Merge pull request #748 from jashapiro/676-trigger-consistency

Make GHA trigger & Dockerfiles consistent
AlexsLemonade · Sep 4, 2024 · d6bea93 · d6bea93
2 parents 609245e + f48d292
commit d6bea93
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Showing 11 changed files with 34 additions and 14 deletions.
diff --git a/.github/workflows/run_cell-type-ewings.yml b/.github/workflows/run_cell-type-ewings.yml
@@ -24,6 +24,7 @@ on:
       - analyses/cell-type-ewings/**
       - "!analyses/cell-type-ewings/Dockerfile"
       - "!analyses/cell-type-ewings/.dockerignore"
+      - .github/workflows/run_cell-type-ewings.yml
 jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'

diff --git a/.github/workflows/run_cell-type-wilms-tumor-06.yml b/.github/workflows/run_cell-type-wilms-tumor-06.yml
@@ -24,9 +24,10 @@ on:
     branches:
       - main
     paths:
-      - "analyses/cell-type-wilms-tumor-06/**"
+      - analyses/cell-type-wilms-tumor-06/**
       - "!analyses/cell-type-wilms-tumor-06/Dockerfile"
       - "!analyses/cell-type-wilms-tumor-06/.dockerignore"
+      - .github/workflows/run_cell-type-wilms-tumor-06.yml
 
 jobs:
   run-module:

diff --git a/.github/workflows/run_doublet-detection.yml b/.github/workflows/run_doublet-detection.yml
@@ -26,7 +26,7 @@ on:
       - analyses/doublet-detection/**
       - "!analyses/doublet-detection/Dockerfile"
       - "!analyses/doublet-detection/.dockerignore"
-      # - .github/workflows/run_doublet-detection.yml
+      - .github/workflows/run_doublet-detection.yml
 
 jobs:
   run-module:

diff --git a/.github/workflows/run_hello-R.yml b/.github/workflows/run_hello-R.yml
@@ -22,6 +22,9 @@ on:
       - main
     paths:
       - analyses/hello-R/**
+      - "!analyses/hello-R/Dockerfile"
+      - "!analyses/hello-R/.dockerignore"
+      - .github/workflows/run_hello-R.yml
 jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'

diff --git a/.github/workflows/run_hello-python.yml b/.github/workflows/run_hello-python.yml
@@ -22,6 +22,9 @@ on:
       - main
     paths:
       - analyses/hello-python/**
+      - "!analyses/hello-python/Dockerfile"
+      - "!analyses/hello-python/.dockerignore"
+      - .github/workflows/run_hello-python.yml
 
 jobs:
   run-module:

diff --git a/.github/workflows/run_metacells.yml b/.github/workflows/run_metacells.yml
@@ -24,7 +24,10 @@ on:
     branches:
       - main
     paths:
-      - "analyses/metacells/**"
+      - analyses/metacells/**
+      - "!analyses/metacells/Dockerfile"
+      - "!analyses/metacells/.dockerignore"
+      - .github/workflows/run_metacells.yml
 
 jobs:
   run-module:

diff --git a/analyses/hello-R/Dockerfile b/analyses/hello-R/Dockerfile
@@ -7,20 +7,20 @@ LABEL org.opencontainers.image.authors="OpenScPCA [email protected]"
 LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/hello-R"
 
 # Set an environment variable to allow checking if we are in an OpenScPCA container
-ENV OPENSCPCA_DOCKER TRUE
+ENV OPENSCPCA_DOCKER=TRUE
 
 # Install additional system dependencies
 RUN apt-get -y update &&  \
-    DEBIAN_FRONTEND=noninteractive \
-    apt-get install --no-install-recommends -y \
-    pandoc \
-    && rm -rf /var/lib/apt/lists/*
+  DEBIAN_FRONTEND=noninteractive \
+  apt-get install --no-install-recommends -y \
+  pandoc \
+  && rm -rf /var/lib/apt/lists/*
 
 # Install renv to enable later package installation
 RUN Rscript -e "install.packages('renv')"
 
 # Disable the renv cache to install packages directly into the R library
-ENV RENV_CONFIG_CACHE_ENABLED FALSE
+ENV RENV_CONFIG_CACHE_ENABLED=FALSE
 
 # Copy the renv.lock file from the host environment to the image
 COPY renv.lock renv.lock

diff --git a/docs/ensuring-repro/docker/docker-images.md b/docs/ensuring-repro/docker/docker-images.md
@@ -80,7 +80,7 @@ FROM bioconductor/r-ver:3.19
 RUN Rscript -e "install.packages('renv')"
 
 # Disable the renv cache to install packages directly into the R library
-ENV RENV_CONFIG_CACHE_ENABLED FALSE
+ENV RENV_CONFIG_CACHE_ENABLED=FALSE
 
 # Copy the renv.lock file from the host environment to the image
 COPY renv.lock renv.lock
@@ -173,7 +173,7 @@ RUN conda install --channel=conda-forge --name=base conda-lock \
 RUN Rscript -e "install.packages('renv')"
 
 # Disable the renv cache to install packages directly into the R library
-ENV RENV_CONFIG_CACHE_ENABLED FALSE
+ENV RENV_CONFIG_CACHE_ENABLED=FALSE
 
 # Copy conda lock file to image
 COPY conda-lock.yml conda-lock.yml

diff --git a/templates/workflows/run_conda-module.yml b/templates/workflows/run_conda-module.yml
@@ -24,7 +24,10 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/{{ openscpca_module }}/**"
+  #     - analyses/{{ openscpca_module }}/**
+  #     - "!analyses/{{ openscpca_module }}/Dockerfile"
+  #     - "!analyses/{{ openscpca_module }}/.dockerignore"
+  #     - .github/workflows/run_{{ openscpca_module }}.yml
 
 jobs:
   run-module:

diff --git a/templates/workflows/run_conda-renv-module.yml b/templates/workflows/run_conda-renv-module.yml
@@ -24,7 +24,10 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/{{ openscpca_module }}/**"
+  #     - analyses/{{ openscpca_module }}/**
+  #     - "!analyses/{{ openscpca_module }}/Dockerfile"
+  #     - "!analyses/{{ openscpca_module }}/.dockerignore"
+  #     - .github/workflows/run_{{ openscpca_module }}.yml
 
 jobs:
   run-module:

diff --git a/templates/workflows/run_renv-module.yml b/templates/workflows/run_renv-module.yml
@@ -24,7 +24,10 @@ on:
   #   branches:
   #     - main
   #   paths:
-  #     - "analyses/{{ openscpca_module }}/**"
+  #     - analyses/{{ openscpca_module }}/**
+  #     - "!analyses/{{ openscpca_module }}/Dockerfile"
+  #     - "!analyses/{{ openscpca_module }}/.dockerignore"
+  #     - .github/workflows/run_{{ openscpca_module }}.yml
 
 jobs:
   run-module: