diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 22c3207..89072b9 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -7,3 +7,8 @@ updates: time: "07:00" timezone: Europe/London open-pull-requests-limit: 10 + labels: + - "dependencies" + - "Technical Debt" + - "python" + diff --git a/.github/workflows/automated_release.yml b/.github/workflows/automated_release.yml index 5209834..016cec3 100644 --- a/.github/workflows/automated_release.yml +++ b/.github/workflows/automated_release.yml @@ -32,17 +32,20 @@ jobs: docker.pkg.github.com/${IMAGE_NAME}:${BRANCH_NAME} python -m pytest --no-cov -vx - - name: Set release tag + - name: Set release name # https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable - # On the develop branch this might create RELEASE_VERSION=2.4.6-987654321-develop - # On the master branch this would then only create RELEASE_VERSION=2.4.6 - run: echo "RELEASE_VERSION=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV + # On the develop branch this might create RELEASE_NAME=2.4.6-987654321-develop + # On the master branch this would then only create RELEASE_NAME=2.4.6 + run: echo "RELEASE_NAME=$(printf -- '%s%s\n' $(cat .release-version) $([ ${BRANCH_NAME} = "develop" ] && printf -- '-%s-develop' ${GITHUB_RUN_ID} || echo ""))" >> $GITHUB_ENV + + - name: Set release tag + run: echo "RELEASE_TAG=v$RELEASE_NAME" >> $GITHUB_ENV - name: Create release uses: ncipollo/release-action@v1.8.8 with: - name: ${{ env.RELEASE_VERSION }} - tag: v${{ env.RELEASE_VERSION }} + name: ${{ env.RELEASE_NAME }} + tag: ${{ env.RELEASE_TAG }} prerelease: ${{ !(github.ref == 'refs/heads/master') }} commit: ${{ github.sha }} @@ -57,14 +60,21 @@ jobs: run: >- docker tag docker.pkg.github.com/${IMAGE_NAME}:${BRANCH_NAME} - docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }} + docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }} - name: Push release tag image to registry run: >- - docker push docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_VERSION }} + docker push docker.pkg.github.com/${IMAGE_NAME}:${{ env.RELEASE_TAG }} - - name: Remove the oldest package - uses: actions/delete-package-versions@v1 - if: false + - name: Remove old releases + uses: snok/container-retention-policy@v2 with: - package-name: "${{ github.event.repository.name }}" + image-names: ${{ github.event.repository.name }}/* + cut-off: Four months ago UTC + timestamp-to-use: updated_at + account-type: org + org-name: sanger + keep-at-least: 5 + skip-tags: latest + token: ${{ secrets.REMOVE_OLD_IMAGES }} + diff --git a/.github/workflows/check_release_version.yml b/.github/workflows/check_release_version.yml index 8901979..bd49a9e 100644 --- a/.github/workflows/check_release_version.yml +++ b/.github/workflows/check_release_version.yml @@ -14,7 +14,7 @@ jobs: - name: Get specific changed files id: changed-files-specific - uses: tj-actions/changed-files@v23 + uses: tj-actions/changed-files@v41 with: files: | .release-version diff --git a/.release-version b/.release-version index 31e5c84..d0149fe 100644 --- a/.release-version +++ b/.release-version @@ -1 +1 @@ -1.3.3 +1.3.4 diff --git a/.vscode/settings.json b/.vscode/settings.json index 53c94d3..211e298 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -7,7 +7,7 @@ "python.analysis.typeCheckingMode": "basic", "[python]": { "editor.codeActionsOnSave": { - "source.organizeImports": true + "source.organizeImports": "explicit" } } } diff --git a/LICENSE b/LICENSE index f288702..f8d7d74 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,21 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. - - If the disclaimer of warranty