Merge pull request #190 from icenet-ai/v0.2.7_dev

V0.2.7 dev

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+exclude: (LICENSE|README.md|setup.py)
+repos:
+  # General pre-commit hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        language_version: python3
+
+  # # isort - Sorting imports
+  # - repo: https://github.com/pycqa/isort
+  #   rev: 5.12.0
+  #   hooks:
+  #     - id: isort
+  #       args: ["--filter-files"]
+
+  # yapf - is doing my head in with making modifications, so removing as it make non-pep8
+  # compliant changes
+  #- repo: https://github.com/google/yapf
+  #  rev: v0.40.2
+  #  hooks:
+  #    - id: yapf
+  #      name: "yapf"
+  #      args: ["--in-place", "--parallel"]
+  #      exclude: "docs/"
+
+  # ruff - Linting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+        args: []
+
+  - repo: local
+    hooks:
+      # Run pytest
+      - id: pytest
+        name: Run pytest
+        entry: pytest
+        language: system
+        pass_filenames: false

.ruff.toml

@@ -0,0 +1,6 @@
+line-length = 120
+
+[lint]
+select = ["E", "F"]
+ignore = ["E721"]
+exclude = ["setup.py"]

CONTRIBUTING.rst

@@ -68,30 +68,36 @@ Ready to contribute? Here's how to set up `icenet` for local development.
 
     $ mkvirtualenv icenet
     $ cd icenet/
-    $ python setup.py develop
+    $ pip install -e .
 
 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::
+5. Install development packages::
 
-    $ flake8 icenet tests
-    $ python setup.py test or pytest
-    $ tox
+    $ pip install -r requirements_dev.txt
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+6. Set up pre-commit hooks to run automatically. This will run through linting checks, formatting, and pytest. It will format new code using yapf and prevent code committing that does not pass linting or testing checks until fixed::
 
-6. Commit your changes and push your branch to GitHub::
+    $ pre-commit install
+
+7. When you're done making changes, check that your changes pass flake8 and the tests::
+
+    $ make lint
+    $ pytest
+
+8. 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.
+   Note: When committing, if pre-commit is installed, the commit might be prevented if there are problems with formatting. In this case, deal with the file(s) and commit again.
+
+9.  Submit a pull request through the GitHub website.
 
 Pull Request Guidelines
 -----------------------
@@ -112,12 +118,12 @@ TODO
 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::
+A reminder for the maintainers on how to deploy::
 
-# Update icenet/__init__.py
-$ git push
-$ git push --tags
+$ make clean
+$ make lint # Ignore black moaning at present
+$ make docs
+$ make install
+$ make release
 
-Travis will then deploy to PyPI if tests pass.
+If anything looks really wrong, abandon and fix!

HISTORY.rst

@@ -2,13 +2,14 @@
 History
 =======
 
-0.2.* (2022-11-22)
+0.2.* (2022-2024)
 ------------------
 
 * First releases to PyPI
 * Still under development but usable codebase for training and prediction
 * Use alongside icenet-pipeline and icenet-notebooks
-* Proper releases will follow >=0.2.1, otherwise alpha versioned for the mo
+* Alpha only, beta releases will follow 0.2
+* 0.2 is maintained for the sake of adoption, with 0.3 to be a beta version
 
 0.1.* (2021-2022)
 -----------------

MANIFEST.in

@@ -3,6 +3,8 @@ include CONTRIBUTING.rst
 include HISTORY.rst
 include LICENSE
 include README.md
+include requirements*.txt
+include docs/requirements.txt
 
 recursive-include tests *
 recursive-exclude * __pycache__

Makefile

@@ -86,4 +86,4 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+	pip install -e .

docs/Makefile

@@ -12,7 +12,12 @@ BUILDDIR      = _build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help html Makefile
+
+# When running "make html": Run pyreverse to generate UML diagram if outputting html docs.
+html:
+	pyreverse --output puml --output-directory ./ --project icenet ../icenet --colorized
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).