Merge branch 'main' into fix-docker-ci

scverse · Sep 25, 2024 · 822a405 · 822a405
2 parents c2db4e7 + b0a2efe
commit 822a405
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diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         RAPIDS_VER:
-          - 24.04
+          - 24.08
     name: Build Docker images
     runs-on: ubuntu-latest
     permissions:
@@ -105,7 +105,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           #cache-from: type=registry,ref=ghcr.io/${{ github.repository }}
           build-contexts: |
-            rapids-singlecell-deps=docker-image://${{ steps.meta-base.outputs.tags }}
+            rapids-singlecell-deps=docker-image://${{ fromJSON(steps.meta-base.outputs.json).tags[0] }}
 
       - name: Generate artifact attestation for main image
         if: github.event_name == 'release'

diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
@@ -26,6 +26,8 @@ jobs:
     name: GPU Tests
     needs: check
     runs-on: "cirun-aws-gpu--${{ github.run_id }}"
+    timeout-minutes: 30
+
     defaults:
       run:
         shell: bash -el {0}
@@ -37,20 +39,21 @@ jobs:
       - name: Nvidia SMI sanity check
         run: nvidia-smi
 
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
 
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Install UV
+        uses: hynek/setup-cached-uv@v2
         with:
-          micromamba-version: "1.5.6-0"
-          environment-file: ci/rsc_test_env.yml
-          post-cleanup: 'all'
+          cache-dependency-path: pyproject.toml
 
       - name: Install rapids-singlecell
-        run: uv pip install -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com
+        run: uv pip install --system -e .[test,rapids12] --extra-index-url=https://pypi.nvidia.com
 
-      - name: Mamba list
-        run: |
-          micromamba list
-          pip list
+      - name: Pip list
+        run: pip list
 
       - name: Run test
         run: pytest
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4
+    rev: v0.6.7
     hooks:
     -   id: ruff
         types_or: [python, pyi, jupyter]
@@ -26,7 +26,7 @@ repos:
         args: [--branch=main]
     -   id: detect-private-key
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
     -   id: codespell
         additional_dependencies:

diff --git a/README.md b/README.md
@@ -16,30 +16,9 @@ Rapids-singlecell offers enhanced single-cell data analysis as a near drop-in re
 
 Our commitment with rapids-singlecell is to deliver a powerful, user-centric tool that significantly enhances single-cell data analysis capabilities in bioinformatics.
 
-## Installation
-### Conda
-The easiest way to install *rapids-singlecell* is to use one of the *yaml* file provided in the [conda](https://github.com/scverse/rapids_singlecell/tree/main/conda) folder. These *yaml* files install everything needed to run the example notbooks and get you started.
-```
-conda env create -f conda/rsc_rapids_24.02.yml
-# or
-mamba env create -f conda/rsc_rapids_24.04.yml
-```
-### PyPI
-```
-pip install rapids-singlecell
-```
-The default installer doesn't cover RAPIDS nor cupy. Information on how to install RAPIDS & cupy can be found [here](https://rapids.ai/start.html).
-
-If you want to use RAPIDS PyPI packages, the whole library with all dependencies can be install with:
-````
-pip install 'rapids-singlecell[rapids11]' --extra-index-url=https://pypi.nvidia.com #CUDA11.X
-pip install 'rapids-singlecell[rapids12]' --extra-index-url=https://pypi.nvidia.com #CUDA12
-````
-It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and Cupy can locate the necessary libraries.
-
 ## Documentation
 
-Please have a look through the [documentation](https://rapids-singlecell.readthedocs.io/en/latest/)
+For more information please have a look through the [documentation](https://rapids-singlecell.readthedocs.io/en/latest/)
 
 
 ## Citation

diff --git a/ci/rsc_test_env.yml b/ci/rsc_test_env.yml
diff --git a/ci/rsc_test_env_backup.yml b/ci/rsc_test_env_backup.yml
diff --git a/conda/rsc_rapids_24.04.yml → conda/rsc_rapids_24.06.yml b/conda/rsc_rapids_24.04.yml → conda/rsc_rapids_24.06.yml
@@ -5,7 +5,7 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=24.04
+ - rapids=24.06
  - python=3.11
  - cuda-version=11.8
  - cudnn

diff --git a/conda/rsc_rapids_24.02.yml → conda/rsc_rapids_24.08.yml b/conda/rsc_rapids_24.02.yml → conda/rsc_rapids_24.08.yml
@@ -5,9 +5,9 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=24.02
- - python=3.10
- - cuda-version=11.8
+ - rapids=24.08
+ - python=3.11
+ - cuda-version=12.5
  - cudnn
  - cutensor
  - cusparselt

diff --git a/docker/Dockerfile.deps b/docker/Dockerfile.deps
@@ -1,4 +1,4 @@
-ARG CUDA_VER=11.8.0
+ARG CUDA_VER=12.5.0
 ARG LINUX_VER=ubuntu22.04
 
