scale = ""
if unit.scale is not None and unit.scale != 1:
scale = "<br/>" + spacer4 + "Scale: " + str(unit.scale)
contents += spacer4 + "Dimension: " + dimension(
unit.dimension, "",
"") + "<br/>" + spacer4 + "Power of 10: " + str(
unit.power) + offset + scale + "<br/>\n"
for unit2 in model.units:
if unit.symbol != unit2.symbol and unit.dimension == unit2.dimension:
'''diff = unit.power - unit2.power
factor = "10<sup>%i</sup>"%diff
if diff == 0:
factor = 1'''
factor1 = model.get_numeric_value("1%s" % unit.symbol,
unit.dimension)
factor2 = model.get_numeric_value("1%s" % unit2.symbol,
unit2.dimension)
contents += "<br/>" + spacer4 + "1 %s = %s <a href='#%s'>%s</a>" % (
unit.symbol, "%s" %
(factor1 / factor2), unit2.symbol, unit2.symbol)
contents += " </td>\n"
contents += " </tr>\n"
contents += "</table>\n"
for o_comp_type in ordered_comp_types[file]:
comp_type = model.component_types[o_comp_type]
#print "ComponentType %s is %s"%(comp_type.name, comp_type.description)
ext = "" if comp_type.extends is None else "<p>%sextends %s</p>" % (
if unit.offset is not None and unit.offset != 0:
offset = "<br/>"+spacer4+"Offset: "+str(unit.offset)
scale = ""
if unit.scale is not None and unit.scale != 1:
scale = "<br/>"+spacer4+"Scale: "+str(unit.scale)
contents += spacer4+"Dimension: "+dimension(unit.dimension, "", "")+"<br/>"+spacer4+"Power of 10: "+str(unit.power)+offset+scale+"<br/>\n"
for unit2 in model.units:
if unit.symbol != unit2.symbol and unit.dimension == unit2.dimension:
'''diff = unit.power - unit2.power
factor = "10<sup>%i</sup>"%diff
if diff == 0:
factor = 1'''
factor1 = model.get_numeric_value("1%s"%unit.symbol, unit.dimension)
factor2 = model.get_numeric_value("1%s"%unit2.symbol, unit2.dimension)
contents += "<br/>"+spacer4+"1 %s = %s <a href='#%s'>%s</a>" % (unit.symbol, "%s"%(factor1/factor2), unit2.symbol, unit2.symbol)
contents += " </td>\n"
contents += " </tr>\n"
contents += "</table>\n"
for o_comp_type in ordered_comp_types[file]:
comp_type = model.component_types[o_comp_type]
#print "ComponentType %s is %s"%(comp_type.name, comp_type.description)
def main(srcdir, destdir):
"""Main parser and generator function.
:param srcdir: directory holding source NeuroML Core Type XML files
:type srcdir: str
:param destdir: directory where generated files should be stored
:type destdir: str
:returns: nothing
"""
# If not defined or empty, download a new copy to a temporary directory
if not srcdir or src == "":
print("No src directory specified. Cloning NeuroML2 repo")
tempdir = tempfile.TemporaryDirectory()
tmpsrcdir = tempdir.name
print("Temporariy directory: {}".format(tmpsrcdir))
clone_command = [
"git", "clone", "--depth", "1", "--branch", nml_branch, GitHubRepo,
tmpsrcdir
]
subprocess.run(clone_command)
else:
tmpsrcdir = srcdir
# TODO: add LEMS examples
# We can't do this at the moment, because the LEMS python bits are in
# pyneuroml, while we point to the libNeuroML docs for the NeuroML2 usage
# examples. pyneuroml does not currently have docs on RTD, and some more
# work will be required to tell our templates when an example is NeuroML
# and when it is LEMS so it can point to the correct docs.
# exampledirs = [tmpsrcdir + "/examples/", tmpsrcdir + "/LEMSexamples/"]
exampledirs = [tmpsrcdir + "/examples/"]
tmpsrcdir = tmpsrcdir + "/NeuroML2CoreTypes/"
# Get current commit
commit_command = ["git", "log", "-1", "--pretty=format:%H"]
output = subprocess.run(commit_command,
capture_output=True,
cwd=tmpsrcdir,
text=True)
nml_commit = output.stdout
# read the downloaded files
get_component_types(tmpsrcdir)
# get examples
get_comp_examples(exampledirs)
# get python signatures
get_libneuroml_signatures()
if not destdir or destdir == "":
destdir = "."
