Merge development into master

.github/workflows/publish_release.yaml

@@ -0,0 +1,20 @@
+name: Publish release
+on:
+    push:
+        tags:
+            - "v[0-9]+.[0-9]+.[0-9]+.[0-9]+"
+jobs:
+    publish-release:
+        runs-on: ubuntu-latest
+        env:
+            VERSION: ${{ github.ref_name }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v5
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv build
+            - run: uv publish -u __token__ -p ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yaml

@@ -0,0 +1,68 @@
+name: Tests
+on:
+    push:
+        branches:
+            - master
+    pull_request:
+    workflow_dispatch:
+jobs:
+    ruff:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv sync --all-extras --dev
+            - run: uv run ruff check src/ tests/ docs/source/ examples/
+    mypy:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv sync --all-extras --dev
+            - run: uv run mypy src/ tests/ docs/source/ examples/
+    ruff-format:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv sync --all-extras --dev
+            - run: uv run ruff format --check src/ tests/ docs/source/ examples/
+    pytest:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv sync --all-extras --dev
+            - run: uv run pytest
+    doctest:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v3
+              with:
+                  enable-cache: true
+            - uses: actions/setup-python@v5
+              with:
+                  python-version-file: "pyproject.toml"
+            - run: uv sync --all-extras --dev
+            - run: uv run make -C docs doctest

.gitignore

@@ -1,10 +1,3 @@
-# Marcin add-ons
-TEST.ipynb
-tests/
-pywindow/shape.py
-pywindow/graph.py
-pywindow/postprocess.py
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -94,3 +87,7 @@ ENV/
 
 # Rope project settings
 .ropeproject
+
+.pytest_cache
+.ruff_cache
+.venv

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+    os: ubuntu-lts-latest
+    tools:
+        python: "3.11"
+
+sphinx:
+    configuration: docs/source/conf.py
+
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - dev

README.rst

@@ -0,0 +1,45 @@
+:maintainers:
+  `marcinmiklitz <https://github.com/marcinmiklitz/>`_
+  `andrewtarzia <https://github.com/andrewtarzia/>`_
+:documentation: https://pywindowx.readthedocs.io/en/latest/
+
+.. figure:: docs/source/_static/pyWINDOW_logo.png
+
+Overview
+========
+
+``pywindow`` is a Python package for the analysis of structural properties of
+molecular pores (*porous organic cages*, but also *MOFs* and
+*metal-organic cages* - see examples directory).
+
+.. warning::
+  This package is currently under development and differs
+  from the published
+  `pywindow <https://github.com/andrewtarzia/pywindow>`_ but
+  should work with Python >= 3.9.
+
+Installation
+============
+
+``pywindow`` can be installed with pip:
+
+.. code-block:: bash
+
+  pip install pywindowx
+
+Developer Setup
+---------------
+
+To develop with ``pywindow``, you can clone the repo and use
+`just <https://github.com/casey/just>`_ to setup the dev environment:
+
+.. code-block:: bash
+
+  just setup
+
+How To Cite
+===========
+
+If you use ``pywindow`` please cite
+
+  https://pubs.acs.org/doi/10.1021/acs.jcim.8b00490

docs/Makefile

@@ -1,12 +1,12 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = pywindow
-SOURCEDIR     = ./source/
-BUILDDIR      = ..
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?= -W --keep-going
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help: