Merge pull request #3348 from kbase/develop

Merge to main for 5.2.0 release
kbase · Aug 31, 2023 · bf8a3a2 · bf8a3a2
2 parents 9f1b0c0 + aa86e40
commit bf8a3a2
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diff --git a/.flake8 b/.flake8
@@ -1,5 +1,5 @@
 [flake8]
-max-line-length = 88
+max-line-length = 100
 # E203: whitespace before ‘,’, ‘;’, or ‘:’
 # E501: line length
 # W503: line break after binary operator

diff --git a/.github/workflows/ReleaseCycleProposal.md b/.github/workflows/ReleaseCycleProposal.md
diff --git a/.github/workflows/build_and_push_image.yml b/.github/workflows/build_and_push_image.yml
@@ -1,3 +1,4 @@
+---
 name: Build and push narrative images
 
 on:
@@ -17,55 +18,56 @@ jobs:
       name: Check out GitHub Repo
       with:
         ref: "${{ github.event.pull_request.head.sha }}"
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     -
       name: Set up environment
       run: |
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
+            branch=`echo "-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`
         echo "APP_IMAGE_TAG=ghcr.io/${{ github.repository }}${branch}:pr-${{ github.event.pull_request.number }}" >> $GITHUB_ENV
         echo "APP_VERSION_IMAGE_TAG=ghcr.io/${{ github.repository }}${branch}_version:pr-${{ github.event.pull_request.number }}" >> $GITHUB_ENV
         echo "BRANCH=${branch}" >> $GITHUB_ENV
-        echo "BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")" >> $GITHUB_ENV
         echo "NARRATIVE_GIT_HASH=${narrative_git_hash}" >> $GITHUB_ENV
         echo "NARRATIVE_VERSION=${narrative_version}" >> $GITHUB_ENV
         echo "PR=pr-${{ github.event.pull_request.number }}" >> $GITHUB_ENV
         echo "VCS_REF=$(echo "${{ github.event.pull_request.head.sha }}" | cut -c -7)" >> $GITHUB_ENV
     -
-      name: Set up QEMU
-      uses: docker/setup-qemu-action@v1
+      name: Get current date
+      id: date
+      run: echo "date=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT
     -
       name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
+      uses: docker/setup-buildx-action@v2
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Build narrative image
-      uses: docker/build-push-action@v2
+      uses: docker/build-push-action@v3
       with:
         context: .
+        file: ./Dockerfile
+        pull: true
         push: true
         tags: ${{ env.APP_IMAGE_TAG }}
         build-args: |
           BRANCH=${{ github.head_ref }}
-          BUILD_DATE=${{ env.BUILD_DATE }}
+          BUILD_DATE=${{ steps.date.output.date }}
           NARRATIVE_VERSION=${{ env.NARRATIVE_VERSION }}
-          VCS_REF=${{ env.VCS_REF }}
-        labels: |
-          us.kbase.vcs-pull-req=pr-${{ env.PR }}
+          VCS_REF=${{ github.sha }}
+          TAG='${{ github.ref }}'
     -
       name: Build version image
-      uses: docker/build-push-action@v2
+      uses: docker/build-push-action@v3
       if: ${{ github.base_ref }} == 'main' || ${{ github.base_ref }} == 'develop'
       with:
         context: .
@@ -74,9 +76,8 @@ jobs:
         tags: ${{ env.APP_VERSION_IMAGE_TAG }}
         build-args: |
           BRANCH=${{ github.head_ref }}
-          BUILD_DATE=${{ env.BUILD_DATE }}
+          BUILD_DATE=${{ steps.date.output.date }}
           NARRATIVE_VERSION=${{ env.NARRATIVE_VERSION }}
           NARRATIVE_GIT_HASH=${{ env.NARRATIVE_GIT_HASH }}
-          VCS_REF=${{ env.VCS_REF }}
-        labels: |
-          us.kbase.vcs-pull-req=pr-${{ env.PR }}
+          VCS_REF=${{ github.sha }}
+          TAG='${{ github.ref }}'
diff --git a/.github/workflows/build_test_pr.yaml b/.github/workflows/build_test_pr.yaml
@@ -16,6 +16,11 @@ jobs:
       GHCR_USERNAME: ${{ secrets.GHCR_USERNAME }}
       GHCR_TOKEN: ${{ secrets.GHCR_TOKEN }}
 
+  trivy-scans:
+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit
+
   run_unit_tests:
     uses: ./.github/workflows/unit_test.yml
     needs: run_build_and_push

diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml
@@ -16,21 +16,21 @@ jobs:
     steps:
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Repo checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     -
       name: Set up environment
       run: |
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
+            branch=`echo "-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`
@@ -47,10 +47,10 @@ jobs:
       shell: bash -l {0}
       run: docker pull ${{ env.APP_IMAGE_TAG }}
     -
-      name: Use Node JS 16.x
-      uses: actions/setup-node@v2
+      name: Use Node JS 16
+      uses: actions/setup-node@v3
       with:
-        node-version: 16.x
+        node-version: 16
     -
       name: Install JS dependencies
       run: |

diff --git a/.github/workflows/manual-build.yml b/.github/workflows/manual-build.yml
@@ -0,0 +1,11 @@
+---
+name: Manual Build & Push
+on:
+ workflow_dispatch:
+jobs:
+  build-push:
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: br-${{ github.ref_name }}
+    secrets: inherit
diff --git a/.github/workflows/pr_build.yml b/.github/workflows/pr_build.yml
@@ -0,0 +1,44 @@
+---
+name: Pull Request Build, Tag, & Push
+on:
+  workflow_dispatch:
+  # pull_request:
+  #   branches:
+  #     - develop
+  #     - main
+  #     - master
+  #   types:
+  #     - opened
+  #     - reopened
+  #     - synchronize
+  #     - closed
+jobs:
+  build-develop-open:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build.yml@main
+    secrets: inherit
+  build-develop-merge:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: pr-${{ github.event.number }},latest
+    secrets: inherit
+  build-main-open:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }}
+    secrets: inherit
+  build-main-merge:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }},latest-rc
+    secrets: inherit
+  trivy-scans:
+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit
diff --git a/.github/workflows/release-main.yml b/.github/workflows/release-main.yml
@@ -0,0 +1,25 @@
+---
+name: Release - Build & Push Image
+on:
+  release:
+    branches:
+      - main
+      - master
+    types: [ published ]
+jobs:
+  check-source-branch:
+    uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
+    with:
+      build_branch: '${{ github.event.release.target_commitish }}'
+  validate-release-tag:
+    needs: check-source-branch
+    uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
+    with:
+      release_tag: '${{ github.event.release.tag_name }}'
+  build-push:
+    needs: validate-release-tag
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: '${{ github.event.release.tag_name }},latest'
+    secrets: inherit
diff --git a/.github/workflows/tag_environments.yaml b/.github/workflows/tag_environments.yaml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Check out GitHub Repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Log in to the Container registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}

diff --git a/.github/workflows/tag_latest_image.yaml b/.github/workflows/tag_latest_image.yaml
@@ -16,10 +16,10 @@ jobs:
     - name: Check out GitHub Repo
       with:
         ref: "${{ github.event.pull_request.head.sha }}"
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
@@ -21,14 +21,14 @@ jobs:
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Repo checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     -
       name: Set up environment
       run: |
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
+            branch=`echo "-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`
@@ -55,10 +55,10 @@ jobs:
         docker run -v "${{ github.workspace }}/output:/tmp/output" --user nobody ${{ env.APP_IMAGE_TAG }} /bin/bash scripts/narrative_backend_tests.sh
       continue-on-error: true
     -
-      name: Use Node JS 16.x
+      name: Use Node JS 16
       uses: actions/setup-node@v2
       with:
-        node-version: 16.x
+        node-version: 16
     -
       name: Install JS dependencies
       run: |
@@ -74,10 +74,10 @@ jobs:
     -
       name: Send to Codecov
       id: send_to_codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       continue-on-error: true
       with:
-        files: ./output/coverage.xml, ./js-coverage/lcov/lcov.info
+        files: ./output/coverage.xml,./js-coverage/lcov/lcov.info
         fail_ci_if_error: true
     -
       name: outcome

diff --git a/.isort.cfg b/.isort.cfg
@@ -0,0 +1,2 @@
+[settings]
+profile=black