diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..9096371 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,6 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "daily" \ No newline at end of file diff --git a/.github/workflows/daily-build.yaml b/.github/workflows/daily-build.yaml index 8631ed8..1628392 100644 --- a/.github/workflows/daily-build.yaml +++ b/.github/workflows/daily-build.yaml @@ -4,6 +4,8 @@ on: push: branches: - main + paths: + - 'base_images/**' pull_request: schedule: # build daily diff --git a/base_images/.gitignore b/base_images/.gitignore new file mode 100644 index 0000000..485dee6 --- /dev/null +++ b/base_images/.gitignore @@ -0,0 +1 @@ +.idea diff --git a/base_images/CHANGELOG.md b/base_images/CHANGELOG.md new file mode 100644 index 0000000..8d659bf --- /dev/null +++ b/base_images/CHANGELOG.md @@ -0,0 +1,7 @@ +# OpenProblems Base Images v1.0.0 + +Relocated the base images from base_images repo to core repo. + +## MAJOR CHANGES + +* Change container registry from `ghcr.io/openproblems-bio/base_images` to docker hub `openproblems/base_*` (PR #5). \ No newline at end of file diff --git a/base_images/README.md b/base_images/README.md new file mode 100644 index 0000000..e562377 --- /dev/null +++ b/base_images/README.md @@ -0,0 +1,13 @@ +# Base images + + + + +Repository for base Docker images for openproblems-bio on Docker-hub. + +This repository currently contains the following images: + +- [`openproblems/base_python:1.0.0`](src/python) +- [`openproblems/base_pytorch_nvidia:1.0.0`](src/pytorch_nvidia) +- [`openproblems/base_r:1.0.0`](src/r) +- [`openproblems/base_tensorflow_nvidia:1.0.0`](src/tensorflow_nvidia) diff --git a/base_images/README.qmd b/base_images/README.qmd new file mode 100644 index 0000000..7054dab --- /dev/null +++ b/base_images/README.qmd @@ -0,0 +1,29 @@ +--- +title: Base images +format: gfm +--- + + + +```{r include=FALSE} +# run 'viash ns list' and read as yaml + +ns_list_yaml <- system("viash ns list --format yaml", intern = TRUE) +ns_list <- yaml::yaml.load(ns_list_yaml) +``` + +Repository for base Docker images for openproblems-bio on Docker-hub. + +This repository currently contains the following images: + +```{r echo=FALSE, output="asis"} +for (comp in ns_list) { + image_name <- paste0( + comp$package_config$organization, "/", + comp$name, ":", + comp$version + ) + cat(paste0("* [`", image_name, "`](", dirname(comp$build_info$config), ")")) + cat("\n") +} +``` diff --git a/base_images/_viash.yaml b/base_images/_viash.yaml new file mode 100644 index 0000000..c21962c --- /dev/null +++ b/base_images/_viash.yaml @@ -0,0 +1,5 @@ +organization: openproblems +version: 1.0.0 +viash_version: 0.9.0-RC6 +links: + repository: https://github.com/openproblems-bio/base_images diff --git a/base_images/src/python/config.vsh.yaml b/base_images/src/python/config.vsh.yaml new file mode 100644 index 0000000..006e322 --- /dev/null +++ b/base_images/src/python/config.vsh.yaml @@ -0,0 +1,16 @@ +name: base_python +description: A Python 3.11 image with anndata preinstalled. +engines: + - type: docker + image: python:3.11 + setup: + - type: apt + packages: + - procps + - type: python + packages: + - anndata~=0.10.0 + - scanpy~=1.10.0 + - pyyaml + - requests + - jsonschema diff --git a/base_images/src/pytorch_nvidia/config.vsh.yaml b/base_images/src/pytorch_nvidia/config.vsh.yaml new file mode 100644 index 0000000..77e4268 --- /dev/null +++ b/base_images/src/pytorch_nvidia/config.vsh.yaml @@ -0,0 +1,16 @@ +name: base_pytorch_nvidia +description: An nvcr.io pytorch 24.06-py3 with anndata preinstalled. +engines: + - type: docker + image: nvcr.io/nvidia/pytorch:24.06-py3 + setup: + - type: apt + packages: + - procps + - type: python + packages: + - anndata~=0.10.0 + - scanpy~=1.10.0 + - pyyaml + - requests + - jsonschema diff --git a/base_images/src/r/config.vsh.yaml b/base_images/src/r/config.vsh.yaml new file mode 100644 index 0000000..37e941f --- /dev/null +++ b/base_images/src/r/config.vsh.yaml @@ -0,0 +1,29 @@ +name: base_r +description: An R2U 22.04 image with anndata preinstalled. +engines: + - type: docker + image: rocker/r2u:22.04 + setup: + - type: apt + packages: + - procps + - libhdf5-dev + - libgeos-dev + - python3 + - python3-pip + - python3-dev + - python-is-python3 + - type: python + packages: + - rpy2 + - anndata~=0.10.0 + - scanpy~=1.10.0 + - pyyaml + - requests + - jsonschema + - type: r + packages: + - anndata + - BiocManager + - reticulate + - bit64 diff --git a/base_images/src/tensorflow_nvidia/config.vsh.yaml b/base_images/src/tensorflow_nvidia/config.vsh.yaml new file mode 100644 index 0000000..71a3547 --- /dev/null +++ b/base_images/src/tensorflow_nvidia/config.vsh.yaml @@ -0,0 +1,16 @@ +name: base_tensorflow_nvidia +description: An nvcr.io tensorflow 24.06-tf2-py3 with anndata preinstalled. +engines: + - type: docker + image: nvcr.io/nvidia/tensorflow:24.06-tf2-py3 + setup: + - type: apt + packages: + - procps + - type: python + packages: + - anndata~=0.10.0 + - scanpy~=1.10.0 + - pyyaml + - requests + - jsonschema