Merge pull request #3384 from kbase/nov_2023_py_deps

PyDeps Nov 2023

RELEASE_NOTES.md

@@ -4,6 +4,14 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v6.4.12 and IPython 8.5.0 (more notes will follow).
 
+## Version unreleased
+
+### Dependency Changes
+
+- Python dependency updates
+  - black: 23.7.0 -> 23.11.0
+  - pytest: 7.4.0 -> 7.4.3
+
 ## Version 5.2.1
 -   PTV-1900 - a previous bugfix exposed an issue in the SpeciesTreeBuilder apps. This provides a workaround to keep those apps running.
 -   PTV-1687 - update favicon
@@ -19,7 +27,7 @@ This is built on the Jupyter Notebook v6.4.12 and IPython 8.5.0 (more notes will
 ## Version 5.2.0
 A new feature here is that app cells now store object information internally as UPAs, instead of object names. This will lead to more reproducible results, and is on the path to fixing the long-standing copy-of-a-copy problem.
 
--   PTV-1810 - address object name display issues in the View Configure tab of app cells. This now saves all app inputs as UPAs in the cell. It also includes an update to input transforms to properly convert from UPAs <-> names or references as appropriate before starting the app. 
+-   PTV-1810 - address object name display issues in the View Configure tab of app cells. This now saves all app inputs as UPAs in the cell. It also includes an update to input transforms to properly convert from UPAs <-> names or references as appropriate before starting the app.
 -   PTV-1875 - fix public data paging issue by removing paging from workspace data sources
 -   PTV-1877 - fix app descriptions to replace the documentation link for the upload / download guide
 -   PTV-1878 - fix some failing front end unit tests

package.json

@@ -149,7 +149,7 @@
         "test_local": "karma start test/unit/karma.local.conf.js",
         "test": "karma start test/unit/karma.conf.js",
         "uglify": "terser kbase-extension/static/kbase-narrative.js -c --source-map --output kbase-extension/static/kbase-narrative-min.js",
-        "update_browserslist": "npx browserslist@latest --update-db",
+        "update_browserslist": "npx update-browserslist-db@latest",
         "watch_css": "grunt watch"
     },
     "lint-staged": {

src/biokbase/narrative/jobs/appmanager.py

@@ -19,10 +19,7 @@
 )
 from biokbase.narrative.common import kblogging
 from biokbase.narrative.exception_util import transform_job_exception
-from biokbase.narrative.system import (
-    strict_system_variable,
-    system_variable
-)
+from biokbase.narrative.system import strict_system_variable, system_variable
 
 from biokbase.narrative.widgetmanager import WidgetManager
 
@@ -289,9 +286,9 @@ def run_legacy_batch_app(
         kblogging.log_event(self._log, "run_batch_app", log_info)
 
         try:
-            job_id = clients.get(
-                "execution_engine2", token=agent_token.token
-            ).run_job(job_runner_inputs)
+            job_id = clients.get("execution_engine2", token=agent_token.token).run_job(
+                job_runner_inputs
+            )
         except Exception as e:
             log_info.update({"err": str(e)})
             kblogging.log_event(self._log, "run_batch_app_error", log_info)
@@ -386,9 +383,9 @@ def run_app(
         kblogging.log_event(self._log, "run_app", log_info)
 
         try:
-            job_id = clients.get(
-                "execution_engine2", token=agent_token.token
-            ).run_job(job_runner_inputs)
+            job_id = clients.get("execution_engine2", token=agent_token.token).run_job(
+                job_runner_inputs
+            )
         except Exception as e:
             log_info.update({"err": str(e)})
             kblogging.log_event(self._log, "run_app_error", log_info)

src/requirements.txt

@@ -3,7 +3,7 @@
 # sklearn
 # clustergrammer_widget
 beautifulsoup4==4.12.2
-black==23.7.0
+black==23.11.0
 coverage==7.3.1
 cryptography==41.0.4
 decorator==5.1.1
@@ -18,7 +18,7 @@ ndg-httpsclient==0.5.1
 pygments==2.16.1
 pymongo==4.5.0
 pyopenssl==23.2.0
-pytest==7.4.0
+pytest==7.4.3
 pytest-cov==4.1.0
 requests==2.31.0
 requests-mock==1.11.0