Merge branch 'main' into add_devel_image

pharmaverse · Nov 7, 2023 · 0c23a4a · 0c23a4a
2 parents b2c7ab6 + b7c8e96
commit 0c23a4a
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diff --git a/.github/actions/cran-status-extract/Dockerfile b/.github/actions/cran-status-extract/Dockerfile
diff --git a/.github/actions/cran-status-extract/action.yml b/.github/actions/cran-status-extract/action.yml
diff --git a/.github/actions/cran-status-extract/check-status.R b/.github/actions/cran-status-extract/check-status.R
diff --git a/.github/actions/cran-status-extract/entrypoint.sh b/.github/actions/cran-status-extract/entrypoint.sh
diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
@@ -1,5 +1,25 @@
 on:
   workflow_dispatch:
+    inputs:
+      r-version:
+        description: 'The version of R to use'
+        default: '4.1'
+        required: false
+        type: choice
+        options:
+          - '4.1'
+          - '4.2'
+          - '4.3'
+      push-templates-data:
+        description: 'Push generated templates data to pharmaverseadam repo'
+        default: false
+        required: false
+        type: boolean
+      exclude-templates-data:
+        description: 'List of data generated by templates to exclude (templates script will run, but results will not be push to pharmaverseadam repo) - comma seperated list'
+        default: ''
+        required: false
+        type: string
   workflow_call:
     inputs:
       r-version:
@@ -17,16 +37,6 @@ on:
         default: ''
         required: false
         type: string
-  push:
-    branches:
-      - main
-      - devel
-      - pre-release
-  pull_request:
-    branches:
-      - main
-      - devel
-      - pre-release
 
 env:
   # branch name for PR
@@ -58,35 +68,13 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  get_r_version:
-    name: Get R version
-    runs-on: ubuntu-latest
-    if: >
-      !contains(github.event.commits[0].message, '[skip check_templates]')
-    outputs:
-      r-version: ${{ steps.normalizer.outputs.R_VERSION }}
-    steps:
-      - name: Normalize inputs
-        id: normalizer
-        run: |
-          R_VERSION="${{ inputs.r-version }}"
-          if [ "$R_VERSION" == "" ]
-          then {
-            R_VERSION="4.1"
-          }
-          fi
-          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
-        shell: bash
-
   check_templates:
     name: Verify
     if: >
       !contains(github.event.commits[0].message, '[skip check_templates]')
     runs-on: ubuntu-latest
     container:
-      image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest"
-    needs: get_r_version
-
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:

diff --git a/.github/workflows/code-coverage.yml b/.github/workflows/code-coverage.yml
@@ -1,5 +1,20 @@
 on:
   workflow_dispatch:
+    inputs:
+      r-version:
+        description: 'The version of R to use'
+        default: '4.1'
+        required: false
+        type: choice
+        options:
+          - '4.1'
+          - '4.2'
+          - '4.3'
+      skip-coverage-badges:
+        description: 'Skip code coverage badge creation'
+        default: false
+        required: false
+        type: boolean
   workflow_call:
     inputs:
       r-version:
@@ -12,16 +27,6 @@ on:
         default: false
         required: false
         type: boolean
-  push:
-    branches:
-      - main
-      - devel
-      - pre-release
-  pull_request:
-    branches:
-      - main
-      - devel
-      - pre-release
 
 name: Code Coverage
 
@@ -30,37 +35,17 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  get_r_version:
-    name: Get R version
-    runs-on: ubuntu-latest
-    if: >
-      !contains(github.event.commits[0].message, '[skip coverage]')
-    outputs:
-      r-version: ${{ steps.normalizer.outputs.R_VERSION }}
-    steps:
-      - name: Normalize inputs
-        id: normalizer
-        run: |
-          R_VERSION="${{ inputs.r-version }}"
-          if [ "$R_VERSION" == "" ]
-          then {
-            R_VERSION="4.1"
-          }
-          fi
-          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
-        shell: bash
   coverage:
     name: Test Coverage
     runs-on: ubuntu-latest
     container:
-      image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest"
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
     if: >
       !contains(github.event.commits[0].message, '[skip coverage]')
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     outputs:
       coverage-percent: ${{ steps.set-coverage-percentage.outputs.coverage-percentage }}
-    needs: get_r_version
     steps:
       ##################### BEGIN boilerplate steps #####################
       - name: Get branch names