subprocess.check_call(["/bin/bash", "-c",
'cd %s; %s' % (fmindexV2_home, command)], **kwargs)
objects_files = [pjoin(fmindexV2_home,'fm_index.a'),
pjoin(ds_ssort_home, 'ds_ssort.a')]
fmindex_ext = Extension('fmindex._fmindex',
sources=['fmindex/src/fmindex_py.c'],
extra_objects=objects_files,
include_dirs=[fmindexV2_home,
ds_ssort_home,
'fmindex/src'],
)
# Find all fmindex data files
fmi_files = [rpath(pjoin(root, f), package_path) for root, _, files in
os.walk(fmindexV2_home) for f in files]
setup(
name=DISTNAME,
maintainer=AUTHORS,
packages=['fmindex'],
package_data={'fmindex': fmi_files},
ext_modules=[fmindex_ext],
include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs(),
maintainer_email=EMAIL,
description=DESCRIPTION,
license=LICENSE,
url=URL,
download_url=DOWNLOAD_URL,
long_description=LONG_DESCRIPTION,
$ pip install cadnano
''' % (version)
LONG_DESCRIPTION = __doc__
PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
MODULE_PATH = pjoin(PACKAGE_PATH, 'cadnano')
INSTALL_EXE_PATH = pjoin(MODULE_PATH, 'extras', 'install_exe')
TESTS_PATH = pjoin(MODULE_PATH, 'tests')
TEST_DATA_PATH = pjoin(TESTS_PATH, 'data')
IMAGES_PATH1 = pjoin(MODULE_PATH, 'gui', 'mainwindow', 'images')
IMAGES_PATH2 = pjoin(MODULE_PATH, 'gui', 'dialogs', 'images')
# batch files and launch scripts
test_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(TESTS_PATH) for f in files]
test_data_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(TEST_DATA_PATH) for f in files]
cn_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(IMAGES_PATH1) for f in files]
cn_files += [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(IMAGES_PATH2) for f in files]
cn_files += test_files + test_data_files
entry_points = {'console_scripts': [
'cadnano = cadnano.bin.main:main',
'cadnanoinstall = cadnano.extras.install_exe.cadnanoinstall:post_install'
]}
if sys.platform == 'win32':
input_text="Files or folders that end with this text should be excluded: ",
function=lambda excl, path: os.path.splitext(
os.path.split(path)[1])[0].endswith(excl.data),
ui_input=lambda m: tk.Entry(m),
ui_edit=lambda m, excl: tk.Entry(m, textvariable=tk.StringVar(m, value=excl.data)),
ui_submit=lambda e: e.get()),
ExclusionType(code="ext", menu_text="Specific file extension",
input_text="Files with this extension should be excluded (the . before the " +
"extension is needed): ",
function=lambda excl, path: os.path.splitext(path)[1] == excl.data,
ui_input=lambda m: tk.Entry(m),
ui_edit=lambda m, excl: tk.Entry(m, textvariable=tk.StringVar(m, value=excl.data)),
ui_submit=lambda e: e.get()),
ExclusionType(code="directory", accepts_limitations=False, menu_text="Specific directory path",
input_text="Folders with this absolute path will be excluded: ",
function=lambda excl, path: os.path.isdir(path) and rpath(path) == rpath(excl.data),
ui_input=lambda m: Fileview(master=m),
ui_edit=lambda m, excl: Fileview(master=m, default_focus=excl.data),
ui_submit=lambda e: e.get_focus_path()),
ExclusionType(code="file", menu_text="Specific filename",
input_text="Files with this name and extension will be excluded: ",
function=lambda excl, path: os.path.isfile(path) and os.path.split(
path)[1] == excl.data,
ui_input=lambda m: tk.Entry(m),
ui_edit=lambda m, excl: tk.Entry(m, textvariable=tk.StringVar(m, value=excl.data)),
ui_submit=lambda e: e.get()),
ExclusionType(code="dir_name", menu_text="Specific directory name",
input_text="Directories with this name will be excluded: ",
function=lambda excl, path: os.path.isdir(path) and os.path.split(
path)[1] == excl.data,
ui_input=lambda m: tk.Entry(m),
def p3Build():
# Build primer3
p3build = subprocess.Popen(['make clean; make'], shell=True,
cwd=LIBPRIMER3_PATH)
p3build.wait()
P3_BUILT = False
# Find all necessary primer3 binaries / data files to include with the package
p3_binaries = ['oligotm', 'ntthal', 'primer3_core']
p3_binary_fps = [pjoin(LIBPRIMER3_PATH, fn) for fn in p3_binaries]
thermo_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(THERMO_PARAMS_PATH) for f in files]
test_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(TESTS_PATH) for f in files]
p3_files = thermo_files + test_files + ['thermoanalysis.pxd', 'thermoanalysis.pyx']
# Insure that the copied binaries are executable
def makeExecutable(fp):
''' Adds the executable bit to the file at filepath `fp`
'''
mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
setup_log.info("Adding executable bit to %s (mode is now %o)", fp, mode)
os.chmod(fp, mode)
p3clean.wait()
def p3Build():
# Build primer3
p3build = subprocess.Popen(['make clean; make'], shell=True,
cwd=LIBPRIMER3_PATH)
p3build.wait()
P3_BUILT = False
# Find all necessary primer3 binaries / data files to include with the package
p3_binaries = ['oligotm', 'ntthal', 'primer3_core']
p3_binary_fps = [pjoin(LIBPRIMER3_PATH, fn) for fn in p3_binaries]
thermo_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(THERMO_PARAMS_PATH) for f in files]
test_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(TESTS_PATH) for f in files]
p3_files = thermo_files + test_files
# Insure that the copied binaries are executable
def makeExecutable(fp):
''' Adds the executable bit to the file at filepath `fp`
'''
mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
setup_log.info("Adding executable bit to %s (mode is now %o)", fp, mode)
os.chmod(fp, mode)
UIC_PATH = pjoin(MODULE_PATH, 'uic')
search_path = pjoin(MODULE_PATH, '*.pyd')
filepath_list = glob.glob(search_path)
file_list = [os.path.basename(x) for x in filepath_list]
search_path = pjoin(MODULE_PATH, '*.pyi')
filepath_list = glob.glob(search_path)
file_list += [os.path.basename(x) for x in filepath_list]
search_path = pjoin(MODULE_PATH, '*.dll')
filepath_list = glob.glob(search_path)
file_list += [os.path.basename(x) for x in filepath_list]
package_files = [
rpath(pjoin(root, f), MODULE_PATH) for root, _, files in os.walk(Qt5_PATH)
for f in files
]
package_files += [
rpath(pjoin(root, f), MODULE_PATH) for root, _, files in os.walk(UIC_PATH)
for f in files
]
packages = find_packages()
setup(
name='PyQt5',
version='5.6.1',
license='GPLv3',
url='https://www.riverbankcomputing.com/software/pyqt/download5',
description='PyQt5',
Qt5_PATH = pjoin(MODULE_PATH, 'Qt')
UIC_PATH = pjoin(MODULE_PATH, 'uic')
search_path = pjoin(MODULE_PATH, '*.pyd')
filepath_list = glob.glob(search_path)
file_list = [os.path.basename(x) for x in filepath_list]
search_path = pjoin(MODULE_PATH, '*.pyi')
filepath_list = glob.glob(search_path)
file_list += [os.path.basename(x) for x in filepath_list]
search_path = pjoin(MODULE_PATH, '*.dll')
filepath_list = glob.glob(search_path)
file_list += [os.path.basename(x) for x in filepath_list]
package_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(Qt5_PATH) for f in files]
package_files += [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(UIC_PATH) for f in files]
packages = find_packages()
setup(
name='PyQt5',
version='5.6.1',
license='GPLv3',
url='https://www.riverbankcomputing.com/software/pyqt/download5',
description='PyQt5',
classifiers=[
'Programming Language :: C',
'Programming Language :: Python',
os_system = platform.system()
if os_system == 'Darwin':
mauve_make = 'build_osx.sh'
elif os_system == 'Linux': # update this for BSD, other POSIX etc
mauve_make = 'build_linux.sh'
else:
raise OSError("Platform %s not supported" % (os_system))
print("Building mauve dependencies...")
mauve_make = pjoin(SRC_PATH, mauve_make)
mauvebuild = subprocess.Popen([mauve_make], shell=True, cwd=SRC_PATH)
mauvebuild.wait()
print("Finished building mauve dependencies")
# Find all mauve data files to include with the package
mauve_files = [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(BIN_PATH) for f in files]
mauve_files += [rpath(pjoin(root, f), MODULE_PATH) for root, _, files in
os.walk(INCLUDE_PATH) for f in files]
DESCRIPTION = ("Python wrapper for progressive mauve genome aligner")
DISTNAME = 'mauve-py'
LICENSE = 'GPLv2'
AUTHORS = "Nick Conway, Ben Pruitt"
EMAIL = "*****@*****.**"
URL = ""
DOWNLOAD_URL = ''
CLASSIFIERS = [
'Development Status :: 1 - Beta',
MAKE_BIN = 'mingw32-make' if sys.platform == 'win32' else 'make'
# Indicates whether the Primer3 library has been built during install
P3_BUILT = False
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Package paths ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
MODULE_PATH = pjoin(PACKAGE_PATH, 'primer3')
SRC_PATH = pjoin(MODULE_PATH, 'src')
TESTS_PATH = pjoin(MODULE_PATH, 'tests')
LIBPRIMER3_PATH = pjoin(SRC_PATH, 'libprimer3')
THERMO_PARAMS_PATH = pjoin(LIBPRIMER3_PATH, 'primer3_config')
KLIB_PATH = pjoin(LIBPRIMER3_PATH, 'klib')
LIBPRIMER3_FPS = [
rpath(pjoin(LIBPRIMER3_PATH, 'thal.c')),
rpath(pjoin(LIBPRIMER3_PATH, 'oligotm.c')),
rpath(pjoin(LIBPRIMER3_PATH, 'p3_seq_lib.c')),
rpath(pjoin(LIBPRIMER3_PATH, 'libprimer3.c')),
rpath(pjoin(LIBPRIMER3_PATH, 'dpal.c')),
rpath(pjoin(SRC_PATH, 'primerdesign_helpers.c')),
]
LIBPRIMER3_BINARIES = ['oligotm', 'ntthal', 'primer3_core']
if sys.platform == 'win32':
LIBPRIMER3_BINARIES = [bin_fn + '.exe' for bin_fn in LIBPRIMER3_BINARIES]
LIBPRIMER3_BINARY_FPS = [
pjoin(LIBPRIMER3_PATH, fn) for fn in LIBPRIMER3_BINARIES
]
''' % (version)
LONG_DESCRIPTION = __doc__
PACKAGE_PATH = os.path.abspath(os.path.dirname(__file__))
MODULE_PATH = pjoin(PACKAGE_PATH, 'cadnano')
INSTALL_EXE_PATH = pjoin(MODULE_PATH, 'extras', 'install_exe')
TESTS_PATH = pjoin(MODULE_PATH, 'tests')
TEST_DATA_PATH = pjoin(TESTS_PATH, 'data')
IMAGES_PATH1 = pjoin(MODULE_PATH, 'gui', 'mainwindow', 'images')
IMAGES_PATH2 = pjoin(MODULE_PATH, 'gui', 'dialogs', 'images')
# batch files and launch scripts
test_files = [
rpath(pjoin(root, f), MODULE_PATH)
for root, _, files in os.walk(TESTS_PATH) for f in files
]
test_data_files = [
rpath(pjoin(root, f), MODULE_PATH)
for root, _, files in os.walk(TEST_DATA_PATH) for f in files
]
cn_files = [
rpath(pjoin(root, f), MODULE_PATH)
for root, _, files in os.walk(IMAGES_PATH1) for f in files
]
cn_files += [
rpath(pjoin(root, f), MODULE_PATH)
for root, _, files in os.walk(IMAGES_PATH2) for f in files
]
cn_files += test_files + test_data_files
from os import remove as rem # imports os.remove() and names it "rem"
from time import sleep as t # imports time.sleep() and names it "t"
from os.path import dirname as fpath # imports os.path.dirname() and names it "fpath"
from os.path import realpath as rpath # imports os.path.realpath() and names it "rpath"
from sys import exit as quit # imports sys.exit() and names it "quit"
# this is used to find the directory this file is in, it is later used
# to move the other files to "/release/file.pyc," I just hadn't wanted
# clutter in the building directory. (These notes are for the
# "path = fpath(rpath(__file__))" bit below this note, I know it's bit lengthy)
path = fpath(rpath(__file__))
# these make a .pyc version of all these files
pyc("Read.py")
pyc("Settings.py")
pyc("Socket.py")
pyc("Commands.py")
pyc("Run.py")
pyc("Threads.py")
try: # if the file does not exist, it will bring up an error
# these remove the current file because on windows,
# moving a file to another file's directory even if they
# are the same file, brings up an error.
rem(path + "/release/Read.pyc")
rem(path + "/release/Settings.pyc")
if os_system == 'Darwin':
mauve_make = 'build_osx.sh'
elif os_system == 'Linux': # update this for BSD, other POSIX etc
mauve_make = 'build_linux.sh'
else:
raise OSError("Platform %s not supported" % (os_system))
print("Building mauve dependencies...")
mauve_make = pjoin(SRC_PATH, mauve_make)
mauvebuild = subprocess.Popen([mauve_make], shell=True, cwd=SRC_PATH)
mauvebuild.wait()
print("Finished building mauve dependencies")
# Find all mauve data files to include with the package
mauve_files = [
rpath(pjoin(root, f), MODULE_PATH) for root, _, files in os.walk(BIN_PATH)
for f in files
]
mauve_files += [
rpath(pjoin(root, f), MODULE_PATH)
for root, _, files in os.walk(INCLUDE_PATH) for f in files
]
DESCRIPTION = ("Python wrapper for progressive mauve genome aligner")
DISTNAME = 'mauve-py'
LICENSE = 'GPLv2'
AUTHORS = "Nick Conway, Ben Pruitt"
EMAIL = "*****@*****.**"
URL = ""
DOWNLOAD_URL = ''
