Merge pull request #2538 from kbase/develop

Merge to main branch for 5.6.0 release
kbase · Oct 28, 2021 · 52de0e2 · 52de0e2
2 parents f151891 + 68b3e2b
commit 52de0e2
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diff --git a/.github/workflows/build_prodrc_pr.yaml b/.github/workflows/build_prodrc_pr.yaml
@@ -4,6 +4,7 @@ name: Build Prod RC Image
   pull_request:
     branches:
     - master
+    - main
     types:
     - opened
     - synchronize
@@ -22,6 +23,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/build_prodrc_pr.sh\n"
diff --git a/.github/workflows/build_test_pr.yaml b/.github/workflows/build_test_pr.yaml
@@ -22,6 +22,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/build_test_pr.sh\n"
diff --git a/.github/workflows/build_truss_pr.yaml b/.github/workflows/build_truss_pr.yaml
@@ -22,6 +22,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/build_truss_pr.sh\n"
diff --git a/.github/workflows/build_truss_push.yaml b/.github/workflows/build_truss_push.yaml
@@ -18,6 +18,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/build_truss_push.sh\n"
diff --git a/.github/workflows/scripts/build_prodrc_pr.sh b/.github/workflows/scripts/build_prodrc_pr.sh
@@ -16,6 +16,7 @@ docker build --build-arg BUILD_DATE="$DATE" \
              --build-arg BRANCH="$GITHUB_HEAD_REF" \
              --build-arg PULL_REQUEST="$PR" \
              --label us.kbase.vcs-pull-req="$PR" \
+             --label us.kbase.narrative-version="$NARRATIVE_VERSION_NUM" \
              -t ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" .
 docker push ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR"
 
@@ -25,8 +26,8 @@ docker build -t ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" \
                 --build-arg BRANCH="$GITHUB_HEAD_REF" \
                 --build-arg PULL_REQUEST="$PR" \
                 --label us.kbase.vcs-pull-req="$PR" \
-                --build-arg NARRATIVE_VERSION=$NARRATIVE_VERSION_NUM \
-                --build-arg NARRATIVE_GIT_HASH=$NARRATIVE_GIT_HASH \
+                --build-arg NARRATIVE_VERSION="$NARRATIVE_VERSION_NUM" \
+                --build-arg NARRATIVE_GIT_HASH="$NARRATIVE_GIT_HASH" \
                 -f Dockerfile2 \
                 .
 docker push ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR"
diff --git a/.github/workflows/scripts/build_test_pr.sh b/.github/workflows/scripts/build_test_pr.sh
@@ -14,6 +14,7 @@ docker build --build-arg BUILD_DATE="$DATE" \
              --build-arg BRANCH="$GITHUB_HEAD_REF" \
              --build-arg PULL_REQUEST="$PR" \
              --label us.kbase.vcs-pull-req="$PR" \
+             --label us.kbase.narrative-version="$NARRATIVE_VERSION_NUM" \
              -t ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" .
 docker push ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR"
 
@@ -25,7 +26,7 @@ docker build -t ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" \
                 --build-arg BRANCH="$GITHUB_HEAD_REF" \
                 --build-arg PULL_REQUEST="$PR" \
                 --label us.kbase.vcs-pull-req="$PR" \
-                --build-arg NARRATIVE_VERSION=$NARRATIVE_VERSION_NUM \
+                --build-arg NARRATIVE_VERSION="$NARRATIVE_VERSION_NUM" \
                 -f Dockerfile2 \
                 .
 docker rmi kbase/narrative:tmp

diff --git a/.github/workflows/scripts/tag_prod_latest.sh b/.github/workflows/scripts/tag_prod_latest.sh
@@ -6,12 +6,17 @@ export DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 export BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 export COMMIT=$(echo "$SHA" | cut -c -7)
 export MY_APP2="$MY_APP"_version
+export NARRATIVE_VERSION_NUM=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
 
 docker login -u "$DOCKER_ACTOR" -p "$DOCKER_TOKEN" ghcr.io
 docker pull ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR"
 docker tag ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP":"latest"
+docker tag ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP":"$NARRATIVE_VERSION_NUM"
+docker push ghcr.io/"$MY_ORG"/"$MY_APP":"$NARRATIVE_VERSION_NUM"
 docker push ghcr.io/"$MY_ORG"/"$MY_APP":"latest"
 
 docker pull ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR"
 docker tag ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP2":"latest"
+docker tag ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP2":"$NARRATIVE_VERSION_NUM"
+docker push ghcr.io/"$MY_ORG"/"$MY_APP2":"$NARRATIVE_VERSION_NUM"
 docker push ghcr.io/"$MY_ORG"/"$MY_APP2":"latest"
diff --git a/.github/workflows/scripts/tag_test_latest.sh b/.github/workflows/scripts/tag_test_latest.sh
@@ -6,12 +6,17 @@ export DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 export BUILD_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
 export COMMIT=$(echo "$SHA" | cut -c -7)
 export MY_APP2="$MY_APP"_version
+export NARRATIVE_VERSION_NUM=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
 
 docker login -u "$DOCKER_ACTOR" -p "$DOCKER_TOKEN" ghcr.io
 docker pull ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR"
 docker tag ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP":"latest"
+docker tag ghcr.io/"$MY_ORG"/"$MY_APP":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP":"$NARRATIVE_VERSION_NUM"
+docker push ghcr.io/"$MY_ORG"/"$MY_APP":"$NARRATIVE_VERSION_NUM"
 docker push ghcr.io/"$MY_ORG"/"$MY_APP":"latest"
 
 docker pull ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR"
 docker tag ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP2":"latest"
+docker tag ghcr.io/"$MY_ORG"/"$MY_APP2":"pr-""$PR" ghcr.io/"$MY_ORG"/"$MY_APP2":"$NARRATIVE_VERSION_NUM"
+docker push ghcr.io/"$MY_ORG"/"$MY_APP2":"$NARRATIVE_VERSION_NUM"
 docker push ghcr.io/"$MY_ORG"/"$MY_APP2":"latest"
diff --git a/.github/workflows/tag_environments.yaml b/.github/workflows/tag_environments.yaml
@@ -10,7 +10,7 @@ jobs:
       uses: actions/checkout@v2
     - name: Tag Deploy Environments  
       env:
-        DOCKER_ACTOR: jsfillman
+        DOCKER_ACTOR: ${{ secrets.GHCR_USERNAME }}
         DOCKER_TOKEN: ${{ secrets.GHCR_TOKEN  }}
         IMAGE_TAG: ${{ github.event.client_payload.image_tag }}
         SHA: ${{ github.event.pull_request.head.sha }}

diff --git a/.github/workflows/tag_prod_latest.yaml b/.github/workflows/tag_prod_latest.yaml
@@ -4,6 +4,7 @@ name: Tag Prod Latest
   pull_request:
     branches:
     - master
+    - main
     types:
     - closed
 jobs:
@@ -21,6 +22,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/tag_prod_latest.sh\n"
diff --git a/.github/workflows/tag_test_latest.yaml b/.github/workflows/tag_test_latest.yaml
@@ -21,6 +21,6 @@ jobs:
       env:
         PR: "${{ github.event.pull_request.number }}"
         SHA: "${{ github.event.pull_request.head.sha }}"
-        DOCKER_ACTOR: "jsfillman"
+        DOCKER_ACTOR: "${{ secrets.GHCR_USERNAME }}"
         DOCKER_TOKEN: "${{ secrets.GHCR_TOKEN }}"
       run: "./.github/workflows/scripts/tag_test_latest.sh\n"
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -4,6 +4,36 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v6.0.2 (more notes will follow).
 
+### Version 4.6.0
+Code changes
+- DATAUP-599 - Adjusted the kernel code and tests to account for a Workspace service update.
+- PTV-1703 - Fix DifferentialExpressionSet and DifferentialExpressionMatrixSet viewers
+- SCT-3088 - Add Narrative Outline View. Allows scrolling through a minimal view of Narrative cells more quickly. 
+
+Dependency Changes
+- Python dependency updates
+  - pillow 8.3.1 -> 8.3.2
+  - plotly 5.1.0 -> 5.3.1
+  - pygments 2.9.0 -> 2.10.0
+  - pytest 6.2.4 -> 6.2.5
+  - terminado 0.10.1 -> 0.11.1
+- Javascript dependency updates
+  - @wdio/browserstack-service 7.9.1 -> 7.11.1
+  - @wdio/cli 7.9.1 -> 7.11.1
+  - @wdio/local-runner 7.9.1 -> 7.11.1 
+  - @wdio/mocha-framework 7.9.1 -> 7.11.1
+  - @wdio/selenium-standalone-service 7.7.7 -> 7.10.1
+  - @wdio/spec-reporter 7.9.0 -> 7.10.1
+  - chromedriver 92.0.1 -> 93.0.1
+  - husky 7.0.1 -> 7.0.2
+  - jasmine-core 3.8.0 -> 3.9.0
+  - msw 0.34.0 -> 0.35.0
+  - puppeteer 10.1.0 -> 10.4.0
+  - terser 5.7.1 -> 5.7.2
+  - webdriverio 7.9.1 -> 7.11.1
+- Javascript dependency additions
+  - expect-webdriverio 3.1.4
+
 ### Version 4.5.0
 - PTV-1561 - SampleSet viewer fixes to allow AMA features; not complete support for AMA features as GenomeSearchUtil does not yet support AMA.
 - SCT-3100 - Improve SampleSet viewer; add improved JSON-RPC 1.1 client and associatedKBase service client; add msw (Mock Service Worker) support;

diff --git a/bower.json b/bower.json
@@ -1,10 +1,10 @@
 {
   "name": "kbase-narrative",
-  "version": "4.5.0",
+  "version": "4.6.0",
   "homepage": "https://kbase.us",
   "dependencies": {
     "bluebird": "3.7.2",
-    "bootstrap-slider": "*",
+    "seiyria-bootstrap-slider": "10.6.2",
     "bowser": "1.0.0",
     "corejs-typeahead": "1.0.1",
     "d3": "3.5.6",

diff --git a/kbase-extension/static/kbase/css/bootstrapHelper.css b/kbase-extension/static/kbase/css/bootstrapHelper.css
@@ -32,9 +32,9 @@
     The BS checkbox appears too low, due to the top margin, when used with a label
     in the recommended manner.
     Note: I don't understand why BS handles checkbox styling as they do, turning
-    the checkbox into relatively posiioned and then pushing the label to checkbox
+    the checkbox into relatively positioned and then pushing the label to checkbox
     to the left and down (at the same time given the container extra margin to
-    accomodate this.) Anyway, we roll with it but try to patch up the styling
+    accommodate this.) Anyway, we roll with it but try to patch up the styling
     as it breaks.
 */
 
@@ -98,7 +98,7 @@
 }
 
 /*
-  The button bar in a cell widgetis located at the bottom of the inputs, but
+  The button bar in a cell widget is located at the bottom of the inputs, but
   above any outputs.
   These styles attempt to help the button toolbar, which represents the actions
   the user can take, be visually distinct from the other bits surrounding it.