Merge pull request #18 from anergictcell/refactor/pyproject

Use pyproject.toml and HPO version update

.github/workflows/create_release.yaml

@@ -5,7 +5,7 @@ on:
     tags:
       - "v*"
 
-name: Upload Release Asset
+name: Release on PyPI
 
 jobs:
   build:

.github/workflows/test_coverage.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Complete unit, integration tests and test coverage measurement
+name: Full Tests
 
 on:
   push:
@@ -35,3 +35,7 @@ jobs:
     - name: Unittesting (complete-check)
       run: |
         coverage run -m unittest discover complete-check -s tests && coverage report
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_python_versions.yaml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Basic Unittesting all Python versions
+name: Unittesting all Python versions
 
 on:
   pull_request:

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Changelog
 =========
 
+3.2.3
+-----
+Data update to 2023-07-21
+Migrate documentations to ReadTheDocs
+Transfer repository ownership back to ``anergictcell``.
+
 3.2.0
 -----
 Update Pydantic dependency to 2.0

Makefile

@@ -7,11 +7,13 @@ fulltests:
 	python -m unittest discover complete-check -s tests
 
 check:
-	@echo "Checking flake8"
-	flake8 pyhpo
+	@echo "Checking black linting"
+	black --check .
+	@echo "Checking ruff"
+	ruff .
 	@echo "Checking mypy standard"
 	mypy pyhpo
-	@echo "Checking mypy more stict"
+	@echo "Checking mypy more strict"
 	mypy --disallow-untyped-calls --disallow-untyped-defs --disallow-incomplete-defs --warn-redundant-casts --warn-unreachable pyhpo
 
 docs:

README.rst

@@ -1,3 +1,16 @@
+.. image:: https://codecov.io/gh/anergictcell/pyhpo/branch/master/graph/badge.svg?token=33ZGNQD61W 
+    :target: https://codecov.io/gh/anergictcell/pyhpo
+
+.. image:: https://github.com/anergictcell/pyhpo/actions/workflows/test_coverage.yml/badge.svg
+    :target: https://github.com/anergictcell/pyhpo/actions/workflows/test_coverage.yml/
+
+.. image:: https://img.shields.io/pypi/dm/pyhpo.svg?label=Pypi%20downloads
+    :target: https://pypi.org/project/pyhpo/
+
+.. image:: https://img.shields.io/pypi/v/pyhpo?label=Latest%20Release
+    :target: https://pypi.org/project/pyhpo/#history
+
+
 *****
 PyHPO
 *****
@@ -27,6 +40,9 @@ Internally the ontology is represented as a branched linked list, every term con
 
 It provides an interface to create ``Pandas Dataframe`` from its data, allowing integration in already existing data anlysis tools.
 
+.. hint::
+
+    Check out `hpo3 <https://pypi.org/project/hpo3/>`_ (`Documentation <https://hpo3.readthedocs.io/en/stable/>`_) for an alternative implementation. ``hpo3`` has the exact same functionality, but is much faster 🚀 and supports multithreading for even faster large data processing.
 
 Getting started
 ===============
@@ -37,26 +53,36 @@ The easiest way to install **PyHPO** is via pip
 
     pip install pyhpo
 
-or, you can additionally install optional packages for extra functionality
+This will install a base version of **PyHPO** that offers most functionality.
+
+.. note::
+
+    Some features of PyHPO require ``pandas`` and ``scipy``. The standard installation via pip will not include pandas or scipy and PyHPO will work just fine. (You will get a warning on the initial import though).
+
+    Without installing ``pandas``, you won't be able to export the Ontology as a ``Dataframe``, everything else will work fine.
+
+    Without installing ``scipy``, you won't be able to use the ``stats`` module, especially the enrichment calculations.
+
+
+If you want to do enrichment analysis, you must also install ``scipy``.
 
 .. code:: bash
 
-    # Include pandas during install
-    pip install pyhpo[pandas]
+    pip install 'pyhpo[scipy]'
 
-    # Include scipy
-    pip install pyhpo[scipy]
+If you want to work with **PyHPO** using ``pandas`` dataframes, you can install the ``pandas`` dependency
 
-    # Include all dependencies
-    pip install pyhpo[all]
+.. code:: bash
 
-.. note::
+    pip install 'pyhpo[pandas]'
 
-    Some features of PyHPO require ``pandas`` and ``scipy``. The standard installation via pip will not include pandas or scipy and PyHPO will work just fine. (You will get a warning on the initial import though).
+Or simply install both together:
 
-    Without installing ``pandas``, you won't be able to export the Ontology as a ``Dataframe``, everything else will work fine.
+.. code:: bash
+
+    # Include all dependencies
+    pip install 'pyhpo[all]'
 
-    Without installing ``scipy``, you won't be able to use the ``stats`` module, especially the enrichment calculations.
 
 
 Usage example

RELEASE_CHECKLIST.md

@@ -0,0 +1,19 @@
+# Release checklist
+
+Before creating a new release, follow all the below steps:
+
+- [ ] Create release branch from master
+- [ ] Merge all feature branches into release branch
+- [ ] Check if new HPO version is available
+- [ ] Run all checks `make check`
+- [ ] Run full test suite `make fulltests`
+- [ ] Check test coverage `make coverage`
+- [ ] Decide which type of version bump is required (master, minor, path)
+- [ ] Update version in `pyhpo.__init__`
+- [ ] Update `CHANGELOG.rst`
+- [ ] Create new documentation
+- [ ] Create version bump commit
+- [ ] Push commit
+- [ ] Crate version tag, push tag
+- [ ] Merge into master
+