Merge pull request #283 from nlesc-nano/toml

MAINT: General maintenance in preperation for Auto-FOX 1.0.0

.github/workflows/cff.yml

@@ -0,0 +1,19 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v3
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--validate"

.github/workflows/pypi.yml

@@ -38,7 +38,7 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           name: wheels
-          path: ./build/*
+          path: ./dist/*
 
       - name: Publish the package
         if: github.event_name == 'release'

.github/workflows/pythonpackage.yml

@@ -103,7 +103,7 @@ jobs:
                     python-version: "3.x"
 
             -   name: Install linters
-                run: pip install flake8 pydocstyle
+                run: pip install flake8 "pydocstyle[toml]>=6.1" "Flake8-pyproject>=1.0.1"
 
             -   name: Python info
                 run: |

CHANGELOG.rst

@@ -6,8 +6,8 @@ All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
 
-0.10.3
-******
+1.0.0
+*****
 * *Placeholder*.
 
 

CITATION.cff

@@ -0,0 +1,23 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+title: Auto-FOX
+abstract: A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
+authors:
+- given-names: Bas
+  family-names: van Beek
+  orcid: "https://orcid.org/0000-0003-2463-6559"
+keywords:
+ - computational-chemistry
+ - materials-science
+ - python
+ - Workflows
+ - forcefield
+ - forcefield-parameterization
+version: '0.10.2'
+date-released: "2022-08-31"
+repository-code: https://github.com/nlesc-nano/auto-FOX
+license: "GPL-3.0"
+doi: 10.5281/zenodo.3988142
+type: software

FOX/__version__.py

@@ -1,3 +1,3 @@
 """The Auto-FOX version."""
 
-__version__ = '0.10.3.dev0'
+__version__ = '1.0.0.dev0'

pyproject.toml

@@ -14,3 +14,30 @@ module = [
     "h5py.*",
 ]
 ignore_missing_imports = true
+
+[tool.pydocstyle]
+convention = "numpy"
+add_ignore = ["D401", "D103", "D102", "D105"]
+ignore_decorators = "set_docstring"
+
+[tool.flake8]
+ignore = ["E226", "E704", "E731", "W503", "W504", "E721"]
+exclude = ["FOX/examples/ ALL", "FOX/properties/*.pyi ALL"]
+max-line-length = 100
+
+[tool.pytest.ini_options]
+testpaths = "FOX tests"
+addopts = "--tb=short --cov=FOX --cov-report xml --cov-report term --cov-report html --pdbcls=IPython.terminal.debugger:TerminalPdb"
+filterwarnings = [
+    "ignore::pandas.errors.PerformanceWarning",
+    "ignore:numpy\\.ufunc size changed, may indicate binary incompatibility\\. Expected [0-9]+ from C header, got [0-9]+ from PyObject:RuntimeWarning",
+    "ignore::DeprecationWarning:numpy.distutils.*",
+    "ignore:elementwise comparison failed:FutureWarning:pandas",
+    "error::qmflows.warnings_qmflows.QMFlows_Warning",
+    "ignore:Generic keyword '_pytestfixturefunction' not implemented for package \\w:qmflows.warnings_qmflows.Key_Warning",
+]
+
+[tool.coverage.run]
+branch = true
+source = ["FOX"]
+omit = ["FOX/examples"]

setup.py

@@ -21,7 +21,7 @@
 ]
 
 tests_require_no_optional = [
-    'pytest>=5.4.0',
+    'pytest>=6.0.0',
     'pytest-cov',
 ]
 tests_require = [
@@ -77,21 +77,19 @@
         'chemistry',
         'forcefield-parameterization',
         'forcefield',
+        'python',
         'python-3',
-        'python-3.7',
-        'python-3.8',
-        'python-3.9',
-        'python-3.10',
     ],
     classifiers=[
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
         'Natural Language :: English',
         'Operating System :: Unix',
         'Operating System :: MacOS',
         'Programming Language :: Python',
         'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3 :: Only',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',