Weekly release 2024-11-04

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,4 @@
+- [ ] I have read the [section on commits and pull requests](https://github.com/NaturalHistoryMuseum/ckanext-gbif/blob/main/CONTRIBUTING.md#commits-and-pull-requests) in `CONTRIBUTING.md`
+
+
+Describe your changes, tagging relevant issues where possible.

.github/workflows/bump.yml

@@ -7,12 +7,12 @@ on:
 
 jobs:
   bump-version:
-    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    name: Bump version and create changelog
     runs-on: ubuntu-latest
-    name: "Bump version and create changelog"
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
     steps:
-      - name: Check out
-        uses: actions/checkout@v3
+      - name: Checkout source code
+        uses: actions/checkout@v4
         with:
           token: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
           fetch-depth: 0

.github/workflows/pull-requests.yml

@@ -0,0 +1,27 @@
+name: Validate pull requests
+
+on:
+  pull_request:
+    types: [opened, edited, reopened, synchronize]
+
+jobs:
+  validate-commits:
+    name: Validate commit messages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v4
+      - name: Check commit message format
+        uses: webiny/[email protected]
+        with:
+          allowed-commit-types: 'feat,fix,refactor,perf,docs,style,test,build,ci,chore,new,patch,revert,ui,merge'
+  pre-commit:
+    name: Run pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+      - name: Run pre-commit
+        uses: pre-commit/[email protected]

.github/workflows/pypi-publish.yml

@@ -10,17 +10,16 @@ permissions:
 
 jobs:
   deploy:
+    name: Deploy package to PyPI
     runs-on: ubuntu-latest
     steps:
-      - name: Check out
-        uses: actions/checkout@v3
+      - name: Checkout source code
+        uses: actions/checkout@v4
         with:
           token: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v3
-        with:
-          python-version: '3.x'
+        uses: actions/setup-python@v5
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/sync.yml

@@ -7,11 +7,11 @@ on:
 
 jobs:
   sync-branches:
+    name: Sync dev and patch branches to latest commit
     runs-on: ubuntu-latest
-    name: "Sync dev and patch branches to latest commit"
     steps:
-      - name: Check out
-        uses: actions/checkout@v3
+      - name: Checkout source code
+        uses: actions/checkout@v4
         with:
           token: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
           fetch-depth: 0

.github/workflows/main.yml → .github/workflows/tests.yml

@@ -3,18 +3,18 @@ name: Tests
 on:
   push:
   workflow_dispatch:
+  pull_request:
+    types: [opened, edited, reopened, synchronize]
 
 jobs:
   test:
+    name: Run tests
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout source code
-        uses: actions/checkout@v3
-
+        uses: actions/checkout@v4
       - name: Build images
         run: docker compose build
-
       - name: Run tests
         env:
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

.pre-commit-config.yaml

@@ -1,33 +1,34 @@
 exclude: /(vendor|dist)/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
       - id: check-merge-conflict
       - id: detect-private-key
       - id: end-of-file-fixer
       - id: name-tests-test
-        args: ["--pytest-test-first"]
+        args: ['--pytest-test-first']
         exclude: ^tests/helpers/
       - id: trailing-whitespace
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v2.37.0
+    rev: v3.30.0
     hooks:
       - id: commitizen
-        additional_dependencies: ["cz-nhm"]
-  - repo: https://github.com/psf/black
-    rev: 22.10.0
+        additional_dependencies: ['cz-nhm']
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.1
     hooks:
-      - id: black
+      - id: ruff
+        args: [ '--fix', '--select', 'I', '--select', 'F401', '--fix-only' ]
+      - id: ruff-format
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.5.0
+    rev: eb1df34
     hooks:
       - id: docformatter
-        # these can't be pulled directly from the config atm, not sure why
-        args: ["-i", "--wrap-summaries=88", "--wrap-descriptions=88",
-               "--pre-summary-newline", "--make-summary-multi-line"]
+        args: [ '-i', '--config', './pyproject.toml' ]
+        additional_dependencies: ['tomli']
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         types_or: [ javascript, vue, less, sass, scss, css ]

CONTRIBUTING.md

@@ -41,7 +41,7 @@ This extension and [several others](https://github.com/search?q=topic:ckan+org:N
 
 The current core team consists of:
 - Josh ([@jrdh](https://github.com/jrdh)) - Technical Lead
-- Ginger ([@alycejenni](https://github.com/alycejenni)) - Software Engineer
+- Ginger ([@alycejenni](https://github.com/alycejenni)) - Senior Software Engineer
 
