Fix docker build (#406)

* touch manually

* push separately again

* don't need to remote update files

Author: scottgigante-immunai

.github/workflows/run_tests.yml

@@ -53,19 +53,18 @@ jobs:
         python -c "import openproblems"
 
     - name: Build Docker images
-      if: "!startsWith(github.ref, 'refs/heads/main')"
       run: |
         cd workflow
         snakemake -j $(nproc) docker_build
         cd ..
 
-    - name: Build and push Docker images
+    - name: Push Docker images
       if: "startsWith(github.ref, 'refs/heads/main')"
       env:
         DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
       run: |
         cd workflow
-        snakemake -j $(nproc) docker_build docker_push
+        snakemake -j $(nproc) docker_push
         cd ..
         echo "CHANGED=`git diff --exit-code > /dev/null && echo false || echo true`" >> $GITHUB_ENV
 

.gitignore

@@ -148,8 +148,4 @@ nf-openproblems
 .idea
 
 # snakemake
-.docker_build
-.docker_pull
-.docker_refresh
 .docker_update
-.docker_push

workflow/Snakefile

@@ -31,7 +31,7 @@ rule refresh_docker_image:
         dockerfile = "{}/{{image}}/refresh.Dockerfile".format(tools.IMAGES_DIR),
         requirements = tools.docker_refresh_requirements,
     output:
-        touch("{}/{{image}}/.docker_refresh".format(tools.IMAGES_DIR))
+        temp(touch("{}/{{image}}/.docker_refresh".format(tools.IMAGES_DIR)))
     params:
         sourcedir = os.path.dirname(tools.SCRIPTS_DIR),
         user = "singlecellopenproblems",
@@ -67,14 +67,16 @@ rule update_docker_image:
     input:
         tools.docker_update_requirements
     output:
-        touch("{}/{{image}}/.docker_update".format(tools.IMAGES_DIR))
+        "{}/{{image}}/.docker_update".format(tools.IMAGES_DIR)
+		shell:
+        "touch {output}"
 
 rule build_docker_image:
     input:
         dockerfile = "{}/{{image}}/Dockerfile".format(tools.IMAGES_DIR),
         requirements = tools.docker_build_requirements,
     output:
-        touch("{}/{{image}}/.docker_build".format(tools.IMAGES_DIR))
+        temp(touch("{}/{{image}}/.docker_build".format(tools.IMAGES_DIR)))
     params:
         sourcedir = os.path.dirname(tools.SCRIPTS_DIR),
         user = "singlecellopenproblems",
@@ -102,13 +104,13 @@ rule push_docker_image:
         build = "{}/{{image}}/.docker_update".format(tools.IMAGES_DIR),
         login = ".docker_login",
     output:
-        touch("{}/{{image}}/.docker_push".format(tools.IMAGES_DIR))
+        temp(touch("{}/{{image}}/.docker_push".format(tools.IMAGES_DIR)))
     shell:
         "docker push --quiet singlecellopenproblems/{wildcards.image}"
 
 rule pull_docker_image:
     output:
-        touch("{}/{{image}}/.docker_pull".format(tools.IMAGES_DIR))
+        temp(touch("{}/{{image}}/.docker_pull".format(tools.IMAGES_DIR)))
     shell:
         "DOCKER_CLI_EXPERIMENTAL=enabled docker manifest inspect singlecellopenproblems/{wildcards.image} > /dev/null && \
         docker pull --quiet singlecellopenproblems/{wildcards.image} || true"

workflow/snakemake_tools.py

@@ -390,16 +390,3 @@ def docker_command(wildcards, output):
     """Get the Docker command to be run given a set of wildcards."""
     image = docker_image_name(wildcards)
     return DOCKER_EXEC.format(image=image)
-
-
-for image in _images(""):
-    for filename in [
-        ".docker_push",
-        ".docker_pull",
-        ".docker_build",
-        ".docker_refresh",
-    ]:
-        try:
-            os.remove(os.path.join(image, filename))
-        except FileNotFoundError:
-            pass