refactor into viash components

.github/workflows/daily-build.yml

@@ -0,0 +1,75 @@
+name: daily build
+
+on:
+  schedule:
+    # build daily
+    - cron: '0 0 * * *'
+  workflow_dispatch:
+
+jobs:
+  # phase 1
+  list:
+    runs-on: ubuntu-latest
+
+    outputs:
+      component_matrix: ${{ steps.set_matrix.outputs.matrix }}
+      cache_key: ${{ steps.cache.outputs.cache_key }}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: viash-io/viash-actions/setup@v3
+
+    - id: ns_list
+      uses: viash-io/viash-actions/ns-list@v3
+      with:
+        platform: docker
+        src: src
+        format: json
+
+    - id: set_matrix
+      run: |
+        echo "matrix=$(jq -c '[ .[] | 
+          { 
+            "name": (.functionality.namespace + "/" + .functionality.name),
+            "config": .info.config,
+            "dir": .info.config | capture("^(?<dir>.*\/)").dir
+          }
+        ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT
+
+  # phase 2
+  build:
+    needs: list
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        component: ${{ fromJson(needs.list.outputs.component_matrix) }}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: viash-io/viash-actions/setup@v3
+
+    - name: Login to container registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ secrets.GTHB_USER }}
+        password: ${{ secrets.GTHB_PAT }}
+
+    - name: Build container
+      uses: viash-io/viash-actions/ns-build@v3
+      with:
+        platform: docker
+        src: ${{ matrix.component.dir }}
+        setup: build
+
+    - name: Push container
+      uses: viash-io/viash-actions/ns-build@v3
+      with:
+        platform: docker
+        src: ${{ matrix.component.dir }}
+        setup: push

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 OpenPipelines
+Copyright (c) 2021 OpenPipelines
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

_viash.yaml

@@ -0,0 +1,9 @@
+viash_version: 0.7.3
+
+source: src
+target: target
+
+config_mods: |
+  .functionality.version := '1.0.0'
+  .platforms[.type == 'docker'].target_registry := 'ghcr.io/openpipelines-bio/base'
+  .platforms[.type == 'docker'].target_image_source := 'https://github.com/openpipelines-bio/base-images'

base-python-3.10/CHANGELOG.md → src/python_3_10/CHANGELOG.md

@@ -1,4 +1,4 @@
-# `ghcr.io/openpipelines-bio/base-python-3.10:v1.0.0`
+# `ghcr.io/openpipelines-bio/base/python_3_10:1.0.0`
 
 * Initial release. An Python 3.10 image with the following packages installed:
   - `anndata~=0.8.0`

src/python_3_10/config.vsh.yaml

@@ -0,0 +1,15 @@
+functionality:
+  name: python_3_10
+  description: A Python 3.10 slim with anndata and mudata preinstalled.
+platforms:
+  - type: docker
+    image: python:3.10-slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+      - type: python
+        packages:
+          - anndata~=0.8.0
+          - mudata~=0.2.0
+          - scanpy~=1.9.2

base-r2u-22.04/CHANGELOG.md → src/r2u_22_04/CHANGELOG.md

@@ -1,4 +1,4 @@
-# `ghcr.io/openpipelines-bio/base-r:v1.0.0`
+# `ghcr.io/openpipelines-bio/base/r2u_22_04:1.0.0`
 
 * Initial release. An R2U 22.04 image with the following packages installed:
   - R release

src/r2u_22_04/config.vsh.yaml

@@ -0,0 +1,24 @@
+functionality:
+  name: r2u_22_04
+  description: An R2U 22.04 with anndata and mudata preinstalled.
+platforms:
+  - type: docker
+    image: eddelbuettel/r2u:22.04
+    setup:
+      - type: apt
+        packages:
+          - procps
+          - libhdf5-dev
+          - libgeos-dev
+          - python3
+          - python3-pip
+          - python3-dev
+          - python-is-python3
+      - type: python
+        packages:
+          - anndata~=0.8.0
+          - mudata~=0.2.0
+          - scanpy~=1.9.2
+      - type: r
+        packages:
+          - anndata