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working but needs to be cleaned up
1 parent 58981c2 commit 29398cf

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-90
lines changed

Diff for: ‎MANIFEST.in

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
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recursive-include data *
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recursive-include out/NR_files/ *.dat
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recursive-include lib/ pygfunc.f90
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recursive-include lib/ pygfunc.pyf
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recursive-include lib/ *.f90
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recursive-include work/ *
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recursive-include DOCUMENTATION/ *

Diff for: ‎Makefile

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Original file line numberDiff line numberDiff line change
@@ -8,21 +8,18 @@ install:
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sudo python2 setup.py install
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.PHONY: phantom
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phantom: lib/pygfunc.c
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python setup.py build_ext --inplace
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phantom: lib/pygfunc.pyf
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lib/pygfunc.c:
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cython -a lib/pygfunc.pyx
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.PHONY: dist
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dist:
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python2 setup.py sdist
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dist: phantom
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python3 setup.py sdist
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.PHONY: upload
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upload: dist
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twine upload --verbose dist/*
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2522
.PHONY: clean
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clean:
27-
rm -f *.mod lib/*.o lib/pygfunc.c lib/pygfunc.html pygfunc.so
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rm -f *.mod lib/*.o lib/pygfunc.pyf pygfunc.*.so
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rm -rf build dist

Diff for: ‎install_phantom.sh

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@@ -0,0 +1,13 @@
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#!/bin/bash
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pushd lib
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# -m is name the module pygfunc
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# generates the pygfunc.pyf file
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f2py3 pygfunc.f90 -m pygfunc -h pygfunc.pyf
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# generates .so file
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f2py3 -c pygfunc.pyf write_data_phantom.f90 pygfunc.f90 -m pygfunc
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popd

Diff for: ‎lib/io_lib.py

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@@ -24,7 +24,7 @@
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import sys
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from MESA2HYDRO.lib import converge_funcs as cf
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from MESA2HYDRO.lib import hdf5lib
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from MESA2HYDRO.lib import pygfunc
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import pygfunc
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###############################################################
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#

Diff for: ‎lib/try.sh

-7
This file was deleted.

Diff for: ‎local_setup.py

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@@ -0,0 +1,32 @@
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#!/usr/bin/env python3
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import os
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import sys
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import subprocess
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################################
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9+
PKG_DIR = os.path.abspath(os.path.dirname(__file__))
10+
PYPATH_DIR = os.path.dirname(PKG_DIR)
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12+
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PYGFUNC_F90_FILE = "lib/pygfunc.f90"
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PYGFUNC_PYF_FILE = "lib/pygfunc.pyf"
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WRITE_DATA_PHANTOM_F90_FILE = "lib/write_data_phantom.f90"
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17+
18+
python_path = os.environ.get('PYTHONPATH') or ''
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python_paths = [os.path.abspath(path) for path in python_path.split(':')]
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if PYPATH_DIR not in python_paths:
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print("{} not in PYTHONPATH, needed for local development of MESA2HYDRO"
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.format(PYPATH_DIR))
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print("Appending {} to PYTHONPATH in ~/.bashrc".format(PYPATH_DIR))
25+
with open(os.path.expanduser('~/.bashrc'), 'w+') as f:
26+
f.write('# ADDED BY MESA2HYDRO FOR LOCAL DEVELOPMENT')
27+
f.write('export PYTHONPATH=$PYTHONPATH:~/')
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subprocess.run("pip install -r requirements.txt", shell=True)
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# install fortran locally
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subprocess.run('./install_phantom.sh', shell=True)

Diff for: ‎requirements.txt

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@@ -0,0 +1,5 @@
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numpy
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scipy
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matplotlib
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healpy
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h5py

Diff for: ‎setup.py

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Original file line numberDiff line numberDiff line change
@@ -1,20 +1,30 @@
11
#!/usr/bin/env python3
22

3-
from setuptools import setup, find_packages
3+
import os
4+
import sys
45

5-
#import os
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#import sys
7-
#import shutil
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#import subprocess
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#from numpy import get_include, f2py
6+
from numpy.distutils.core import setup, Extension
7+
from numpy import f2py
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119
################################
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11+
VERSION = '0.1.2146'
12+
PYGFUNC_F90_FILE = "lib/pygfunc.f90"
13+
PYGFUNC_PYF_FILE = "lib/pygfunc.pyf"
14+
WRITE_DATA_PHANTOM_F90_FILE = "lib/write_data_phantom.f90"
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14-
# TODO: Add "local" option again that adds MESA2HYDRO_ROOT to python path and installs dependencies
16+
if not os.path.exists(PYGFUNC_PYF_FILE):
17+
print("Making {} file".format(PYGFUNC_PYF_FILE))
18+
f2py.run_main([PYGFUNC_F90_FILE, '-m', 'pygfunc', '-h', PYGFUNC_PYF_FILE])
19+
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fortran_ext = Extension(
22+
name = 'pygfunc',
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sources = [PYGFUNC_PYF_FILE, WRITE_DATA_PHANTOM_F90_FILE, PYGFUNC_F90_FILE]
24+
)
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setup(name='MESA2HYDRO',
17-
version='0.1.2146',
27+
version=VERSION,
1828
description=('Convert 1D stellar structure models to 3D particle '
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'distributions using the HEALPix spherical tessellation algorithm'),
2030
long_description=('Convert 1D stellar structure models to 3D particle '
@@ -50,67 +60,5 @@
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'lib/write_data_phantom.f90',
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'lib/pygfunc.f90',
5262
'DOCUMENTATION/*']},
53-
install_requires=['numpy', 'scipy', 'matplotlib', 'healpy', 'h5py', 'setuptools']
63+
ext_modules=[fortran_ext]
5464
)
55-
56-
57-
"""
58-
PKG_DIR = os.path.abspath(os.path.dirname(__file__))
59-
PYGFUNC_F90_FILE = "{}/lib/pygfunc.f90".format(PKG_DIR)
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PYGFUNC_PYF_FILE = "{}/lib/pygfunc.pyf".format(PKG_DIR)
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WRITE_DATA_PHANTOM_F90_FILE = "{}/lib/write_data_phantom.f90".format(PKG_DIR)
62-
63-
64-
65-
if len(sys.argv) > 2 and sys.argv[1] == 'install':
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f2py.run_main([PYGFUNC_F90_FILE, '-m', 'pygfunc', '-h', PYGFUCN_PYF_FILE])
67-
f2py.run_main(['-c', PYGFUNC_PYF_FILE, "--opts='-std=f2003'", WRITE_DATA_PHANTOM_F90_FILE, PYGFUNC_F90_FILE, '-m', 'pygfunc'])
68-
69-
"""
70-
71-
"""
72-
## must explicitly include all f90, h, and pyx files
73-
setup(name='MESA2HYDRO',
74-
scripts=['work/confirm_density_profile.py',
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'work/confirm_mass_profile.py',
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'work/run_conversion.py',
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'uninstall_MESA2HYDRO.py'],
78-
cmdclass={'build_ext': build_ext},
79-
include_dirs=[get_include()],
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ext_modules=cythonize(ext_modules, compiler_directives={'language_level': "3"}),
81-
packages=['MESA2HYDRO',
82-
'MESA2HYDRO.work',
83-
'MESA2HYDRO.lib'],
84-
package_dir={'MESA2HYDRO': '',
85-
'MESA2HYDRO.work': 'work',
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'MESA2HYDRO.lib': 'lib',
87-
'MESA2HYDRO.data': 'data',
88-
'MESA2HYDRO.out': 'out',
89-
'MESA2HYDRO.DOCUMENTATION': 'DOCUMENTATION'},
90-
91-
package_data={'': ['data/*/*',
92-
'work/*.cfg',
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'out/NR_files/*.dat',
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'out/sample_MESA_output/*.data',
95-
'lib/write_data_phantom.f90',
96-
'lib/pygfunc.f90',
97-
'DOCUMENTATION/*']},
98-
99-
version='0.1.2146',
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description='Convert 1D stellar structure models to 3D particle distributions using the HEALPix spherical tessellation algorithm',
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long_description='Convert 1D stellar structure models to 3D particle distributions using the HEALPix spherical tessellation algorithm\
102-
\n\
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see academic paper https://iopscience.iop.org/article/10.3847/1538-4357/ab3405/meta\
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\n\
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and User\'s Guide\
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\n\
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https://github.com/mjoyceGR/MESA2HYDRO/blob/master/DOCUMENTATION/MESA2HYDRO_users_guide.pdf\n\
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for more information',
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author='Meridith Joyce',
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author_email='[email protected]',
111-
url='https://github.com/mjoyceGR/MESA2HYDRO',
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download_url='https://github.com/mjoyceGR/MESA2HYDRO/archive/0.1.0.tar.gz',
113-
keywords=['MESA', 'stellar evolution', 'stellar structure','astronomy', 'stellar modeling','hydrodynamical ICs','HEALPix'],
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classifiers=[]
115-
)
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"""

Diff for: ‎uninstall_MESA2HYDRO.py

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1-
#!/usr/bin/python2
1+
#!/usr/bin/python3
22

33
import os
44
import sys
@@ -25,7 +25,7 @@
2525
location = location[:-1]
2626
if not os.path.isfile(location):
2727
continue
28-
result = raw_input("Remove {}(y/N)?".format(location))
28+
result = input("Remove {}(y/N)?".format(location))
2929
if result.upper().startswith("Y"):
3030
try:
3131
os.remove(location)
@@ -56,7 +56,7 @@
5656
print("Skipping {} because doesn't exist".format(location))
5757
continue
5858

59-
result = raw_input("Remove {}?(y/N)".format(location))
59+
result = input("Remove {}?(y/N)".format(location))
6060
if result.upper().startswith("Y"):
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try:
6262
if os.path.isdir(location):
@@ -70,7 +70,7 @@
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7171
file_path = os.path.abspath(__file__)
7272

73-
result = raw_input("Remove this file ({})?(y/N)".format(file_path))
73+
result = input("Remove this file ({})?(y/N)".format(file_path))
7474
print(result)
7575
if result.upper().startswith("Y"):
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try:

Diff for: ‎work/__init__.py

Whitespace-only changes.

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