add base images to core (#5)

* Add base_images dir

* Update to latest base-images repo

* [WIP] update daily-build action

* remove duplicate build workflow

* update CI to perform when changes on base_images

* fix docker container naming

* Update base_images/CHANGELOG.md

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/daily-build.yaml

@@ -4,6 +4,8 @@ on:
   push:
     branches:
       - main
+    paths:
+      - 'base_images/**'
   pull_request:
   schedule:
     # build daily

base_images/.gitignore

@@ -0,0 +1 @@
+.idea

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).

base_images/README.md

@@ -0,0 +1,13 @@
+# Base images
+
+
+<!-- This file is rendered by running 'quarto render README.qmd' -->
+
+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)

base_images/README.qmd

@@ -0,0 +1,29 @@
+---
+title: Base images
+format: gfm
+---
+
+<!-- This file is rendered by running 'quarto render README.qmd' -->
+
+```{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")
+}
+```

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

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

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

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

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