def main():
(options, args) = parser.parse_args()
sorted_order = tools.get_sorted_order()
if options.module != "":
if options.module == "kernel":
tools.rewrite("lib/IMP/__init__.py", imp_init)
build_wrapper(
options.module, os.path.join(
options.source, "modules", options.module),
options.source, sorted_order,
tools.get_module_description(
options.source,
options.module,
options.datapath),
os.path.join("swig", "IMP_" + options.module + ".i"),
options.datapath)
else:
tools.rewrite("lib/IMP/__init__.py", imp_init)
for m, path in tools.get_modules(options.source):
build_wrapper(m, path, options.source, sorted_order,
tools.get_module_description(
options.source,
m,
options.datapath),
os.path.join("swig", "IMP_" + m + ".i"),
options.datapath)
def get_all_components():
comps = {}
# If RMF is being built as part of IMP, split out its build (rather than
# building it as part of IMP.rmf)
special_dep_targets = {"RMF": RMFDependency}
for dep, cls in special_dep_targets.items():
i = tools.get_dependency_info(dep, "")
if i['ok']:
comps[dep] = cls(dep)
comps[dep].set_dep_modules(comps, [], [], special_dep_targets)
modules = tools.get_sorted_order()
for m in modules:
comps[m] = Module(m)
for m in modules:
i = tools.get_module_info(m, "")
comps[m].set_dep_modules(comps, i['modules'], i['dependencies'],
special_dep_targets)
source_dir = os.path.join(os.path.dirname(sys.argv[0]), '..', '..')
all_modules = [x[0] for x in tools.get_modules(source_dir)]
add_disabled_components(modules, all_modules, comps, "module")
return comps
def link_swig(source):
target = os.path.join("swig")
tools.mkdir(target)
for module, g in tools.get_modules(source):
# they all go in the same dir, so don't remove old links
tools.link_dir(
os.path.join(g,
"pyext"),
target,
match=["*.i"],
clean=False)
if os.path.exists(os.path.join(g, "pyext", "include")):
tools.link_dir(
os.path.join(g,
"pyext",
"include"),
target,
match=["*.i"],
clean=False)
tools.link(
os.path.join(
g,
"pyext",
"swig.i-in"),
os.path.join(
target,
"IMP_%s.impl.i" %
module))
def get_all_components():
comps = {}
# If RMF is being built as part of IMP, split out its build (rather than
# building it as part of IMP.rmf)
special_dep_targets = {"RMF": RMFDependency}
for dep, cls in special_dep_targets.items():
i = tools.get_dependency_info(dep, "")
if i['ok'] and internal_dep(dep):
comps[dep] = cls(dep)
comps[dep].set_dep_modules(comps, [], [], special_dep_targets)
modules = tools.get_sorted_order()
apps = tools.get_all_configured_applications()
for m in modules:
comps[m] = Module(m)
for a in apps:
comps[a] = Application(a)
for m in modules:
i = tools.get_module_info(m, "")
comps[m].set_dep_modules(comps, i['modules'], i['dependencies'],
special_dep_targets)
for a in apps:
i = tools.get_application_info(a, "")
comps[a].set_dep_modules(comps, i['modules'], i['dependencies'],
special_dep_targets)
source_dir = os.path.join(os.path.dirname(sys.argv[0]), '..', '..')
all_modules= [x[0] for x in tools.get_modules(source_dir)]
all_apps= [x[0] for x in tools.get_applications(source_dir)]
add_disabled_components(modules, all_modules, comps, "module")
add_disabled_components(apps, all_apps, comps, "application")
return comps
def generate_overview_pages(source):
name = os.path.join("doxygen", "generated", "cmdline_tools.dox")
contents = []
contents.append("/** ")
contents.append("\\page cmdline_tools All IMP command line tools")
contents.append("""
IMP modules provide a number of command line tools.
These are listed below under their parent module:""")
for bs, g in tools.get_modules(source):
if tools.get_module_info(bs, '')['ok']:
p = pickle.load(
open(os.path.join("data", "build_info", "IMP_%s.pck" % bs)))
if len(p) > 0:
contents.append("- IMP::%s" % bs)
apps = sorted([[k] + list(v) for k, v in p.iteritems() if v],
key=lambda x: x[3])
for app in apps:
contents.append(" - [%s](\\ref %s): %s" %
(app[0], app[1], app[2]))
contents.append("""
See also the [command line tools provided by RMF](http://integrativemodeling.org/rmf/nightly/doc/executables.html)."""
)
contents.append("*/")
g = tools.DoxFileGenerator()
g.write(name, "\n".join(contents))
def check_readme():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "README.md")):
sys.stderr.write(
"Each module must have a file 'README.md' describing what what it does and who wrote it.\n"
)
sys.stderr.write(module, "does not.\n")
exit(1)
def generate_all_cpp(source):
target=os.path.join("src")
tools.mkdir(target)
for module, g in tools.get_modules(source):
sources= tools.get_glob([os.path.join(g, "src", "*.cpp")])\
+tools.get_glob([os.path.join(g, "src", "internal", "*.cpp")])
targetf=os.path.join(target, module+"_all.cpp")
sources.sort()
tools.rewrite(targetf, "\n".join(["#include <%s>"%os.path.abspath(s) for s in sources]) + '\n')
def check_readme():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "README.md")):
print >> sys.stderr, "Each module must have a file 'README.md' describing what what it does and who wrote it."
print >> sys.stderr, module, "does not."
exit(1)
for app, g in tools.get_applications("."):
if not os.path.exists(os.path.join(g, "README.md")):
print >> sys.stderr, "Each application must have a file 'README.md' describing what who wrote it and what it does."
print >> sys.stderr, app, "does not."
exit(1)
def check_readme():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "README.md")):
print >> sys.stderr, "Each module must have a file 'README.md' describing what what it does and who wrote it."
print >> sys.stderr, module, "does not."
exit(1)
for app, g in tools.get_applications("."):
if not os.path.exists(os.path.join(g, "README.md")):
print >> sys.stderr, "Each application must have a file 'README.md' describing what who wrote it and what it does."
print >> sys.stderr, app, "does not."
exit(1)
def generate_overview_pages(source):
ai= open(os.path.join("doxygen", "applications.dox"), "w")
ai.write("/** \\page applications_index Application Index \n")
for bs, g in tools.get_applications(source):
ai.write("- \\subpage IMP_%s_overview \"%s\"\n"%(bs,bs))
ai.write("*/")
ai= open(os.path.join("doxygen", "modules.dox"), "w")
ai.write("/** \\page modules_index Module Index \n")
for bs, g in tools.get_modules(source):
ai.write("- \\subpage IMP_%s_overview \"%s\"\n"%(bs,bs))
ai.write("*/")
def check_dependencies():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "dependencies.py")):
print >> sys.stderr, "Each module must have a file 'dependencies.py' describing what other modules and external dependencies it needs."
print >> sys.stderr, module, "does not."
exit(1)
for app, g in tools.get_applications("."):
if not os.path.exists(os.path.join(g, "dependencies.py")):
print >> sys.stderr, "Each application must have a file 'dependencies.py' describing what other modules and external dependencies it needs."
print >> sys.stderr, app, "does not."
exit(1)
def check_dependencies():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "dependencies.py")):
print >> sys.stderr, "Each module must have a file 'dependencies.py' describing what other modules and external dependencies it needs."
print >> sys.stderr, module, "does not."
exit(1)
for app, g in tools.get_applications("."):
if not os.path.exists(os.path.join(g, "dependencies.py")):
print >> sys.stderr, "Each application must have a file 'dependencies.py' describing what other modules and external dependencies it needs."
print >> sys.stderr, app, "does not."
exit(1)
def link_python(source):
target=os.path.join("lib")
tools.mkdir(target, clean=False)
for module, g in tools.get_modules(source):
path= os.path.join(target, "IMP", module)
tools.mkdir(path, clean=False)
for old in tools.get_glob([os.path.join(path, "*.py")]):
# don't unlink the generated file
if os.path.split(old)[1] != "__init__.py" and os.path.split(old)[1] != "_version_check.py":
os.unlink(old)
#print "linking", path
tools.link_dir(os.path.join(g, "pyext", "src"), path, clean=False)
def link_headers(source):
target=os.path.join("include")
tools.mkdir(target)
root=os.path.join(target, "IMP")
tools.mkdir(root)
for (module, g) in tools.get_modules(source):
#print g, module
if module== "SConscript":
continue
tools.link_dir(os.path.join(g, "include"), os.path.join(root, module), match=["*.h"])
tools.link_dir(os.path.join(g, "include", "internal"), os.path.join(root, module, "internal"),
match=["*.h"])
def link_dox(source):
target = os.path.join("doxygen")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "doc"),
os.path.join("doc", "html", module),
match=["*.png", "*.pdf", "*.gif"], clean=False)
tools.link_dir(os.path.join(source, "doc"), os.path.join("doc", "html"),
match=["*.png", "*.pdf", "*.gif"], clean=False)
tools.link_dir(os.path.join(source, "doc", "tutorial"),
os.path.join("doc", "tutorial"),
match=["*.png", "*.pdf", "*.gif"], clean=False)
def generate_all_cpp(source):
target = os.path.join("src")
tools.mkdir(target)
for module, g in tools.get_modules(source):
sources = tools.get_glob([os.path.join(g, "src", "*.cpp")])\
+ tools.get_glob([os.path.join(g, "src", "internal", "*.cpp")])
targetf = os.path.join(target, module + "_all.cpp")
sources.sort()
tools.rewrite(
targetf,
"\n".join(["#include <%s>" % os.path.abspath(s)
for s in sources]) + '\n')
def main():
parser = OptionParser()
parser.add_option("-s", "--source", dest="source",
help="IMP source directory.")
options, args = parser.parse_args()
# Top-level version
make_version(options.source, '.')
# Submodule versions
for module, module_source in tools.get_modules(options.source):
if os.path.exists(os.path.join(module_source, ".git")):
make_version(module_source, os.path.join("modules", module))
def link_python(source):
target = os.path.join("lib")
tools.mkdir(target, clean=False)
for module, g in tools.get_modules(source):
path = os.path.join(target, "IMP", module)
tools.mkdir(path, clean=False)
for old in tools.get_glob([os.path.join(path, "*.py")]):
# don't unlink the generated file
if os.path.split(old)[1] != "__init__.py" and os.path.split(
old)[1] != "_version_check.py":
os.unlink(old)
# print "linking", path
tools.link_dir(os.path.join(g, "pyext", "src"), path, clean=False)
def link_dox(source):
target=os.path.join("doxygen")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "doc"), os.path.join(target, module))
tools.link_dir(os.path.join(g, "doc"), os.path.join("doc", "html"), match=["*.png", "*.pdf"],
clean=False)
doxygenize_readme(os.path.join(g, "README.md"), "doxygen", module)
for app, g in tools.get_applications(source):
tools.link_dir(g, os.path.join(target, app))
tools.link_dir(g, os.path.join("doc", "html"), match=["*.png", "*.pdf"], clean=False)
doxygenize_readme(os.path.join(g, "README.md"), "doxygen", app)
tools.link_dir(os.path.join(source, "doc"), os.path.join(target, "IMP"))
tools.link_dir(os.path.join(source, "doc"), os.path.join("doc", "html"), match=["*.png", "*.pdf"],
clean=False)
def generate_overview_pages(source):
name = os.path.join("doxygen", "generated", "all.dox")
contents = []
contents.append("/** ")
contents.append("\\page allmod All IMP Modules and Applications")
contents.append("<table><tr>")
contents.append("<th>Modules</th><th>Applications</th></tr><tr><td>")
for bs, g in tools.get_modules(source):
contents.append("- \\subpage imp%s \"IMP.%s\""%(bs,bs))
contents.append("</td><td style=\"vertical-align:top;\">")
for bs, g in tools.get_applications(source):
contents.append("- \subpage imp%s \"IMP.%s\""%(bs,bs))
contents.append("</td></tr></table>")
contents.append("*/")
tools.rewrite(name, "\n".join(contents))
def link_dox(source):
target = os.path.join("doxygen")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "doc"),
os.path.join("doc", "html", module),
match=["*.png", "*.pdf", "*.gif"],
clean=False)
tools.link_dir(os.path.join(source, "doc"),
os.path.join("doc", "html"),
match=["*.png", "*.pdf", "*.gif"],
clean=False)
tools.link_dir(os.path.join(source, "doc", "tutorial"),
os.path.join("doc", "tutorial"),
match=["*.png", "*.pdf", "*.gif"],
clean=False)
def link_dox(source):
target=os.path.join("doxygen")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "doc"),
os.path.join("doc", "html", module),
match=["*.png", "*.pdf"], clean=False)
for app, g in tools.get_applications(source):
tools.link_dir(g, os.path.join("doc", "html", app),
match=["*.png", "*.pdf"], exclude=["README.md"],
clean=False)
tools.link_dir(os.path.join(source, "doc"), os.path.join("doc", "html"), match=["*.png", "*.pdf"],
clean=False)
tools.link_dir(os.path.join(source, "doc", "tutorial"),
os.path.join("doc", "tutorial"), match=["*.png", "*.pdf"],
clean=False)
def link_swig(source):
target = os.path.join("swig")
tools.mkdir(target)
for module, g in tools.get_modules(source):
# they all go in the same dir, so don't remove old links
tools.link_dir(os.path.join(g, "pyext"),
target,
match=["*.i"],
clean=False)
if os.path.exists(os.path.join(g, "pyext", "include")):
tools.link_dir(os.path.join(g, "pyext", "include"),
target,
match=["*.i"],
clean=False)
tools.link(os.path.join(g, "pyext", "swig.i-in"),
os.path.join(target, "IMP_%s.impl.i" % module))
def link_headers(source):
target = os.path.join("include")
tools.mkdir(target)
root = os.path.join(target, "IMP")
tools.mkdir(root)
for (module, g) in tools.get_modules(source):
# print g, module
modroot = os.path.join(root, '' if module == 'kernel' else module)
if module == "SConscript":
continue
tools.link_dir(os.path.join(g, "include"), modroot, match=["*.h"])
tools.link_dir(os.path.join(g, "include", "internal"),
os.path.join(modroot, "internal"), match=["*.h"])
# ick
if os.path.exists(os.path.join(g, "include", "eigen3")):
tools.link_dir(os.path.join(g, "include", "eigen3"),
os.path.join(modroot, "eigen3"),
match=["*"])
def link_headers(source):
target = os.path.join("include")
tools.mkdir(target)
root = os.path.join(target, "IMP")
tools.mkdir(root)
for (module, g) in tools.get_modules(source):
# print g, module
modroot = os.path.join(root, '' if module == 'kernel' else module)
if module == "SConscript":
continue
tools.link_dir(os.path.join(g, "include"), modroot, match=["*.h"])
tools.link_dir(os.path.join(g, "include", "internal"),
os.path.join(modroot, "internal"),
match=["*.h"])
# ick
if os.path.exists(os.path.join(g, "include", "eigen3")):
tools.link_dir(os.path.join(g, "include", "eigen3"),
os.path.join(modroot, "eigen3"),
match=["*"])
def main():
(options, args) = parser.parse_args()
sorted_order = tools.get_sorted_order()
if options.module != "":
if options.module == "kernel":
tools.rewrite("lib/IMP/__init__.py", imp_init)
build_wrapper(
options.module,
os.path.join(options.source, "modules",
options.module), options.source, sorted_order,
tools.get_module_description(options.source, options.module,
options.datapath),
os.path.join("swig", "IMP_" + options.module + ".i"),
options.datapath)
else:
tools.rewrite("lib/IMP/__init__.py", imp_init)
for m, path in tools.get_modules(options.source):
build_wrapper(
m, path, options.source, sorted_order,
tools.get_module_description(options.source, m,
options.datapath),
os.path.join("swig", "IMP_" + m + ".i"), options.datapath)
def main():
source = sys.argv[1]
modules = [m[0] for m in tools.get_modules(source)]
docs = Docs(xml_dir='doxygen/ref/xml',
html_dir='doc/ref',
top_source_dir=source,
source_subdirs=sys.argv[2:] + all_module_docs(modules))
for p in docs.pages:
p.map_location_to_source(source)
for m in modules:
docs.pages.append(get_module_readme(m))
# Difficult to figure out the main/index page, so set this manually
p = docs.page_by_id['indexpage']
p.out_file_name = 'index'
p.source_file_name = 'doc/ref/mainpage.md'
for p in docs.pages:
if os.path.exists(docs.get_html_page(p)):
docs.add_page_navigation(p)
else:
print("Not handling %s: HTML file does not exist" % p.id)
def main():
source = sys.argv[1]
modules = [m[0] for m in tools.get_modules(source)]
docs = Docs(xml_dir='doxygen/ref/xml',
html_dir='doc/ref',
top_source_dir=source,
source_subdirs=sys.argv[2:] + all_module_docs(modules))
for p in docs.pages:
p.map_location_to_source(source)
for m in modules:
docs.pages.append(get_module_readme(m))
# Difficult to figure out the main/index page, so set this manually
p = docs.page_by_id['indexpage']
p.out_file_name = 'index'
p.source_file_name = 'doc/ref/mainpage.md'
for p in docs.pages:
if docs.get_html_pages(p):
docs.add_page_navigation(p)
else:
print("Not handling %s: HTML file does not exist" % p.id)
def generate_overview_pages(source):
name = os.path.join("doxygen", "generated", "cmdline_tools.dox")
contents = []
contents.append("/** ")
contents.append("\\page cmdline_tools All IMP command line tools")
contents.append("""
IMP modules provide a number of command line tools.
These are listed below under their parent module:""")
for bs, g in tools.get_modules(source):
if tools.get_module_info(bs, '')['ok']:
p = pickle.load(open(os.path.join("data", "build_info",
"IMP_%s.pck" % bs)))
if len(p) > 0:
contents.append("- IMP::%s" % bs)
apps = sorted([[k]+list(v) for k,v in p.iteritems() if v],
key=lambda x:x[3])
for app in apps:
contents.append(" - [%s](\\ref %s): %s" % (app[0], app[1],
app[2]))
contents.append("""
See also the [command line tools provided by RMF](http://integrativemodeling.org/rmf/nightly/doc/executables.html).""")
contents.append("*/")
tools.rewrite(name, "\n".join(contents))
def link_examples(source):
target = os.path.join("doc", "examples")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "examples"),
os.path.join(target, module))
def get_output_file_contents(self, options):
template = self.template
name = options.name
modules = self.modules
template = template.replace("@[email protected]", options.source)
template = template.replace("@[email protected]", "NONE")
template = template.replace("@[email protected]", name)
template = template.replace("@[email protected]",
'"The Integrative Modeling Platform"')
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "*/tutorial/*")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "IMP." + name)
template = template.replace("@[email protected]", "../../doc/html/" + name)
template = template.replace("@[email protected]", "xml")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "tags")
template = template.replace(
"@[email protected]",
"%s/doc/doxygen/module_layout.xml" % options.source)
template = template.replace("@[email protected]", "README.md")
template = template.replace("@[email protected]", "include")
template = template.replace("@[email protected]",
"*.cpp *.h *.py *.md *.dox")
template = template.replace("@[email protected]", "warnings.txt")
# include lib and doxygen in input
inputs = []
if options.name == "kernel":
inputs.append("lib/IMP/")
inputs.append("include/IMP/")
exclude = [
"include/IMP/%s include/IMP/%s.h lib/IMP/%s" % (m, m, m)
for m, g in tools.get_modules(options.source)
]
exclude.append("include/IMP/base include/IMP/base.h lib/IMP/base")
template = template.replace(
"@[email protected]", " \\\n ".join(exclude))
else:
template = template.replace("@[email protected]", "")
inputs.append("include/IMP/" + options.name)
inputs.append("lib/IMP/" + options.name)
inputs.append("examples/" + options.name)
# suppress a warning since git removes empty dirs and doxygen
# gets confused if the input path doesn't exist
docpath = os.path.join(options.source, "modules", options.name, "doc")
if os.path.exists(docpath):
inputs.append(docpath)
# overview for module
inputs.append("../generated/IMP_%s.dox" % options.name)
template = template.replace(
"@[email protected]", " \\\n ".join(inputs))
tags = [
os.path.join(options.source, 'doc', 'doxygen',
'dummy_module_tags.xml')
]
for m in modules:
tags.append(os.path.join("../", m, "tags") + "=" + "../" + m)
template = template.replace(
"@[email protected]", " \\\n ".join(tags))
if options.name == "example":
template = template.replace(
"@[email protected]",
"examples/example %s/modules/example" % options.source)
else:
template = template.replace("@[email protected]",
"examples/" + options.name)
return template
def generate_src_dirs(source):
"""Make src directories for each module. This way we don't have to worry about whether
it exists later."""
for module, g in tools.get_modules(source):
tools.mkdir(os.path.join("src", module), clean=False)
def generate_tests(source, scons):
template = """import IMP
import IMP.test
import %(module)s
spelling_exceptions=%(spelling_exceptions)s
class StandardsTest(IMP.test.TestCase):
def test_value_objects(self):
"Test that module classes are either values or objects"
exceptions= %(value_object_exceptions)s
return self.assertValueObjects(%(module)s,exceptions)
def test_classes(self):
"Test that module class names follow the standards"
exceptions=%(value_object_exceptions)s
return self.assertClassNames(%(module)s, exceptions,
spelling_exceptions)
def test_functions(self):
"Test that module function names follow the standards"
exceptions= %(function_name_exceptions)s
return self.assertFunctionNames(%(module)s, exceptions,
spelling_exceptions)
def test_show(self):
"Test all objects have show"
exceptions=%(show_exceptions)s
return self.assertShow(%(module)s, exceptions)
if __name__ == '__main__':
IMP.test.main()
"""
target = os.path.join("test")
tools.mkdir(target)
for module, g in tools.get_modules(source):
targetdir = os.path.join(target, module)
tools.mkdir(targetdir)
exceptions = os.path.join(g, "test", "standards_exceptions")
d = {
'plural_exceptions': [],
'show_exceptions': [],
'function_name_exceptions': [],
'value_object_exceptions': [],
'class_name_exceptions': [],
'spelling_exceptions': []
}
try:
exec(open(exceptions, "r").read(), d)
except IOError:
pass
impmodule = "IMP" if module == 'kernel' else "IMP." + module
test = template % (
{
'module': impmodule,
'plural_exceptions': str(d['plural_exceptions']),
'show_exceptions': str(d['show_exceptions']),
'function_name_exceptions': str(d['function_name_exceptions']),
'value_object_exceptions': str(d['value_object_exceptions']),
'class_name_exceptions': str(d['class_name_exceptions']),
'spelling_exceptions': str(d['spelling_exceptions'])
})
gen = tools.PythonFileGenerator()
gen.write(os.path.join("test", module, "medium_test_standards.py"),
test,
show_diff=False)
cpptests = tools.get_glob([os.path.join(g, "test", "test_*.cpp")])
ecpptests = tools.get_glob(
[os.path.join(g, "test", "expensive_test_*.cpp")])
cppexamples = tools.get_glob([os.path.join(g, "examples", "*.cpp")])
if len(cpptests) > 0 and scons:
_make_test_driver(os.path.join(targetdir, "test_cpp_tests.py"),
cpptests)
if len(ecpptests) > 0 and scons:
_make_test_driver(
os.path.join(targetdir, "expensive_test_cpp_tests.py"),
cpptests)
if len(cppexamples) > 0 and scons:
_make_test_driver(os.path.join(targetdir, "cpp_examples_test.py"),
cppexamples)
def get_output_file_contents(self, output):
is_xml = output['is_xml']
is_html = output['is_html']
manual = output['manual']
source = output['source']
version = "develop"
versionpath = os.path.join("VERSION")
if os.path.exists(versionpath):
version = open(versionpath, "r").read().strip()
if manual:
version = '"for IMP version ' + version + '"'
doxygen = self.template
if manual:
doxygen = doxygen.replace("@[email protected]", '"IMP Manual"')
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/manual/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/manual_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-tags.xml")
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", ".")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref-tags.xml=../ref")
doxygen = doxygen.replace("@[email protected]", "doxygen/manual/xml/")
doxygen = doxygen.replace("@[email protected]", "")
else:
doxygen = doxygen.replace("@[email protected]", '"IMP Reference Guide"')
doxygen = doxygen.replace("@[email protected]",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@[email protected]", "mainpage.md")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/ref/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]",
"doxygen/ref-tags.xml")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]",
