fast-forward cookiecutter, update pre-commit

.codacy.yml

@@ -1,8 +1,8 @@
 ---
 engines:
- pylint:
-   enabled: true
-   python_version: 3
+  pylint:
+    enabled: true
+    python_version: 3
 exclude_paths:
   - 'tests/**'
   - 'docs/source/conf.py'

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/bird-house/cookiecutter-birdhouse.git",
-  "commit": "231d17eca6986f606d280cc25262d0153efd92c4",
+  "commit": "d25191ecc41c091d9b4a392f0ac89d70ff27db55",
   "context": {
     "cookiecutter": {
       "full_name": "Carsten Ehbrecht",
@@ -20,6 +20,7 @@
       "_copy_without_render": [
         "{{cookiecutter.project_slug}}/templates/*.cfg"
       ],
+      "__gh_slug": "roocs/rook",
       "_template": "https://github.com/bird-house/cookiecutter-birdhouse.git"
     }
   },

.gitignore

@@ -122,6 +122,9 @@ target/
 # pyenv
 .python-version
 
+# Dask worker cache
+dask-worker-space/
+
 # celery beat schedule file
 celerybeat-schedule
 

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: setup.cfg
@@ -12,7 +12,7 @@ repos:
       - id: check-yaml
       - id: debug-statements
   - repo: https://github.com/ambv/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: ["--target-version", "py39"]

.yamllint.yaml

@@ -0,0 +1,39 @@
+---
+
+rules:
+
+  brackets:
+    forbid: false
+    min-spaces-inside: 1
+    max-spaces-inside: 1
+
+  commas:
+    min-spaces-after: 1
+
+  document-start: disable
+
+  float-values:
+    require-numeral-before-decimal: true
+
+  hyphens:
+    max-spaces-after: 1
+
+  indentation:
+    indent-sequences: whatever
+    spaces: consistent
+
+  key-duplicates:
+    forbid-duplicated-merge-keys: true
+
+  line-length:
+    allow-non-breakable-words: true
+    allow-non-breakable-inline-mappings: true
+    max: 180
+    level: warning
+
+  new-lines:
+    type: unix
+
+  trailing-spaces: {}
+
+  truthy: disable

CODE_OF_CONDUCT.rst

@@ -0,0 +1,84 @@
+====================================
+Contributor Covenant Code of Conduct
+====================================
+
+Our Pledge
+----------
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to make participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Our Responsibilities
+--------------------
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Scope
+-----
+
+This Code of Conduct applies within all project spaces, and it also applies when
+an individual is representing the project or its community in public spaces.
+Examples of representing a project or community include using an official
+project e-mail address, posting via an official social media account, or acting
+as an appointed representative at an online or offline event. Representation of
+a project may be further defined and clarified by project maintainers.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant`_, version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq
+
+.. _`Contributor Covenant`: https://www.contributor-covenant.org

CONTRIBUTING.rst

@@ -51,8 +51,7 @@ If you are proposing a feature:
 
 * Explain in detail how it would work.
 * Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+* Remember that this is a volunteer-driven project, and that contributions are welcome :)
 
 Get Started!
 ------------
@@ -79,9 +78,10 @@ Ready to contribute? Here's how to set up `rook` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the
    tests, including testing other Python versions with tox::
 
-    $ flake8 rook tests
-    $ python setup.py test or pytest
-    $ tox
+    $ make lint
+    $ make test
+    Or
+    $ make test-all
 
    To get flake8 and tox, just pip install them into your virtualenv.
 
@@ -100,7 +100,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
-3. The pull request should work for Python 3.7, 3.8, 3.9, 3.10 and 3.11. Check https://github.com/roocs/rook/actions and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for all supported Python versions. Check https://github.com/roocs/rook/actions and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
@@ -117,6 +117,14 @@ A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
 Then run::
 
-    $ bump2version patch # possible: major / minor / patch
+    $ bump-my-version bump patch # possible: major / minor / patch
     $ git push
     $ git push --tags
+
+Code of Conduct
+---------------
+
+Please note that this project is released with a `Contributor Code of Conduct`_.
+By participating in this project you agree to abide by its terms.
+
+.. _`Contributor Code of Conduct`: CODE_OF_CONDUCT.rst

Makefile

@@ -101,7 +101,7 @@ clean-docs: ## remove documentation artifacts
 
 lint/flake8: ## check style with flake8
 	@echo "Running flake8 code style checks ..."
-	@bash -c 'flake8 rook tests'
+	@bash -c 'ruff check rook tests'
 
 lint: lint/flake8 ## check style
 
@@ -128,7 +128,6 @@ notebook-sanitizer: ## download notebook output sanitizer
 	@echo "Copying notebook output sanitizer ..."
 	@-bash -c "curl -L $(SANITIZE_FILE) -o $(CURDIR)/docs/source/output-sanitize.cfg --silent"
 
-
 test-notebooks: notebook-sanitizer  ## run notebook-based tests
 	@echo "Running notebook-based tests"
 	@bash -c "env WPS_URL=$(WPS_URL) pytest --nbval --rootdir tests/ --verbose $(CURDIR)/docs/source/notebooks/ --sanitize-with $(CURDIR)/docs/source/output-sanitize.cfg --ignore $(CURDIR)/docs/source/notebooks/.ipynb_checkpoints"
@@ -156,22 +155,17 @@ servedocs: docs ## compile the docs watching for changes
 	@echo "Compiling the docs and watching for changes ..."
 	@watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
-notebook-sanitizer: ## sanitize notebooks with configuration file
-	@echo "Copying notebook output sanitizer ..."
-	@-bash -c "curl -L $(SANITIZE_FILE) -o $(CURDIR)/docs/source/output-sanitize.cfg --silent"
-
-refresh-notebooks: ## refreshing all notebook outputs under docs/source/notebooks
+refresh-notebooks: notebook-sanitizer ## refreshing all notebook outputs under docs/source/notebooks
 	@echo "Refresh all notebook outputs under docs/source/notebooks"
 	@bash -c 'for nb in $(CURDIR)/docs/source/notebooks/*.ipynb; do WPS_URL="$(WPS_URL)" jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=60 --output "$$nb" "$$nb"; sed -i "s@$(WPS_URL)/outputs/@$(OUTPUT_URL)/@g" "$$nb"; done; cd $(APP_ROOT)'
 
 ## Deployment targets:
 
 dist: clean ## build source and wheel package
 	@echo "Building source and wheel package ..."
-	@python setup.py sdist
-	@python setup.py bdist_wheel
+	@python -m build --sdist
 	@bash -c 'ls -l dist/'
 
 release: dist ## upload source and wheel packages
 	@echo "Uploading source and wheel packages ..."
-	@bash -c 'twine upload dist/*'
+	@python -m flit publish dist/*

README.rst

@@ -40,7 +40,7 @@ Contributing
 
 You can find information about contributing in our `Developer Guide`_.
 
-Please use bump2version_ to release a new version.
+Please use bump-my-version_ to release a new version.
 
 Tests
 -----
@@ -61,9 +61,9 @@ Credits
 
 This package was created with Cookiecutter_ and the `bird-house/cookiecutter-birdhouse`_ project template.
 
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _Cookiecutter: https://github.com/cookiecutter/cookiecutter
 .. _`bird-house/cookiecutter-birdhouse`: https://github.com/bird-house/cookiecutter-birdhouse
 .. _`Developer Guide`: https://rook-wps.readthedocs.io/en/latest/dev_guide.html
-.. _bump2version: https://rook.readthedocs.io/en/latest/dev_guide.html#bump-a-new-version
+.. _bump-my-version: https://rook.readthedocs.io/en/latest/dev_guide.html#bump-a-new-version
 .. _daops: https://github.com/roocs/daops
 .. _locust: https://locust.io/

docs/source/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../../CHANGELOG.rst

docs/source/conf.py

@@ -63,7 +63,6 @@
     "hdf5",
     "matplotlib",
     "netCDF4",
-    "networkx",
     "numba",
     "numpy",
     "ocgis",

docs/source/index.rst

@@ -11,7 +11,7 @@
    processes
    authors
    prov
-   changes
+   changelog
 
 Indices and tables
 ==================

environment-dev.yml

@@ -0,0 +1,22 @@
+name: rook-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python >=3.9,<3.13
+  # development
+  - bump-my-version >=0.26.0
+  - coverage >=7.5.0
+  - cruft >=2.15.0
+  - flit >=3.9.0,<4.0
+  - nbsphinx >=0.9.5
+  - nbval >=0.10.0
+  - ruff >=0.5.7
+  - sphinx >=7.0.0
+  - tox >=4.18.0
+  - watchdog >=4.0.0
+  # tests
+  - pytest >=8.0.0
+  - pytest-cov >=5.0.0
+  - pytest-timeout >=2.3.1
+  - beautifulsoup4 >4.12.3

environment-docs.yml

@@ -2,9 +2,10 @@
 name: rook
 channels:
   - conda-forge
+  - defaults
 dependencies:
-  - python >=3.9,<3.10
-  - pywps >=4.5.2,<4.7
+  - python >=3.9,<3.12
+  - pywps >=4.6
   - sphinx >=7.0.0
   - nbsphinx >=0.9.5
-  - ipython >=8.13.0
+  - ipython >=8.5.0

environment.yml

@@ -1,12 +1,13 @@
 name: rook
 channels:
   - conda-forge
+  - defaults
 dependencies:
   - python >=3.9,<3.12
-  - pywps >=4.5.2,<4.7
-  - jinja2
-  - click
-  - psutil
+  - pywps >=4.6
+  - jinja2 >=3.1.4
+  - click >=8.1.7
+  - psutil >=6.0.0
   - requests
   - cftime >=1.2.1
   - xarray >=0.21,<2023.3.0 # https://github.com/pydata/xarray/issues/7794
@@ -31,7 +32,3 @@ dependencies:
   - aiohttp
   # dashboard
   - bokeh
-  # tests
-  - pytest
-  - pytest-timeout
-  - beautifulsoup4