and limitation of liability provided -above cannot be given local legal effect according to their terms, -reviewing courts shall apply local law that most closely approximates -an absolute waiver of all civil liability in connection with the -Program, unless a warranty or assumption of liability accompanies a -copy of the Program in return for a fee. - - END OF TERMS AND CONDITIONS - - How to Apply These Terms to Your New Programs - - If you develop a new program, and you want it to be of the greatest -possible use to the public, the best way to achieve this is to make it -free software which everyone can redistribute and change under these terms. - - To do so, attach the following notices to the program. It is safest -to attach them to the start of each source file to most effectively -state the exclusion of warranty; and each file should have at least -the "copyright" line and a pointer to where the full notice is found. - - - Copyright (C) - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. +MIT License + +Copyright (c) 2024 Wellcome Sanger Institute - PSD + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/Pipfile b/Pipfile index e259f04..1595c09 100644 --- a/Pipfile +++ b/Pipfile @@ -4,7 +4,7 @@ url = "https://pypi.org/simple" verify_ssl = true [dev-packages] -black = "==22.10.0" +black = "==24.3.0" coverage = {extras = ["toml"],version = "*"} flake8 = "*" flake8-bugbear = "*" @@ -13,12 +13,12 @@ pytest = "*" pytest-cov = "*" [packages] -colorlog = "~=6.7" -flask = "~=2.0" -gunicorn = "~=20.0" -python-dotenv = "~=0.21" +colorlog = "~=6.8" +flask = "~=3.0" +gunicorn = "~=21.2" +python-dotenv = "~=1.0" slackclient = "~=2.6" -markupsafe = "==2.1.1" +markupsafe = "==2.1.5" click = "~=8.0" types-flask = "*" diff --git a/Pipfile.lock b/Pipfile.lock index 1cefa3b..fa5b5d2 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "1c681d62cdca7de096a376369b85d2c75dfa9e07859e7d579914a44700880000" + "sha256": "72a694f44fc34c72fabc4940a99136e4d838eadd9d7c26146116efef5c2c0ff2" }, "pipfile-spec": 6, "requires": { @@ -18,241 +18,334 @@ "default": { "aiohttp": { "hashes": [ - "sha256:02f9a2c72fc95d59b881cf38a4b2be9381b9527f9d328771e90f72ac76f31ad8", - "sha256:059a91e88f2c00fe40aed9031b3606c3f311414f86a90d696dd982e7aec48142", - "sha256:05a3c31c6d7cd08c149e50dc7aa2568317f5844acd745621983380597f027a18", - "sha256:08c78317e950e0762c2983f4dd58dc5e6c9ff75c8a0efeae299d363d439c8e34", - "sha256:09e28f572b21642128ef31f4e8372adb6888846f32fecb288c8b0457597ba61a", - "sha256:0d2c6d8c6872df4a6ec37d2ede71eff62395b9e337b4e18efd2177de883a5033", - "sha256:16c121ba0b1ec2b44b73e3a8a171c4f999b33929cd2397124a8c7fcfc8cd9e06", - "sha256:1d90043c1882067f1bd26196d5d2db9aa6d268def3293ed5fb317e13c9413ea4", - "sha256:1e56b9cafcd6531bab5d9b2e890bb4937f4165109fe98e2b98ef0dcfcb06ee9d", - 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create_app(test_config_path: str = None) -> Flask: +def create_app(test_config_path: Optional[str] = None) -> Flask: app = Flask(__name__, instance_relative_config=False) if test_config_path is None: diff --git a/wrangler/exceptions.py b/wrangler/exceptions.py index 4e9d22b..cd5a5b2 100644 --- a/wrangler/exceptions.py +++ b/wrangler/exceptions.py @@ -1,3 +1,6 @@ +from typing import Optional + + class Error(Exception): """Base class for exceptions in this module.""" @@ -5,7 +8,7 @@ class Error(Exception): class CsvNotFoundError(Error): - def __init__(self, tube_rack_barcode: str, message: str = None): + def __init__(self, tube_rack_barcode: str, message: Optional[str] = None): """Raised when a CSV file named after a tube rack barcode is not found in the NFS. Arguments: