Updated environment

Makefile

@@ -1,13 +1,59 @@
+python=./env/bin/python
+
+## Setup
 
 env:
-	conda env create -f ./environment.yml -p ./env --quiet
-	./env/bin/python -m pip install -e .
+	conda env create -f ./environment.yaml -p ./env --quiet
+	${python} -m pre_commit install
+	${python} -m pip install -e .
+
+## Development
 
-env-qml:
-	./env/bin/pip install git+https://github.com/qmlcode/qml@develop
+update-format:
+	${python} -m pre_commit autoupdate
+
+format:
+	${python} -m pre_commit run --all-files
 
 test:
-	python -m pytest -vrs tests
+	${python} -m pytest -rs ./tests
+
+test-dist:
+	${python} -m twine check dist/*
+
+types:
+	${python} -m monkeytype run $$(which ${pytest}) ./tests
+	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j${j} "${python} -m monkeytype apply {} > /dev/null && echo {}"
+
+cov:
+	${python} -m pytest --cov=${pkg} --cov-config .coveragerc --cov-report html tests
+
+compile:
+	${python} _compile.py
+
+build:
+	${python} -m build --sdist --skip-dependency-check  .
+
+upload:
+	${python} -m twine upload ./dist/*.tar.gz
+
+## Version
+
+## Github
+
+## Clean
+
+clean:
+	find ./rmsd/ -type f \
+		-name "*.so" \
+		-name "*.pyc" \
+		-name ".pyo" \
+		-delete
+	rm -rf ./rmsd/*.egg-info/
+	rm -rf *.whl
+	rm -rf ./build/ ./__pycache__/
+	rm -rf ./dist/
 
-test-cov-html:
-	python -m pytest -vrs --cov=rmsd --cov-report html tests
+clean-env:
+	rm -rf ./env/
+	rm ./.git/hooks/pre-commit

environment.yml

@@ -3,11 +3,6 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - matplotlib
-  - mypy
-  - numpy
-  - pre-commit
-  - pylint
-  - pytest
-  - pytest-cov
-  - scipy
+  - pip
+  - pip:
+    - -r requirements.txt

pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rmsd"
+dynamic = ["version"]
+authors = []
+requires-python = ">=3.9"
+readme="README.rst"
+description="Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format "
+classifiers = [
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+keywords = ["pdb", "atoms", "kabsch", "reordering", "rotation", "xyz", "rmsd"]
+dependencies=["numpy", "scipy"]
+
+[project.urls]
+Homepage = "https://github.com/charnley/rmsd"
+
+[options.packages.find]
+where="."
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = {attr = "rmsd.__version__"}

requirements.txt

@@ -1,2 +1,13 @@
 numpy
 scipy
+matplotlib
+qmllib
+mypy
+numpy
+pre-commit
+pylint
+pytest
+pytest-cov
+scipy
+build
+twine

tests/test_reorder_qml.py

@@ -6,7 +6,7 @@
 
 import rmsd as rmsdlib
 
-qml = pytest.importorskip("qmllib")
+qmllib = pytest.importorskip("qmllib")
 
 
 def test_reorder_qml() -> None: