diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml index a3dee200118..9c0d9209b28 100644 --- a/.github/workflows/first_startup.yaml +++ b/.github/workflows/first_startup.yaml @@ -21,7 +21,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.10'] + python-version: ['3.7', '3.11'] defaults: run: shell: bash -l {0} diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 0125f24c4d4..500bb656d9d 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -21,7 +21,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.7', '3.10'] + python-version: ['3.7', '3.11'] env: LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt' TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt' diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml index 00c279d0d5a..7e61918ee13 100644 --- a/.github/workflows/lint_openapi_schema.yml +++ b/.github/workflows/lint_openapi_schema.yml @@ -43,7 +43,7 @@ jobs: path: 'galaxy root/.venv' key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api - name: Install dependencies - run: ./scripts/common_startup.sh --skip-client-build + run: ./scripts/common_startup.sh --dev-wheels --skip-client-build working-directory: 'galaxy root' - name: Lint schema run: make lint-api-schema diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml index 126046c6ee5..1d649d0d858 100644 --- a/.github/workflows/reports_startup.yaml +++ b/.github/workflows/reports_startup.yaml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.10'] + python-version: ['3.7', '3.11'] defaults: run: shell: bash -l {0} diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml index 0f18a52f1be..089d4f45f19 100644 --- a/.github/workflows/test_galaxy_packages.yaml +++ b/.github/workflows/test_galaxy_packages.yaml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.10'] + python-version: ['3.7', '3.11'] steps: - uses: actions/checkout@v3 with: diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml index cef323f1d2c..2d8ae1660ac 100644 --- a/.github/workflows/unit.yaml +++ b/.github/workflows/unit.yaml @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.7', '3.10'] + python-version: ['3.7', '3.11'] steps: - uses: actions/checkout@v3 with: diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js index eb86e05d0ed..42710e2e1ac 100644 --- a/client/src/components/Panels/utilities.js +++ b/client/src/components/Panels/utilities.js @@ -95,7 +95,7 @@ export function searchToolsByKeys(tools, keys, query) { } else { actualValue = tool[key] ? tool[key].toLowerCase() : ""; } - const queryLowerCase = query.toLowerCase(); + const queryLowerCase = query.trim().toLowerCase(); if (actualValue.match(queryLowerCase)) { // do we care for exact matches && is it an exact match ? const order = keys.exact && actualValue === queryLowerCase ? keys.exact : keys[key]; diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js index 05697266a11..3c410cc6c7e 100644 --- a/client/src/components/Panels/utilities.test.js +++ b/client/src/components/Panels/utilities.test.js @@ -38,7 +38,8 @@ describe("test helpers in tool searching utilities", () => { results = searchToolsByKeys(normalizeTools(toolsList), keys, q); expect(results).toEqual(expectedResults); - q = "filter empty datasets"; + // whitespace precedes to ensure query.trim() works + q = " filter empty datasets"; expectedResults = ["__FILTER_EMPTY_DATASETS__"]; keys = { description: 1, name: 2, combined: 0 }; results = searchToolsByKeys(normalizeTools(toolsList), keys, q); diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts index 4b0b6e8dca8..ed9bc4fd31d 100644 --- a/client/src/schema/schema.ts +++ b/client/src/schema/schema.ts @@ -5066,12 +5066,6 @@ export interface components { )[]; metadata: components["schemas"]["LibraryFolderMetadata"]; }; - /** - * LibraryFolderContentsIndexSortByEnum - * @description An enumeration. - * @enum {string} - */ - LibraryFolderContentsIndexSortByEnum: "name" | "description" | "type" | "size" | "update_time"; /** * LibraryFolderCurrentPermissions * @description Base model definition with common configuration used by all derived models. @@ -7348,12 +7342,6 @@ export interface components { [key: string]: number | undefined; }; }; - /** - * WorkflowSortByEnum - * @description An enumeration. - * @enum {string} - */ - WorkflowSortByEnum: "create_time" | "update_time" | "name" | "None"; /** * WriteInvocationStoreToPayload * @description Base model definition with common configuration used by all derived models. @@ -8655,7 +8643,7 @@ export interface operations { offset?: number; search_text?: string; include_deleted?: boolean; - order_by?: components["schemas"]["LibraryFolderContentsIndexSortByEnum"]; + order_by?: "name" | "description" | "type" | "size" | "update_time"; sort_desc?: boolean; }; /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */ @@ -14324,7 +14312,7 @@ export interface operations { missing_tools?: boolean; show_published?: boolean; show_shared?: boolean; - sort_by?: components["schemas"]["WorkflowSortByEnum"]; + sort_by?: "create_time" | "update_time" | "name"; sort_desc?: boolean; limit?: number; offset?: number; diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt index 57493b9389e..0c2e60d96b0 100644 --- a/lib/galaxy/dependencies/conditional-requirements.txt +++ b/lib/galaxy/dependencies/conditional-requirements.txt @@ -1,5 +1,5 @@ # These dependencies are only required when certain config options are set -psycopg2-binary==2.9.1 +psycopg2-binary==2.9.5 mysqlclient fluent-logger sentry-sdk diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index afb44df79cc..07e9ce90740 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,141 +1,143 @@ -aiohttp==3.8.3 ; python_version >= "3.7" and python_version < "3.11" -aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.11" -alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.11" -amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.11" -anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.11" -ase==3.22.1 ; python_version >= "3.7" and python_version < "3.11" -async-generator==1.10 ; python_version >= "3.7" and python_version < "3.11" -async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.11" +aiohttp==3.8.3 ; python_version >= "3.7" and python_version < "3.12" +aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" +alabaster==0.7.13 ; python_version >= "3.7" and python_version < "3.12" +amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" +anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.12" +ase==3.22.1 ; python_version >= "3.7" and python_version < "3.12" +async-generator==1.10 ; python_version >= "3.7" and python_version < "3.12" +async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.12" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" -attrs==22.2.0 ; python_version >= "3.7" and python_version < "3.11" -babel==2.11.0 ; python_version >= "3.7" and python_version < "3.11" -billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.11" -black==22.12.0 ; python_version >= "3.7" and python_version < "3.11" -cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.11" +attrs==22.2.0 ; python_version >= "3.7" and python_version < "3.12" +babel==2.11.0 ; python_version >= "3.7" and python_version < "3.12" +billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" +black==22.12.0 ; python_version >= "3.7" and python_version < "3.12" +cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.12" cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" -celery==5.2.7 ; python_version >= "3.7" and python_version < "3.11" -certifi==2022.12.7 ; python_version >= "3.7" and python_version < "3.11" -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.11" -charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.11" -click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.11" -click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.11" -click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.11" -click==8.1.3 ; python_version >= "3.7" and python_version < "3.11" -codespell==2.2.2 ; python_version >= "3.7" and python_version < "3.11" -colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.11" and sys_platform == "win32" or python_version >= "3.7" and python_version < "3.11" and platform_system == "Windows" -commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.11" -coverage[toml]==7.0.5 ; python_version >= "3.7" and python_version < "3.11" -cwltest==2.3.20230108193615 ; python_version >= "3.7" and python_version < "3.11" -cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.11" -darker==1.6.1 ; python_version >= "3.7" and python_version < "3.11" -defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11" -deprecated==1.2.13 ; python_version >= "3.7" and python_version < "3.11" -docutils==0.16 ; python_version >= "3.7" and python_version < "3.11" +celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" +certifi==2022.12.7 ; python_version >= "3.7" and python_version < "3.12" +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.12" +click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" +click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" +click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" +codespell==2.2.2 ; python_version >= "3.7" and python_version < "3.12" +colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32" or python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" +commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.12" +coverage[toml]==7.0.5 ; python_version >= "3.7" and python_version < "3.12" +cwltest==2.3.20230108193615 ; python_version >= "3.7" and python_version < "3.12" +cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" +darker==1.6.1 ; python_version >= "3.7" and python_version < "3.12" +defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" +deprecated==1.2.13 ; python_version >= "3.7" and python_version < "3.12" +docutils==0.16 ; python_version >= "3.7" and python_version < "3.12" exceptiongroup==1.1.0 ; python_version >= "3.7" and python_version < "3.11" -fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.11" -fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.11" -frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.11" -future==0.18.3 ; python_version >= "3.7" and python_version < "3.11" -h11==0.14.0 ; python_version >= "3.7" and python_version < "3.11" -httpcore==0.16.3 ; python_version >= "3.7" and python_version < "3.11" -httpx==0.23.3 ; python_version >= "3.7" and python_version < "3.11" -idna==3.4 ; python_version >= "3.7" and python_version < "3.11" -imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.11" +fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12" +fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12" +frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" +future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" +h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" +httpcore==0.16.3 ; python_version >= "3.7" and python_version < "3.12" +httpx==0.23.3 ; python_version >= "3.7" and python_version < "3.12" +idna==3.4 ; python_version >= "3.7" and python_version < "3.12" +imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.12" importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.10" -iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.11" -isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.11" -isort==5.11.4 ; python_version >= "3.7" and python_version < "3.11" -jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.11" -junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.11" -kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.11" -kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.11" -lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.11" -lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.11" -markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.11" -markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.11" -markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.11" -matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.11" -mirakuru==2.4.2 ; python_version >= "3.7" and python_version < "3.11" -mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.11" -msgpack==1.0.4 ; python_version >= "3.7" and python_version < "3.11" -multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.11" -mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.11" -numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.11" -outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.11" -packaging==21.3 ; python_version >= "3.7" and python_version < "3.11" -pathspec==0.10.3 ; python_version >= "3.7" and python_version < "3.11" -pillow==9.4.0 ; python_version >= "3.7" and python_version < "3.11" -pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.11" -platformdirs==2.6.2 ; python_version >= "3.7" and python_version < "3.11" -pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.11" -port-for==0.6.3 ; python_version >= "3.7" and python_version < "3.11" -prettytable==3.6.0 ; python_version >= "3.7" and python_version < "3.11" -prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.11" -psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.11" and sys_platform != "cygwin" -py==1.11.0 ; python_version >= "3.7" and python_version < "3.11" -pycparser==2.21 ; python_version >= "3.7" and python_version < "3.11" -pygithub==1.57 ; python_version >= "3.7" and python_version < "3.11" -pygments==2.14.0 ; python_version >= "3.7" and python_version < "3.11" -pyjwt==2.6.0 ; python_version >= "3.7" and python_version < "3.11" -pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.11" -pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.11" -pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.11" -pytest-asyncio==0.20.3 ; python_version >= "3.7" and python_version < "3.11" -pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.11" -pytest-cov==4.0.0 ; python_version >= "3.7" and python_version < "3.11" -pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.11" -pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.11" -pytest-metadata==2.0.4 ; python_version >= "3.7" and python_version < "3.11" -pytest-mock==3.10.0 ; python_version >= "3.7" and python_version < "3.11" -pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.11" -pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.11" -pytest==7.2.1 ; python_version >= "3.7" and python_version < "3.11" -python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.11" -python-irodsclient==1.1.6 ; python_version >= "3.7" and python_version < "3.11" -pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.11" -rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11" -recommonmark==0.7.1 ; python_version >= "3.7" and python_version < "3.11" -requests==2.28.2 ; python_version >= "3.7" and python_version < "3.11" -responses==0.22.0 ; python_version >= "3.7" and python_version < "3.11" -rfc3986[idna2008]==1.5.0 ; python_version >= "3.7" and python_version < "3.11" +iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.12" +isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" +isort==5.11.4 ; python_version >= "3.7" and python_version < "3.12" +jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" +junit-xml==1.9 ; python_version >= "3.7" and python_version < "3.12" +kiwisolver==1.4.4 ; python_version >= "3.7" and python_version < "3.12" +kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" +lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.12" +lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12" +markdown-it-reporter==0.0.2 ; python_version >= "3.7" and python_version < "3.12" +markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.12" +markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.12" +matplotlib==3.5.3 ; python_version >= "3.7" and python_version < "3.12" +mirakuru==2.4.2 ; python_version >= "3.7" and python_version < "3.12" +mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.12" +msgpack==1.0.4 ; python_version >= "3.7" and python_version < "3.12" +multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12" +mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.12" +numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" +numpy==1.24.1 ; python_version >= "3.8" and python_version < "3.12" +outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12" +packaging==21.3 ; python_version >= "3.7" and python_version < "3.12" +pathspec==0.10.3 ; python_version >= "3.7" and python_version < "3.12" +pillow==9.4.0 ; python_version >= "3.7" and python_version < "3.12" +pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12" +platformdirs==2.6.2 ; python_version >= "3.7" and python_version < "3.12" +pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" +port-for==0.6.3 ; python_version >= "3.7" and python_version < "3.12" +prettytable==3.6.0 ; python_version >= "3.7" and python_version < "3.12" +prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.12" +psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin" +py==1.11.0 ; python_version >= "3.7" and python_version < "3.12" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" +pygithub==1.57 ; python_version >= "3.7" and python_version < "3.12" +pygments==2.14.0 ; python_version >= "3.7" and python_version < "3.12" +pyjwt==2.6.0 ; python_version >= "3.7" and python_version < "3.12" +pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" +pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" +pytest-asyncio==0.20.3 ; python_version >= "3.7" and python_version < "3.12" +pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-cov==4.0.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-metadata==2.0.4 ; python_version >= "3.7" and python_version < "3.12" +pytest-mock==3.10.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12" +pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12" +pytest==7.2.1 ; python_version >= "3.7" and python_version < "3.12" +python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" +python-irodsclient==1.1.6 ; python_version >= "3.7" and python_version < "3.12" +pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.12" +rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" +recommonmark==0.7.1 ; python_version >= "3.7" and python_version < "3.12" +requests==2.28.2 ; python_version >= "3.7" and python_version < "3.12" +responses==0.22.0 ; python_version >= "3.7" and python_version < "3.12" +rfc3986[idna2008]==1.5.0 ; python_version >= "3.7" and python_version < "3.12" ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" -ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.11" -schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.11" -scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.11" -selenium==4.7.2 ; python_version >= "3.7" and python_version < "3.11" -seletools==1.3.0 ; python_version >= "3.7" and python_version < "3.11" -setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.11" -six==1.16.0 ; python_version >= "3.7" and python_version < "3.11" -sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.11" -snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.11" -sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.11" -sphinx-markdown-tables==0.0.17 ; python_version >= "3.7" and python_version < "3.11" -sphinx-rtd-theme==1.1.1 ; python_version >= "3.7" and python_version < "3.11" -sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-htmlhelp==2.0.0 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.11" -sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.11" -statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.11" -testfixtures==7.0.4 ; python_version >= "3.7" and python_version < "3.11" -tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.11" -toml==0.10.2 ; python_version >= "3.7" and python_version < "3.11" -tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" -trio-websocket==0.9.2 ; python_version >= "3.7" and python_version < "3.11" -trio==0.22.0 ; python_version >= "3.7" and python_version < "3.11" -tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.11" -twill==3.1 ; python_version >= "3.7" and python_version < "3.11" +ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" +schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.12" +scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8" +scipy==1.10.0 ; python_version >= "3.8" and python_version < "3.12" +selenium==4.7.2 ; python_version >= "3.7" and python_version < "3.12" +seletools==1.3.0 ; python_version >= "3.7" and python_version < "3.12" +setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.12" +six==1.16.0 ; python_version >= "3.7" and python_version < "3.12" +sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12" +snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12" +sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" +sphinx-markdown-tables==0.0.17 ; python_version >= "3.7" and python_version < "3.12" +sphinx-rtd-theme==1.1.1 ; python_version >= "3.7" and python_version < "3.12" +sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-htmlhelp==2.0.0 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12" +sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12" +statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12" +testfixtures==7.0.4 ; python_version >= "3.7" and python_version < "3.12" +tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.12" +toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.7" and python_full_version < "3.11.0a7" +trio-websocket==0.9.2 ; python_version >= "3.7" and python_version < "3.12" +trio==0.22.0 ; python_version >= "3.7" and python_version < "3.12" +tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" +twill==3.1 ; python_version >= "3.7" and python_version < "3.12" typed-ast==1.5.4 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7" -types-toml==0.10.8.1 ; python_version >= "3.7" and python_version < "3.11" -typing-extensions==4.4.0 ; python_version >= "3.7" and python_version < "3.11" -urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.11" -urllib3[socks]==1.26.14 ; python_version >= "3.7" and python_version < "3.11" -vine==5.0.0 ; python_version >= "3.7" and python_version < "3.11" -watchdog==2.2.1 ; python_version >= "3.7" and python_version < "3.11" -wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.11" -wrapt==1.14.1 ; python_version >= "3.7" and python_version < "3.11" -wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.11" -yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.11" +types-toml==0.10.8.1 ; python_version >= "3.7" and python_version < "3.12" +typing-extensions==4.4.0 ; python_version >= "3.7" and python_version < "3.12" +urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.12" +urllib3[socks]==1.26.14 ; python_version >= "3.7" and python_version < "3.12" +vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" +watchdog==2.2.1 ; python_version >= "3.7" and python_version < "3.12" +wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.12" +wrapt==1.14.1 ; python_version >= "3.7" and python_version < "3.12" +wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.12" +yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.12" zipp==3.11.0 ; python_version >= "3.7" and python_version < "3.10" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3cf5b20fd73..b06e4cc7be7 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,198 +1,199 @@ --extra-index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.6.0 ; python_version >= "3.7" and python_version < "3.11" -adal==1.2.7 ; python_version >= "3.7" and python_version < "3.11" -aiofiles==22.1.0 ; python_version >= "3.7" and python_version < "3.11" -aiohttp==3.8.3 ; python_version >= "3.7" and python_version < "3.11" -aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.11" -alembic-utils==0.7.8 ; python_version >= "3.7" and python_version < "3.11" -alembic==1.9.2 ; python_version >= "3.7" and python_version < "3.11" -amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.11" -anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.11" -apispec==6.0.2 ; python_version >= "3.7" and python_version < "3.11" -appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.11" -arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.11" -argcomplete==2.0.0 ; python_version >= "3.7" and python_version < "3.11" -async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.11" +a2wsgi==1.6.0 ; python_version >= "3.7" and python_version < "3.12" +adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12" +aiofiles==22.1.0 ; python_version >= "3.7" and python_version < "3.12" +aiohttp==3.8.3 ; python_version >= "3.7" and python_version < "3.12" +aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" +alembic-utils==0.7.8 ; python_version >= "3.7" and python_version < "3.12" +alembic==1.9.2 ; python_version >= "3.7" and python_version < "3.12" +amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" +anyio==3.6.2 ; python_version >= "3.7" and python_version < "3.12" +apispec==6.0.2 ; python_version >= "3.7" and python_version < "3.12" +appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12" +arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12" +argcomplete==2.0.0 ; python_version >= "3.7" and python_version < "3.12" +async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.12" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" -attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.11" -attrs==22.2.0 ; python_version >= "3.7" and python_version < "3.11" -babel==2.11.0 ; python_version >= "3.7" and python_version < "3.11" -bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.11" -bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.11" -bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.11" -bdbag==1.6.3 ; python_version >= "3.7" and python_version < "3.11" -beaker==1.11.0 ; python_version >= "3.7" and python_version < "3.11" -billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.11" -bioblend==1.0.0 ; python_version >= "3.7" and python_version < "3.11" -bleach==5.0.1 ; python_version >= "3.7" and python_version < "3.11" -boltons==21.0.0 ; python_version >= "3.7" and python_version < "3.11" -boto==2.49.0 ; python_version >= "3.7" and python_version < "3.11" -bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.11" -cachecontrol==0.12.11 ; python_version >= "3.7" and python_version < "3.11" -cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.11" +attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12" +attrs==22.2.0 ; python_version >= "3.7" and python_version < "3.12" +babel==2.11.0 ; python_version >= "3.7" and python_version < "3.12" +bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12" +bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12" +bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.12" +bdbag==1.6.3 ; python_version >= "3.7" and python_version < "3.12" +beaker==1.11.0 ; python_version >= "3.7" and python_version < "3.12" +billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" +bioblend==1.0.0 ; python_version >= "3.7" and python_version < "3.12" +bleach==5.0.1 ; python_version >= "3.7" and python_version < "3.12" +boltons==21.0.0 ; python_version >= "3.7" and python_version < "3.12" +boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12" +bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.12" +cachecontrol==0.12.11 ; python_version >= "3.7" and python_version < "3.12" +cachecontrol[filecache]==0.12.11 ; python_version >= "3.7" and python_version < "3.12" cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" -celery==5.2.7 ; python_version >= "3.7" and python_version < "3.11" -certifi==2022.12.7 ; python_version >= "3.7" and python_version < "3.11" -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.11" -charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.11" -cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.11" -circus==0.18.0 ; python_version >= "3.7" and python_version < "3.11" -click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.11" -click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.11" -click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.11" -click==8.1.3 ; python_version >= "3.7" and python_version < "3.11" -cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.11" -cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.11" -colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.11" and platform_system == "Windows" -coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.11" -cryptography==39.0.0 ; python_version >= "3.7" and python_version < "3.11" -cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.11" -cwl-utils==0.21 ; python_version >= "3.7" and python_version < "3.11" -cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.11" -decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.11" -defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11" -deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.11" -dictobj==0.4 ; python_version >= "3.7" and python_version < "3.11" -dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.11" -docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.11" -docutils==0.16 ; python_version >= "3.7" and python_version < "3.11" -ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.11" -edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.11" -email-validator==1.3.0 ; python_version >= "3.7" and python_version < "3.11" -fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.11" -fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.11" -flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.11" -frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.11" -fs==2.4.16 ; python_version >= "3.7" and python_version < "3.11" -funcsigs==1.0.2 ; python_version >= "3.7" and python_version < "3.11" -future==0.18.3 ; python_version >= "3.7" and python_version < "3.11" -galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.11" -galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.11" -gravity @ git+https://github.com/galaxyproject/gravity.git@release_1.x ; python_version >= "3.7" and python_version < "3.11" -greenlet==2.0.1 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.11" -gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.11" -gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.11" -h11==0.14.0 ; python_version >= "3.7" and python_version < "3.11" -h5py==3.7.0 ; python_version >= "3.7" and python_version < "3.11" -humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.11" -idna==3.4 ; python_version >= "3.7" and python_version < "3.11" +celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" +certifi==2022.12.7 ; python_version >= "3.7" and python_version < "3.12" +cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==2.1.1 ; python_version >= "3.7" and python_version < "3.12" +cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12" +circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12" +click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" +click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" +click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12" +click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" +cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" +cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" +coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12" +cryptography==39.0.0 ; python_version >= "3.7" and python_version < "3.12" +cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.12" +cwl-utils==0.21 ; python_version >= "3.7" and python_version < "3.12" +cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12" +decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12" +defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" +deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12" +dictobj==0.4 ; python_version >= "3.7" and python_version < "3.12" +dnspython==2.3.0 ; python_version >= "3.7" and python_version < "3.12" +docopt==0.6.2 ; python_version >= "3.7" and python_version < "3.12" +docutils==0.16 ; python_version >= "3.7" and python_version < "3.12" +ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12" +edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12" +email-validator==1.3.0 ; python_version >= "3.7" and python_version < "3.12" +fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12" +fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.12" +flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.12" +frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" +fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12" +funcsigs==1.0.2 ; python_version >= "3.7" and python_version < "3.12" +future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" +galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12" +galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12" +gravity @ git+https://github.com/galaxyproject/gravity.git@release_1.x ; python_version >= "3.7" and python_version < "3.12" +greenlet==2.0.1 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12" +gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12" +gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12" +h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" +h5py==3.8.0 ; python_version >= "3.7" and python_version < "3.12" +humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.12" +idna==3.4 ; python_version >= "3.7" and python_version < "3.12" importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.10" -importlib-resources==5.10.2 ; python_version >= "3.7" and python_version < "3.11" -isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.11" -isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.11" -jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.11" -jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.11" -jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.11" -kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.11" -lagom==2.2.0 ; python_version >= "3.7" and python_version < "3.11" -lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.11" -lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.11" -mako==1.2.4 ; python_version >= "3.7" and python_version < "3.11" -markdown-it-py==2.1.0 ; python_version >= "3.7" and python_version < "3.11" -markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.11" -markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.11" -mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.11" -mercurial==6.3.2 ; python_version >= "3.7" and python_version < "3.11" -mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.11" -mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.11" -msgpack==1.0.4 ; python_version >= "3.7" and python_version < "3.11" -multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.11" -mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.11" -networkx==2.5 ; python_version >= "3.7" and python_version < "3.11" -nodeenv==1.7.0 ; python_version >= "3.7" and python_version < "3.11" -numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.11" -oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.11" -oyaml==1.0 ; python_version >= "3.7" and python_version < "3.11" -packaging==21.3 ; python_version >= "3.7" and python_version < "3.11" -paramiko==3.0.0 ; python_version >= "3.7" and python_version < "3.11" -parse==1.19.0 ; python_version >= "3.7" and python_version < "3.11" -parsley==1.3 ; python_version >= "3.7" and python_version < "3.11" -paste==3.5.2 ; python_version >= "3.7" and python_version < "3.11" -pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.11" -pbr==5.11.1 ; python_version >= "3.7" and python_version < "3.11" -pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.11" +importlib-resources==5.10.2 ; python_version >= "3.7" and python_version < "3.12" +isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12" +isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" +jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" +jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.12" +jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.12" +kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" +lagom==2.2.0 ; python_version >= "3.7" and python_version < "3.12" +lockfile==0.12.2 ; python_version >= "3.7" and python_version < "3.12" +lxml==4.9.2 ; python_version >= "3.7" and python_version < "3.12" +mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12" +markdown-it-py==2.1.0 ; python_version >= "3.7" and python_version < "3.12" +markdown==3.4.1 ; python_version >= "3.7" and python_version < "3.12" +markupsafe==2.1.2 ; python_version >= "3.7" and python_version < "3.12" +mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12" +mercurial==6.3.2 ; python_version >= "3.7" and python_version < "3.12" +mistune==2.0.4 ; python_version >= "3.7" and python_version < "3.12" +mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12" +msgpack==1.0.4 ; python_version >= "3.7" and python_version < "3.12" +multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12" +mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.12" +networkx==2.5 ; python_version >= "3.7" and python_version < "3.12" +nodeenv==1.7.0 ; python_version >= "3.7" and python_version < "3.12" +numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" +numpy==1.24.1 ; python_version >= "3.8" and python_version < "3.12" +oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" +oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12" +packaging==21.3 ; python_version >= "3.7" and python_version < "3.12" +paramiko==3.0.0 ; python_version >= "3.7" and python_version < "3.12" +parse==1.19.0 ; python_version >= "3.7" and python_version < "3.12" +parsley==1.3 ; python_version >= "3.7" and python_version < "3.12" +paste==3.5.2 ; python_version >= "3.7" and python_version < "3.12" +pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.12" +pbr==5.11.1 ; python_version >= "3.7" and python_version < "3.12" +pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.12" pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9" -prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.11" -prov==1.5.1 ; python_version >= "3.7" and python_version < "3.11" -psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.11" -pulsar-galaxy-lib==0.15.0.dev0 ; python_version >= "3.7" and python_version < "3.11" -pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.11" -pycparser==2.21 ; python_version >= "3.7" and python_version < "3.11" -pycryptodome==3.16.0 ; python_version >= "3.7" and python_version < "3.11" -pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.11" -pydantic==1.10.4 ; python_version >= "3.7" and python_version < "3.11" -pydantic[email]==1.10.4 ; python_version >= "3.7" and python_version < "3.11" -pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.11" -pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.11" -pyfaidx==0.7.1 ; python_version >= "3.7" and python_version < "3.11" -pygments==2.14.0 ; python_version >= "3.7" and python_version < "3.11" -pyjwt==2.6.0 ; python_version >= "3.7" and python_version < "3.11" -pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.11" -pylibmagic==0.2.2 ; python_version >= "3.7" and python_version < "3.11" -pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.11" -pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.11" -pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.11" +prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.12" +prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12" +psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12" +pulsar-galaxy-lib==0.15.0.dev0 ; python_version >= "3.7" and python_version < "3.12" +pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.12" +pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" +pycryptodome==3.16.0 ; python_version >= "3.7" and python_version < "3.12" +pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12" +pydantic==1.10.4 ; python_version >= "3.7" and python_version < "3.12" +pydantic[email]==1.10.4 ; python_version >= "3.7" and python_version < "3.12" +pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.12" +pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.12" +pyfaidx==0.7.1 ; python_version >= "3.7" and python_version < "3.12" +pygments==2.14.0 ; python_version >= "3.7" and python_version < "3.12" +pyjwt==2.6.0 ; python_version >= "3.7" and python_version < "3.12" +pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12" +pylibmagic==0.2.2 ; python_version >= "3.7" and python_version < "3.12" +pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" +pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" +pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12" pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7" -pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.11" -pysam==0.20.0 ; python_version >= "3.7" and python_version < "3.11" -python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.11" -python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.11" -python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.11" -python-multipart==0.0.5 ; python_version >= "3.7" and python_version < "3.11" -python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.11" -pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.11" -pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.11" -pyzmq==25.0.0 ; python_version >= "3.7" and python_version < "3.11" -rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11" -refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.11" -repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.11" -requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.11" -requests-toolbelt==0.10.1 ; python_version >= "3.7" and python_version < "3.11" -requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.11" -requests==2.28.2 ; python_version >= "3.7" and python_version < "3.11" -rich==13.2.0 ; python_version >= "3.7" and python_version < "3.11" -rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.11" -routes==2.5.1 ; python_version >= "3.7" and python_version < "3.11" -rsa==4.9 ; python_version >= "3.7" and python_version < "3.11" +pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12" +pysam==0.20.0 ; python_version >= "3.7" and python_version < "3.12" +python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" +python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12" +python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12" +python-multipart==0.0.5 ; python_version >= "3.7" and python_version < "3.12" +python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12" +pytz==2022.7.1 ; python_version >= "3.7" and python_version < "3.12" +pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12" +pyzmq==25.0.0 ; python_version >= "3.7" and python_version < "3.12" +rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" +refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12" +repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12" +requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12" +requests-toolbelt==0.10.1 ; python_version >= "3.7" and python_version < "3.12" +requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12" +requests==2.28.2 ; python_version >= "3.7" and python_version < "3.12" +rich==13.2.0 ; python_version >= "3.7" and python_version < "3.12" +rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.12" +routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12" +rsa==4.9 ; python_version >= "3.7" and python_version < "3.12" ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" -ruamel-yaml==0.17.21 ; python_version < "3.11" and python_version >= "3.7" -schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.11" -setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11" -setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.11" -shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.11" -six==1.16.0 ; python_version >= "3.7" and python_version < "3.11" -sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.11" -social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.11" -sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.11" -sqlalchemy-migrate==0.13.0 ; python_version >= "3.7" and python_version < "3.11" -sqlalchemy==1.4.46 ; python_version >= "3.7" and python_version < "3.11" -sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.11" -sqlparse==0.4.3 ; python_version >= "3.7" and python_version < "3.11" -starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.11" -starlette==0.22.0 ; python_version >= "3.7" and python_version < "3.11" -supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.11" -svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.11" -tempita==0.5.2 ; python_version >= "3.7" and python_version < "3.11" -tenacity==8.1.0 ; python_version >= "3.7" and python_version < "3.11" -tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.11" -tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.11" -tornado==6.2 ; python_version >= "3.7" and python_version < "3.11" -tqdm==4.64.1 ; python_version >= "3.7" and python_version < "3.11" -tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.11" -tuswsgi==0.5.4 ; python_version >= "3.7" and python_version < "3.11" -typing-extensions==4.4.0 ; python_version >= "3.7" and python_version < "3.11" -tzlocal==2.1 ; python_version >= "3.7" and python_version < "3.11" -ubiquerg==0.6.2 ; python_version >= "3.7" and python_version < "3.11" -urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.11" -uvicorn==0.20.0 ; python_version >= "3.7" and python_version < "3.11" -uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.11" -vine==5.0.0 ; python_version >= "3.7" and python_version < "3.11" -wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.11" -webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.11" -webob==1.8.7 ; python_version >= "3.7" and python_version < "3.11" -whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.11" -yacman==0.8.4 ; python_version >= "3.7" and python_version < "3.11" -yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.11" +ruamel-yaml==0.17.21 ; python_version < "3.12" and python_version >= "3.7" +schema-salad==8.3.20230109181936 ; python_version >= "3.7" and python_version < "3.12" +setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12" +setuptools==66.1.1 ; python_version >= "3.7" and python_version < "3.12" +shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12" +six==1.16.0 ; python_version >= "3.7" and python_version < "3.12" +sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12" +social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.12" +sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" +sqlalchemy-migrate==0.13.0 ; python_version >= "3.7" and python_version < "3.12" +sqlalchemy==1.4.46 ; python_version >= "3.7" and python_version < "3.12" +sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12" +sqlparse==0.4.3 ; python_version >= "3.7" and python_version < "3.12" +starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12" +starlette==0.22.0 ; python_version >= "3.7" and python_version < "3.12" +supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12" +svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12" +tempita==0.5.2 ; python_version >= "3.7" and python_version < "3.12" +tenacity==8.1.0 ; python_version >= "3.7" and python_version < "3.12" +tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12" +tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.12" +tornado==6.2 ; python_version >= "3.7" and python_version < "3.12" +tqdm==4.64.1 ; python_version >= "3.7" and python_version < "3.12" +tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" +tuswsgi==0.5.4 ; python_version >= "3.7" and python_version < "3.12" +typing-extensions==4.4.0 ; python_version >= "3.7" and python_version < "3.12" +tzlocal==2.1 ; python_version >= "3.7" and python_version < "3.12" +ubiquerg==0.6.2 ; python_version >= "3.7" and python_version < "3.12" +urllib3==1.26.14 ; python_version >= "3.7" and python_version < "3.12" +uvicorn==0.20.0 ; python_version >= "3.7" and python_version < "3.12" +uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.12" +vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" +wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.12" +webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" +webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12" +whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12" +yacman==0.8.4 ; python_version >= "3.7" and python_version < "3.12" +yarl==1.8.2 ; python_version >= "3.7" and python_version < "3.12" zipp==3.11.0 ; python_version >= "3.7" and python_version < "3.10" -zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.11" +zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh index d3a351271a0..8d444070c52 100755 --- a/lib/galaxy/dependencies/update.sh +++ b/lib/galaxy/dependencies/update.sh @@ -6,10 +6,13 @@ set -e +SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11" +NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12" + this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)" usage() { - printf "Usage: %s: [-a] [pkg_spec...]\n" ${0##*/} >&2 + printf "Usage: %s: [-a] [pkg_spec...]\n" "${0##*/}" >&2 } add= @@ -23,7 +26,7 @@ do ;; esac done -shift $(($OPTIND - 1)) +shift $((OPTIND - 1)) if [ -n "$add" ] && [ $# -eq 0 ]; then printf "When adding (-a), you must provide at least one package specification.\n" >&2 @@ -42,6 +45,48 @@ else poetry add -vv --lock "$@" fi -# Update pinned requirements. -poetry export -f requirements.txt --without-hashes --output "$this_directory/pinned-requirements.txt" -poetry export --only dev -f requirements.txt --without-hashes --output "$this_directory/dev-requirements.txt" +# Update pinned requirements files. +PINNED_REQUIREMENTS_FILE=$this_directory/pinned-requirements.txt +PINNED_DEV_REQUIREMENTS_FILE=$this_directory/dev-requirements.txt +poetry export -f requirements.txt --without-hashes --output "$PINNED_REQUIREMENTS_FILE" +poetry export --only dev -f requirements.txt --without-hashes --output "$PINNED_DEV_REQUIREMENTS_FILE" + +# Fix requirements + +latest_package_version_for_python_version () { + PIP_INDEX_OUT=$(pip index versions --python-version "$2" "$1") + echo "$PIP_INDEX_OUT" | head -n 1 | sed -e 's/.* (\(.*\)).*/\1/' +} + +split_requirement () { + PACKAGE_NAME=$1 + + if ! pip index version --help >/dev/null; then + echo "pip >= 21.2.1 required for the 'index' command" + exit 1 + fi + + NEW_REQUIREMENTS= + PREVIOUS_LATEST_PACKAGE_VERSION= + for PYTHON_VERSION in $SUPPORTED_PYTHON_VERSIONS; do + LATEST_PACKAGE_VERSION=$(latest_package_version_for_python_version "$PACKAGE_NAME" "$PYTHON_VERSION") + if [ -z "$NEW_REQUIREMENTS" ]; then + NEW_REQUIREMENTS="$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\"" + elif [ "$LATEST_PACKAGE_VERSION" != "$PREVIOUS_LATEST_PACKAGE_VERSION" ]; then + NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$PYTHON_VERSION\"\n$PACKAGE_NAME==$LATEST_PACKAGE_VERSION ; python_version >= \"$PYTHON_VERSION\"" + fi + PREVIOUS_LATEST_PACKAGE_VERSION=$LATEST_PACKAGE_VERSION + done + if [ -n "$NOT_SUPPORTED_NEXT_PYTHON_VERSION" ]; then + NEW_REQUIREMENTS="$NEW_REQUIREMENTS and python_version < \"$NOT_SUPPORTED_NEXT_PYTHON_VERSION\"" + fi + + sed -i.orig -e "s/^$PACKAGE_NAME==.*/$NEW_REQUIREMENTS/" "$PINNED_REQUIREMENTS_FILE" "$PINNED_DEV_REQUIREMENTS_FILE" +} + +# For some packages there is no recent version that works on all Python versions +# supported by Galaxy, so Poetry resorts to an old version that didn't have a +# maximum Python version pin. Here we replace any such requirement with multiple +# Python-version-specific requirements. +split_requirement numpy +split_requirement scipy diff --git a/lib/galaxy/managers/folders.py b/lib/galaxy/managers/folders.py index 0796836b16c..784e0a063f1 100644 --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -37,10 +37,7 @@ from galaxy.exceptions import ( RequestParameterInvalidException, ) from galaxy.model.scoped_session import galaxy_scoped_session -from galaxy.schema.schema import ( - LibraryFolderContentsIndexQueryPayload, - LibraryFolderContentsIndexSortByEnum, -) +from galaxy.schema.schema import LibraryFolderContentsIndexQueryPayload from galaxy.security import RBACAgent from galaxy.security.idencoding import IdEncodingHelper @@ -57,17 +54,17 @@ class SecurityParams: LDDA_SORT_COLUMN_MAP = { - LibraryFolderContentsIndexSortByEnum.name: lambda ldda, dataset: ldda.name, - LibraryFolderContentsIndexSortByEnum.description: lambda ldda, dataset: ldda.message, - LibraryFolderContentsIndexSortByEnum.type: lambda ldda, dataset: ldda.extension, - LibraryFolderContentsIndexSortByEnum.size: lambda ldda, dataset: dataset.file_size, - LibraryFolderContentsIndexSortByEnum.update_time: lambda ldda, dataset: ldda.update_time, + "name": lambda ldda, dataset: ldda.name, + "description": lambda ldda, dataset: ldda.message, + "type": lambda ldda, dataset: ldda.extension, + "size": lambda ldda, dataset: dataset.file_size, + "update_time": lambda ldda, dataset: ldda.update_time, } FOLDER_SORT_COLUMN_MAP = { - LibraryFolderContentsIndexSortByEnum.name: lambda folder: folder.name, - LibraryFolderContentsIndexSortByEnum.description: lambda folder: folder.description, - LibraryFolderContentsIndexSortByEnum.update_time: lambda folder: folder.update_time, + "name": lambda folder: folder.name, + "description": lambda folder: folder.description, + "update_time": lambda folder: folder.update_time, } diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py index 658a20c3eaf..e462c3a7bc2 100644 --- a/lib/galaxy/schema/schema.py +++ b/lib/galaxy/schema/schema.py @@ -1093,11 +1093,7 @@ class ExportHistoryArchivePayload(Model): ) -class WorkflowSortByEnum(str, Enum): - create_time = "create_time" - update_time = "update_time" - name = "name" - none = None +WorkflowSortByEnum = Literal["create_time", "update_time", "name"] class WorkflowIndexQueryPayload(Model): @@ -2718,12 +2714,7 @@ class LibraryFolderCurrentPermissions(Model): ) -class LibraryFolderContentsIndexSortByEnum(str, Enum): - name = "name" - description = "description" - type = "type" - size = "size" - update_time = "update_time" +LibraryFolderContentsIndexSortByEnum = Literal["name", "description", "type", "size", "update_time"] class LibraryFolderContentsIndexQueryPayload(Model): @@ -2731,7 +2722,7 @@ class LibraryFolderContentsIndexQueryPayload(Model): offset: int = 0 search_text: Optional[str] = None include_deleted: Optional[bool] = None - order_by: LibraryFolderContentsIndexSortByEnum = LibraryFolderContentsIndexSortByEnum.name + order_by: LibraryFolderContentsIndexSortByEnum = "name" sort_desc: Optional[bool] = False diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 72674bd9832..f67c12749a8 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -54,7 +54,7 @@ IncludeDeletedQueryParam: Optional[bool] = Query( ) SortByQueryParam: LibraryFolderContentsIndexSortByEnum = Query( - default=LibraryFolderContentsIndexSortByEnum.name, + default="name", title="Sort By", description="Sort results by specified field.", ) diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index adc8796fce2..81f631c9f75 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 6b86b8dd6fe..615a6ce60eb 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 9405aff43c4..4cc99e3e3ec 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 27e9fc753dd..151c44a2479 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index e8511c90416..122fdb2083d 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 116b60e5b21..6a600a38747 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index 0f55a4adc52..c69ef01cb39 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg index e19979aceaa..516107f5088 100644 --- a/packages/meta/setup.cfg +++ b/packages/meta/setup.cfg @@ -14,6 +14,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Scientific/Engineering :: Bio-Informatics Topic :: Software Development Topic :: Software Development :: Code Generators diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 9caab3cfb17..58052a4b1ea 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 6316e72eca6..13e31e2c89d 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 74f7511f7fd..5ceca67497d 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 3836355f36a..dddffc3e7b4 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 0bac97973a7..df459991ea1 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 3c288983d1e..615d32c3fbd 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg index 9c464931d09..086d0243571 100644 --- a/packages/test_selenium/setup.cfg +++ b/packages/test_selenium/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index cf9990cf587..c042b12eeab 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 5181c6a1ad4..e82ae80c593 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 7a0ddbe6179..6c5a02f3cc1 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index b5a0b374fba..712ba80e82f 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 4959b5df6ab..9db956776d0 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/packages/webapps/setup.cfg b/packages/webapps/setup.cfg index 9971ec2182b..298304a4f16 100644 --- a/packages/webapps/setup.cfg +++ b/packages/webapps/setup.cfg @@ -13,6 +13,7 @@ classifiers = Programming Language :: Python :: 3.8 Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 + Programming Language :: Python :: 3.11 Topic :: Software Development Topic :: Software Development :: Code Generators Topic :: Software Development :: Testing diff --git a/pyproject.toml b/pyproject.toml index d8b3484a6e4..0f669a3bda8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -84,7 +84,7 @@ pykwalify = "*" pylibmagic = "*" pyparsing = "*" pysam = ">=0.20" -python = ">=3.7,<3.11" # Keep maximum version strict to appease numpy and scipy +python = ">=3.7,<3.12" # Keep maximum version strict to appease numpy and scipy python-dateutil = "*" python-magic = "*" python-multipart = "*" # required to support form parsing in FastAPI/Starlette