From be7c6caec0af3157b64e3e2bafdad49d688e1361 Mon Sep 17 00:00:00 2001 From: Bill Riehl Date: Thu, 25 Jul 2024 16:47:19 -0400 Subject: [PATCH 1/5] update dependencies for July 2024 based on dependabot --- RELEASE_NOTES.md | 30 ++++++++ package-lock.json | 135 +++++++++++++++++++++++------------ package.json | 10 +-- src/requirements-dev.txt | 2 +- src/requirements-general.txt | 34 ++++----- src/requirements.txt | 2 +- 6 files changed, 145 insertions(+), 68 deletions(-) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 390e900ccf..fd5386efbd 100644 --- 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 v6.5.6 and IPython 8.25.0 (more notes will follow). +## Version 5.4.1 +### Dependency Changes +- Python dependency updates + - biopython 1.79 -> 1.84 + - bokeh 3.0.3 -> 3.4.2 + - networkx 3.0 -> 3.3 + - numpy 1.24.1 -> 2.0.0 + - plotly 5.13.0 -> 5.22.0 + - pyasn1 0.4.8 -> 0.6.0 + - ruff 0.4.7 -> 0.5.0 + - pygments 2.17.2 -> 2.18.0 + - pexpect 4.8.0 -> 4.9.0 + - seaborn 0.12.0 -> 0.13.2 + - setuptools 69.5.1 -> 70.1.1 + - certifi 2024.6.2 -> 2024.7.4 + - sympy 1.10.1 -> 1.12.1 + - pillow 10.3.0 -> 10.4.0 + - python-daemon 2.3.2 -> 3.0.1 + - chardet 5.0.0 -> 5.2.0 + - python-dateutil 2.8.2 -> 2.9.0.post0 + - scipy 1.10.0 -> 1.14.0 + - ipython 8.25.0 -> 8.26.0 + +- JavaScript dependency updates + - chromedriver 126.0.0 -> 126.0.4 + - postcss 8.4.38 -> 8.4.39 + - chrome-launcher 1.1.1 -> 1.1.2 + - @wdio/mocha-framework 8.38.2 -> 8.39.0 + - selenium-webdriver 4.21.0 -> 4.22.0 + ## Version 5.4.0 - UIP-43 - Change Narrative JSON downloads to use a download-to-staging app. diff --git a/package-lock.json b/package-lock.json index ee36c24f21..a95009826e 100644 --- a/package-lock.json +++ b/package-lock.json @@ -57,14 +57,14 @@ "@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": "^126.0.4", "commander": "^12.1.0", "cssnano": "^7.0.2", "ejs": "^3.1.10", @@ -101,7 +101,7 @@ "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", @@ -111,7 +111,7 @@ "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", @@ -449,6 +449,12 @@ "node": ">=6.9.0" } }, + "node_modules/@bazel/runfiles": { + "version": "5.8.1", + "resolved": "https://registry.npmjs.org/@bazel/runfiles/-/runfiles-5.8.1.tgz", + "integrity": "sha512-NDdfpdQ6rZlylgv++iMn5FkObC/QlBQvipinGLSOguTYpRywmieOyJ29XHvUilspwTFSILWpoE9CqMGkHXug1g==", + "dev": true + }, "node_modules/@colors/colors": { "version": "1.5.0", "resolved": "https://registry.npmjs.org/@colors/colors/-/colors-1.5.0.tgz", @@ -1868,23 +1874,58 @@ } }, "node_modules/@wdio/mocha-framework": { - "version": "8.38.2", - "resolved": "https://registry.npmjs.org/@wdio/mocha-framework/-/mocha-framework-8.38.2.tgz", - "integrity": "sha512-qJmRL5E6/ypjCUACH4hvCAAmTdU4YUrUlp9o/IKvTIAHMnZPE0/HgUFixCeu8Mop+rdzTPVBrbqxpRDdSnraYA==", + "version": "8.39.0", + "resolved": "https://registry.npmjs.org/@wdio/mocha-framework/-/mocha-framework-8.39.0.tgz", + "integrity": "sha512-OFau1dd5mUAqC70gkx0WeZ8rJG191Snb4qhOTS18FpszUoZgoHtgjFICC0cxqZBFtmT9j7+22hNrj6d4sQVPJw==", "dev": true, - "license": "MIT", "dependencies": { "@types/mocha": "^10.0.0", "@types/node": "^20.1.0", "@wdio/logger": "8.38.0", - "@wdio/types": "8.38.2", - "@wdio/utils": "8.38.2", + "@wdio/types": "8.39.0", + "@wdio/utils": "8.39.0", "mocha": "^10.0.0" }, "engines": { "node": "^16.13 || >=18" } }, + "node_modules/@wdio/mocha-framework/node_modules/@wdio/types": { + "version": "8.39.0", + "resolved": "https://registry.npmjs.org/@wdio/types/-/types-8.39.0.tgz", + "integrity": "sha512-86lcYROTapOJuFd9ouomFDfzDnv3Kn+jE0RmqfvN9frZAeLVJ5IKjX9M6HjplsyTZhjGO1uCaehmzx+HJus33Q==", + "dev": true, + "dependencies": { + "@types/node": "^20.1.0" + }, + "engines": { + "node": "^16.13 || >=18" + } + }, + "node_modules/@wdio/mocha-framework/node_modules/@wdio/utils": { + "version": "8.39.0", + "resolved": "https://registry.npmjs.org/@wdio/utils/-/utils-8.39.0.tgz", + "integrity": "sha512-jY+n6jlGeK+9Tx8T659PKLwMQTGpLW5H78CSEWgZLbjbVSr2LfGR8Lx0CRktNXxAtqEVZPj16Pi74OtAhvhE6Q==", + "dev": true, + "dependencies": { + "@puppeteer/browsers": "^1.6.0", + "@wdio/logger": "8.38.0", + "@wdio/types": "8.39.0", + "decamelize": "^6.0.0", + "deepmerge-ts": "^5.1.0", + "edgedriver": "^5.5.0", + "geckodriver": "^4.3.1", + "get-port": "^7.0.0", + "import-meta-resolve": "^4.0.0", + "locate-app": "^2.1.0", + "safaridriver": "^0.1.0", + "split2": "^4.2.0", + "wait-port": "^1.0.4" + }, + "engines": { + "node": "^16.13 || >=18" + } + }, "node_modules/@wdio/protocols": { "version": "8.38.0", "resolved": "https://registry.npmjs.org/@wdio/protocols/-/protocols-8.38.0.tgz", @@ -3513,11 +3554,10 @@ } }, "node_modules/chrome-launcher": { - "version": "1.1.1", - "resolved": "https://registry.npmjs.org/chrome-launcher/-/chrome-launcher-1.1.1.tgz", - "integrity": "sha512-OAQgBmpUzrIuShApIwOpjt7WFripGKcDMW/qeYU+kcl6jBPg87mRG+N2C3Vu+VeCVPqZ/ds3GfI2TK7tpz3Yyw==", + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/chrome-launcher/-/chrome-launcher-1.1.2.tgz", + "integrity": "sha512-YclTJey34KUm5jB1aEJCq807bSievi7Nb/TU4Gu504fUYi3jw3KCIaH6L7nFWQhdEgH3V+wCh+kKD1P5cXnfxw==", "dev": true, - "license": "Apache-2.0", "dependencies": { "@types/node": "*", "escape-string-regexp": "^4.0.0", @@ -3544,12 +3584,11 @@ } }, "node_modules/chromedriver": { - "version": "126.0.0", - "resolved": "https://registry.npmjs.org/chromedriver/-/chromedriver-126.0.0.tgz", - "integrity": "sha512-rzwKp1okI9RmFtSyIzkk9+GTlTK62ai5P3/AS2qMwl86+gw84d2S/IyLkQMm5cqieFs4dgDAuqqPu0AqQACScg==", + "version": "126.0.5", + "resolved": "https://registry.npmjs.org/chromedriver/-/chromedriver-126.0.5.tgz", + "integrity": "sha512-xXVxwxd8CJ6yg2KEvFqLQi7V0RvF78xFnLB+xo9g9MoJNHMQccD7b4OWaxtKDy5RXrMgQ6Jb6vUN3SjTYXHLEQ==", "dev": true, "hasInstallScript": true, - "license": "Apache-2.0", "dependencies": { "@testim/chrome-version": "^1.1.4", "axios": "^1.6.7", @@ -13972,9 +14011,9 @@ "dev": true }, "node_modules/picocolors": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.0.tgz", - "integrity": "sha512-1fygroTLlHu66zi26VoTDv8yRgm0Fccecssto+MhsZ0D/DGW2sm8E8AjW7NU5VVTRt5GxbeZ5qBuJr+HyLYkjQ==" + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.1.tgz", + "integrity": "sha512-anP1Z8qwhkbmu7MFP5iTt+wQKXgwzf7zTyGlcdzabySa9vd0Xt392U0rVmz9poOaBj0uHJKyyo9/upk0HrEQew==" }, "node_modules/picomatch": { "version": "2.3.1", @@ -14297,9 +14336,9 @@ } }, "node_modules/postcss": { - "version": "8.4.38", - "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.38.tgz", - "integrity": "sha512-Wglpdk03BSfXkHoQa3b/oulrotAkwrlLDRSOb9D0bN86FdRyE9lppSp33aHNPgBa0JKCoB+drFLZkQoRRYae5A==", + "version": "8.4.40", + "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.40.tgz", + "integrity": "sha512-YF2kKIUzAofPMpfH6hOi2cGnv/HrUlfucspc7pDyvv7kGdqXrfj8SCl/t8owkEgKEuu8ZcRjSOxFxVLqwChZ2Q==", "dev": true, "funding": [ { @@ -14315,10 +14354,9 @@ "url": "https://github.com/sponsors/ai" } ], - "license": "MIT", "dependencies": { "nanoid": "^3.3.7", - "picocolors": "^1.0.0", + "picocolors": "^1.0.1", "source-map-js": "^1.2.0" }, "engines": { @@ -16852,20 +16890,41 @@ } }, "node_modules/selenium-webdriver": { - "version": "4.21.0", - "resolved": "https://registry.npmjs.org/selenium-webdriver/-/selenium-webdriver-4.21.0.tgz", - "integrity": "sha512-WaEJHZjOWNth1QG5FEpxpREER0qptZBMonFU6GtAqdCNLJVxbtC3E7oS/I/+Q1sf1W032Wg0Ebk+m46lANOXyQ==", + "version": "4.23.0", + "resolved": "https://registry.npmjs.org/selenium-webdriver/-/selenium-webdriver-4.23.0.tgz", + "integrity": "sha512-DdvtInpnMt95Td8VApvmAw7oSydBD9twIRXqoMyRoGMvL1dAnMFxdrwnW6L0d/pF/uoNTjbVUarwGZ9wIGNStA==", "dev": true, - "license": "Apache-2.0", "dependencies": { + "@bazel/runfiles": "^5.8.1", "jszip": "^3.10.1", "tmp": "^0.2.3", - "ws": ">=8.16.0" + "ws": "^8.17.1" }, "engines": { "node": ">= 14.21.0" } }, + "node_modules/selenium-webdriver/node_modules/ws": { + "version": "8.18.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", + "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", + "dev": true, + "engines": { + "node": ">=10.0.0" + }, + "peerDependencies": { + "bufferutil": "^4.0.1", + "utf-8-validate": ">=5.0.2" + }, + "peerDependenciesMeta": { + "bufferutil": { + "optional": true + }, + "utf-8-validate": { + "optional": true + } + } + }, "node_modules/semver": { "version": "6.3.1", "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz", @@ -18767,12 +18826,6 @@ "integrity": "sha512-sBPIUGTNF0czz0mwGGUoKKJC8Q7On1GPbCSFPfyEsfHb2DyBG0Y4QtV+EVWpINSaiGKZblDNuF5AezxSgOhesQ==", "dev": true }, - "node_modules/stylelint/node_modules/picocolors": { - "version": "1.0.1", - "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.1.tgz", - "integrity": "sha512-anP1Z8qwhkbmu7MFP5iTt+wQKXgwzf7zTyGlcdzabySa9vd0Xt392U0rVmz9poOaBj0uHJKyyo9/upk0HrEQew==", - "dev": true - }, "node_modules/stylelint/node_modules/resolve-from": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-5.0.0.tgz", @@ -19714,12 +19767,6 @@ "browserslist": ">= 4.21.0" } }, - "node_modules/update-browserslist-db/node_modules/picocolors": { - "version": "1.0.1", - "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.1.tgz", - "integrity": "sha512-anP1Z8qwhkbmu7MFP5iTt+wQKXgwzf7zTyGlcdzabySa9vd0Xt392U0rVmz9poOaBj0uHJKyyo9/upk0HrEQew==", - "dev": true - }, "node_modules/update-notifier": { "version": "4.1.3", "resolved": "https://registry.npmjs.org/update-notifier/-/update-notifier-4.1.3.tgz", diff --git a/package.json b/package.json index dab50166f6..eb9ae14f77 100644 --- a/package.json +++ b/package.json @@ -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": "^126.0.4", "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", diff --git a/src/requirements-dev.txt b/src/requirements-dev.txt index bce8fd4146..d9ba789407 100644 --- a/src/requirements-dev.txt +++ b/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==0.5.0 vcrpy==6.0.1 diff --git a/src/requirements-general.txt b/src/requirements-general.txt index c681a2df5b..a2fdd5b0f4 100644 --- a/src/requirements-general.txt +++ b/src/requirements-general.txt @@ -1,7 +1,7 @@ appdirs==1.4.4 beautifulsoup4==4.12.3 -certifi==2024.6.2 -chardet==5.0.0 +certifi==2024.7.4 +chardet==5.2.0 cryptography==42.0.8 decorator==5.1.1 html5lib==1.1 @@ -10,28 +10,28 @@ jsonschema==4.16.0 markdown==3.4.1 markupsafe==2.1.4 ndg-httpsclient==0.5.1 -pexpect==4.8.0 +pexpect==4.9.0 pickleshare==0.7.5 -pillow==10.3.0 -pyasn1==0.4.8 +pillow==10.4.0 +pyasn1==0.6.0 pycurl==7.45.1 -pygments==2.17.2 +pygments==2.18.0 pyopenssl==24.1.0 -python-daemon==2.3.2 -python-dateutil==2.8.2 +python-daemon==3.0.1 +python-dateutil==2.9.0.post0 rsa==4.9 -setuptools==69.5.1 +setuptools==70.1.1 six==1.16.0 terminado==0.18.0 -biopython==1.79 -bokeh==3.0.3 +biopython==1.84 +bokeh==3.4.2 chart_studio==1.1.0 ete3==3.1.2 -networkx==3.0 -numpy==1.24.1 -plotly==5.13.0 +networkx==3.3 +numpy==2.0.0 +plotly==5.22.0 qgrid==1.3.1 -seaborn==0.12.0 -scipy==1.10.0 -sympy==1.10.1 +seaborn==0.13.2 +scipy==1.14.0 +sympy==1.12.1 wordcloud==1.9.3 diff --git a/src/requirements.txt b/src/requirements.txt index 1ec0f76bfa..8159cabd76 100644 --- a/src/requirements.txt +++ b/src/requirements.txt @@ -1,5 +1,5 @@ clustergrammer2==0.18.0 -ipython==8.25.0 +ipython==8.26.0 ipywidgets==7.7.1 jinja2==3.1.4 notebook==6.5.6 From 0bec5e851a03adebf57951893e6d5abac172c868 Mon Sep 17 00:00:00 2001 From: Bill Riehl Date: Thu, 25 Jul 2024 17:08:39 -0400 Subject: [PATCH 2/5] fix bug with inputs not getting populated in staging download apps --- .../kbaseNarrativeDownloadPanel.js | 2 +- .../kbaseNarrativeDownloadPanel-spec.js | 40 +++++++++---------- 2 files changed, 21 insertions(+), 21 deletions(-) diff --git a/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeDownloadPanel.js b/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeDownloadPanel.js index a406ffa9b1..531e53cdb5 100644 --- a/kbase-extension/static/kbase/js/widgets/narrative_core/kbaseNarrativeDownloadPanel.js +++ b/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); diff --git a/test/unit/spec/narrative_core/kbaseNarrativeDownloadPanel-spec.js b/test/unit/spec/narrative_core/kbaseNarrativeDownloadPanel-spec.js index 8c0f1f7bd6..4818b60f1c 100644 --- a/test/unit/spec/narrative_core/kbaseNarrativeDownloadPanel-spec.js +++ b/test/unit/spec/narrative_core/kbaseNarrativeDownloadPanel-spec.js @@ -12,20 +12,20 @@ define([ describe('The kbaseNarrativeDownloadPanel widget', () => { let $div = null; - const ws = 1111, - oid = 2222, - ver = 3333, - name = 'fake_test_object', - objType = 'FakeModule.FakeType', - upa = `${ws}/${oid}/${ver}`; + const WS = 1111, + OBJ_ID = 2222, + OBJ_VER = 3333, + OBJ_NAME = 'fake_test_object', + OBJ_TYPE = 'FakeModule.FakeType', + INPUT_UPA = `${WS}/${OBJ_ID}/${OBJ_VER}`; const initDownloadPanel = async (authToken, exporterCache) => { return await new kbaseNarrativeDownloadPanel($div, { token: authToken, - type: objType, - objId: oid, - ref: upa, - objName: name, + type: OBJ_TYPE, + objId: OBJ_ID, + upa: INPUT_UPA, + objName: OBJ_NAME, downloadSpecCache: exporterCache, }); }; @@ -65,7 +65,7 @@ define([ const exporterCache = { lastUpdateTime: 100, types: { - [objType]: { export_functions: exporters }, + [OBJ_TYPE]: { export_functions: exporters }, }, }; @@ -141,7 +141,7 @@ define([ exporterCache = { lastUpdateTime: 100, types: { - [objType]: { + [OBJ_TYPE]: { export_functions: { SOME_FORMAT: exportApp, }, @@ -215,7 +215,7 @@ define([ exporterCache = { lastUpdateTime: 100, types: { - [objType]: { + [OBJ_TYPE]: { export_functions: { SOME_FORMAT: exportApp, }, @@ -254,7 +254,7 @@ define([ exporterCache = { lastUpdateTime: 100, types: { - [objType]: { + [OBJ_TYPE]: { export_functions: { SOME_FORMAT: exportApp, }, @@ -355,7 +355,7 @@ define([ exporterCache = { lastUpdateTime: 100, types: { - [objType]: { + [OBJ_TYPE]: { export_functions: { SOME_FORMAT: exportApp, }, @@ -401,7 +401,7 @@ define([ const exporterCache = { lastUpdateTime: 100, types: { - [objType]: { + [OBJ_TYPE]: { export_functions: { STAGING: 'gets_overwritten_right_now', }, @@ -416,14 +416,14 @@ define([ expect(Jupyter.narrative.addAndPopulateApp).toHaveBeenCalledOnceWith( STAGING_EXPORT_APP, 'release', - { input_ref: 'fake_test_object' } + { input_ref: INPUT_UPA } ); }); it('Should create an app cell with the JSON exporter', async () => { /* use mock for Jupyter.narrative.addAndPopulateApp */ spyOn(Jupyter.narrative, 'addAndPopulateApp'); - await initDownloadPanel(null, { lastUpdateTime: 100, types: { [objType]: {} } }); + await initDownloadPanel(null, { lastUpdateTime: 100, types: { [OBJ_TYPE]: {} } }); const exportBtn = $div.find('.kb-data-list-btn'); // only one is JSON expect(exportBtn.length).toEqual(1); @@ -431,14 +431,14 @@ define([ expect(Jupyter.narrative.addAndPopulateApp).toHaveBeenCalledOnceWith( JSON_EXPORT_APP, 'release', - { input_ref: 'fake_test_object' } + { input_ref: INPUT_UPA } ); }); it('Should have a cancel button that empties the widget', async () => { const widget = await initDownloadPanel(null, { lastUpdateTime: 100, - types: { [objType]: {} }, + types: { [OBJ_TYPE]: {} }, }); const cancelBtn = $div.find('.kb-data-list-cancel-btn'); cancelBtn.click(); From 24bd5a5a3aa2f0d736549dbb444ac4760ed8e1c2 Mon Sep 17 00:00:00 2001 From: Bill Riehl Date: Thu, 25 Jul 2024 17:10:50 -0400 Subject: [PATCH 3/5] bump release notes --- RELEASE_NOTES.md | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index fd5386efbd..ee80948170 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -2,36 +2,38 @@ 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 -> 3.4.2 + - 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 -> 2.0.0 + - pexpect 4.8.0 -> 4.9.0 + - pillow 10.3.0 -> 10.4.0 - plotly 5.13.0 -> 5.22.0 - pyasn1 0.4.8 -> 0.6.0 - - ruff 0.4.7 -> 0.5.0 - pygments 2.17.2 -> 2.18.0 - - pexpect 4.8.0 -> 4.9.0 - - seaborn 0.12.0 -> 0.13.2 - - setuptools 69.5.1 -> 70.1.1 - - certifi 2024.6.2 -> 2024.7.4 - - sympy 1.10.1 -> 1.12.1 - - pillow 10.3.0 -> 10.4.0 - python-daemon 2.3.2 -> 3.0.1 - - chardet 5.0.0 -> 5.2.0 - python-dateutil 2.8.2 -> 2.9.0.post0 - scipy 1.10.0 -> 1.14.0 - - ipython 8.25.0 -> 8.26.0 + - seaborn 0.12.0 -> 0.13.2 + - setuptools 69.5.1 -> 70.1.1 + - sympy 1.10.1 -> 1.12.1 + - ruff 0.4.7 -> 0.5.0 - 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 - - chrome-launcher 1.1.1 -> 1.1.2 - - @wdio/mocha-framework 8.38.2 -> 8.39.0 - selenium-webdriver 4.21.0 -> 4.22.0 ## Version 5.4.0 From 50925fe7c4c4aa96a74046b8ad6cf350e2f05e5a Mon Sep 17 00:00:00 2001 From: Bill Riehl Date: Mon, 29 Jul 2024 13:34:25 -0400 Subject: [PATCH 4/5] another round of updates --- RELEASE_NOTES.md | 12 ++++++------ package-lock.json | 8 ++++---- package.json | 2 +- src/requirements-dev.txt | 2 +- src/requirements-general.txt | 10 +++++----- 5 files changed, 17 insertions(+), 17 deletions(-) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index ee80948170..d6f7646c3a 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -10,24 +10,24 @@ This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will ### Dependency Changes - Python dependency updates - biopython 1.79 -> 1.84 - - bokeh 3.0.3 -> 3.4.2 + - 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 -> 2.0.0 + - 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 -> 5.22.0 + - 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 -> 70.1.1 - - sympy 1.10.1 -> 1.12.1 - - ruff 0.4.7 -> 0.5.0 + - 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 diff --git a/package-lock.json b/package-lock.json index a95009826e..ccfe5bee67 100644 --- a/package-lock.json +++ b/package-lock.json @@ -64,7 +64,7 @@ "axios": "^1.7.2", "bootstrap-sass": "^3.4.3", "chrome-launcher": "^1.1.2", - "chromedriver": "^126.0.4", + "chromedriver": "^127.0.0", "commander": "^12.1.0", "cssnano": "^7.0.2", "ejs": "^3.1.10", @@ -3584,9 +3584,9 @@ } }, "node_modules/chromedriver": { - "version": "126.0.5", - "resolved": "https://registry.npmjs.org/chromedriver/-/chromedriver-126.0.5.tgz", - "integrity": "sha512-xXVxwxd8CJ6yg2KEvFqLQi7V0RvF78xFnLB+xo9g9MoJNHMQccD7b4OWaxtKDy5RXrMgQ6Jb6vUN3SjTYXHLEQ==", + "version": "127.0.0", + "resolved": "https://registry.npmjs.org/chromedriver/-/chromedriver-127.0.0.tgz", + "integrity": "sha512-/Jla24iL0ly/EI7i/q0ukANkpAWvAkSHbvC7FtBZXFJXe6klH0n/XT56VSBcBYB1iMgWM8kPwqF8pb9gdqN9UA==", "dev": true, "hasInstallScript": true, "dependencies": { diff --git a/package.json b/package.json index eb9ae14f77..bd7bcf8cf6 100644 --- a/package.json +++ b/package.json @@ -22,7 +22,7 @@ "axios": "^1.7.2", "bootstrap-sass": "^3.4.3", "chrome-launcher": "^1.1.2", - "chromedriver": "^126.0.4", + "chromedriver": "^127.0.0", "commander": "^12.1.0", "cssnano": "^7.0.2", "ejs": "^3.1.10", diff --git a/src/requirements-dev.txt b/src/requirements-dev.txt index d9ba789407..e155571c3b 100644 --- a/src/requirements-dev.txt +++ b/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==0.5.0 +ruff==0.5.5 vcrpy==6.0.1 diff --git a/src/requirements-general.txt b/src/requirements-general.txt index a2fdd5b0f4..39126ee294 100644 --- a/src/requirements-general.txt +++ b/src/requirements-general.txt @@ -20,18 +20,18 @@ pyopenssl==24.1.0 python-daemon==3.0.1 python-dateutil==2.9.0.post0 rsa==4.9 -setuptools==70.1.1 +setuptools==71.1.0 six==1.16.0 terminado==0.18.0 biopython==1.84 -bokeh==3.4.2 +bokeh==3.5.1 chart_studio==1.1.0 ete3==3.1.2 networkx==3.3 -numpy==2.0.0 -plotly==5.22.0 +numpy==2.0.1 +plotly==5.23.0 qgrid==1.3.1 seaborn==0.13.2 scipy==1.14.0 -sympy==1.12.1 +sympy==1.13.1 wordcloud==1.9.3 From 3277bab8cf19466bf56cd547004d07423ac592be Mon Sep 17 00:00:00 2001 From: Bill Riehl Date: Mon, 29 Jul 2024 15:03:54 -0400 Subject: [PATCH 5/5] bump version to 5.4.1 --- package-lock.json | 4 ++-- package.json | 2 +- src/biokbase/narrative/__init__.py | 2 +- src/config.json | 2 +- src/config.json.templ | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index ccfe5bee67..9e27a03af5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "kbase-narrative-core", - "version": "5.4.0", + "version": "5.4.1", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "kbase-narrative-core", - "version": "5.4.0", + "version": "5.4.1", "dependencies": { "bluebird": "3.7.2", "bootstrap": "3.4.1", diff --git a/package.json b/package.json index bd7bcf8cf6..b644bd04d6 100644 --- a/package.json +++ b/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": { diff --git a/src/biokbase/narrative/__init__.py b/src/biokbase/narrative/__init__.py index 0655b4df1a..6a3ae3a3d1 100644 --- a/src/biokbase/narrative/__init__.py +++ b/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(): diff --git a/src/config.json b/src/config.json index 11f7c9173b..b7db42979c 100644 --- a/src/config.json +++ b/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" } diff --git a/src/config.json.templ b/src/config.json.templ index d8aa3181e9..584693c13f 100644 --- a/src/config.json.templ +++ b/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" }