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* Fixed syntax errors in checking for max python version (#208) * Fixed syntax errors in checking for max python version * Switch OS specification to absolute versions and reduce places where those are specified * Update Windows config to Visual Studio 17 2022 * skip ci -- Updated releases.rst with update info * [skip ci] Added release note Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Change OS specification in build workflow (#210) * Switch OS specification to absolute versions and reduce places where those are specified * Update Windows config to Visual Studio 17 2022 * skip ci -- Updated releases.rst with update info Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> Co-authored-by: Darren Curtis <Darren.Curtis@pnnl.gov> * Nsoblath/issue 212 (#217) * Turn off debugging steps * Only install python in Windows for "Test Usage" job, as we'll be statically linking Python in Mac and Linux. * Search for static python libs in linux and mac when doing a static build * Turn on tmate to check library linking * Find threads explicitly * Tmate only on failure * Verbose build for debugging * Added two more missing libraries: libdl and libutil * Enable tmate for the mac use-test job * Test with Python 3.10 * Test with Python 3.10 revealed we needed libintl. So that's added now. Should be mac-specific * Can't include_directories() on an empty variable * Typo fix * Find Iconv * Add linking of APBS to CoreFoundation framework under macOS * Remove debugging * Removing some of the debugging tools used in testing the build. * Switch back to the standard build with Python 3.9 * Removed last tmate debugging * [skip ci] Document changes Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Nsoblath/issue 222 (#223) * First committed version of Dockerfile.centos * Add alt config workflow * Alt config build: test docker builds * In Dockerfile, specify APBS_STATIC_BUILD instead of BUILD_SHARED_LIBS * Missing backslash found * Fixing bugs in both Dockerfiles * Dockerfile bug fixing * Complete missing pieces of ensuring a position-independent-code build * Minor fixes * Switch to a shared-library build in the Ubuntu Docker build * Rename Dockerfile --> Dockerfile.ubuntu * Override APBS_STATIC_BUILD when needed Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Remove all mention of ENABLE_FETK (#225) Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Nsoblath/issue 226: FETK update (#227) * Address missing linkages * Cleanup FETK import * Multithreaded build in docker now controlled by a build argument * Install superlu as a dependency in the Ubuntu docker build * Update the FETK version in use by the automatic builds (still on a development branch) * Add in debugging tmate session for mac * Manually build arpack to get the static lib (which seems to have disappeared?) * Remove -j flags * Set fortran compiler for arpack build * Engaging brain, fixing mac-build commands * Comment out tmate session * Update the FETK commit to be the main branch, pre-release * Update the changelog * Updated default FETK build to commit v1.9.3 (57195e) Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Nsoblath/new issue 207: Addressing python version test (#229) * Fix python test max-version test in apbs/CMakeLists.txt * Turn on the alternate non-docker builds, with updates from the main build * Fixing the python max version test in apbs/tests/CMakeLists.txt * Fixing the python max version test in apbs/tools/python/CMakeLists.txt * Test commit: remove python-max-version definition * Simplify the Python search by looking for an exact version * Add a default PYTHON_VERSION * Adapt the various files involved in building APBS to the new Python version setup * Didn't setup the python version correctly in the GHA builds Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Updated installation documentation (#231) Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> * Updated license, version, and release info for pending release Co-authored-by: Noah Oblath <noah.oblath@pnnl.gov> Co-authored-by: Darren Curtis <Darren.Curtis@pnnl.gov>
README for tools/Python directory
---------------------------------
Author: Todd Dolinsky (todd@ccb.wustl.edu)
Date: 9/12/2005
This directory contains Python wrappers for APBS.
Files:
apbslib.i - SWIG interface file
apbslib.c - SWIG generated C file
apbslib.py - SWIG generated Python file containing wrappers
for the APBS functions defined in routines.c
_apbslib.so - Generated shared object file
NOTE: This file used to be called apbslibc.so in APBS
0.3.2 and below.
main.py - Driver file for APBS code; mimics main.c
noinput.py - Example driver file for APBS code that does not need
PQR/.in input files - all input is handled at the Python
level
apbs.in - Example APBS input file for Born Ion example
To run the Python-wrapper version of APBS, make sure you have a working
version of Python installed. By default, the wrappers are compiled during the
initial configure process if Python is detected on the system.* Type
python main.py <input file> or
python noinput.py
to run APBS on an input file in Python. The input file must be the same
format as the standard APBS input files - see documentation for formatting.
* The main configure script needs additional libraries to compile correctly,
and thus may not work on all systems. Current status:
Linux - Working
Mac G5 - Working
Irix/SGI - Untested
Sun/Solaris - Untested
Mingw - Working, but users will need to copy the resulting
_apbslib.so.exe to _apbslib.dll:
cd /path/to/apbs/tools/python
cp _apbslib.so.exe _apbslib.dll
cp vgrid/_vgrid.so.exe vgrid/_vgrid.dll
Cygwin - No support (by default, the directory is not compiled)