Merge pull request #280 from Becksteinlab/versioningit

General clean up and modernization
- fix #278
- update to using pyproject.toml only #278
- replace setup.py with full pyproject.toml
- replace versioneer with versioningit
- clean up old code in tests (setup method replace with fixtures, removed old Python 2 cruft)

supported packages
- test GROMACS 2024 (also now on macOS)

CI
- fix RTD build
- fix macOS runners (2018.6 needed to be replaced by 2024.2)

release 0.9.0
- finalized CHANGES

.github/workflows/ci.yaml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         gromacs-version: ["2023.1"]
         # Test other GROMACS versions selectively on a recent Python.
         # On macOS only test one GROMACS version and two Python versions
@@ -50,25 +50,33 @@ jobs:
           - os: ubuntu-latest
             python-version: "3.11"
             gromacs-version: "2022.4"
-          # explicitly include a few macOS runners: MUST use 2018.6:
-          # (conda-forge GROMACS >= 2021 is compiled to use rdtscp CPU instruction but these
-          # are not available in the macOS GitHub runner so we need to use a different GROMACS
-          # version. 2018.5 from bioconda works. (2021.5 worked previously but not anymore.)
-          # Locally 2023.1 was successfully tested on Intel macOS 13.5.)
+          - os: ubuntu-latest
+            python-version: "3.11"
+            gromacs-version: "2023.4"       
+          - os: ubuntu-latest
+            python-version: "3.11"
+            gromacs-version: "2024.2"
+          # explicitly include a few macOS runners; finding a version that works
+          # on the GH runners is tricky (eg some are compiled for rdtscp CPU instructions
+          # that are not available); 2018.6 (bioconda) worked for a while, but then stopped
+          # being resolved. 2024.2 (conda-forge) runs at the moment
           - os: macOS-latest
             python-version: "3.11"
-            gromacs-version: "2018.6"
+            gromacs-version: "2024.2"
           - os: macOS-latest
             python-version: "3.12"
-            gromacs-version: "2018.6"
-            
+            gromacs-version: "2024.2"
+
 
     env:
       MPLBACKEND: agg
 
 
     steps:
-    - uses: actions/checkout@v3
+    - name: git checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-tags: true
 
     - name: micromamba package and testing environment installation (Python ${{ matrix.python-version }}, GROMACS ${{ matrix.gromacs-version }})
       uses: mamba-org/setup-micromamba@v1

.gitignore

@@ -14,3 +14,6 @@ dist
 gromacs.log
 doc/sphinx/*.log
 *~
+
+# aut-generated by versioningit
+gromacs/_version.py

.readthedocs.yml

@@ -15,12 +15,12 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
 
-#### Ignored when using conda
-# python:
-#     install:
-#       - method: pip
-#         path: .
-#       - requirements: ci/readthedocs/requirements.txt
+
+# install package
+python:
+   install:
+      - method: pip
+        path: .
 
 conda:
     environment: ci/readthedocs/environment.yml

CHANGES

@@ -2,16 +2,25 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
-2023-xx-xx      0.9.0
+2024-06-15      0.9.0
 orbeckst, jandom, njzjz
 
 * officially support Python 3.12 (PR #271, issue #263)
-* removed support for legacy Python (<= 3.7) (#259)
+* supports GROMACS 2024.2 (PR #280)
+* removed support for legacy Python (<= 3.8) (#259)
 * fixed GROMACS TOP reader not reading angle parameters from topology
   file (#261)
 * fixed Python 3.12: No module named ('pkg_resources' #263)
 * fixed AttributeDict does not support hasattr (#214)
 * fixed handle KeyboardInterrupts when using MDRunner.run() (#252)
+* internally switched to pyproject.toml (#278)
+* Pending Deprecation for the gw-*.py scripts:
+
+  The gw-*.py scripts are NOT anymore installed (it's technically
+  messy with the new system #278 and requires code refactoring). They
+  will likely be DEPRECATED. See issue #279 for more details and voice
+  your opinion if you really need these scripts.
+
 
 
 2023-09-16      0.8.5

MANIFEST.in

@@ -1,5 +1,4 @@
-include   setup.py COPYING README.rst CHANGES AUTHORS
+include   COPYING README.rst CHANGES AUTHORS
 recursive-include scripts *.py
 graft     gromacs/templates/
-include versioneer.py
 include gromacs/_version.py

README.rst

@@ -11,8 +11,8 @@
 
 A primitive Python wrapper around the Gromacs_ tools. The library is
 tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x,
-2023.x (and 5.x and 2016.x should also work). It supports Python
-3.8--3.12 on Linux and macOS.
+2023.x, 2024.x (and 5.x and 2016.x should also work). It supports
+Python 3.9--3.12 on Linux and macOS.
 
 GromacsWrapper also provides a small library (cook book) of often-used
 recipes and helper functions to set up MD simulations.
@@ -22,9 +22,9 @@ available at https://gromacswrapper.readthedocs.org for recent releases.
 
 The source code is available in the `GromacsWrapper git repository`_.
 
-Please be aware that this is **beta** software that most definitely
-contains bugs. It is *your* responsibility to ensure that you are
-running simulations with sensible parameters.
+Please be aware that this software is only minimally maintained and it
+most definitely contains bugs. It is *your* responsibility to ensure
+that you are running simulations with sensible parameters.
 
 .. _Gromacs: http://www.gromacs.org
 .. _Documentation: 
@@ -165,7 +165,7 @@ your own development::
 Questions
 =========
 
-Please ask questions in the `Issue Tracker`_ (instead of private email).
+Please ask questions in the `Discussion forum`_ (instead of private email).
 
 
 Reporting Bugs and Contributing to GromacsWrapper

doc/sphinx/source/index.txt

@@ -19,7 +19,7 @@ errors are logged to a file so that there exists a complete history of
 what has been done.
 
 GROMACS_ versions 4.6.x, 2016.x, 2018.x, 2019.x, 2020.x, 2021.x,
-2022.x, and 2023.x are all supported. GromacsWrapper detects your
+2022.x, 2023.x, 2024.x are all supported. GromacsWrapper detects your
 Gromacs tools and provides them as :func:`gromacs.grompp`,
 :func:`gromacs.mdrun`, etc, regardless of your Gromacs version, which
 allows one to write scripts that are broadly Gromacs-version

doc/sphinx/source/installation.txt

@@ -14,7 +14,6 @@ these instructions. Ask for help in the `discussions`_ forum.
 .. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues
 .. _discussions:
    https://github.com/Becksteinlab/GromacsWrapper/discussions
-.. _setuptools: https://pypi.org/project/setuptools/
 
 
 ``pip`` installation
@@ -70,12 +69,12 @@ If your prefer to download manually, get the latest stable release
 from https://github.com/Becksteinlab/GromacsWrapper/releases and
 either ::
 
-  pip install GromacsWrapper-0.8.5.tar.gz
+  pip install GromacsWrapper-0.9.0.tar.gz
 
 or install from the unpacked source::
 
-  tar -zxvf GromacsWrapper-0.8.5.tar.gz
-  cd GromacsWrapper-0.8.5
+  tar -zxvf GromacsWrapper-0.9.0.tar.gz
+  cd GromacsWrapper-0.9.0
   pip install .
 
 
@@ -102,16 +101,16 @@ formatting so please install black_ and run it on your code.
 Requirements
 ============
 
-Python_ >= 3.8 and GROMACS_ (4.6.x, 2016, 2018, 2019, 2020, 2021,
-2022, 2023) must be installed.
+Python_ >= 3.9 and GROMACS_ (4.6.x, 2016, 2018, 2019, 2020, 2021,
+2022, 2023, 2024) must be installed.
 
 .. _Python: http://www.python.org
 
 
 System requirements
 -------------------
 
-Tested with Python 3.8--3.12 on Linux and Mac OS X. Earlier Python
+Tested with Python 3.9--3.12 on Linux and Mac OS X. Earlier Python
 versions were only supported until release 0.8.5.
 
 

gromacs/__init__.py

@@ -193,7 +193,8 @@
 #: the commit ID encoded in the trailing string.
 #:
 #: .. _`semantic versioning`: https://semver.org/
-__version__ = _version.get_versions()["version"]
+__version__ = _version.__version__
+del _version
 
 from . import fileformats
 from .exceptions import (