From 6e58be3fa94c9eb857084a2dbd4cea7b8d7849f4 Mon Sep 17 00:00:00 2001
From: Christoph Knote <christoph.knote@physik.uni-muenchen.de>
Date: Wed, 16 Sep 2020 12:04:05 +0200
Subject: [PATCH] Make compatible with Python 3
---
.gitignore | 7 +++++++
CHANGES.rst | 5 +++++
boxmox/.gitignore | 4 +++-
boxmox/__init__.py | 14 +++++++-------
boxmox/data.py | 41 ++++++++++++++++++++++-------------------
boxmox/experiment.py | 6 +++---
boxmox/plotter.py | 2 +-
examples/run_tests.bash | 27 +++++++++++++++++++++++++++
setup.py | 6 ++----
9 files changed, 77 insertions(+), 35 deletions(-)
create mode 100644 .gitignore
create mode 100644 examples/run_tests.bash
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..881b75f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,7 @@
+boxmox.egg-info/dependency_links.txt
+boxmox.egg-info/entry_points.txt
+boxmox.egg-info/not-zip-safe
+boxmox.egg-info/PKG-INFO
+boxmox.egg-info/requires.txt
+boxmox.egg-info/SOURCES.txt
+boxmox.egg-info/top_level.txt
diff --git a/CHANGES.rst b/CHANGES.rst
index 83dc67b..16b0e2c 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,6 +1,11 @@
Changelog
=========
+1.1.0 (2020-09-16)
+------------------
+
+- Python 3 compatible
+
1.0.0 (2017-12-19)
------------------
diff --git a/boxmox/.gitignore b/boxmox/.gitignore
index 94d8735..3bc2d2d 100644
--- a/boxmox/.gitignore
+++ b/boxmox/.gitignore
@@ -1,2 +1,4 @@
work
-work/*
\ No newline at end of file
+work/*
+**/*.pyc
+**/__pycache__
diff --git a/boxmox/__init__.py b/boxmox/__init__.py
index d0ebe91..2a50f12 100644
--- a/boxmox/__init__.py
+++ b/boxmox/__init__.py
@@ -1,25 +1,25 @@
try:
- from _site_specific import *
+ from ._site_specific import *
except:
pass
-import _installation
+from . import _installation
-from data import InputFile, InputFileOrig, InputFile17, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
-from fluxes import FluxParser
+from .data import InputFile, InputFileOrig, InputFile17, Output, ConcentrationOutput, RatesOutput, AdjointOutput, JacobianOutput, HessianOutput
+from .fluxes import FluxParser
work_path = _installation.validate()
if work_path is None:
import warnings
warnings.warn("BOXMOX unusable - experiment execution disabled.")
else:
- from experiment import Experiment, ExperimentFromExample, ExperimentFromExistingRun, Namelist, examples, compiledMechs
+ from .experiment import Experiment, ExperimentFromExample, ExperimentFromExistingRun, Namelist, examples, compiledMechs
try:
import matplotlib
- from plotter import ExperimentPlotter
+ from .plotter import ExperimentPlotter
except:
import warnings
warnings.warn('matplotlib not found - plotting disabled.')
-import _console
\ No newline at end of file
+from . import _console
diff --git a/boxmox/data.py b/boxmox/data.py
index 8a875f8..3fd18ea 100644
--- a/boxmox/data.py
+++ b/boxmox/data.py
@@ -1,7 +1,10 @@
import os
import sys
import shutil
-import StringIO
+try:
+ from StringIO import StringIO ## for Python 2
+except ImportError:
+ from io import StringIO ## for Python 3
import csv
import numpy as np
@@ -18,7 +21,7 @@ def _mygenfromtxt2(f):
f.seek(curpos)
spamreader = csv.reader(f, skipinitialspace = True, delimiter=" ")
# twice as fast as np.genfromtxt(..., names=True)
- hdr = spamreader.next()
+ hdr = next(spamreader)
dat = []
for row in spamreader:
dat.append( tuple(map(float, row)) )
@@ -36,7 +39,7 @@ def _mygenfromtxt(f):
f.seek(curpos)
spamreader = csv.reader(f, skipinitialspace = True, delimiter=" ")
# twice as fast as np.genfromtxt(..., names=True)
- hdr = spamreader.next()
+ hdr = next(spamreader)
dat = []
for row in spamreader:
dat.append( tuple(map(float, row)) )
@@ -50,7 +53,7 @@ def InputFile(fpath=None, version=1.7):
'''
if not fpath is None:
# file format discovery: 3 lines with numbers ==> 1.7
- with open(fpath, 'rb') as f:
+ with open(fpath, 'r') as f:
one = f.readline()
two = f.readline()
tre = f.readline()
@@ -102,7 +105,7 @@ class InputFile17:
'''
Read input file from path.
'''
- with open(fpath, 'rb') as f:
+ with open(fpath, 'r') as f:
nvar = int(f.readline().replace(',', ''))
nanc = int(f.readline().replace(',', ''))
self.timeFormat = int(f.readline().replace(',', ''))
@@ -117,7 +120,7 @@ class InputFile17:
self._data = { hdr[i]: [ x[i] for x in dmp ] for i in range(ntime+nanc, len(dmp[0])) }
def __str__(self):
- f = StringIO.StringIO()
+ f = StringIO()
self.write(f)
return(f.getvalue())
@@ -170,10 +173,10 @@ class InputFile17:
#: File path of the underlying file (if it exists (yet))
self.fpath = fpath
if not self.fpath is None:
- try:
- self.read(self.fpath)
- except Exception as e:
- print("Reading input file {:s} failed: {:s}".format(self.fpath, str(e)))
+# try:
+ self.read(self.fpath)
+# except Exception as e:
+# print("Reading input file {:s} failed: {:s}".format(self.fpath, str(e)))
class InputFileOrig:
'''
@@ -205,7 +208,7 @@ class InputFileOrig:
'''
Read input file from path.
'''
- with open(fpath, 'rb') as f:
+ with open(fpath, 'r') as f:
self.nvar = int(f.readline().replace(',', ''))
self.timeFormat = int(f.readline().replace(',', ''))
dmp = _mygenfromtxt(f)
@@ -215,7 +218,7 @@ class InputFileOrig:
self._data = { x: dmp[x] for x in dmp.dtype.names }
def __str__(self):
- f = StringIO.StringIO()
+ f = StringIO()
self.write(f)
return(f.getvalue())
@@ -279,7 +282,7 @@ class Output(object):
:param File f: file object or stream where to write to, defaults to sysout.
'''
- with open(self.fpath, 'rb') as i:
+ with open(self.fpath, 'r') as i:
for line in i:
f.write(line)
@@ -321,17 +324,17 @@ class ConcentrationOutput(Output):
out = self.data
return out
def __str__(self):
- fout = StringIO.StringIO()
- with open(self.fpath, 'rb') as f:
+ fout = StringIO()
+ with open(self.fpath, 'r') as f:
fout.write(f.read())
return fout.getvalue()
def __init__(self, fpath, vars=None):
self.fpath = fpath
- with open(fpath, 'rb') as f:
+ with open(fpath, 'r') as f:
# not using mygenfromtxt as we know the file format and this is way faster...
spamreader = csv.reader(f, skipinitialspace = True, delimiter=" ")
- hdr = spamreader.next()
+ hdr = next(spamreader)
dat = []
for row in spamreader:
dat.append( tuple(map(float, row)) )
@@ -365,14 +368,14 @@ class RatesOutput(Output):
# line 2 -> 10001 10002 10003 10004 ... 20000
# line 3 -> 20001 20002 20003 20004 ... 30000
# and so on ...
- rateFormat = num_of_reacs/10000 + 1
+ rateFormat = int(num_of_reacs/10000 + 1)
for x in range( rateFormat ):
# Column names are not needed ...
_ = f.readline()
# Length :: number_of_timesteps * rateFormat:
- ratesRaw = [map(float, xline.strip().split()) for xline in f.readlines()]
+ ratesRaw = [list(map(float, xline.strip().split())) for xline in f.readlines()]
# "Unfold" the raw data:
ratesUnfold = ratesRaw[ ::rateFormat]
diff --git a/boxmox/experiment.py b/boxmox/experiment.py
index dd4e975..d785dbe 100644
--- a/boxmox/experiment.py
+++ b/boxmox/experiment.py
@@ -90,7 +90,7 @@ class Namelist:
def __init__(self, path = None):
self._namelist = None
- firstExample = examples[examples.keys()[0]]
+ firstExample = examples[list(examples.keys())[0]]
self.read(os.path.join(firstExample.path, "BOXMOX.nml"))
if not path is None:
if os.path.exists(path):
@@ -139,7 +139,7 @@ class Experiment:
versionFile = os.path.join(path, 'VERSION')
if os.path.exists(versionFile):
try:
- with open(versionFile, 'rb') as f:
+ with open(versionFile, 'r') as f:
line = f.readline().rstrip()
line = ".".join(line.split(".")[0:min(2, len(line.split(".")))])
# for development only:
@@ -230,7 +230,7 @@ class Experiment:
self.namelist.write(os.path.join(self.path, 'BOXMOX.nml'))
for type in self.input:
- with open( os.path.join(self.path, type + '.csv'), 'wb') as f:
+ with open( os.path.join(self.path, type + '.csv'), 'w') as f:
self.input[type].write(f, version=self.version)
pwd = os.getcwd()
diff --git a/boxmox/plotter.py b/boxmox/plotter.py
index ee01ac5..e57af61 100644
--- a/boxmox/plotter.py
+++ b/boxmox/plotter.py
@@ -19,7 +19,7 @@ class ExperimentPlotter:
fig, ax = plt.subplots()
- if isinstance(specs, (str, unicode)):
+ if isinstance(specs, (str)):
specs = [ specs ]
nspecs = len(specs)
diff --git a/examples/run_tests.bash b/examples/run_tests.bash
new file mode 100644
index 0000000..c540750
--- /dev/null
+++ b/examples/run_tests.bash
@@ -0,0 +1,27 @@
+export KPP_HOME=/Users/lechriso/git/boxmox/boxmox/
+export PATH="$KPP_HOME/bin:$KPP_HOME/boxmox/bin:$PATH"
+export BOXMOX_WORK_PATH=/tmp/
+
+echo " - - - - "
+echo "PYTHON 2"
+echo
+echo "simple.py"
+echo
+python2 simple.py
+echo
+echo "intermediate.py"
+echo
+python2 intermediate.py
+echo
+
+echo " - - - - "
+echo "PYTHON 3"
+echo
+echo "simple.py"
+echo
+python3 simple.py
+echo
+echo "intermediate.py"
+echo
+python3 intermediate.py
+echo
diff --git a/setup.py b/setup.py
index 3db26b4..03f5695 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@ def read(filename):
setup(name='boxmox',
description='Python wrapper for the chemical box model BOXMOX',
long_description=read('README.rst') + '\n\n' + read('INSTALL.rst') + '\n\n' + read('CHANGES.rst'),
- version='1.0.0',
+ version='1.1.0',
url='https://boxmodeling.meteo.physik.uni-muenchen.de',
author='Christoph Knote',
author_email='christoph.knote@physik.uni-muenchen.de',
@@ -22,15 +22,13 @@ setup(name='boxmox',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'Operating System :: POSIX',
- 'Programming Language :: Python :: 2 :: Only',
+ 'Programming Language :: Python',
'Topic :: Education',
'Topic :: Scientific/Engineering',
'Topic :: Utilities'
],
keywords='',
- python_requires='<3',
packages=['boxmox'],
-# install_requires=['subprocess32;python_version<"3.0"', 'numpy', 'f90nml', 'pyparsing' ],
install_requires=['numpy', 'f90nml', 'pyparsing' ],
entry_points={
'console_scripts':
--
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