ci: docker push (-> ghcr)

.github/workflows/build-containers.yml

@@ -12,57 +12,57 @@ jobs:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/OmicsIntegrator1
-      container: reedcompbio/omics-integrator-1
+      container: ghcr.io/reed-compbio/omics-integrator-1
   build-and-remove-omics2:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/OmicsIntegrator2
-      container: reedcompbio/omics-integrator-2
+      container: ghcr.io/reed-compbio/omics-integrator-2
   build-and-remove-pathlinker:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/PathLinker
-      container: reedcompbio/pathlinker
+      container: ghcr.io/reed-compbio/pathlinker
   build-and-remove-meo:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/MEO
-      container: reedcompbio/meo
+      container: ghcr.io/reed-compbio/meo
   build-and-remove-mincostflow:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/MinCostFlow
-      container: reedcompbio/mincostflow
+      container: ghcr.io/reed-compbio/mincostflow
   build-and-remove-allpairs:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/AllPairs
-      container: reedcompbio/allpairs
+      container: ghcr.io/reed-compbio/allpairs
   build-and-remove-domino:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/DOMINO
-      container: reedcompbio/domino
+      container: ghcr.io/reed-compbio/domino
   build-and-remove-btb:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/BowTieBuilder
-      container: reedcompbio/bowtiebuilder
+      container: ghcr.io/reed-compbio/bowtiebuilder
   build-and-remove-cytoscape:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/Cytoscape
-      container: reedcompbio/py4cytoscape
+      container: ghcr.io/reed-compbio/py4cytoscape
   build-and-remove-responsenet:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/ResponseNet
-      container: reedcompbio/responsenet
+      container: ghcr.io/reed-compbio/responsenet
   build-and-remove-spras:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/SPRAS
-      container: reedcompbio/spras
+      container: ghcr.io/reed-compbio/spras
       # Since any change to the SPRAS codebase would constitute a change to
       # the container we produce in this step, build the container regardless
       # of detected changes.

.github/workflows/push-docker.yml

@@ -0,0 +1,30 @@
+name: Push to Docker
+
+on:
+  workflow_dispatch:
+    inputs:
+      folder:
+        description: 'The folder to push'
+        required: true
+        type: string
+      version:
+        description: 'The version to use (e.g. v1)'
+        required: true
+        type: string
+
+jobs:
+  push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Run build.py
+        run: python3 docker-wrappers/build.py --dir ${{ inputs.folder }} --version ${{ inputs.version }} --yes

.github/workflows/release.yml

@@ -19,25 +19,12 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Log in to Docker Hub
+      - name: Login to GitHub Container Registry
         uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          # Passwords are set up through the GitHub control panel. The docs for
-          # the login action are explicit about never using a real password, and
-          # instead setting up a DockerHub personal access token:
-          # https://github.com/docker/login-action?tab=readme-ov-file#docker-hub
-          password: ${{ secrets.DOCKER_PASSWORD }}
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v6
-        with:
-          context: ./
-          file: docker-wrappers/SPRAS/Dockerfile
-          tags: |
-            reedcompbio/spras:${{ github.ref_name }}
-            reedcompbio/spras:latest
-          # Use the previous latest for the build cache, assuming they're probably
-          # relatively similar
-          cache-from: type=registry,ref=reedcompbio/spras:latest
-          push: true
+        run: python3 docker-wrappers/build.py --dir SPRAS --version ${{ github.ref_name }} --yes

README.md

@@ -72,7 +72,7 @@ Large SPRAS workflows may benefit from execution with HTCondor, a scheduler/mana
 **Dockerized pathway reconstruction algorithms**: Pathway reconstruction algorithms are run via Docker images using the docker-py Python package.
 [PathLinker](https://github.com/Murali-group/PathLinker), [Omics Integrator](https://github.com/fraenkel-lab/OmicsIntegrator), [Omics Integrator 2](https://github.com/fraenkel-lab/OmicsIntegrator2), and [Maximum Edge Orientation](https://github.com/agitter/meo/) are the first supported algorithms.
 The files to create these Docker images are in the `docker-wrappers` subdirectory along with links to algorithms' original repositories.
-The Docker images are available on [DockerHub](https://hub.docker.com/orgs/reedcompbio).
+The Docker images are available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages).
 