 
 ## Questions
@@ -81,7 +81,10 @@ The process is generally as follows:
 3. Make your changes, and commit often; each commit should only contain one change. See below for specifics on how to word your commits.
 4. Push your changes back to your fork.
 5. [Open a pull request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) in this repository, with the base branch set to **dev** and the compare branch set to your new branch. Provide a summary of your changes in the description.
-6. If the automatic tests fail (these may take a while), please go back to your code and try to make them pass. You may have to update the tests themselves. You don't have to close the pull request while you're doing this; it'll update as you add further commits.
+6. There are several automated checks that will run when you open the pull request. Try to make all of them pass. If you do not at least _attempt_ to make them pass, we will not merge your pull request.
+   1. Tests. Update them so that they pass, if necessary. New tests are always welcome in any pull request, but if you have added a new feature that has decreased the coverage, new tests are required.
+   2. Commit format validation. If you have not followed the conventional commits format for one or more of your commits, this will fail.
+   3. Code format validation. If you have not formatted your code correctly (using Ruff, docformatter, and/or Prettier), this will fail.
 7. Wait for feedback from one of the core maintainers. If it's been a week or so and we haven't responded, we may not have seen it. You can find other places to contact us in [SUPPORT.md](./.github/SUPPORT.md).
 
 ### Commits
@@ -142,9 +145,9 @@ cz c
 
 ##### pre-commit
 
-pre-commit is a tool that runs a variety of checks and modifications before a commit is made. You can check the [.pre-commit-config.yaml](./.pre-commit-config.yaml) file to see eaxtly what it's currently configured to do for this repository, but of particular note:
+pre-commit is a tool that runs a variety of checks and modifications before a commit is made. You can check the [.pre-commit-config.yaml](./.pre-commit-config.yaml) file to see exactly what it's currently configured to do for this repository, but of particular note:
 
-- reformats Python code with [Black](https://github.com/psf/black)
+- reformats Python code with [Ruff](https://docs.astral.sh/ruff)
 - reformats JavaScript and stylesheets with [Prettier](https://prettier.io)
 - reformats docstrings with [docformatter](https://github.com/PyCQA/docformatter)
 - checks your commit message is correcly formatted
@@ -161,15 +164,15 @@ pre-commit run
 
 Don't forget to stage any modifications that it makes! Once it runs without failing, then you can make your commit.
 
-Something to remember is that empty docstrings will cause conflicts between Black and docformatter and the checks will fail repeatedly - so don't leave your docstrings empty!
+Something to remember is that empty docstrings will cause conflicts between Ruff and docformatter and the checks will fail repeatedly - so don't leave your docstrings empty!
 
 ### Code changes and style guide
 
-We generally use external style guides and tools to help us maintain standardised code. Black and Prettier will be run with pre-commit.
+We generally use external style guides and tools to help us maintain standardised code. Ruff and Prettier will be run with pre-commit.
 
 #### Python
 
-We follow the [Black style](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html), with the notable exception that we use single quotes.
+We use [Ruff](https://docs.astral.sh/ruff) to format our code, using defaults for everything except quote style (we use single quotes).
 
 We also _mostly_ use [CKAN's style](http://docs.ckan.org/en/latest/contributing/python.html), with the following exceptions:
 - prefer `f''` strings over `.format()`
@@ -178,7 +181,7 @@ We also _mostly_ use [CKAN's style](http://docs.ckan.org/en/latest/contributing/
 
 #### JavaScript and stylesheets (CSS, LESS, etc)
 
-We use [Prettier](https://prettier.io) to format these files.
+We use [Prettier](https://prettier.io) to format these files. As with Ruff, we use defaults for everything except quote style (we use single quotes).
 
 #### Accessibility
 

README.md

@@ -1,9 +1,13 @@
 <!--header-start-->
-<img src="https://data.nhm.ac.uk/images/nhm_logo.svg" align="left" width="150px" height="100px" hspace="40"/>
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://data.nhm.ac.uk/images/nhm_logo.svg">
+  <source media="(prefers-color-scheme: light)" srcset="https://data.nhm.ac.uk/images/nhm_logo_black.svg">
+  <img alt="The Natural History Museum logo." src="https://data.nhm.ac.uk/images/nhm_logo_black.svg" align="left" width="150px" height="100px" hspace="40">
+</picture>
 
 # ckanext-gbif
 
-[![Tests](https://img.shields.io/github/actions/workflow/status/NaturalHistoryMuseum/ckanext-gbif/main.yml?style=flat-square)](https://github.com/NaturalHistoryMuseum/ckanext-gbif/actions/workflows/main.yml)
+[![Tests](https://img.shields.io/github/actions/workflow/status/NaturalHistoryMuseum/ckanext-gbif/tests.yml?style=flat-square)](https://github.com/NaturalHistoryMuseum/ckanext-gbif/actions/workflows/tests.yml)
 [![Coveralls](https://img.shields.io/coveralls/github/NaturalHistoryMuseum/ckanext-gbif/main?style=flat-square)](https://coveralls.io/github/NaturalHistoryMuseum/ckanext-gbif)
 [![CKAN](https://img.shields.io/badge/ckan-2.9.7-orange.svg?style=flat-square)](https://github.com/ckan/ckan)
 [![Python](https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8-blue.svg?style=flat-square)](https://www.python.org/)

ckanext/gbif/lib/__init__.py

@@ -9,5 +9,5 @@ def main():
     pass
 
 
-if __name__ == u'__main__':
+if __name__ == '__main__':
     main()

ckanext/gbif/lib/helpers.py

@@ -20,7 +20,7 @@ def dqi_parse_errors(errors):
     Convert each DQI status string into a more detailed dict.
 
