Merge branch 'main' into jandom/ci/simplify-ci-yaml

.github/workflows/ci.yaml

@@ -50,14 +50,17 @@ jobs:
           - os: ubuntu-latest
             python-version: "3.11"
             gromacs-version: "2022.4"
-          # explicitly include a few macOS runners
+          # 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. Try 2018.5 from bioconda. (2021.5 worked previously but not anymore.)
+          # 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: macOS-latest
             python-version: "3.11"
             gromacs-version: "2018.6"
+          - os: macOS-latest
+            python-version: "3.12"
+            gromacs-version: "2018.6"
 
 
     env:

AUTHORS

@@ -63,6 +63,11 @@ year of their first commit. GitHub handle is optional.
 ----
 
 - Yury Polyachenko (@polyachenkoya)
+
+2023
+----
+
+- Jinzhe Zeng (@njzjz)
 
 We gratefully acknowledge code fixes contributed by
 @quantifiedcode-bot from Quantified Code https://www.quantifiedcode.com

CHANGES

@@ -3,11 +3,13 @@
 ==============================
 
 2023-xx-xx      0.9.0
-orbeckst, jandom
+orbeckst, jandom, njzjz
 
+* officially support Python 3.12 (PR #271, issue #263)
 * removed support for legacy Python (<= 3.7) (#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)
 
 

README.rst

@@ -12,7 +12,7 @@
 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--3.11 on Linux and macOS.
+3.8--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.

ci/conda-envs/test_env.yaml

@@ -7,8 +7,9 @@ dependencies:
 - numpy>=1.0
 - pandas>=0.17
 - pocl
+- setuptools
 # dev tools
 - codecov
 - pytest 
 - pytest-cov 
-- pytest-pep8 
+- pytest-pep8 

ci/readthedocs/requirements.txt

@@ -2,4 +2,4 @@ numpy>=1.0
 matplotlib
 pandas
 numkit>=1.0
-
+setuptools; python_version >= "3.12"

doc/sphinx/source/installation.txt

@@ -70,12 +70,12 @@ If your prefer to download manually, get the latest stable release
 from https://github.com/Becksteinlab/GromacsWrapper/releases and
 either ::
 
-  pip install GromacsWrapper-0.8.3.tar.gz
+  pip install GromacsWrapper-0.8.5.tar.gz
 
 or install from the unpacked source::
 
-  tar -zxvf GromacsWrapper-0.8.3.tar.gz
-  cd GromacsWrapper-0.8.3
+  tar -zxvf GromacsWrapper-0.8.5.tar.gz
+  cd GromacsWrapper-0.8.5
   pip install .
 
 
@@ -111,7 +111,7 @@ Python_ >= 3.8 and GROMACS_ (4.6.x, 2016, 2018, 2019, 2020, 2021,
 System requirements
 -------------------
 
-Tested with Python 3.8--3.11 on Linux and Mac OS X. Earlier Python
+Tested with Python 3.8--3.12 on Linux and Mac OS X. Earlier Python
 versions were only supported until release 0.8.5.
 
 

setup.py

@@ -39,6 +39,7 @@
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Chemistry",
         "Topic :: Software Development :: Libraries :: Python Modules",
@@ -66,6 +67,7 @@
         "matplotlib",
         "numkit",  # numerical helpers
         "numpy>=1.0",
+        'setuptools; python_version >= "3.12"',  # contains 'pkg_resources' for versioneer
     ],
     tests_require=["pytest", "pandas>=0.17"],
     zip_safe=True,