview", "--select=PLR0917"] - repo: https://github.com/biomejs/pre-commit - rev: v2.0.0-beta.1 + rev: v1.9.4 hooks: - id: biome-format - repo: https://github.com/ComPWA/taplo-pre-commit 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, + }, + }, + }, + ], +} From bc6d795507a4781df084927dcff20f66c0cdf4d2 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Tue, 6 May 2025 08:56:50 +0200 Subject: [PATCH 2/4] add in tracer for rapids team --- .github/workflows/test-gpu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index 253d7616..0b999e55 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -62,7 +62,7 @@ jobs: run: pip list - name: Run test - run: pytest + run: pytest --setup-show -vv -s - name: Remove 'run-gpu-ci' Label if: always() From dc679948e7e320aea3bea53d601ae3a7b76c67a0 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Tue, 6 May 2025 09:02:54 +0200 Subject: [PATCH 3/4] add back org installer --- .github/workflows/test-gpu.yml | 22 +++++++++++++++------- notebooks | 2 +- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml index d1986965..0b999e55 100644 --- a/.github/workflows/test-gpu.yml +++ b/.github/workflows/test-gpu.yml @@ -39,16 +39,24 @@ 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 diff --git a/notebooks b/notebooks index 2dd93f91..6c8d8a7f 160000 --- a/notebooks +++ b/notebooks @@ -1 +1 @@ -Subproject commit 2dd93f91eb57d65c978ddb85737eaa1d43ee270d +Subproject commit 6c8d8a7f51f759184604d0474f2d93da7180e3fa From 70d24fcaf45c4215106395a15debea50c1b1f31c Mon Sep 17 00:00:00 2001 From: Intron7 Date: Tue, 6 May 2025 09:04:56 +0200 Subject: [PATCH 4/4] update notebook --- notebooks | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks b/notebooks index 6c8d8a7f..2dd93f91 160000 --- a/notebooks +++ b/notebooks @@ -1 +1 @@ -Subproject commit 6c8d8a7f51f759184604d0474f2d93da7180e3fa +Subproject commit 2dd93f91eb57d65c978ddb85737eaa1d43ee270d