     :param errors: a list of error names
-    :return: a list of dicts of information about each error
+    :returns: a list of dicts of information about each error
     """
     if not errors:
         return []
@@ -36,7 +36,7 @@ def dqi_get_severity(errors, gbif_id):
 
     :param errors: a list of errors
     :param gbif_id: the GBIF occurrence id for this record
-    :return: the status to show
+    :returns: the status to show
     """
     if not gbif_id:
         return 'unknown'
@@ -83,9 +83,9 @@ def gbif_get_classification(gbif_record):
 
 
 def gbif_get_geography(occurrence):
-    '''
+    """
     :param occurrence:
-    '''
+    """
     geography = []
     for geographic_part in ['continent', 'country', 'stateprovince']:
         value = occurrence.get(geographic_part, None)
@@ -113,7 +113,7 @@ def get_gbif_record_url(pkg, res, rec):
     :param pkg: the package dict
     :param res: the resource dict
     :param rec: the record dict
-    :return: the link to the GBIF view for this record/resource/package combo
+    :returns: the link to the GBIF view for this record/resource/package combo
     """
     # return the url for package/resource/record combo requested
     return toolkit.url_for(
@@ -133,7 +133,7 @@ def build_gbif_nav_item(package_name, resource_id, record_id, version=None):
     :param resource_id: the resource id
     :param record_id: the record id
     :param version: the version of the record, or None if no version is present
-    :return: a nav items
+    :returns: a nav items
     """
     kwargs = {
         'package_name': package_name,

ckanext/gbif/logic/action.py

@@ -5,7 +5,6 @@
 # Created by the Natural History Museum in London, UK
 
 import requests
-
 from ckan.plugins import toolkit
 
 
@@ -16,17 +15,17 @@ def gbif_record_show(context, data_dict):
     :param context: CKAN context
     :param data_dict: dict of parameters, only one is required: gbif_id
     """
-    gbif_id = toolkit.get_or_bust(data_dict, "gbif_id")
+    gbif_id = toolkit.get_or_bust(data_dict, 'gbif_id')
     try:
         response = requests.get(
-            f"https://api.gbif.org/v1/occurrence/{gbif_id}", timeout=5
+            f'https://api.gbif.org/v1/occurrence/{gbif_id}', timeout=5
         )
     except requests.Timeout:
-        raise toolkit.ObjectNotFound("GBIF request timed out")
+        raise toolkit.ObjectNotFound('GBIF request timed out')
     # if there was an error getting the record, raise a not found error
     if 400 <= response.status_code < 600:
         raise toolkit.ObjectNotFound(
-            f"GBIF request failed with code {response.status_code}"
+            f'GBIF request failed with code {response.status_code}'
         )
     else:
         return response.json()

ckanext/gbif/plugin.py

@@ -5,13 +5,14 @@
 # Created by the Natural History Museum in London, UK
 
 from ckan.plugins import SingletonPlugin, implements, interfaces, toolkit
+
 from ckanext.gbif import routes
 from ckanext.gbif.lib import helpers
 from ckanext.gbif.logic.action import gbif_record_show
 
 
 class GBIFPlugin(SingletonPlugin):
-    '''GBIF plugin - Data Quality Indicators'''
+    """GBIF plugin - Data Quality Indicators"""
 
     implements(interfaces.IActions, inherit=True)
     implements(interfaces.IConfigurer)

ckanext/gbif/routes/gbif.py

@@ -4,9 +4,8 @@
 # This file is part of ckanext-gbif
 # Created by the Natural History Museum in London, UK
 
-from flask import Blueprint
-
 from ckan.plugins import toolkit
+from flask import Blueprint
 
 blueprint = Blueprint(
     name='gbif',

docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3"
-
 services:
   ckan:
     build:

docs/_scripts/gen_api_pages.py

@@ -1,6 +1,5 @@
 # !/usr/bin/env python
 # encoding: utf-8
-
 """
 Generate the code reference pages and navigation.
 

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = [
 dependencies = [
     "python-dateutil",
     "requests",
-    "ckantools>=0.3.0"
+    "ckantools>=0.4.1"
 ]
 
 [project.optional-dependencies]
@@ -66,9 +66,8 @@ version_files = [
     "CITATION.cff:^version"
 ]
 
-[tool.black]
-line-length = 88
-skip_string_normalization = true
+[tool.ruff.format]
+quote-style = "single"
 
 [tool.pylint]
 max-line-length = 88