 **Python wrapper for calling algorithms**: Wrapper functions provide an interface between the common file formats for input and output data and the algorithm-specific file formats and reconstruction commands.
 These wrappers are in the `spras/` subdirectory.

config/config.yaml

@@ -24,10 +24,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
   # Enabling profiling adds a file called 'usage-profile.tsv' to the output directory of each algorithm.
   # The contents of this file describe the CPU utilization and peak memory consumption of the algorithm

config/egfr.yaml

@@ -21,10 +21,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
 algorithms:
   - name: pathlinker

docker-wrappers/AllPairs/Dockerfile

@@ -1,5 +1,6 @@
 # AllPairs wrapper
 FROM python:3.12-alpine3.21
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # bash is required for dsub in the All of Us cloud environment
 RUN apk add --no-cache bash

docker-wrappers/AllPairs/README.md

@@ -1,17 +1,17 @@
 # All Pairs Shortest Paths Docker image
 
-A Docker image for All Pairs Shortest Paths that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/allpairs).
+A Docker image for All Pairs Shortest Paths that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/allpairs).
 This [algorithm](https://github.com/Reed-CompBio/all-pairs-shortest-paths) was implemented by the SPRAS team and relies on the NetworkX [`shortest_path`](https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html) function.
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/allpairs -f Dockerfile .
+docker build -t reed-compbio/allpairs -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-docker run reedcompbio/allpairs pip list
+docker run reed-compbio/allpairs pip list
 ```
 
 
@@ -29,3 +29,4 @@ The Docker wrapper can be tested with `pytest -k test_ap.py` from the root of th
 ## Versions:
 - v1: Initial version. Copies source file from SPRAS repository.
 - v2: Add bash, which is not available in Alpine Linux.
+- v3: AllPairs directionality

docker-wrappers/AllPairs/metadata.json

@@ -0,0 +1,4 @@
+{
+    "imageName": "allpairs",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}

docker-wrappers/BowTieBuilder/Dockerfile

@@ -1,4 +1,5 @@
 FROM python:3.8-bullseye
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /btb
 RUN wget https://raw.githubusercontent.com/Reed-CompBio/BowTieBuilder-Algorithm/dd8519cd8a8397c0e0724106f498b6002d3f7be2/btb.py

docker-wrappers/BowTieBuilder/README.md

@@ -1,15 +1,20 @@
 # BowTieBuilder Docker image
 
-A Docker image for [BowTieBuilder](https://github.com/Reed-CompBio/BowTieBuilder-Algorithm) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/bowtiebuilder).
+A Docker image for [BowTieBuilder](https://github.com/Reed-CompBio/BowTieBuilder-Algorithm) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/bowtiebuilder).
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/bowtiebuilder:v2 -f Dockerfile .
+docker build -t reed-compbio/bowtiebuilder:v1 -f Dockerfile .
 ```
 from this directory.
 
 ## Original Paper
 
 The original paper for [BowTieBuilder] can be accessed here:
 
-Supper, J., Spangenberg, L., Planatscher, H. et al. BowTieBuilder: modeling signal transduction pathways. BMC Syst Biol 3, 67 (2009). https://doi.org/10.1186/1752-0509-3-67
+Supper, J., Spangenberg, L., Planatscher, H. et al. BowTieBuilder: modeling signal transduction pathways. BMC Syst Biol 3, 67 (2009). https://doi.org/10.1186/1752-0509-3-67
+
+## Versions
+
+- `v1`: Initial docker container
+- `v2`: Pin BTB file version for reproducible docker builds.

docker-wrappers/BowTieBuilder/metadata.json

@@ -0,0 +1,4 @@
+{
+    "imageName": "bowtiebuilder",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}

docker-wrappers/Cytoscape/Dockerfile

@@ -2,6 +2,7 @@
 # https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile
 # by Kozo Nishida
 FROM python:3.9.13
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # Versions
 ENV CYTOSCAPE_VERSION=3.9.1

docker-wrappers/Cytoscape/README.md

@@ -1,6 +1,6 @@
 # Cytoscape image
 
-A Docker image for [Cytoscape](https://cytoscape.org/) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/py4cytoscape).
+A Docker image for [Cytoscape](https://cytoscape.org/) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/py4cytoscape).
 It was originally derived from the [`docker-cytoscape-desktop/py4cytoscape`](https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile) image.
 
 Thank you to Scooter Morris for help debugging problems running Cytoscape in Singularity.
@@ -9,7 +9,7 @@ Thank you to Scooter Morris for help debugging problems running Cytoscape in Sin
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/py4cytoscape -f Dockerfile .
+docker build -t reed-compbio/py4cytoscape -f Dockerfile .
 ```
 from this directory.
 

docker-wrappers/Cytoscape/metadata.json

@@ -0,0 +1,4 @@
+{
+    "imageName": "py4cytoscape",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}

docker-wrappers/DOMINO/Dockerfile

@@ -1,6 +1,7 @@
 # DOMINO wrapper
 # https://github.com/Shamir-Lab/DOMINO
 FROM python:3.7
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 RUN pip install domino-python==0.1.1
 

docker-wrappers/DOMINO/README.md

@@ -1,22 +1,27 @@
 # DOMINO Docker image
 
-A Docker image for [DOMINO](https://github.com/Shamir-Lab/DOMINO) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/domino).
+A Docker image for [DOMINO](https://github.com/Shamir-Lab/DOMINO) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/domino).
 
 DOMINO outputs multiple active modules, which SPRAS combines into a single pathway.
 It is [non-deterministic](https://github.com/Shamir-Lab/DOMINO/issues/5) and cannot be made deterministic with a seed.
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/domino -f Dockerfile .
+docker build -t reed-compbio/domino -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-winpty docker run reedcompbio/domino pip list
+winpty docker run reed-compbio/domino pip list
 ```
 The `winpty` prefix is only needed on Windows.
 
 ## TODO
 - Resolve upstream ValueError with small inputs https://github.com/Shamir-Lab/DOMINO/issues/11
 - Use cache or reuse slices files from previous runs on the same network
+- Investigate why DOMINO does not build on amd64 after https://github.com/Reed-CompBio/spras/pull/235.
+
+## Versions
+
+- `v1`: Initial DOMINO container.

docker-wrappers/DOMINO/metadata.json

@@ -0,0 +1,4 @@
+{
+    "imageName": "domino",
+    "architectures": ["linux/amd64"]
+}

docker-wrappers/MEO/Dockerfile

@@ -1,6 +1,7 @@
 # Maximum Edge Orientation wrapper
 # https://github.com/agitter/meo/
 FROM amazoncorretto:8-alpine3.19
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /meo
 RUN export MEO_TAG=v1.1.0 && \

docker-wrappers/MEO/README.md

@@ -1,13 +1,13 @@
 # Maximum Edge Orientation Docker image
 
-A Docker image for [Maximum Edge Orientation](https://github.com/agitter/meo/) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/meo).
+A Docker image for [Maximum Edge Orientation](https://github.com/agitter/meo/) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/meo).
 Only supports the Random orientation algorithm, not MINSAT or MAXCSP.
 
 ## Building the Docker image
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/meo -f Dockerfile .
+docker build -t reed-compbio/meo -f Dockerfile .
 ```
 from this directory.
 
@@ -24,5 +24,5 @@ The Docker wrapper can be tested with `pytest`.
 
 ## Versions
 
-- `v1`: Initial version
+- `v1`: Initial MEO container
 - `v2`: Use `amazoncorretto` alpine base image

docker-wrappers/MEO/metadata.json

@@ -0,0 +1,4 @@
+{
+    "imageName": "meo",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}

docker-wrappers/MinCostFlow/Dockerfile

@@ -1,5 +1,6 @@
 #uses ubuntu as the base
 FROM python:3.10.7
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /MinCostFlow
 

docker-wrappers/MinCostFlow/README.md

@@ -1,20 +1,20 @@
 # MinCostFlow Docker image
 
-A Docker image for [MinCostFlow](https://github.com/gitter-lab/min-cost-flow) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/mincostflow).
+A Docker image for [MinCostFlow](https://github.com/gitter-lab/min-cost-flow) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/mincostflow).
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/mincostflow -f Dockerfile .
+docker build -t reed-compbio/mincostflow -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-docker run reedcompbio/mincostflow pip list
+docker run reed-compbio/mincostflow pip list
 ```
 or inspect the Python script arguments:
 ```
-docker run reedcompbio/mincostflow python /MinCostFlow/minCostFlow.py -h
+docker run reed-compbio/mincostflow python /MinCostFlow/minCostFlow.py -h
 ```
 Windows users may need to add the prefix `winpty` prefix before these commands.
 
@@ -30,9 +30,13 @@ The Docker wrapper can be tested with `pytest -k test_mcf.py` from the root of t
 
 Alternatively, to run the Docker image directly, run the following command from the root of the `spras` repository
 ```
-docker run -w /data --mount type=bind,source=/${PWD},target=/data reedcompbio/mincostflow python /MinCostFlow/minCostFlow.py --edges_file /data/test/MinCostFlow/input/graph1/edges.txt --sources_file /data/test/MinCostFlowinput/graph1/sources.txt --targets_file /data/test/MinCostFlowinput/graph1/targets.txt --flow 1 --output graph1 --capacity 1  
+docker run -w /data --mount type=bind,source=/${PWD},target=/data reed-compbio/mincostflow python /MinCostFlow/minCostFlow.py --edges_file /data/test/MinCostFlow/input/graph1/edges.txt --sources_file /data/test/MinCostFlowinput/graph1/sources.txt --targets_file /data/test/MinCostFlowinput/graph1/targets.txt --flow 1 --output graph1 --capacity 1  
 ```
 
 This will run MinCostFlow on the test input files and write the output files to the root of the `spras` repository.
 
 Windows users may need to escape the absolute paths so that `/data` becomes `//data`, etc.
+
+## Versions
+
+- `v1`: Initial MinCostFlow docker container.