ci: docker push (-> ghcr)

.github/workflows/build-containers.yml

@@ -12,47 +12,47 @@ 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:
@@ -62,7 +62,7 @@ jobs:
     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 +1,27 @@
+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
+    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 push.py
+        run: python3 docker-wrappers/push.py --dir ${{ inputs.folder }} --version ${{ inputs.version }} --yes

config/config.yaml

@@ -23,10 +23,10 @@ unpack_singularity: false
 # Note that this assumes container names are consistent across registries, and that the
 # registry being passed doesn't require authentication for pull actions
 container_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
 
 # This list of algorithms should be generated by a script which checks the filesystem for installs.
 # It shouldn't be changed by mere mortals. (alternatively, we could add a path to executable for each algorithm

docker-wrappers/AllPairs/metadata.json

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

docker-wrappers/BowTieBuilder/metadata.json

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

docker-wrappers/Cytoscape/metadata.json

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

docker-wrappers/DOMINO/metadata.json

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

docker-wrappers/MEO/metadata.json

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

docker-wrappers/MinCostFlow/metadata.json

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

docker-wrappers/OmicsIntegrator1/Dockerfile

@@ -1,12 +1,10 @@
 # Omics Integrator 1 wrapper
 # https://github.com/fraenkel-lab/OmicsIntegrator
-# Activates the conda environment before running command inside container
-# Uses the strategy from https://pythonspeed.com/articles/activate-conda-dockerfile/
-# by Itamar Turner-Trauring
-FROM continuumio/miniconda3:4.9.2
+# This version does not use conda
+FROM python:2.7.18
 
 # Need to install msgsteiner-1.3 and dependencies
-RUN apt-get -qq update --allow-releaseinfo-change && \
+RUN apt-get -qq update && \
     apt-get install -y build-essential libx11-dev libboost-dev libboost-program-options-dev
 
 RUN commit=0a57ede6beeef6e63b86d19898e560d62015e85d && \
@@ -24,7 +22,5 @@ RUN commit=0a57ede6beeef6e63b86d19898e560d62015e85d && \
 ENV MSGSTEINER_PATH=/OmicsIntegrator/msgsteiner-1.3/msgsteiner
 WORKDIR /OmicsIntegrator
 
-COPY environment.yml .
-RUN conda env create -f environment.yml
-
-ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "oi1"]
+COPY requirements.txt .
+RUN pip install -r requirements.txt

docker-wrappers/OmicsIntegrator1/metadata.json

@@ -0,0 +1,4 @@
+{
+    "dockerName": "omics-integrator-1",
+    "architectures": ["linux/amd64"]
+}

docker-wrappers/OmicsIntegrator2/metadata.json

@@ -0,0 +1,4 @@
+{
+    "dockerName": "omics-integrator-2",
+    "architectures": ["linux/amd64"]
+}

docker-wrappers/PathLinker/metadata.json

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

docker-wrappers/README.md

@@ -0,0 +1,20 @@
+# docker-wrappers
+
+This folder contains the list of all docker wrappers.
+
+We build these docker images with `buildx` to support multiple docker architectures.
+
+For convenience, we provide a `push.py` python file which pushes a docker image with the architectures
+that we want to support.
+
+```
+usage: push.py [-h] --tag TAG --dir DIR
+push.py: error: the following arguments are required: --tag, --dir
+```
+
+For example, using the default supported `ghcr.io` registry that SPRAS uses, we can push RWR v1:
+
+```
+docker login ghcr.io -u reed-compbio
+python push.py --dir RWR --version v1
+```

docker-wrappers/RWR/metadata.json

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

docker-wrappers/SPRAS/metadata.json

@@ -0,0 +1,5 @@
+{
+    "dockerName": "spras",
+    "architectures": ["linux/arm64", "linux/amd64"],
+    "cwd": "../../"
+}

docker-wrappers/ST_RWR/README.md

@@ -9,7 +9,7 @@ The random walk with restarts algorithm requires a directed input network. Howev
 To build a new docker image for ST_RWR navigate to the /docker-wrappers/ST_RWR directory and enter:
 
 ```
-docker build -t reedcompbio/str-wr -f Dockerfile .
+docker build -t reedcompbio/st-rwr -f Dockerfile .
 ```
 
 ## Testing

docker-wrappers/ST_RWR/metadata.json

@@ -0,0 +1,4 @@
+{
+    "dockerName": "st-rwr",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}

docker-wrappers/push.py

@@ -0,0 +1,73 @@
+import argparse
+import json
+import os
+import subprocess
+from pathlib import Path
+
+COMMAND_BUILDX = ["docker", "buildx"]
+
+COMMAND_BUILDER_LS = COMMAND_BUILDX + ["ls"]
+COMMAND_BUILDER_INSTANCE = COMMAND_BUILDX + ["create", "--name", "container", "--driver=docker-container"]
+
+# https://stackoverflow.com/a/5137509/7589775
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
+def construct_push_command(tags: list[str], dir: str, architectures: list[str]):
+    base_cmd = ["build"]
+    for tag in tags:
+        base_cmd.extend(["--tag", tag])
+    base_cmd = base_cmd + ["--file", Path(dir_path, dir, "Dockerfile"), "--platform",
+                ",".join(architectures), "--builder", "container", "--push", "."]
+    return COMMAND_BUILDX + base_cmd
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description="Docker Wrapper builder python wrapper"
+    )
+    parser.add_argument("--dir", type=str, required=True, help="The directory of the docker wrapper to use")
+    parser.add_argument("--version", type=str, required=True, help="The version (tag name) to use for the container")
+    parser.add_argument("--org-name", type=str, help="The organization to push to", default="ghcr.io/reed-compbio/")
+    parser.add_argument("--yes", type=bool, help="Whether to automatically agree to pushing a container", action=argparse.BooleanOptionalAction)
+    parser.add_argument("--relax", type=bool, help="Whether to not be strict on tag naming", action=argparse.BooleanOptionalAction)
+
+    return parser.parse_args()
+
+def main():
+    # We need a buildx environment
+    # This is a terrible check. Yes, docker buildx has no API exposed on docker-py.
+    if f"\ncontainer" not in subprocess.check_output(COMMAND_BUILDER_LS).decode("utf-8"):
+        out = subprocess.run(COMMAND_BUILDER_INSTANCE)
+        if out.returncode != 0:
+            raise RuntimeError(f"Command {COMMAND_BUILDER_INSTANCE} exited with non-zero exit code.")
+
+    args = parse_arguments()
+
+    if not args.org_name.endswith("/"):
+        args.org_name = f"{args.org_name}/"
+
+    if not args.version.startswith("v"):
+        if not args.relax:
+            raise ValueError("All versions start with v (v1, v2, ...)")
+
+    metadata_path = Path(dir_path, args.dir, "metadata.json")
+    metadata = json.loads(metadata_path.read_text())
+    name = metadata['dockerName']
+    architectures = metadata['architectures']
+    cwd = str(Path(dir_path, args.dir, metadata['cwd']) if 'cwd' in metadata else Path(dir_path, args.dir))
+    tag = args.org_name + name + ":" + args.version
+    tag_latest = args.org_name + name + ":latest"
+
+    print(f"Building {name} over {architectures} with:")
+    print(f"- CWD: {cwd}")
+    print(f"- Specified tag: {tag}")
+    print(f"-    Latest tag: {tag_latest}")
+    if not args.yes:
+        confirm = input("[y/n] Are you sure you want to push to these tags over these architectures? ")
+        if confirm.strip().lower() not in ('y', 'yes'):
+            raise RuntimeError("Did not confirm dialog.")
+
+    push_command = construct_push_command([tag, tag_latest], args.dir, architectures)
+    subprocess.run(push_command, capture_output=False, cwd=cwd)
+
+if __name__ == '__main__':
+    main()

spras/allpairs.py

@@ -104,7 +104,7 @@ def run(nodetypes=None, network=None, directed_flag=None, output_file=None, cont
         if Path(directed_flag).read_text().strip() == "true":
             command.append("--directed")
 
-        container_suffix = "allpairs:v4"
+        container_suffix = "allpairs:v1"
         run_container_and_log(
             'All Pairs Shortest Paths',
             container_framework,

spras/analysis/cytoscape.py

@@ -46,7 +46,7 @@ def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, contai
         # Provided the mapped pathway file path and the original file path as the label Cytoscape
         command.extend(['--pathway', f'{mapped_pathway}|{pathway}'])
 
-    container_suffix = "py4cytoscape:v3"
+    container_suffix = "py4cytoscape:v1"
     run_container_and_log('Cytoscape',
                          container_framework,
                          container_suffix,

spras/btb.py

@@ -132,7 +132,7 @@ def run(sources=None, targets=None, edges=None, output_file=None, container_fram
                    '--output_file',
                    mapped_out_prefix]
 
-        container_suffix = "bowtiebuilder:v2"
+        container_suffix = "bowtiebuilder:v1"
         run_container_and_log('BowTieBuilder',
                               container_framework,
                               container_suffix,

spras/domino.py

@@ -111,7 +111,7 @@ def run(network=None, active_genes=None, output_file=None, slice_threshold=None,
                           '--network_file', network_file,
                           '--output_file', mapped_slices_file]
 
-        container_suffix = "domino"
+        container_suffix = "domino:v1"
         run_container_and_log('slicer',
                              container_framework,
                              container_suffix,

spras/meo.py

@@ -178,7 +178,7 @@ def run(edges=None, sources=None, targets=None, output_file=None, max_path_lengt
 
         command = ['java', '-jar', '/meo/EOMain.jar', properties_file]
 
-        container_suffix = "meo"
+        container_suffix = "meo:v1"
         run_container_and_log('Maximum Edge Orientation',
                              container_framework,
                              container_suffix,

spras/mincostflow.py

@@ -113,7 +113,7 @@ def run(sources=None, targets=None, edges=None, output_file=None, flow=None, cap
             command.extend(['--capacity', str(capacity)])
 
         # choosing to run in docker or singularity container
-        container_suffix = "mincostflow"
+        container_suffix = "mincostflow:v1"
 
         # constructs a docker run call
         run_container_and_log('MinCostFlow',

spras/omicsintegrator1.py

@@ -195,10 +195,10 @@ def run(edges=None, prizes=None, dummy_nodes=None, dummy_mode=None, mu_squared=N
         if seed is not None:
             command.extend(['--seed', str(seed)])
 
-        container_suffix = "omics-integrator-1:no-conda" # no-conda version is the default
+        container_suffix = "omics-integrator-1:v1"
         run_container_and_log('Omics Integrator 1',
                              container_framework,
-                             container_suffix,  # no-conda version is the default
+                             container_suffix,
                              command,
                              volumes,
                              work_dir,