minor

.github/workflows/build_test_publish_docker_images.yml → .github/workflows/docker.yml

@@ -1,12 +1,8 @@
 # From https://docs.github.com/en/actions/publishing-packages/publishing-docker-images
-
 name: Build, Test, and Publish Docker images
 
-# Trigger on *publish* of a release
-# See: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#release
 on:
-  release:
-    types: [published]
+  push
 
 jobs:
   matrixed-docker-build-test-publish:

docs/install.md

@@ -77,11 +77,4 @@ For certain features, however, additional optional dependencies are necessary:
 - scanorama: For the `snapatac2.pp.scanorama_integrate` function.
 - xgboot: For network structure inference.
 
-To install these optional dependencies, use `pip install snapatac2[extra]`.
-
-For downstream analysis, some helpful but not mandatory packages, such as scanpy and scvi-tools, are available.
-They can be installed with `pip install snapatac2[recommend]`.
-
-To obtain all optional dependencies at once, use `pip install snapatac2[all]`.
-
-Note that the detailed dependencies of SnapATAC2 can be found in the [setup.py](https://github.com/kaizhang/SnapATAC2/blob/main/snapatac2-python/setup.py).
+To install these optional dependencies, use `pip install snapatac2[recommend]`.

snapatac2-python/pyproject.toml

@@ -56,7 +56,14 @@ Issues = "https://github.com/kaizhang/SnapATAC2/issues"
 Changelog = "https://kzhang.org/SnapATAC2/version/dev/changelog.html"
 
 [project.optional-dependencies]
-extra = ["scanorama>=1.7.3", "harmonypy>=0.0.9", "xgboost>=1.4", "umap-learn>=0.5.0"]
-recommend = ["scanpy[scanorama, skmisc, magic, harmony]>=1.9", "scvi-tools>=1.0"]
-all = ["snapatac2[extra]", "snapatac2[recommend]"]
+recommend = [
+    "scanorama>=1.7.3",
+    "harmonypy>=0.0.9",
+    "xgboost>=1.4",
+    "umap-learn>=0.5.0",
+    "scanpy>=1.9",
+    "scvi-tools>=1.0",
+    "scikit-misc>=0.1.3",
+    "magic-impute>=2.0",
+]
 test = ["pytest", "hypothesis==6.72.4"]