 FROM nvidia/cuda:${CUDA_VER}-base-${LINUX_VER}

diff --git a/docker/docker-push.sh b/docker/docker-push.sh
@@ -2,7 +2,7 @@
 set -euxo pipefail
 
 docker_account=scverse
-rapids_version=24.04
+rapids_version=24.08
 grep -v -- '- rapids-singlecell' conda/rsc_rapids_${rapids_version}.yml > rsc_rapids.yml
 docker build -t rapids-singlecell-deps:latest -f docker/Dockerfile.deps .
 rm rsc_rapids.yml

diff --git a/docs/Installation.md b/docs/Installation.md
@@ -2,9 +2,9 @@
 ## Conda
 The easiest way to install *rapids-singlecell* is to use one of the *yaml* file provided in the [conda](https://github.com/scverse/rapids_singlecell/tree/main/conda) folder. These *yaml* files install everything needed to run the example notebooks and get you started.
 ```
-conda env create -f conda/rsc_rapids_24.02.yml
+conda env create -f conda/rsc_rapids_24.06.yml #default CUDA-11.8
 # or
-mamba env create -f conda/rsc_rapids_24.04.yml
+mamba env create -f conda/rsc_rapids_24.08.yml #default CUDA-12.5
 ```
 ## PyPI
 As of version 0.4.0 *rapids-singlecell* is now on PyPI.

diff --git a/docs/api/decoupler_gpu.md b/docs/api/decoupler_gpu.md
@@ -10,5 +10,7 @@
     :toctree: generated
 
     dcg.run_mlm
+    dcg.run_ulm
     dcg.run_wsum
+    dcg.run_aucell
 ```
diff --git a/docs/api/get.md b/docs/api/get.md
@@ -12,4 +12,6 @@ These functions offer convineant ways to move arrays and matrices from and to th
     get.aggregate
     get.anndata_to_GPU
     get.anndata_to_CPU
+    get.X_to_GPU
+    get.X_to_CPU
 ```
diff --git a/docs/api/scanpy_gpu.md b/docs/api/scanpy_gpu.md
@@ -89,6 +89,16 @@ Any transformation of the data matrix that is not a tool. Other than `tools`, pr
     tl.leiden
 ```
 
+### Gene scores, Cell cycle
+
+```{eval-rst}
+.. autosummary::
+   :toctree: generated/
+
+    tl.score_genes
+    tl.score_genes_cell_cycle
+```
+
 ### Marker genes
 
 ```{eval-rst}

diff --git a/docs/conf.py b/docs/conf.py
@@ -78,7 +78,7 @@
     "html_image",
     "html_admonition",
 ]
-myst_url_schemes = ("http", "https", "mailto")
+myst_url_schemes = ("http", "https", "mailto", "ftp")
 nb_output_stderr = "remove"
 nb_execution_mode = "off"
 nb_merge_streams = True
@@ -135,6 +135,10 @@
 html_css_files = ["_static/css/override.css"]
 html_title = "rapids-singlecell"
 
+qualname_overrides = {
+    "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
+}
+
 nitpick_ignore = [
     ("py:class", "scipy.sparse.base.spmatrix"),
     ("py:meth", "pandas.DataFrame.iloc"),

diff --git a/docs/release-notes/0.10.3.md b/docs/release-notes/0.10.3.md
@@ -15,7 +15,6 @@
 * updates `gr.spatial_autocorr` to use a preallocation during the iterations {pr}`188` {smaller}`S Dicks`
 * `_get_mean_var` for dense input now uses `cupy.ReductionKernel` to improve precision and speed {pr}`190` {smaller}`S Dicks`
 
-#190
 ```{rubric} Bug fixes
 ```
 * fixes a bug where the `pp.scale` would have issues with `int64` indexing {pr}`187` {smaller}`S Dicks`

diff --git a/docs/release-notes/0.10.4.md b/docs/release-notes/0.10.4.md
@@ -0,0 +1,15 @@
+### 0.10.4 {small}`2024-05-14`
+
+```{rubric} Features
+```
+
+```{rubric} Performance
+```
+
+```{rubric} Bug fixes
+```
+* fixes the creation of the docker container on release {pr}`193` {smaller}`T Korten (HZDR/Helmholtz AI)`
+
+
+```{rubric} Misc
+```
diff --git a/docs/release-notes/0.10.5.md b/docs/release-notes/0.10.5.md
@@ -0,0 +1,11 @@
+### 0.10.5 {small}`2024-06-11`
+
+```{rubric} Bug fixes
+```
+* fixes an issue with `tl.umap` and `init_pos` {pr}`197` {smaller}`S Dicks`
+* fixes an issue with `pp.highly_variable_genes` for `flavor = 'seurat_v3'` with sparse `csc` {pr}`199` {smaller}`S Dicks`
+* adds `AnyRandom` to `_utils` {pr}`200` {smaller}`S Dicks`
+
+```{rubric} Misc
+```
+* updates installer for `rapids-24.06` {pr}`205` {smaller}`S Dicks`
diff --git a/docs/release-notes/0.10.6.md b/docs/release-notes/0.10.6.md
@@ -0,0 +1,9 @@
+### 0.10.6 {small}`2024-06-25`
+
+```{rubric} Bug fixes
+```
+ * removes `.A` to be compatible with scipy 1.14.0 {pr}`214` {smaller}`S Dicks`
+
+```{rubric} Misc
+```
+* updates tests to work without `scanpy.testing` {pr}`215` {smaller}`S Dicks`
diff --git a/docs/release-notes/0.10.7.md b/docs/release-notes/0.10.7.md
@@ -0,0 +1,21 @@
+### 0.10.7 {small}`2024-07-23`
+
+```{rubric} Features
+```
+* adds `decoupler_gpu.run_ulm` {pr}`224` {smaller}`S Dicks`
+
+```{rubric} Performance
+```
+* adds `_sparse2dense` for better performance {pr}`220` {smaller}`S Dicks`
+* refactors `regress_out` {pr}`222` {smaller}`S Dicks`
+* refactors `decoupler_gpu` dataloading {pr}`224` {smaller}`S Dicks`
+* updates `regress_out` for better memory use {pr}`227` {smaller}`S Dicks`
+* avoid `.toarray()` in sparse PCA transform {pr}`228` {smaller}`S Dicks`
+
+
+```{rubric} Bug fixes
+```
+* Removes support for older rapids with `tl.louvain` that cause issues {pr}`226` {smaller}`S Dicks`
+
+```{rubric} Misc
+```
diff --git a/docs/release-notes/0.10.8.md b/docs/release-notes/0.10.8.md
@@ -0,0 +1,21 @@
+### 0.10.8 {small}`2024-08-09`
+
+```{rubric} Features
+```
+* adds `tl.score_genes` {pr}`235` {smaller}`S Dicks`
+* adds `tl.score_genes_cell_cycle` {pr}`235` {smaller}`S Dicks`
+* adds `get.X_to_GPU` and `get.X_to_CPU` {pr}`235` {smaller}`S Dicks`
+* adds `dcg.run_aucell` {pr}`236` {smaller}`S Dicks`
+
+
+```{rubric} Performance
+```
+
+```{rubric} Bug fixes
+```
+
+```{rubric} Misc
+```
+* updates tests to run on rapids-24.08 {pr}`241` {smaller}`S Dicks`
+* updates docker to on rapids-24.08 {pr}`241` {smaller}`S Dicks`
+* updates docker to run with cuda-12 {pr}`241` {smaller}`S Dicks`
diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md
@@ -0,0 +1,17 @@
+### 0.10.8 {small}`the future`
+
+```{rubric} Features
+```
+* add `key_added` parameter to `tl.pca`, `tl.tsne`, and `tl.umap` that allows to control where to put the output within the AnnData object {pr}`244` {smaller}`P Angerer`
+
+```{rubric} Performance
+```
+
+```{rubric} Bug fixes
+```
+
+```{rubric} Misc
+```
+* refactor docstrings to work better in RTD {pr}`242` {smaller}`S Dicks`
+* remove Conda from CI {pr}`247` {smaller}`S Dicks`
+* add `cupy` as rapids dependency {pr}`254` {smaller}`S Dicks`
diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md
@@ -3,6 +3,18 @@
 # Release notes
 
 ## Version 0.10.0
+```{include} /release-notes/0.10.9.md
+```
+```{include} /release-notes/0.10.8.md
+```
+```{include} /release-notes/0.10.7.md
+```
+```{include} /release-notes/0.10.6.md
+```
+```{include} /release-notes/0.10.5.md
+```
+```{include} /release-notes/0.10.4.md
+```
 ```{include} /release-notes/0.10.3.md
 ```
 ```{include} /release-notes/0.10.2.md

diff --git a/notebooks b/notebooks