Support newer pyogrio, re-add cruft, fix documentation (#535)

## Overview

Supersedes #534

Changes:

* Allowed for larger int fields when writing to GeoJSON
* Ensured that JSON-serialized output does not include numpy complex
types
* Updates a few dependencies to ensure that the notebooks render
properly
* Revamped documentation

.cruft.json

@@ -0,0 +1,29 @@
+{
+  "template": "https://github.com/bird-house/cookiecutter-birdhouse",
+  "commit": "2964f01a05703d88c087bb491811d16c703307b6",
+  "skip": [],
+  "context": {
+    "cookiecutter": {
+      "full_name": "David Huard",
+      "email": "[email protected]",
+      "github_username": "Ouranosinc",
+      "project_name": "Raven",
+      "project_slug": "raven",
+      "project_repo_name": "raven",
+      "project_readthedocs_name": "pavics-raven",
+      "project_short_description": "A WPS service that offers processes related to hydrological modelling.",
+      "version": "0.17.1",
+      "open_source_license": "MIT license",
+      "http_port": "9099",
+      "use_pytest": "y",
+      "use_black": "n",
+      "create_author_file": "y",
+      "_copy_without_render": [
+        "{{cookiecutter.project_slug}}/templates/*.cfg"
+      ],
+      "__gh_slug": "Ouranosinc/raven",
+      "_template": "https://github.com/bird-house/cookiecutter-birdhouse"
+    }
+  },
+  "checkout": null
+}

.github/workflows/main.yml

@@ -81,11 +81,10 @@ jobs:
         uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0
         with:
           cache-downloads: true
-          cache-environment: false
+          cache-environment: true
           environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python-version }}
-          micromamba-version: "1.5.10-0" # pinned to avoid the breaking changes with mamba and micromamba (2.0.0).
       - name: Install RavenWPS
         run: |
           python -m pip install --no-user --editable ".[dev]"

.gitignore

@@ -1,46 +1,75 @@
-# installer
-#Makefile
-
-# Docker
-#Dockerfile
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
 # PyWPS
 custom.cfg
 .custom.cfg
 *.pid
 
+# C extensions
+*.so
+
 # Python / Extensions etc.
 *~
-*.mo
-*.so
 *.pyc
 *.pyo
-*.egg
-*.egg-info
 *.sqlite
 *.bak
 __pycache__
 
++# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+
 # Unit test / Coverage reports
+*.cover
+*.lock
+*.log
 .cache
-.pytest_cache
 .coverage
-.tox
+.coverage.*
+.hypothesis/
+.pytest_cache/
+.tox/
+coverage.xml
+coverage/
+htmlcov/
 nosetests.xml
+testdata.json
 unit_tests/testdata.json
-coverage/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
 # Raven specific
 Raven_errors.txt
 
 # R
 *.Rhistory
 
-# Eclipse / PyDev
-.project
-.pydevproject
-.settings
-
 # PyCharm
 *.idea
 
@@ -53,6 +82,10 @@ Raven_errors.txt
 # Sublime Text Editor
 *.sublime*
 
+# Translations
+*.mo
+*.pot
+
 # buildout
 bin
 develop-eggs
@@ -61,38 +94,54 @@ parts
 build
 dist
 downloads
-.installed.cfg
 .mr.developer.cfg
 bootstrap-buildout.py
 bootstrap.py
-#generated by buildout
-
-*.pid
 
-# sphinx
-#docs/Makefile
-docs/make.bat
+# Sphinx documentation
+docs/Makefile
+docs/_build/
+docs/_html/
+docs/build/
 docs/doctrees/
 docs/html/
-docs/build/
+docs/make.bat
+docs/source/modules.rst
 docs/source/output-sanitize.cfg
+docs/source/raven.*.rst
+docs/source/raven.rst
+
+# PyBuilder
+target/
 
 # External Sources
 #src/external
 src/
 
 # tests
-*.log
-*.lock
-testdata.json
 tests/*/*/processor_0
 tests/*/*/OstOutput*
 tests/*/*/*.nc
 
 # IPython
-.ipynb_checkpoints
 docs/source/notebooks/*.nc
 
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Dask worker cache
+dask-worker-space/
+
+# Scrapy stuff:
+.scrapy
+
+# pyenv
+.python-version
+
 # gcc/fortran
 *.o
 *.a
@@ -102,4 +151,37 @@ docs/source/notebooks/*.nc
 # Merge conflict
 *.orig
 
-venv
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode/
+
+# Eclipse / PyDev
+.project
+.pydevproject
+.settings

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.17.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         args: [ '--py39-plus' ]
@@ -40,7 +40,6 @@ repos:
       - id: flake8
         args: [ '--config=.flake8' ]
         additional_dependencies:
-          - "flake8-alphabetize==0.0.21"
           - "flake8-rst-docstrings==0.3.0"
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
@@ -51,9 +50,9 @@ repos:
     hooks:
       - id: nbqa-pyupgrade
         args: [ '--py39-plus' ]
-        additional_dependencies: [ 'pyupgrade==v3.15.2' ]
+        additional_dependencies: [ 'pyupgrade==v3.18.0' ]
       - id: nbqa-black
-        additional_dependencies: [ 'black==24.4.2' ]
+        additional_dependencies: [ 'black==24.10.0' ]
       - id: nbqa-isort
         additional_dependencies: [ 'isort==5.13.2' ]
   - repo: https://github.com/pycqa/pydocstyle
@@ -65,14 +64,15 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==24.4.2' ]
+        additional_dependencies: [ 'black==24.10.0' ]
+      - id: blackdoc-autoupdate-black
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.35.1
     hooks:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.3
+    rev: 0.29.4
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

.readthedocs.yml

@@ -15,7 +15,7 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
+    python: "mambaforge-22.9"
 
 formats: all
 

AUTHORS.rst

@@ -12,7 +12,7 @@ Co-Developers
 * Richard Arsenault `@richardarsenault <https://github.com/richardarsenault>`_
 * Juliane Mai <[email protected]> `@julemai <https://github.com/julemai>`_
 * Trevor James Smith <[email protected]> `@Zeitsperre <https://github.com/Zeitsperre>`_
-* Christian Jauvin <[email protected]> `@cjauvin <https://github.com/cjauvin>`_
+* Christian Jauvin `@cjauvin <https://github.com/cjauvin>`_
 
 Contributors
 ------------