diff --git a/.github/workflows/ci_codecov.yml b/.github/workflows/ci_codecov.yml
index e537b8ae..81e9fcbf 100644
--- a/.github/workflows/ci_codecov.yml
+++ b/.github/workflows/ci_codecov.yml
@@ -21,19 +21,16 @@ on:
- cron: "0 0 * * *"
jobs:
- run:
+ test:
name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
-
- env:
- OS: ${{ matrix.os }}
- python-version: "3.7"
+ python-version: ["3.11"]
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- name: Additional info about the build
shell: bash
run: |
@@ -42,7 +39,7 @@ jobs:
ulimit -a
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
architecture: x64
@@ -51,22 +48,27 @@ jobs:
shell: bash
run: |
python -m pip install --upgrade pip
+ python -m pip install -r requirements_dev.txt
+ python -m pip install -U pytest pytest-cov codecov
+
+ - name: Install package
+ shell: bash
+ run: |
python -m pip install .
# pip install tox tox-gh-actions
- python -m pip install -r requirements.txt
- python -m pip install -U pytest pytest-cov
- name: Run tests
shell: bash
run: |
- pytest --cov=./ --cov-config=.coveragerc --cov-report=xml --color=yes procrustes/test/
+ python -m pytest -c pyproject.toml --cov-config=.coveragerc --cov-report=xml --color=yes selector
- name: CodeCov
- uses: codecov/codecov-action@v3.1.0
+ uses: codecov/codecov-action@v4.5.0
with:
+ token: ${{ secrets.CODECOV_TOKEN }}
+ # Temp fix for https://github.com/codecov/codecov-action/issues/1487
+ version: v0.6.0
fail_ci_if_error: true
- directory: ./coverage/reports/
file: ./coverage.xml
- verbose: true
flags: unittests
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/.github/workflows/ci_tox.yml b/.github/workflows/ci_tox.yml
index f75230c1..7576bb06 100644
--- a/.github/workflows/ci_tox.yml
+++ b/.github/workflows/ci_tox.yml
@@ -1,30 +1,63 @@
name: CI Tox
+
on:
- push:
- # branches: [master, tox]
- pull_request:
- branches: [master]
+ # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+ # Existing codes likely still have "master" as the primary branch
+ # Both are tracked here to keep legacy and new codes working
+ push:
+ branches:
+ - "master"
+ - "main"
+ pull_request:
+ branches:
+ - "master"
+ - "main"
+ schedule:
+ # Nightly tests run on master by default:
+ # Scheduled workflows run on the latest commit on the default or base branch.
+ # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+ - cron: "0 0 * * *"
jobs:
- test:
- strategy:
- fail-fast: false
- matrix:
- os: [ubuntu-latest, macos-latest, windows-latest]
- python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+ test:
+ name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ # os: [macOS-latest, windows-latest, ubuntu-latest]
+ os: [macos-13, windows-latest, ubuntu-latest]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: Additional info about the build
+ shell: bash
+ run: |
+ uname -a
+ df -h
+ ulimit -a
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+ architecture: x64
+
+ - name: Install dependencies
+ shell: bash
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install -r requirements_dev.txt
+ # python -m pip install -U pytest pytest-cov codecov
+ python -m pytest -c pyproject.toml --cov-config=.coveragerc --cov-report=xml --color=yes procrustes
- runs-on: ${{ matrix.os }}
- steps:
- - uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- architecture: x64
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install tox tox-gh-actions
- - name: Testing with tox
- run: tox
+ - name: Install package
+ shell: bash
+ run: |
+ python -m pip install .
+ pip install tox tox-gh-actions
+ - name: Run tests
+ shell: bash
+ run: |
+ tox
diff --git a/README.md b/README.md
index 9e78cab6..74ce3ea1 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,12 @@
Procrustes
==========
-[](https://python.org/downloads)
+[](https://python.org/downloads)
[](https://opensource.org/licenses/)
[](https://github.com/theochem/procrustes/actions/workflows/ci_tox.yml)
[](https://procrustes.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/theochem/procrustes)
[](https://mybinder.org/v2/gh/theochem/procrustes/master?filepath=doc%2Fnotebooks%2F)
-[](https://lgtm.com/projects/g/theochem/procrustes/context:python)
The Procrustes library provides a set of functions for transforming a matrix to make it
as similar as possible to a target matrix. For more information, visit
@@ -55,7 +54,7 @@ first, and then:
```bash
# Create and activate myenv conda environment (optional, but recommended)
-conda create -n myenv python=3.6
+conda create -n myenv python=3.11
conda activate myenv
# Install the stable release.
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..cdca03b0
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,266 @@
+# -*- coding: utf-8 -*-
+# The Procrustes library provides a set of functions for transforming
+# a matrix to make it as similar as possible to a target matrix.
+#
+# Copyright (C) 2017-2022 The QC-Devs Community
+#
+# This file is part of Procrustes.
+#
+# Procrustes is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# Procrustes is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see
+#
+# --
+
+[project]
+name = "qc-procrustes"
+description = "Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other."
+readme = {file = 'README.md', content-type='text/markdown'}
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+authors = [
+ {name = "QC-Devs Community", email = "qcdevs@gmail.com"},
+]
+keywords = [
+ "procrustes analysis",
+ "statistical shape analysis",
+ "qudratic assignment problem",
+ "matrix transformation",
+ "generalized procrustes analysis",
+ "orthogonal procrustes problem",
+ "symmetric procrustes problem",
+ "rotational procrustes problem",
+ "permutation procrustes problem",
+ "softassign method",
+ "molecule alignment",
+ "chemical structure similarity",
+
+]
+
+classifiers = [
+ "Development Status :: 5 - Production/Stable",
+ "Environment :: Console",
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Natural Language :: English",
+ "Operating System :: MacOS",
+ "Operating System :: Microsoft :: Windows",
+ "Operating System :: Unix",
+ "Operating System :: POSIX",
+ "Operating System :: POSIX :: Linux",
+ "Programming Language :: Python",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+ "Programming Language :: Python :: 3.12",
+ "Topic :: Scientific/Engineering",
+ "Topic :: Scientific/Engineering :: Mathematics",
+ 'Topic :: Scientific/Engineering :: Physics',
+ 'Topic :: Scientific/Engineering :: Chemistry',
+ 'Intended Audience :: Science/Research',
+]
+
+dynamic = [
+ "dependencies",
+ "optional-dependencies",
+ "version",
+]
+
+[project.scripts]
+# # Command line interface entrypoint scripts
+# procrustes = "procrustes.__main__:main"
+
+[project.urls]
+homepage = "https://github.com/theochem/procrustes"
+documentation = "https://procrustes.qcdevs.org/"
+repository = "https://github.com/theochem/procrustes/"
+
+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}
+
+[tool.setuptools_scm]
+# can be empty if no extra settings are needed, presence enables setuptools-scm
+
+[tool.setuptools]
+platforms = ["Linux", "Windows", "MacOS"]
+include-package-data = true
+zip-safe = true
+
+[tool.setuptools.package-data]
+procrustes = ["*.xml"]
+
+[tool.setuptools.packages.find]
+exclude = ["*/*/tests", "tests_*", "doc", "tools/conda.recipe", "tools/conda.recipe/*"]
+
+[tool.black]
+line-length = 100
+
+[tool.isort]
+profile = "black"
+known_first_party = ["procrustes"]
+
+[tool.ruff]
+line-length = 100
+show-source = true
+# Rules: https://beta.ruff.rs/docs/rules
+# If you violate a rule, lookup the rule on the Rules page in ruff docs.
+# Many rules have links you can click with a explanation of the rule and how to fix it.
+# If there isn't a link, go to the project the rule was source from (e.g. flake8-bugbear)
+# and review it's docs for the corresponding rule.
+# If you're still confused, ask a fellow developer for assistance.
+# You can also run "ruff rule " to explain a rule on the command line, without a browser or internet access.
+select = [
+ "E", # pycodestyle
+ "F", # Pyflakes
+ "W", # Warning
+ "B", # flake8-bugbear
+ "A", # flake8-builtins
+ "C4", # flake8-comprehensions
+ "T10", # flake8-debugger
+ "EXE", # flake8-executable,
+ "ISC", # flake8-implicit-str-concat
+ "G", # flake8-logging-format
+ "PIE", # flake8-pie
+ "T20", # flake8-print
+ "PT", # flake8-pytest-style
+ "RSE", # flake8-raise
+ "RET", # flake8-return
+ "TID", # flake8-tidy-imports
+ "ARG", # flake8-unused-arguments
+ "PGH", # pygrep-hooks
+ "PLC", # Pylint Convention
+ "PLE", # Pylint Errors
+ "PLW", # Pylint Warnings
+ "RUF", # Ruff-specific rules
+
+ # ** Things to potentially enable in the future **
+ # DTZ requires all usage of datetime module to have timezone-aware
+ # objects (so have a tz argument or be explicitly UTC).
+ # "DTZ", # flake8-datetimez
+ # "PTH", # flake8-use-pathlib
+ # "SIM", # flake8-simplify
+]
+
+# Files to exclude from linting
+extend-exclude = [
+ "*.pyc",
+ "__pycache__",
+ "*.egg-info",
+ ".eggs",
+ # check point files of jupyter notebooks
+ "*.ipynb_checkpoints",
+ ".tox",
+ ".git",
+ "build",
+ "dist",
+ "docs",
+ "examples",
+ "htmlcov",
+ "notebooks",
+ ".cache",
+ "_version.py",
+]
+
+# Linting error codes to ignore
+ignore = [
+ "F403", # unable to detect undefined names from star imports
+ "F405", # undefined locals from star imports
+ "W605", # invalid escape sequence
+ "A003", # shadowing python builtins
+ "RET505", # unnecessary 'else' after 'return' statement
+ "RET504", # Unnecessary variable assignment before return statement
+ "RET507", # Unnecessary {branch} after continue statement
+ "PT011", # pytest-raises-too-broad
+ "PT012", # pytest.raises() block should contain a single simple statement
+ "PLW0603", # Using the global statement to update is discouraged
+ "PLW2901", # for loop variable overwritten by assignment target
+ "G004", # Logging statement uses f-string
+ "PIE790", # no-unnecessary-pass
+ "PIE810", # multiple-starts-ends-with
+ "PGH003", # Use specific rule codes when ignoring type issues
+ "PLC1901", # compare-to-empty-string
+]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401", "E501"]
+"procrustes/somefile.py" = ["E402", "E501"]
+"procrustes/somedir/*" = ["E501"]
+
+[tool.mypy]
+python_version = "3.11"
+follow_imports = "skip"
+ignore_missing_imports = true
+files = "procrustes"
+exclude = [
+ "doc",
+ "docs",
+ "tools/conda.recipe",
+ "tools/conda.recipe/*",
+]
+
+# Configuration for pytest
+# https://docs.pytest.org/en/latest/reference/customize.html#pyproject-toml
+[tool.pytest.ini_options]
+addopts = [
+ "--import-mode=importlib",
+ "--cache-clear",
+ "--showlocals",
+ "-v",
+ "-r a",
+ "--cov-report=term-missing",
+ "--cov=procrustes",
+]
+# directory containing the tests
+testpaths = [
+ "procrustes/tests",
+ "procrustes/test",
+]
+norecursedirs = [
+ ".vscode",
+ "__pycache__",
+ "build",
+]
+filterwarnings = [
+ "ignore::DeprecationWarning"
+]
+markers = [
+ "slow: lower-importance tests that take an excessive amount of time",
+]
+
+[tool.coverage.run]
+omit = [
+ 'procrustes/test/*',
+]
+
+[tool.vulture]
+exclude = [
+ "somedir",
+ "*somefile.py",
+]
+
+[tool.bandit]
+exclude_dirs = [
+ "procrustes/tests",
+ "procrustes/test",
+]
+skips = [
+ "B101", # Ignore assert statements
+ "B311", # Ignore pseudo-random generators
+ "B404", # Ignore subprocess import
+ "B603", # Ignore subprocess call
+ "B607", # Ignore subprocess call
+]
diff --git a/requirements_dev.txt b/requirements_dev.txt
new file mode 100644
index 00000000..a235283a
--- /dev/null
+++ b/requirements_dev.txt
@@ -0,0 +1,4 @@
+numpy>=1.19.5
+scipy>=1.5.0
+pytest>=5.4.3
+sphinx>=2.3.0
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 4ee8e7de..00000000
--- a/setup.py
+++ /dev/null
@@ -1,74 +0,0 @@
-# -*- coding: utf-8 -*-
-# The Procrustes library provides a set of functions for transforming
-# a matrix to make it as similar as possible to a target matrix.
-#
-# Copyright (C) 2017-2022 The QC-Devs Community
-#
-# This file is part of Procrustes.
-#
-# Procrustes is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 3
-# of the License, or (at your option) any later version.
-#
-# Procrustes is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, see
-#
-# --
-"""Setup and Install Script."""
-
-
-import os
-
-from setuptools import setup
-
-
-def get_version_info():
- """Read __version__ and DEV_CLASSIFIER from version.py, using exec, not import."""
- fn_version = os.path.join("procrustes", "_version.py")
- if os.path.isfile(fn_version):
- myglobals = {}
- with open(fn_version, "r") as f:
- exec(f.read(), myglobals) # pylint: disable=exec-used
- return myglobals["__version__"], myglobals["DEV_CLASSIFIER"]
- return "0.0.0.post0", "Development Status :: 2 - Pre-Alpha"
-
-
-def get_readme():
- """Load README.rst for display on PyPI."""
- with open('README.md') as fhandle:
- return fhandle.read()
-
-
-VERSION, DEV_CLASSIFIER = get_version_info()
-
-setup(
- name="qc-procrustes",
- version=VERSION,
- description="Procrustes Package",
- long_description=get_readme(),
- long_description_content_type='text/markdown',
- url="http://github.com/theochem/procrustes",
- license="GNU (Version 3)",
- author="QC-Devs Community",
- author_email="qcdevs@gmail.com",
- package_dir={"procrustes": "procrustes"},
- packages=["procrustes", "procrustes.test"],
- include_package_data=True,
- classifiers=[
- DEV_CLASSIFIER,
- 'Environment :: Console',
- 'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
- 'Operating System :: POSIX :: Linux',
- 'Programming Language :: Python :: 3',
- 'Topic :: Scientific/Engineering :: Physics',
- 'Topic :: Scientific/Engineering :: Chemistry',
- 'Intended Audience :: Science/Research',
- ],
- install_requires=["numpy>=1.19.5", "scipy>=1.5.0", "pytest>=5.4.3", "sphinx>=2.3.0"],
-)