Merge pull request #3618 from kbase/develop

Merge to main for version 5.4.1 release.

RELEASE_NOTES.md

@@ -2,7 +2,39 @@
 
 The Narrative Interface allows users to craft KBase Narratives using a combination of GUI-based commands, Python and R scripts, and graphical output elements.
 
-This is built on the Jupyter Notebook v6.5.6 and IPython 8.25.0 (more notes will follow).
+This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will follow).
+
+## Version 5.4.1
+- UIP-51 fix issue where JSON and STAGING download apps aren't getting properly instantiated with object inputs.
+
+### Dependency Changes
+- Python dependency updates
+  - biopython 1.79 -> 1.84
+  - bokeh 3.0.3 -> 3.5.1
+  - certifi 2024.6.2 -> 2024.7.4
+  - chardet 5.0.0 -> 5.2.0
+  - ipython 8.25.0 -> 8.26.0
+  - networkx 3.0 -> 3.3
+  - numpy 1.24.1 -> 2.0.1
+  - pexpect 4.8.0 -> 4.9.0
+  - pillow 10.3.0 -> 10.4.0
+  - plotly 5.13.0 -> 5.23.0
+  - pyasn1 0.4.8 -> 0.6.0
+  - pygments 2.17.2 -> 2.18.0
+  - python-daemon 2.3.2 -> 3.0.1
+  - python-dateutil 2.8.2 -> 2.9.0.post0
+  - scipy 1.10.0 -> 1.14.0
+  - seaborn 0.12.0 -> 0.13.2
+  - setuptools 69.5.1 -> 71.1.0
+  - sympy 1.10.1 -> 1.13.1
+  - ruff 0.4.7 -> 0.5.5
+
+- JavaScript dependency updates
+  - @wdio/mocha-framework  8.38.2 -> 8.39.0 
+  - chrome-launcher  1.1.1 -> 1.1.2 
+  - chromedriver  126.0.0 -> 126.0.4 
+  - postcss  8.4.38 -> 8.4.39 
+  - selenium-webdriver  4.21.0 -> 4.22.0 
 
 ## Version 5.4.0
 -   UIP-43

kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeDownloadPanel.js

@@ -76,7 +76,7 @@ define([
             $dlBtn.click(() => {
                 if (makeCell) {
                     Jupyter.narrative.addAndPopulateApp(dlInfo.appId, APIUtil.getAppVersionTag(), {
-                        input_ref: this.objName,
+                        input_ref: this.upa,
                     });
                 } else {
                     $dlBtn.parent().find('.kb-data-list-btn').prop('disabled', true);

package.json

@@ -1,7 +1,7 @@
 {
     "name": "kbase-narrative-core",
     "description": "Core components for the KBase Narrative Interface",
-    "version": "5.4.0",
+    "version": "5.4.1",
     "private": true,
     "repository": "github.com/kbase/narrative",
     "engines": {
@@ -15,14 +15,14 @@
         "@wdio/browserstack-service": "^8.38.2",
         "@wdio/cli": "^8.38.2",
         "@wdio/local-runner": "^8.38.2",
-        "@wdio/mocha-framework": "^8.38.2",
+        "@wdio/mocha-framework": "^8.39.0",
         "@wdio/selenium-standalone-service": "^8.15.0",
         "@wdio/spec-reporter": "^8.38.2",
         "autoprefixer": "^10.4.19",
         "axios": "^1.7.2",
         "bootstrap-sass": "^3.4.3",
-        "chrome-launcher": "^1.1.1",
-        "chromedriver": "^126.0.0",
+        "chrome-launcher": "^1.1.2",
+        "chromedriver": "^127.0.0",
         "commander": "^12.1.0",
         "cssnano": "^7.0.2",
         "ejs": "^3.1.10",
@@ -59,7 +59,7 @@
         "lint-staged": "^15.2.6",
         "load-grunt-tasks": "^5.1.0",
         "msw": "^0.40.2",
-        "postcss": "^8.4.38",
+        "postcss": "^8.4.39",
         "postcss-cli": "^11.0.0",
         "postcss-discard-comments": "^7.0.0",
         "postcss-scss": "^4.0.9",
@@ -69,7 +69,7 @@
         "requirejs": "^2.3.6",
         "sass": "^1.77.5",
         "selenium-standalone": "^9.5.0",
-        "selenium-webdriver": "^4.21.0",
+        "selenium-webdriver": "^4.22.0",
         "string-template": "^1.0.0",
         "string.prototype.endswith": "^1.0.2",
         "string.prototype.startswith": "^1.0.0",

src/biokbase/narrative/__init__.py

@@ -1,5 +1,5 @@
 __all__ = ["magics", "common", "handlers", "contents", "services", "widgetmanager"]
-__version__ = "5.4.0"
+__version__ = "5.4.1"
 
 
 def version():

src/config.json

@@ -391,5 +391,5 @@
         "globus_upload_url": "https://app.globus.org/file-manager?destination_id=c3c0a65f-5827-4834-b6c9-388b0b19953a"
     },
     "use_local_widgets": true,
-    "version": "5.4.0"
+    "version": "5.4.1"
 }

src/config.json.templ

@@ -391,5 +391,5 @@
         "globus_upload_url": "https://app.globus.org/file-manager?destination_id=c3c0a65f-5827-4834-b6c9-388b0b19953a"
     },
     "use_local_widgets": true,
-    "version": "5.4.0"
+    "version": "5.4.1"
 }

src/requirements-dev.txt

@@ -3,5 +3,5 @@ pytest==8.2.2
 pytest-cov==5.0.0
 pytest-recording==0.13.1
 requests-mock==1.12.1
-ruff==0.4.7
+ruff==0.5.5
 vcrpy==6.0.1