From 04c80b233f0c4f00a4ce5e5b65effb5d124d953e Mon Sep 17 00:00:00 2001 From: ialarmedalien Date: Wed, 8 Nov 2023 10:13:47 -0800 Subject: [PATCH] updating python deps for Nov 2023, reformatting one file that had gone astray --- RELEASE_NOTES.md | 10 +++++++++- package.json | 2 +- src/biokbase/narrative/jobs/appmanager.py | 17 +++++++---------- src/requirements.txt | 4 ++-- 4 files changed, 19 insertions(+), 14 deletions(-) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index a46c863154..f328389839 100644 --- a/RELEASE_NOTES.md +++ b/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 diff --git a/package.json b/package.json index a895c93373..e961fcdbb9 100644 --- a/package.json +++ b/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": { diff --git a/src/biokbase/narrative/jobs/appmanager.py b/src/biokbase/narrative/jobs/appmanager.py index 2ed1333a88..8480c57d9b 100644 --- a/src/biokbase/narrative/jobs/appmanager.py +++ b/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) diff --git a/src/requirements.txt b/src/requirements.txt index e4e1365bd8..d3516036e9 100644 --- a/src/requirements.txt +++ b/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