Implement Connectivity Strategy

.coveragerc

@@ -0,0 +1,4 @@
+[report]
+exclude_lines =
+    @abstractmethod
+    @abc.abstractmethod

.github/workflows/tests.yaml

@@ -0,0 +1,59 @@
+name: "CI"
+on:
+  # on PR to main
+  pull_request:
+    branches:
+      - main
+  # on push to main
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} python-${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version:
+          - "3.10"
+          - "3.11"
+          - "3.12"
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: stratocaster-test
+          init-shell: bash
+          cache-environment: true
+          # Since gufe the single dependency, install it without env file
+          create-args: >-
+            python=${{ matrix.python-version }}
+            gufe
+
+      - name: Install stratocaster
+        # install test dependencies
+        run: python -m pip install -e ".[test]"
+
+      - name: Environment information
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: Run tests
+        run: |
+          pytest -v src/stratocaster/tests/

.gitignore

@@ -1,2 +1,3 @@
-/stratocaster.egg-info/
-/stratocaster/__pycache__/
+/src/stratocaster/stratocaster.egg-info/
+/src/stratocaster/__pycache__/
+docs/_build/

README.md

@@ -1,5 +1,7 @@
 # stratocaster
 
+[![CI](https://github.com/OpenFreeEnergy/stratocaster/actions/workflows/tests.yaml/badge.svg)](https://github.com/OpenFreeEnergy/stratocaster/actions/workflows/tests.yaml)
+
 A library for proposing a prioritization of Transformations within AlchemicalNetworks.
 
 ## Installation

devtools/conda-envs/docs.yaml

@@ -0,0 +1,6 @@
+name: stratocaster-docs
+channels:
+  - conda-forge
+
+dependencies:
+  - python>=3.12

devtools/conda-envs/test.yaml

@@ -0,0 +1,8 @@
+name: stratocaster-test
+channels:
+  - conda-forge
+
+dependencies:
+  - python>=3.10
+
+  - gufe>=1.2.0

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

@@ -0,0 +1,3 @@
+API Reference
+=============
+

docs/conf.py

@@ -0,0 +1,27 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'stratocaster'
+copyright = '2024, Ian Kenney'
+author = 'Ian Kenney'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'ofe_sphinx_theme'
+html_static_path = ['_static']

docs/developer_guide.rst

@@ -0,0 +1,2 @@
+Developer Guide
+===============

docs/getting_started.rst

@@ -0,0 +1,31 @@
+Getting Started
+===============
+
+This guide will help you quickly get started using stratocaster.
+
+1. Installation
+~~~~~~~~~~~~~~~
+
+For installation instructions, refer to the :ref:`installation page<installation-label>`.
+
+2. Verify the installation
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Verify the installation was successful in a Python interpreter
+
+.. code:: python
+
+   import statocaster
+   print(stratocaster.__version__)
+
+3. Quick-start example
+~~~~~~~~~~~~~~~~~~~~~~
+
+TODO
+
+Other resources
+~~~~~~~~~~~~~~~
+
+- `Source code repository <https://github.com/OpenFreeEnergy/stratocaster>`_
+- `GitHub issue tracker <https://github.com/OpenFreeEnergy/stratocaster/issues>`_
+

docs/index.rst

@@ -0,0 +1,17 @@
+stratocaster
+============
+
+The stratocaster library is complimentary to gufe and provides suggestions, via Strategies, for optimally executing Transformation Protocols defined in AlchemicalNetworks.
+
+This library includes a set of Strategy implementations as well as base classes to facilitate the creation of custom Strategy implementations.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   :hidden:
+
+   installation
+   getting_started
+   user_guide
+   developer_guide
+   api

docs/installation.rst

@@ -0,0 +1,28 @@
+.. _installation-label:
+
+Installation
+============
+
+The only requirement for installing statocaster is a working installation of gufe with a version 1.2.0 or higher.
+For general use, we recommend installing from the conda-forge channel, which will also install gufe in the process.
+
+conda-forge channel
+~~~~~~~~~~~~~~~~~~~
+
+If you use conda, stratocaster can be installed through the conda-forge channel.
+
+.. code::
+
+   conda create -n statocaster-env
+   conda activate stratocaster-env
+   conda install -c conda-forge stratocaster
+
+Development version
+~~~~~~~~~~~~~~~~~~~
+
+If you want to install the latest development version of stratocaster, you can do so using pip, provided that you have a working installation of gufe (version >=1.2.0) in your environment.
+
+.. code::
+
+   pip install git+https://github.com/OpenFreeEnergy/stratocaster.git@main
+

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/user_guide.rst

@@ -0,0 +1,2 @@
+User guide
+==========

pyproject.toml

@@ -24,10 +24,16 @@ Issues = "https://github.com/OpenFreeEnergy/stratocaster/issues"
 [project.optional-dependencies]
 test = [
      "pytest",
+     "pytest-cov",
 ]
 dev = [
     "stratocaster[test]",
     "black",
+    "isort",
+]
+docs = [
+     "sphinx",
+     "ofe-sphinx-theme @ git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme.git@main",
 ]
 
 [build-system]
@@ -37,6 +43,9 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[tool.isort]
+profile = "black"
+
 [tool.versioningit]
 default-version = "1+unknown"
 

src/stratocaster/base/__init__.py

@@ -1,2 +1,2 @@
-from .strategy import Strategy, StrategyResult
 from .models import StrategySettings
+from .strategy import Strategy, StrategyResult

src/stratocaster/base/models.py

@@ -1,7 +1,6 @@
 from gufe.settings.models import SettingsBaseModel
 
 
+# TODO: docstrings
 class StrategySettings(SettingsBaseModel):
-
-    def __init__(self):
-        normalize_weights: bool = True
+    pass