From 8f17f47ef50cc91dbfbc695fecad8916a666fcb3 Mon Sep 17 00:00:00 2001 From: Kai Zhang Date: Sun, 31 Mar 2024 13:59:07 +0800 Subject: [PATCH] minor --- ...ld_test_publish_docker_images.yml => docker.yml} | 6 +----- docs/install.md | 9 +-------- snapatac2-python/pyproject.toml | 13 ++++++++++--- 3 files changed, 12 insertions(+), 16 deletions(-) rename .github/workflows/{build_test_publish_docker_images.yml => docker.yml} (96%) diff --git a/.github/workflows/build_test_publish_docker_images.yml b/.github/workflows/docker.yml similarity index 96% rename from .github/workflows/build_test_publish_docker_images.yml rename to .github/workflows/docker.yml index 9cc8be5fc..abac5e9d7 100644 --- a/.github/workflows/build_test_publish_docker_images.yml +++ b/.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: diff --git a/docs/install.md b/docs/install.md index 659ef1b9d..ed9c2ba5d 100644 --- a/docs/install.md +++ b/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). \ No newline at end of file +To install these optional dependencies, use `pip install snapatac2[recommend]`. \ No newline at end of file diff --git a/snapatac2-python/pyproject.toml b/snapatac2-python/pyproject.toml index 702fa8ba7..75d2648fa 100644 --- a/snapatac2-python/pyproject.toml +++ b/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"]