def mac_setup(self):
"""Mac OS X setup."""
# The relax settings.
self.APP = ['relax_gui_mode.py']
self.NAME = 'relax'
self.VERSION = version_full()
self.OPTIONS = {}
self.OPTIONS['py2app'] = {
'argv_emulation': False,
'iconfile': status.install_path + sep + 'graphics' + sep + 'ulysses_shadowless_trans_128x128.icns',
'packages': 'wx',
'site_packages': True,
'includes': self.get_includes(),
'excludes': ['build', 'dist'],
'plist': {
'CFBundleName': 'relax',
'CFBundleShortVersionString': version_full(),
'CFBundleGetInfoString': 'relax %s' % version_full(),
'CFBundleIdentifier': 'com.nmr-relax.relax'
}
}
self.REQUIRES = ['py2app']
def mac_setup(self):
"""Mac OS X setup."""
# The relax settings.
self.APP = ['relax_gui_mode.py']
self.NAME = 'relax'
self.VERSION = version_full()
self.OPTIONS = {}
self.OPTIONS['py2app'] = {
'argv_emulation': False,
'iconfile': status.install_path + sep + 'graphics' + sep +
'ulysses_shadowless_trans_128x128.icns',
'packages': 'wx',
'site_packages': True,
'includes': self.get_includes(),
'excludes': ['build', 'dist'],
'plist': {
'CFBundleName': 'relax',
'CFBundleShortVersionString': version_full(),
'CFBundleGetInfoString': 'relax %s' % version_full(),
'CFBundleIdentifier': 'com.nmr-relax.relax'
}
}
self.REQUIRES = ['py2app']
def write(file=None, dir=None, version='3.1', force=False):
"""Create a BMRB NMR-STAR formatted file.
@keyword file: The name of the file to create or a file object.
@type file: str or file object
@keyword dir: The optional directory to place the file into. If set to 'pipe_name', then it will be placed in a directory with the same name as the current data pipe.
@type dir: str or None
@keyword version: The NMR-STAR version to create. This can be either '2.1', '3.0', or '3.1'.
@type version: str
@keyword force: A flag which if True will allow a currently existing file to be overwritten.
@type force: bool
"""
# Test if bmrblib is installed.
if not dep_check.bmrblib_module:
raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')
# Test if the current data pipe exists.
pipe_name = cdp_name()
if not pipe_name:
raise RelaxNoPipeError
# Check the file name.
if file == None:
raise RelaxError("The file name must be specified.")
# A file object.
if isinstance(file, str):
# The special data pipe name directory.
if dir == 'pipe_name':
dir = pipe_name
# Get the full file path.
file = get_file_path(file, dir)
# Fail if the file already exists and the force flag is False.
if access(file, F_OK) and not force:
raise RelaxFileOverwriteError(file, 'force flag')
# Print out.
print("Opening the file '%s' for writing." % file)
# Create the directories.
mkdir_nofail(dir, verbosity=0)
# Get the info box.
info = Info_box()
# Add the relax citations.
for id, key in zip(['relax_ref1', 'relax_ref2'],
['dAuvergneGooley08a', 'dAuvergneGooley08b']):
# Alias the bib entry.
bib = info.bib[key]
# Add.
exp_info.citation(cite_id=id,
authors=bib.author2,
doi=bib.doi,
pubmed_id=bib.pubmed_id,
full_citation=bib.cite_short(doi=False, url=False),
title=bib.title,
status=bib.status,
type=bib.type,
journal_abbrev=bib.journal,
journal_full=bib.journal_full,
volume=bib.volume,
issue=bib.number,
page_first=bib.page_first,
page_last=bib.page_last,
year=bib.year)
# Add the relax software package.
exp_info.software(name=exp_info.SOFTWARE['relax'].name,
version=version_full(),
vendor_name=exp_info.SOFTWARE['relax'].authors,
url=exp_info.SOFTWARE['relax'].url,
cite_ids=['relax_ref1', 'relax_ref2'],
tasks=exp_info.SOFTWARE['relax'].tasks)
# Execute the specific BMRB writing code.
api = return_api(pipe_name=pipe_name)
api.bmrb_write(file, version=version)
# Add the file to the results file list.
if isinstance(file, str):
add_result_file(type='text', label='BMRB', file=file)
def write(file=None, dir=None, version='3.1', force=False):
"""Create a BMRB NMR-STAR formatted file.
@keyword file: The name of the file to create or a file object.
@type file: str or file object
@keyword dir: The optional directory to place the file into. If set to 'pipe_name', then it will be placed in a directory with the same name as the current data pipe.
@type dir: str or None
@keyword version: The NMR-STAR version to create. This can be either '2.1', '3.0', or '3.1'.
@type version: str
@keyword force: A flag which if True will allow a currently existing file to be overwritten.
@type force: bool
"""
# Test if bmrblib is installed.
if not dep_check.bmrblib_module:
raise RelaxNoModuleInstallError('BMRB library', 'bmrblib')
# Test if the current data pipe exists.
pipe_name = cdp_name()
if not pipe_name:
raise RelaxNoPipeError
# Check the file name.
if file == None:
raise RelaxError("The file name must be specified.")
# A file object.
if isinstance(file, str):
# The special data pipe name directory.
if dir == 'pipe_name':
dir = pipe_name
# Get the full file path.
file = get_file_path(file, dir)
# Fail if the file already exists and the force flag is False.
if access(file, F_OK) and not force:
raise RelaxFileOverwriteError(file, 'force flag')
# Print out.
print("Opening the file '%s' for writing." % file)
# Create the directories.
mkdir_nofail(dir, verbosity=0)
# Specific results writing function.
write_function = specific_analyses.setup.get_specific_fn('bmrb_write', ds[pipe_name].pipe_type)
# Get the info box.
info = Info_box()
# Add the relax citations.
for id, key in zip(['relax_ref1', 'relax_ref2'], ['dAuvergneGooley08a', 'dAuvergneGooley08b']):
# Alias the bib entry.
bib = info.bib[key]
# Add.
exp_info.citation(cite_id=id, authors=bib.author2, doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False, url=False), title=bib.title, status=bib.status, type=bib.type, journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume, issue=bib.number, page_first=bib.page_first, page_last=bib.page_last, year=bib.year)
# Add the relax software package.
exp_info.software(name=exp_info.SOFTWARE['relax'].name, version=version_full(), vendor_name=exp_info.SOFTWARE['relax'].authors, url=exp_info.SOFTWARE['relax'].url, cite_ids=['relax_ref1', 'relax_ref2'], tasks=exp_info.SOFTWARE['relax'].tasks)
# Execute the specific BMRB writing code.
write_function(file, version=version)
# Add the file to the results file list.
if isinstance(file, str):
add_result_file(type='text', label='BMRB', file=file)
def software_select(name, version=None):
"""Select by name the software used in the analysis.
@param name: The name of the software program.
@type name: str
@keyword version: The program version.
@type version: None or str
"""
# Test if the current pipe exists.
pipes.test()
# Unknown program.
if name not in ['relax', 'NMRPipe', 'Sparky', 'Bruker DC']:
raise RelaxError("The software '%s' is unknown. Please use the user function for manually specifying software details instead." % name)
# Set up the experimental info data container, if needed.
if not hasattr(cdp, 'exp_info'):
cdp.exp_info = ExpInfo()
# Init.
cite_ids = []
keys = []
software_keys = []
versions = []
# relax.
if name == 'relax':
# The info.
cite_ids.append(['relax_ref1', 'relax_ref2'])
keys.append(['dAuvergneGooley08a', 'dAuvergneGooley08b'])
software_keys.append('relax')
versions.append(version_full())
# NMRPipe.
elif name == 'NMRPipe':
# The info.
cite_ids.append(['nmrpipe_ref'])
keys.append(['Delaglio95'])
software_keys.append('NMRPipe')
versions.append(version)
# Sparky.
elif name == 'Sparky':
# Check if the version information has been supplied.
if not version:
raise RelaxError("The Sparky version number has not been supplied.")
# The info.
cite_ids.append(['sparky_ref'])
keys.append(['GoddardKneller'])
software_keys.append('Sparky')
versions.append(version)
# Bruker Dynamics Center.
elif name == 'Bruker DC':
# The info.
software_keys.append('DC')
versions.append(version)
# Get the info box.
info = Info_box()
# Loop over the citations.
for i in range(len(cite_ids)):
for j in range(len(cite_ids[i])):
# Alias the bib entry.
bib = info.bib[keys[i][j]]
# Add the citations.
cdp.exp_info.add_citation(cite_id=cite_ids[i][j], authors=bib.author2, doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False, url=False), title=bib.title, status=bib.status, type=bib.type, journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume, issue=bib.number, page_first=bib.page_first, page_last=bib.page_last, year=bib.year)
# Add the software info.
cdp.exp_info.software_setup(name=SOFTWARE[software_keys[i]].name, version=versions[i], vendor_name=SOFTWARE[software_keys[i]].authors, url=SOFTWARE[software_keys[i]].url, cite_ids=cite_ids, tasks=SOFTWARE[software_keys[i]].tasks)
def run(self):
"""Execute relax.
This is the application callback method executed by the multi-processor framework.
"""
# Set up the warning system.
lib.warnings.setup()
# Logging.
if self.log_file:
io_streams_log(self.log_file)
# Tee.
elif self.tee_file:
io_streams_tee(self.tee_file)
# Show the version number and exit.
if self.mode == 'version':
print('relax ' + version.version_full())
return
# Show the relax info and exit.
if self.mode == 'info':
# Initialise the information box.
info = Info_box()
# Print the program intro.
print(info.intro_text())
# Print the system info.
print(info.sys_info())
# Stop execution.
return
# Run the interpreter for the prompt or script modes.
if self.mode == 'prompt' or self.mode == 'script':
# Run the interpreter.
self.interpreter = interpreter.Interpreter()
self.interpreter.run(self.script_file)
# Execute the relax GUI.
elif self.mode == 'gui':
# Dependency check.
if not dep_check.wx_module:
sys.stderr.write("Please install the wx Python module to access the relax GUI.\n\n")
return
# Only import the module in this mode (to improve program start up speeds).
import gui
# Set the GUI flag in the status object.
status.show_gui = True
# Start the relax GUI wx application.
app = gui.App(script_file=self.script_file)
app.MainLoop()
# Execute the relax test suite
elif self.mode == 'test suite':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Load the interpreter and turn intros on.
self.interpreter = interpreter.Interpreter(show_script=False, raise_relax_error=True)
self.interpreter.on()
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_all_tests()
# Execute the relax system tests.
elif self.mode == 'system tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Load the interpreter and turn intros on.
self.interpreter = interpreter.Interpreter(show_script=False, raise_relax_error=True)
self.interpreter.on()
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_system_tests()
# Execute the relax unit tests.
elif self.mode == 'unit tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_unit_tests()
# Execute the relax GUI tests.
elif self.mode == 'GUI tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_gui_tests()
# Execute the relax verification tests.
elif self.mode == 'verification tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_verification_tests()
# Test mode.
elif self.mode == 'test':
self.test_mode()
# Licence mode.
elif self.mode == 'licence':
self.licence()
# Unknown mode.
else:
raise lib.errors.RelaxError("The '%s' mode is unknown." % self.mode)
def run(self):
"""Execute relax.
This is the application callback method executed by the multi-processor framework.
"""
# Set up the warning system.
lib.warnings.setup()
# Logging.
if self.log_file:
io_streams_log(self.log_file)
# Tee.
elif self.tee_file:
io_streams_tee(self.tee_file)
# Show the version number and exit.
if self.mode == 'version':
print('relax ' + version.version_full())
return
# Show the relax info and exit.
if self.mode == 'info':
# Initialise the information box.
info = Info_box()
# Print the program intro.
print(info.intro_text())
# Print the system info.
print(info.sys_info())
# Stop execution.
return
# Run the interpreter for the prompt or script modes.
if self.mode == 'prompt' or self.mode == 'script':
# Run the interpreter.
self.interpreter = interpreter.Interpreter()
self.interpreter.run(self.script_file)
# Execute the relax GUI.
elif self.mode == 'gui':
# Dependency check.
if not dep_check.wx_module:
sys.stderr.write(
"Please install the wx Python module to access the relax GUI.\n\n"
)
return
# Only import the module in this mode (to improve program start up speeds).
import gui
# Set the GUI flag in the status object.
status.show_gui = True
# Start the relax GUI wx application.
app = gui.App(script_file=self.script_file)
app.MainLoop()
# Execute the relax test suite
elif self.mode == 'test suite':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Load the interpreter and turn intros on.
self.interpreter = interpreter.Interpreter(show_script=False,
raise_relax_error=True)
self.interpreter.on()
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_all_tests()
# Execute the relax system tests.
elif self.mode == 'system tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Load the interpreter and turn intros on.
self.interpreter = interpreter.Interpreter(show_script=False,
raise_relax_error=True)
self.interpreter.on()
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_system_tests()
# Execute the relax unit tests.
elif self.mode == 'unit tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_unit_tests()
# Execute the relax GUI tests.
elif self.mode == 'GUI tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_gui_tests()
# Execute the relax verification tests.
elif self.mode == 'verification tests':
# Only import the module in the test modes (to improve program start up speeds).
from test_suite.test_suite_runner import Test_suite_runner
# Run the tests.
runner = Test_suite_runner(self.tests, timing=self.test_timings)
runner.run_verification_tests()
# Test mode.
elif self.mode == 'test':
self.test_mode()
# Licence mode.
elif self.mode == 'licence':
self.licence()
# Unknown mode.
else:
raise lib.errors.RelaxError("The '%s' mode is unknown." %
self.mode)
def software_select(name, version=None):
"""Select by name the software used in the analysis.
@param name: The name of the software program.
@type name: str
@keyword version: The program version.
@type version: None or str
"""
# Test if the current pipe exists.
check_pipe()
# Unknown program.
if name not in ['relax', 'NMRPipe', 'Sparky', 'Bruker DC']:
raise RelaxError("The software '%s' is unknown. Please use the user function for manually specifying software details instead." % name)
# Set up the experimental info data container, if needed.
if not hasattr(cdp, 'exp_info'):
cdp.exp_info = ExpInfo()
# Init.
cite_ids = []
keys = []
software_keys = []
versions = []
# relax.
if name == 'relax':
# The info.
cite_ids.append(['relax_ref1', 'relax_ref2'])
keys.append(['dAuvergneGooley08a', 'dAuvergneGooley08b'])
software_keys.append('relax')
versions.append(version_full())
# NMRPipe.
elif name == 'NMRPipe':
# The info.
cite_ids.append(['nmrpipe_ref'])
keys.append(['Delaglio95'])
software_keys.append('NMRPipe')
versions.append(version)
# Sparky.
elif name == 'Sparky':
# Check if the version information has been supplied.
if not version:
raise RelaxError("The Sparky version number has not been supplied.")
# The info.
cite_ids.append(['sparky_ref'])
keys.append(['GoddardKneller'])
software_keys.append('Sparky')
versions.append(version)
# Bruker Dynamics Center.
elif name == 'Bruker DC':
# The info.
software_keys.append('DC')
versions.append(version)
# Get the info box.
info = Info_box()
# Loop over the citations.
for i in range(len(cite_ids)):
for j in range(len(cite_ids[i])):
# Alias the bib entry.
bib = info.bib[keys[i][j]]
# Add the citations.
cdp.exp_info.add_citation(cite_id=cite_ids[i][j], authors=bib.author2, doi=bib.doi, pubmed_id=bib.pubmed_id, full_citation=bib.cite_short(doi=False, url=False), title=bib.title, status=bib.status, type=bib.type, journal_abbrev=bib.journal, journal_full=bib.journal_full, volume=bib.volume, issue=bib.number, page_first=bib.page_first, page_last=bib.page_last, year=bib.year)
# Add the software info.
cdp.exp_info.software_setup(name=SOFTWARE[software_keys[i]].name, version=versions[i], vendor_name=SOFTWARE[software_keys[i]].authors, url=SOFTWARE[software_keys[i]].url, cite_ids=cite_ids, tasks=SOFTWARE[software_keys[i]].tasks)