print("Output files will be written to {} directory".format(destdir))
for comp_definition in comp_definitions:
fullpath = "{}/{}.xml".format(tmpsrcdir, comp_definition)
outputfile = "{}/{}.md".format(destdir, comp_definition)
"""Stage 1"""
model = Model(include_includes=False)
model.import_from_file(fullpath)
print("Processing {}".format(fullpath))
print("Writing output to {}".format(outputfile))
ast_doc = open(outputfile, 'w')
"""Page header"""
print(asttemplates.page_header.render(
comp_definition=comp_definition,
comp_description=format_description(model.description),
GitHubCompSources=GitHubCompSources,
nml_version=nml_version,
nml_branch=nml_branch,
nml_date=nml_date,
nml_commit=nml_commit),
file=ast_doc)
"""Dimensions and units"""
if "Dimensions" in comp_definition:
dimensions = model.dimensions
dimensions = sorted(dimensions, key=lambda dim: dim.name)
units = model.units
units = sorted(units, key=lambda unit: unit.symbol)
# lables are translated as lowercase in jupyter, so we append two
# consecutive underscores to differentiate same ones, like M and m.
symbols = []
for unit in units:
if unit.symbol.lower() in symbols:
unit.symbol = unit.symbol + "__"
symbols.append(unit.symbol.lower())
print(asttemplates.dimension.render(
comp_definition=comp_definition,
dimensions=dimensions,
units=units),
file=ast_doc)
# Get factors
for unit in units:
unit.factors = []
for unit2 in units:
if unit.symbol != unit2.symbol and unit.dimension == unit2.dimension:
si_val = model.get_numeric_value(
"1%s" % unit.symbol.replace("__", ""),
unit.dimension)
unit_val = (
(Decimal(si_val) /
Decimal(math.pow(10, unit2.power))) /
Decimal(unit2.scale)) - Decimal(unit2.offset)
conversion = float(unit_val)
# to catch 60.0001 etc.
if conversion > 1 and int(conversion) != conversion:
if conversion - int(conversion) < 0.001:
conversion = int(conversion)
if conversion > 10000:
conversion = '%.2e' % conversion
else:
conversion = '%s' % conversion
if conversion.endswith('.0'):
conversion = conversion[:-2]
unit.factors.append([conversion, unit2.symbol])
print(asttemplates.unit.render(comp_definition=comp_definition,
units=units),
file=ast_doc)
"""Component Types"""
for o_comp_type in ordered_comp_types[comp_definition]:
o_comp_type = o_comp_type.replace('rdf:', 'rdf_')
comp_type = model.component_types[o_comp_type]
"""Header"""
cno = None
if " cno_00" in str(comp_type.description):
cno = comp_type.description.split(" ")[-1]
comp_type.description = comp_type.description.replace(cno, "")
comp_type.description = format_description(comp_type.description)
if len(comp_type.description) > 0:
if comp_type.description[-1] not in "!.":
comp_type.description += "."
else:
comp_type.description = ""
print(asttemplates.comp.render(comp_definition=comp_definition,
comp_type=comp_type,
cno=cno),
file=ast_doc)
"""Process parameters, derived parameters, texts, paths, expsures,
requirements and ports"""
params = {}
derived_params = {}
texts = {}
paths = {}
exposures = {}
requirements = {}
eventPorts = {}
"""Get lists of them all"""
for param in comp_type.parameters:
params[param] = comp_type.name
for derived_param in comp_type.derived_parameters:
derived_params[derived_param] = comp_type.name
for text in comp_type.texts:
texts[text] = comp_type.name
for path in comp_type.paths:
paths[path] = comp_type.paths
for exp in comp_type.exposures:
exposures[exp] = comp_type.name
for req in comp_type.requirements:
requirements[req] = comp_type.name
for ep in comp_type.event_ports:
eventPorts[ep] = comp_type.name
"""Get parent ComponentType if derived from one."""
extd_comp_type = get_extended_from_comp_type(comp_type.name)
"""Recursively go up the tree and get attributes inherited from ancestors."""
while extd_comp_type is not None:
for param in extd_comp_type.parameters:
pk = params.copy().keys()
for pp0 in pk:
if pp0.name == param.name:
del params[pp0]
params[param] = extd_comp_type.name
for derived_param in extd_comp_type.derived_parameters:
derived_params[derived_param] = extd_comp_type.name
for text in extd_comp_type.texts:
texts[text] = extd_comp_type.name
for path in extd_comp_type.paths:
paths[path] = extd_comp_type.paths
for exp in extd_comp_type.exposures:
ek = exposures.copy().keys()
for ee0 in ek:
if ee0.name == exp.name:
del exposures[ee0]
exposures[exp] = extd_comp_type.name
for req in extd_comp_type.requirements:
requirements[req] = extd_comp_type.name
for ep in extd_comp_type.event_ports:
eventPorts[ep] = extd_comp_type.name
"""Recurse up the next parent"""
extd_comp_type = get_extended_from_comp_type(
extd_comp_type.name)
if len(params) > 0:
keysort = sorted(params.keys(), key=lambda param: param.name)
print(asttemplates.params.render(title="Parameters",
comp_type=comp_type,
entries=params,
keysort=keysort),
file=ast_doc)
if len(derived_params) > 0:
keysort = sorted(derived_params.keys(),
key=lambda derived_param: derived_param.name)
print(asttemplates.params.render(title="Derived parameters",
comp_type=comp_type,
entries=derived_params,
keysort=keysort),
file=ast_doc)
if len(comp_type.texts
) > 0: # TODO: Check if Text elements are inherited...
print(asttemplates.misc2c.render(title="Text fields",
textlist=comp_type.texts),
file=ast_doc)
if len(comp_type.paths
) > 0: # TODO: Check if Path elements are inherited...
print(asttemplates.misc2c.render(title="Paths",
textlist=comp_type.paths),
file=ast_doc)
if len(comp_type.component_references) > 0:
print(asttemplates.misc3c.render(
title="Component References",
textlist=comp_type.component_references),
file=ast_doc)
if len(comp_type.children) > 0:
childlist = []
childrenlist = []
for child_or_children in comp_type.children:
if not child_or_children.multiple:
childlist.append(child_or_children)
else:
childrenlist.append(child_or_children)
if len(childlist) > 0:
print(asttemplates.misc3c.render(title="Child list",
textlist=childlist),
file=ast_doc)
if len(childrenlist) > 0:
print(asttemplates.misc3c.render(title="Children list",
textlist=childrenlist),
file=ast_doc)
if len(comp_type.constants) > 0:
print(asttemplates.constants.render(
title="Constants", textlist=comp_type.constants),
file=ast_doc)
if len(comp_type.properties) > 0:
print(asttemplates.properties.render(
title="Properties", textlist=comp_type.properties),
file=ast_doc)
if len(exposures) > 0:
keysort = sorted(exposures, key=lambda entry: entry.name)
print(asttemplates.exposures.render(title="Exposures",
comp_type=comp_type,
entries=exposures,
keysort=keysort),
file=ast_doc)
if len(requirements) > 0:
keysort = sorted(requirements, key=lambda entry: entry.name)
print(asttemplates.requirements.render(title="Requirements",
comp_type=comp_type,
entries=requirements,
keysort=keysort),
file=ast_doc)
if len(eventPorts) > 0:
keysort = sorted(eventPorts, key=lambda entry: entry.name)
print(asttemplates.eventPorts.render(title="Event Ports",
comp_type=comp_type,
entries=eventPorts,
keysort=keysort),
file=ast_doc)
if len(comp_type.attachments) > 0:
print(asttemplates.misc3c.render(
title="Attachments", textlist=comp_type.attachments),
file=ast_doc)
if comp_type.dynamics and comp_type.dynamics.has_content():
print(asttemplates.dynamics.render(title="Dynamics",
comp_type=comp_type),
file=ast_doc)
# Examples
"""
print("{} has: ".format(comp_type.name))
if comp_type_py_api[comp_type.name]:
print("\t1 Py def")
if len(comp_type_examples[comp_type.name]) > 0:
print("\t{} XML examples".format(len(comp_type_examples[comp_type.name])))
"""
if comp_type_py_api[comp_type.name] or len(
comp_type_examples[comp_type.name]) > 0:
print(asttemplates.examples.render(
title="Usage",
comp_type=comp_type,
lemsexamples=comp_type_examples[comp_type.name],
pysig=comp_type_py_api[comp_type.name]),
file=ast_doc)
ast_doc.close()
print("Finished processing {}".format(fullpath))
if not srcdir:
tempdir.cleanup()
