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python 3+ ctypes wrapper for selected function prototypes defined by IPhreeqc version 3 in IPhreeqc.h and Var.h

Project description

iphreeqc-py

A python 3+ ctypes wrapper for selected function prototypes defined by IPhreeqc version 3 in IPhreeqc.h and Var.h.

Version 0.3.1.

See "Change Log" below for recent changes.

This package is tailored to the author's preference but is made available in the event others find it useful.

The author is not affiliated with the USGS or the PHREEQC project.

Install

Option 1

pip install iphreeqc-py

Option 2

pip install git+https://github.com/stuart-nolan/iphreeqc-py.git@v0.3.1

Option 3

git clone -b 'v0.3.1' --single-branch https://github.com/stuart-nolan/iphreeqc-py.git
cd iphreeqc-py; python setup.py install

This python package intentionally does not install or come with an IPhreeqc instance. An IPhreeqc shared library must be built and installed by the user. An example IPhreeqc install is below.

Additional Documentation

See IPhreeqc.h and Var.h.

Example iphreeqc-3.7.3-15968.tar.gz install

Using Ubuntu 20.04.3 LTS with gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0:

screen # optional, start screen session
tmpDir=$(mktemp -d)
cd $tmpDir
wget https://water.usgs.gov/water-resources/software/PHREEQC/iphreeqc-3.7.3-15968.tar.gz
tar xvf ./iphreeqc-3.7.3-15968.tar.gz
cd iphreeqc*/
# configure options used by the author
./configure --libdir=${HOME}/local/lib/iphreeqc-3.7.3-15968 --includedir=${HOME}/local/include/iphreeqc-3.7.3-15968 --docdir=${HOME}/local/share/doc/iphreeqc-3.7.3-15968 CFLAGS="-g -O2 -march=native" CXXFLAGS="-g -O2 -march=native"
ncp1=$(expr $(cat /proc/cpuinfo | grep processor | wc -l) + 1)
make -j $ncp1 V=s 2>&1 | tee ipcBuild-$(date +"%Y%m%d-%H%M").log | grep -i '[^_\"a-z-]error[^_.a-z-]'
make install

Example iphreeqc-py tests

Assuming iphreeqc-py is installed and an IPhreeqc shared library has been configured, built, and installed as described above, try:

python -c "import iphreeqc; print(iphreeqc.ex1_mod(lib=\"${HOME}/local/lib/iphreeqc-3.7.3-15968/libiphreeqc.so\", database=\"${HOME}/local/share/doc/iphreeqc-3.7.3-15968/database/phreeqc.dat\"))"
python -c "from test_iphreeqc.test_ex2 import ex2; print(ex2(lib=\"${HOME}/local/lib/iphreeqc-3.7.3-15968/libiphreeqc.so\", database=\"${HOME}/local/share/doc/iphreeqc-3.7.3-15968/database/phreeqc.dat\"))"

Clean up

cd /tmp
rm -fr $tmpDir
exit # screen session

Notes

For the above examples, IPhreeqc.h and Var.h are in

${HOME}/local/include/iphreeqc-3.7.3-15968/

Last tested with iphreeqc-3.7.3-15968 and python 3.10.2 in a virtual environment on Ubuntu 20.04.3 LTS, January 2022.

References & Attribution

<https://www.usgs.gov/software/phreeqc-version-3>
    Note the files in the examples directory and content used from 
    these files elsewhere in iphreeqc-py are copied from:

    <http://water.usgs.gov/water-resources/software/PHREEQC/phreeqc-3.7.3-15968.tar.gz>

    and are distributed under the terms of the PHREEQC Public Domain
    declaration (see the "phreeqc-version-3" link above).

<https://www.phreeqpy.com/>
PhreeqPy, Python Tools for PHREEQC
Copyright 2011 Mike Mueller and contributors

<http://raviapatel.bitbucket.io/IPhreeqcPy>
IPhreeqcPy, a python wrapper for IPhreeqc
Copyright 2016 Ravi Patel

This work is derived from IPhreeqcPy.

License Notice

iphreeqc-py Copyright (C) 2020 Stuart Nolan

This program is free software: you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation, version 3.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.

License Usage Reference

<https://www.gnu.org/licenses/gpl-howto.html>

Change Log

Notable changes from 0.2.2:

  • update for iphreeqc-3.7.3-15968 release December 5, 2021
  • revert license notices from LGPL-3.0-or-later to LGPL-3.0-only
  • fix setup.py pypi license classifier

See here for specifics.

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