Update cookiecutter (#312)

## Overview

Changes:

* Updated the project to the latest cookiecutter
(`bc8a389e02a3e55e55dad7657671d91e2f238ed9`) via cruft
* Fixed several URLs to point to the proper targets
* Updated development status to beta
* Finch is now a bird with characteristics

## Related Issue / Discussion

This PR is in advance of a proper release on PyPI and conda-forge. 

## Additional Information

Closes #288

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/bird-house/cookiecutter-birdhouse",
-  "commit": "b6969697401008114c8e25846ae5801e7e65224d",
+  "commit": "bc8a389e02a3e55e55dad7657671d91e2f238ed9",
   "skip": [
     "finch/processes/wps_say_hello.py",
     "tests/test_wps_hello.py",
@@ -25,10 +25,13 @@
       "version": "0.11.3",
       "open_source_license": "Apache Software License 2.0",
       "http_port": "5000",
+      "use_pytest": "y",
+      "create_author_file": "y",
       "_copy_without_render": [
         "{{cookiecutter.project_slug}}/templates/*.cfg"
       ],
       "_template": "https://github.com/bird-house/cookiecutter-birdhouse"
     }
-  }
+  },
+  "checkout": null
 }

.gitignore

@@ -77,6 +77,9 @@ docs/doctrees/
 docs/html/
 docs/build/
 docs/source/output-sanitize.cfg
+docs/finch.rst
+docs/finch.*.rst
+docs/modules.rst
 
 # External Sources
 #src/external
@@ -98,3 +101,19 @@ testdata.json
 
 # Merge conflict
 *.orig
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/

CONTRIBUTING.rst

@@ -0,0 +1,121 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+Please read the Birdhouse [Developer Guide](https://birdhouse.readthedocs.io/en/latest/guide_dev.html)
+and the [Finch Documentation](https://finch.readthedocs.io/en/latest/) to get started.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/bird-house/finch/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Finch could always use more documentation, whether as part of the official Finch docs, in docstrings, or even on the web in blog posts, articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/bird-house/finch/issues.
+
+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 :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `finch` for local development.
+
+1. Fork the `finch` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/finch.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv finch
+    $ cd finch/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 finch tests
+    $ python setup.py test or pytest
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+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 3.8, 3.9, 3.10 and 3.11. Check https://travis-ci.com/bird-house/finch/pull_requests and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ pytest tests.test_finch
+
+Deploying
+---------
+
+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
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

LICENSE.txt → LICENSE

@@ -1,4 +1,20 @@
-Apache License
+Apache Software License 2.0
+
+Copyright (c) 2023, David Huard
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+                                 Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
 

MANIFEST.in

@@ -1,3 +1,4 @@
+include LICENSE
 include Makefile
 include *.txt
 include *.rst

README.rst

@@ -1,36 +1,19 @@
 Finch
-===============================
-
-.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
-   :target: http://finch.readthedocs.io/en/latest/?badge=latest
-   :alt: Documentation Status
-
-.. image:: https://github.com/bird-house/finch/actions/workflows/main.yml/badge.svg
-   :target: https://github.com/bird-house/finch/actions/workflows/main.yml
-   :alt: GitHub CI
-
-.. image:: https://img.shields.io/github/license/bird-house/finch.svg
-    :target: https://github.com/bird-house/finch/blob/master/LICENSE.txt
-    :alt: GitHub license
-
-.. image:: https://badges.gitter.im/bird-house/birdhouse.svg
-    :target: https://gitter.im/bird-house/birdhouse?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
-    :alt: Join the chat at https://gitter.im/bird-house/birdhouse
+=====
 
+|docs| |pypi| |ci| |license| |gitter|
 
 Finch (the bird)
-  *Finch is a bird ...*
+  *Finch is a bird that can adapt to many different climates and ecological niches*
 
 A Web Processing Service for Climate Indicators.
 
 Documentation
 -------------
 
-Learn more about Finch in its official documentation at
-https://finch.readthedocs.io.
+Learn more about Finch in its official documentation at: https://pavics-sdi.readthedocs.io/projects/finch
 
-Submit bug reports, questions and feature requests at
-https://github.com/bird-house/finch/issues
+Submit bug reports, questions and feature requests at: https://github.com/bird-house/finch/issues
 
 Contributing
 ------------
@@ -42,7 +25,7 @@ Please use bumpversion_ to release a new version.
 License
 -------
 
-Free software: Apache Software License 2.0
+* Free software: Apache Software License 2.0
 
 Credits
 -------
@@ -51,5 +34,24 @@ This package was created with Cookiecutter_ and the `bird-house/cookiecutter-bir
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`bird-house/cookiecutter-birdhouse`: https://github.com/bird-house/cookiecutter-birdhouse
-.. _`Developer Guide`: https://finch.readthedocs.io/en/latest/dev_guide.html
+.. _`Developer Guide`: https://pavics-sdi.readthedocs.io/projects/finch/en/latest/dev_guide.html
 .. _bumpversion: https://finch.readthedocs.io/en/latest/dev_guide.html#bump-a-new-version
+
+.. |docs| image:: https://readthedocs.org/projects/finch/badge/?version=latest
+    :target: https://pavics-sdi.readthedocs.io/projects/finch/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. |pypi| image:: https://img.shields.io/pypi/v/birdhouse-finch.svg
+        :target: https://pypi.python.org/pypi/birdhouse-finch
+
+.. |ci| image:: https://github.com/bird-house/finch/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/bird-house/finch/actions/workflows/main.yml
+   :alt: GitHub CI
+
+.. |license| image:: https://img.shields.io/github/license/bird-house/finch.svg
+    :target: https://github.com/bird-house/finch/blob/master/LICENSE.txt
+    :alt: GitHub license
+
+.. |gitter| image:: https://badges.gitter.im/bird-house/birdhouse.svg
+    :target: https://gitter.im/bird-house/birdhouse?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+    :alt: Join the chat at https://gitter.im/bird-house/birdhouse

docs/source/authors.rst

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

docs/source/conf.py

@@ -1,17 +1,11 @@
 #!/usr/bin/env python
 # noqa: D100
 #
-# finch documentation build configuration file, created by
-# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
+# finch documentation build configuration file, created by sphinx-quickstart on Fri Jun 9 13:47:02 2017.
 #
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+# This file is execfile()d with the current directory set to its containing dir.
+# Note that not all possible configuration values are present in this autogenerated file.
+# All configuration values have a default; values that are commented out serve to show the default.
 
 import os
 import sys

docs/source/index.rst

@@ -9,6 +9,7 @@
    notebooks/index
    dev_guide
    processes
+   authors
    changes
 
 Indices and tables

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - clisops >=0.9.3
   - dask
   - distributed
-  - geopandas!=0.13.1
+  - geopandas !=0.13.1
   - h5netcdf
   - netcdf4
   - numpy

requirements_dev.txt

@@ -1,21 +1,24 @@
-pytest
+pytest>=6.0
+pytest-cov
 flake8
 pytest-flake8
 ipython
 pytest-notebook
 nbsphinx
-nbval
+nbval>=0.9.6
 nbconvert
-sphinx>=1.7
-bumpversion
+sphinx>=1.8.5
+bump2version
 twine
 cruft
 jupyter_client
 # Changing dependencies above this comment will create merge conflicts when updating the cookiecutter template with cruft. Add extra requirements below this line.
 birdhouse-birdy>=0.8.1
 geojson
+jupyter-server>=2.7.2 # not directly required, pinned by Snyk to avoid a vulnerability
+lxml
 matplotlib
+owslib
+pillow>=10.0.1 # not directly required, pinned by Snyk to avoid a vulnerability
 pre-commit
 tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability
-jupyter-server>=2.7.2 # not directly required, pinned by Snyk to avoid a vulnerability
-pillow>=10.0.1 # not directly required, pinned by Snyk to avoid a vulnerability

requirements_docs.txt

@@ -2,12 +2,12 @@ birdhouse-birdy>=0.8.1
 ipython
 matplotlib
 nbsphinx
+pillow>=10.0.1 # not directly required, pinned by Snyk to avoid a vulnerability
 pywps>=4.5.1
+setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability
 sphinx>=4.0
 sphinxcontrib-bibtex
 unidecode
 xclim==0.43
-pillow>=10.0.1 # not directly required, pinned by Snyk to avoid a vulnerability
-setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability
 werkzeug>=3.0.1 # not directly required, pinned by Snyk to avoid a vulnerability
 tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability