Migrate to rye

.github/workflows/build.yml

@@ -1,4 +1,4 @@
-name: build
+name: Build
 
 on:
   push:
@@ -9,68 +9,73 @@ on:
     branches: [ master ]
 
 jobs:
-  publish:
-    runs-on: ubuntu-22.04
-
+  build:
+    name: Build
+    runs-on: ubuntu-24.04
     steps:
-    - uses: actions/checkout@v4
-    - name: Decide image tags
-      id: info
-      shell: python
-      run: |
-        import os
-        import itertools
-        
-        registries = ['docker.io', 'ghcr.io']
-        repos = ['${{ github.repository }}'.lower()]
-        if '${{ github.ref_type }}' == 'branch':
-            tags = ['latest']
-        elif '${{ github.ref_type }}' == 'tag':
-            version = '${{ github.ref_name }}'[1:]
-            tags = ['latest', version]
-        else:
-            tags = []
-
-        def join_tag(t):
-            registry, repo, tag = t
-            return f'{registry}/{repo}:{tag}'
-
-        product = itertools.product(registries, repos, tags)
-        tags_csv = ','.join(map(join_tag, product))
-        push = 'true' if tags_csv else 'false'
-
-        with open(os.environ['GITHUB_OUTPUT'], 'a') as out:
-            out.write(f'tags={tags_csv}\n')
-            out.write(f'push={push}\n')
-
-    - uses: docker/setup-buildx-action@v3
-    - name: Login to DockerHub
-      if: github.event_name == 'push' || github.event_name == 'release'
-      id: dockerhub_login
-      uses: docker/login-action@v3
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
-    - name: Login to GitHub Container Registry
-      if: github.event_name == 'push' || github.event_name == 'release'
-      uses: docker/login-action@v3
-      with:
-        registry: ghcr.io
-        username: ${{ github.repository_owner }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-    - name: Build image
-      uses: docker/build-push-action@v5
-      with:
-        context: .
-        platforms: linux/amd64,linux/ppc64le,linux/arm64
-        tags: ${{ steps.info.outputs.tags }}
-        push: ${{ steps.info.outputs.push }}
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
-    - name: Update DockerHub description
-      uses: peter-evans/dockerhub-description@v3
-      if: ${{ steps.info.outputs.push }}
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
-        short-description: ${{ github.event.repository.description }}
+      - uses: actions/checkout@v4
+      - name: Install rye
+        uses: eifinger/setup-rye@d4c3ac7b15d8bf2e0b45e2d257c6b5cdbebc3643  # v4.2.1
+        with:
+          version: '0.36.0'
+          enable-cache: true
+          cache-prefix: ${{ github.workflow }}
+      - name: Decide image tags
+        id: info
+        shell: python
+        run: |
+          import os
+          import itertools
+          
+          registries = ['docker.io', 'ghcr.io']
+          repos = ['${{ github.repository }}'.lower()]
+          if '${{ github.ref_type }}' == 'branch':
+              tags = ['latest']
+          elif '${{ github.ref_type }}' == 'tag':
+              version = '${{ github.ref_name }}'[1:]
+              tags = ['latest', version]
+          else:
+              tags = []
+  
+          def join_tag(t):
+              registry, repo, tag = t
+              return f'{registry}/{repo}:{tag}'
+
+          product = itertools.product(registries, repos, tags)
+          tags_csv = ','.join(map(join_tag, product))
+          push = 'true' if tags_csv else 'false'
+
+          with open(os.environ['GITHUB_OUTPUT'], 'a') as out:
+              out.write(f'tags={tags_csv}\n')
+              out.write(f'push={push}\n')
+      - name: Build Python wheel
+        run: rye build --wheel --clean
+      - uses: docker/setup-buildx-action@v3
+      - name: Login to DockerHub
+        if: github.event_name == 'push' || github.event_name == 'release'
+        id: dockerhub_login
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Login to GitHub Container Registry
+        if: github.event_name == 'push' || github.event_name == 'release'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Build image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          platforms: linux/amd64,linux/ppc64le,linux/arm64
+          tags: ${{ steps.info.outputs.tags }}
+          push: ${{ steps.info.outputs.push }}
+      - name: Update DockerHub description
+        uses: peter-evans/dockerhub-description@v4
+        if: ${{ steps.info.outputs.push }}
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          short-description: ${{ github.event.repository.description }}

.gitignore

@@ -2,3 +2,4 @@
 .venv/
 __pycache__/
 *.egg-info/
+dist/

.python-version

@@ -0,0 +1 @@
+3.12.3

Dockerfile

@@ -1,4 +1,8 @@
-FROM docker.io/fnndsc/python-poetry:1.5.1
+# Build instructions: see https://rye.astral.sh/guide/docker/
+
+FROM python:3.12.3-alpine
+
+RUN --mount=source=dist,target=/dist PYTHONDONTWRITEBYTECODE=1 pip install --no-cache-dir /dist/*.whl
 
 LABEL org.opencontainers.image.authors="Jennings Zhang <[email protected]>, FNNDSC <[email protected]>" \
       org.opencontainers.image.title="ChRISomatic" \
@@ -7,11 +11,5 @@ LABEL org.opencontainers.image.authors="Jennings Zhang <Jennings.Zhang@childrens
       org.opencontainers.image.source="https://github.com/FNNDSC/chrisomatic" \
       org.opencontainers.image.licenses="MIT"
 
-WORKDIR /usr/local/src/chrisomatic
-COPY . .
-RUN poetry install --no-dev
-
 WORKDIR /
-# needs to write to docker daemon
-USER root
 CMD ["chrisomatic"]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2023 FNNDSC / BCH
+Copyright (c) 2021-2024 FNNDSC / BCH
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -3,7 +3,6 @@
 [![Version](https://img.shields.io/docker/v/fnndsc/chrisomatic?sort=semver)](https://hub.docker.com/r/fnndsc/chrisomatic)
 [![MIT License](https://img.shields.io/github/license/fnndsc/chrisomatic)](https://github.com/FNNDSC/chrisomatic/blob/master/LICENSE)
 [![Build](https://github.com/FNNDSC/chrisomatic/actions/workflows/build.yml/badge.svg)](https://github.com/FNNDSC/chrisomatic/actions)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 `chrisomatic` is a tool for automatic administration of _ChRIS_ backends.
 It is particularly useful for the recreation of setups for testing or development,

dev.Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.12.3-alpine
+
+WORKDIR /app
+COPY requirements-dev.lock requirements-dev.lock
+RUN --mount=type=cache,sharing=locked,target=/root/.cache/pip \
+    sed -i' ' -e '/-e file:\./d' requirements-dev.lock \
+    && env PYTHONDONTWRITEBYTECODE=1 pip install -r requirements-dev.lock
+
+CMD ["pytest"]

docker-compose.yml

@@ -0,0 +1,26 @@
+services:
+  dev:
+    build:
+      context: .
+      dockerfile: dev.Dockerfile
+    command: pytest --color=yes --code-highlight=yes
+    networks:
+      minichris:
+    userns_mode: host
+    user: root
+    working_dir: /app
+    volumes:
+      - "wd:/app:rw"
+      - "./src/chrisomatic:/app/chrisomatic:ro"
+      - "./tests:/app/tests:ro"
+      - "./scripts:/app/scripts:ro"
+      - "./pytest.ini:/app/pytest.ini:ro"
+      - "/var/run/docker.sock:/var/run/docker.sock:rw"
+
+networks:
+  minichris:
+    external: true
+    name: minichris-local
+
+volumes:
+  wd: