Correct/Update CI

.bumpversion.cfg

@@ -15,6 +15,10 @@ tag_message =
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'
 
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
 [bumpversion:file:docs/rst/conf.py]
 search = version = release = '{current_version}'
 replace = version = release = '{new_version}'

.github/workflows/build.yml

@@ -12,13 +12,13 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - run: pip install tox

.github/workflows/docs.yml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
       with:
         python-version: "3.10"
     - run: pip install tox

.github/workflows/lint.yml

@@ -13,13 +13,13 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - run: pip install tox

.github/workflows/test.yml

@@ -12,13 +12,13 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - run: pip install tox
@@ -27,7 +27,7 @@ jobs:
       run: tox -e test
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         env_vars: OS,PYTHON
         files: ./coverage.xml

.github/workflows/version-bump-and-package.yml

@@ -13,12 +13,12 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         token: ${{ secrets.AC_GITHUB_TOKEN }}
 
     - name: Set up Python
-      uses: actions/setup-python@v2.2.2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/rst/conf.py

docs/CHANGELOG.rst

@@ -2,6 +2,10 @@
 Changelog
 =========
 
+* set `long-description` to single file
+* remove Py3.8
+* Fixing codecov upload
+* Translate ```setup.py`` into ``pyproject.toml``
 
 v0.1.24 (2023-01-27)
 ------------------------------------------

pyproject.toml

@@ -3,3 +3,97 @@
 # https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
 requires = ["setuptools>=43.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "mdacli"
+version = "0.1.24"
+description = "A command line client for MDAnalysis Analysis classes."
+authors = [
+    {name = "MDAnalysis Development Team and contributors", email = "mdanalysis@numfocus.org"},
+]
+readme = "README.rst"
+requires-python = ">=3.8"
+keywords = ["Science", "Molecular Dynamics", "MDAnalysis"]
+license = {text = "GPL-3.0-or-later"}
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: System :: Shells",
+]
+
+dependencies = [
+    "MDAnalysis>=2.1.0",
+    "threadpoolctl",
+]
+
+[project.urls]
+homepage = "https://github.com/MDAnalysis/mdacli"
+documentation = "https://mdacli.readthedocs.io/en/latest"
+repository = "https://github.com/MDAnalysis/mdacli"
+changelog = "https://github.com/MDAnalysis/mdacli/blob/main/docs/CHANGELOG.rst"
+issues = "https://github.com/MDAnalysis/mdacli/issues/"
+discord = "https://discord.com/channels/807348386012987462"
+twitter = "https://twitter.com/mdanalysis"
+blog = "https://www.mdanalysis.org/blog"
+user_group = " https://groups.google.com/g/mdnalysis-discussion"
+
+[project.scripts]
+mda = "mdacli.__main__:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.flake8]
+max_line_length = 80
+hang-closing = true
+ignore = [
+    "W293",
+    "W503",
+    "D412",
+    "D105",
+]
+docstring-convention = "numpy"
+
+[tool.isort]
+line_length = 80
+indent = 4
+multi_line_output = 8
+include_trailing_comma = true
+lines_after_imports = 2
+sections = "FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
+known_first_party = "mdacli"
+known_third_party = [
+    "MDAnalysis",
+    "hypothesis",
+    "matplotlib",
+    "numpy",
+    "pytest",
+]
+
+[tool.pytest.ini_options]
+addopts = "-p pytest_cov"
+python_files = [
+    "test_*.py",
+    "*_test.py",
+    "tests.py",
+]
+testpaths = [
+    "tests"
+]

src/mdacli/libcli.py

@@ -759,13 +759,10 @@ def init_base_argparse(name, version, description):
 
     Parameters
     ----------
-
     name : str
         Name of the cli program
-
     version : str
         Version of the cli program
-
     description : str
         Description of the cli program