re-adding one image per workflow structure

.github/workflows/release-workflow.yml

@@ -155,6 +155,13 @@ jobs:
   buildtestandpushsingularity:
     needs: [buildandpushkipoibaseenvandsharedpy3keras2, buildandtestsharedpy3keras2,
       buildtestandpush]
+    strategy:
+      fail-fast: false
+      matrix:
+        image: ["sharedpy3keras1.2", "sharedpy3keras2", "mpra-dragonn", "extended_coda", "mmsplice",
+          "mmsplice-mtsplice", "deepmel", "framepool", "kipoisplice", "deeptarget",
+          "attentivechrome", "bpnet-oskn", "seqvec", "deepflybrain", "aparent-site_probabilities",
+          "aparent-veff", "deepstarr"]  
     runs-on: ubuntu-latest
     env:
       SINGULARITY_PULL_FOLDER: "/home/runner/singularity/"
@@ -191,4 +198,4 @@ jobs:
       shell: bash -l {0}
       if: ${{ success() }}
       run: |
-        update_all_singularity
+        update_all_singularity kipoi/kipoi-docker:${{ matrix.image }}

kipoi_containers/update_all_singularity_images.py

@@ -20,16 +20,20 @@
 
 
 @click.command()
-def run_update() -> None:
-    """Update all singularity images. By default, it will push the image to
-    zenodo by creating a new version of an existing deposition and updating
-    the metadata and file after deleting the existing file. Obviously, this
-    will update content of model_group_to_singularity_dict. The image specific
-    entry in model_group_to_singularity_dict will be updated with url and md5
-    values of the new deposition and kipoi_containers/container-info/
-    model-group-to-singularity.json will be updated.
+@click.argument("docker_image", required=True, type=str)
+def run_update(docker_image: str) -> None:
+    """Update the singularity image corresponding to the docker image.
+    By default, it does not push the image to zenodo but creates a new
+    version of an existing deposition and updates the metadata and file
+    after deleting the existing file. Obviously, this does not update
+    content of model_group_to_singularity_dict. However, if push is
+    enabled in SingularityHandler.udpate, the draft entry will be
+    pushed to zenodo, the image specific entry in model_group_to_singularity_dict
+    will be updated with url and md5 values of the new deposition and
+    kipoi_containers/container-info/model-group-to-singularity.json will be
+    updated.
     """
-    click.echo("Updating all singularity containers")
+    click.echo(f"Updating the singularity container for {docker_image}")
     github_obj = Github(os.environ["GITHUB_TOKEN"])
     kipoi_model_repo = github_obj.get_organization("kipoi").get_repo("models")
     model_group_to_singularity_dict = populate_json_from_kipoi(
@@ -47,34 +51,32 @@ def run_update() -> None:
         else:
             docker_to_model_group_dict_ci[kipoi_docker_image] = [model_group]
 
-    for docker_image in docker_to_model_group_dict_ci.keys():
-        model_or_model_group_list = docker_to_model_group_dict_ci[docker_image]
-        singularity_pull_folder = os.environ.get(
-            "SINGULARITY_PULL_FOLDER", Path(__file__).parent.resolve()
-        )
-        docker_to_model_dict = populate_json(DOCKER_TO_MODEL_JSON)
+    # for docker_image in docker_to_model_group_dict_ci.keys():
+    model_or_model_group_list = docker_to_model_group_dict_ci[docker_image]
+    singularity_pull_folder = os.environ.get(
+        "SINGULARITY_PULL_FOLDER", Path(__file__).parent.resolve()
+    )
+    docker_to_model_dict = populate_json(DOCKER_TO_MODEL_JSON)
 
-        singularity_handler = singularityhandler.SingularityHandler(
-            model_group=model_or_model_group_list[0],
-            docker_image_name=docker_image,
-            singularity_image_folder=singularity_pull_folder,
-            model_group_to_singularity_dict=model_group_to_singularity_dict,
+    singularity_handler = singularityhandler.SingularityHandler(
+        model_group=model_or_model_group_list[0],
+        docker_image_name=docker_image,
+        singularity_image_folder=singularity_pull_folder,
+        model_group_to_singularity_dict=model_group_to_singularity_dict,
+    )
+    if "shared" in docker_image:
+        models_to_test = one_model_per_modelgroup(
+            docker_to_model_dict[docker_image]
         )
-        if "shared" in docker_image:
-            models_to_test = one_model_per_modelgroup(
-                docker_to_model_dict[docker_image]
-            )
-            # Otherwise it will take more than 6 hours - available time on actions ci
-        else:
-            models_to_test = docker_to_model_dict[docker_image]
-        singularity_handler.update(models_to_test)
-        if len(model_or_model_group_list) > 1:
-            for model_or_model_group in model_or_model_group_list[1:]:
-                model_group_to_singularity_dict[
-                    model_or_model_group
-                ] = model_group_to_singularity_dict[
-                    model_or_model_group_list[0]
-                ]
+        # Otherwise it will take more than 6 hours - available time on actions ci
+    else:
+        models_to_test = docker_to_model_dict[docker_image]
+    singularity_handler.update(models_to_test)
+    if len(model_or_model_group_list) > 1:
+        for model_or_model_group in model_or_model_group_list[1:]:
+            model_group_to_singularity_dict[
+                model_or_model_group
+            ] = model_group_to_singularity_dict[model_or_model_group_list[0]]
 
     write_json_to_kipoi(
         model_group_to_singularity_dict,

test-containers/test_update_all_singularity_images.py

@@ -11,6 +11,15 @@ def runner():
     yield runner
 
 
+def test_cli_incorrect_use(runner):
+    result = runner.invoke(
+        update_all_singularity_images.run_update,
+        [],
+    )
+    assert "Error: Missing argument 'DOCKER_IMAGE'" in result.output
+    assert result.exit_code == 2
+
+
 def test_cli_correct_use(runner, monkeypatch):
     def mock_populate_singularity_json(*args, **kwargs):
         if args[0] == "model-to-docker.json":
@@ -88,6 +97,8 @@ def mock_cleanup(*args, **kwargs):
         "kipoi_containers.update_all_singularity_images.write_json_to_kipoi",
         mock_write_singularity_json,
     )
-    result = runner.invoke(update_all_singularity_images.run_update)
-    print(result.output)
+    result = runner.invoke(
+        update_all_singularity_images.run_update,
+        ["kipoi/kipoi-docker:mmsplice-mtsplice"],
+    )
     assert result.exit_code == 0