"doc/examples %s/modules/example" % source)
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-tags.xml=../manual")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref/xml/")
doxygen = doxygen.replace("@[email protected]",
"lib/IMP/kernel lib/IMP/base")
doxygen = doxygen.replace("@[email protected]", "IMP")
doxygen = doxygen.replace("@[email protected]", source) \
.replace("@[email protected]", version)
doxygen = doxygen.replace("@[email protected]", "include")
doxygen = doxygen.replace("@[email protected]",
"*.cpp *.h *.py *.md *.dox")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if is_html:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if manual:
inputsh = [source + "/doc/manual",
source + "/tools/README.md",
source + "/ChangeLog.md"]
else:
inputsh = ["doxygen/generated", source + "/doc/ref",
"include", "doc/examples", "lib/IMP"]
for m, p in tools.get_modules(source):
doc = os.path.join(p, "doc")
if os.path.exists(doc):
inputsh.append(doc + "/")
doxygen = doxygen.replace("@[email protected]", " ".join(inputsh))
return doxygen
def link_data(source):
target = os.path.join("data")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "data"), os.path.join(target, module))
def generate_doxyfile(source,
target,
is_xml=False,
is_html=False,
tutorial=False):
doxyin = os.path.join(source, "tools", "build", "doxygen_templates",
"Doxyfile.in")
version = "develop"
versionpath = os.path.join("VERSION")
if os.path.exists(versionpath):
version = open(versionpath, "r").read().strip()
if tutorial:
version = '"for IMP version ' + version + '"'
doxygen = open(doxyin, "r").read()
if tutorial:
doxygen = doxygen.replace("@[email protected]", '"IMP Tutorial"')
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]", "doc/tutorial/")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]",
"doxygen/tutorial-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", ".")
doxygen = doxygen.replace("@[email protected]", "doxygen/tags.html=../html")
else:
doxygen = doxygen.replace("@[email protected]", "IMP")
doxygen = doxygen.replace("@[email protected]",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@[email protected]", "mainpage.md")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/html/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]", "doxygen/tags.html")
doxygen = doxygen.replace("@[email protected]", "doxygen/warnings.txt")
doxygen = doxygen.replace("@[email protected]", "*/tutorial/*")
doxygen = doxygen.replace("@[email protected]",
"doc/examples %s/modules/example" % source)
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "IMP")
doxygen = doxygen.replace("@[email protected]",
source).replace("@VERSION@", version)
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "include")
doxygen = doxygen.replace("@[email protected]", "*.cpp *.h *.py *.md *.dox")
doxygen = doxygen.replace("@[email protected]", "doxygen/xml/")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if is_html:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
# skip linking later
inputsh = [
"doxygen/generated", source + "/doc", source + "/ChangeLog.md",
source + "/tools/README.md", "include", "doc/examples"
]
for m, p in tools.get_modules(source):
doc = os.path.join(p, "doc")
inputsh.append(os.path.join("lib", "IMP", m))
if os.path.exists(doc):
inputsh.append(doc + "/")
if not tutorial:
doxygen = doxygen.replace("@[email protected]", " ".join(inputsh))
open(target, "w").write(doxygen)
def generate_src_dirs(source):
"""Make src directories for each module. This way we don't have to worry about whether
it exists later."""
for module, g in tools.get_modules(source):
tools.mkdir(os.path.join("src", module), clean=False)
def get_output_file_contents(self, output):
is_xml = output['is_xml']
is_html = output['is_html']
manual = output['manual']
source = output['source']
version = "develop"
versionpath = os.path.join("VERSION")
if os.path.exists(versionpath):
version = open(versionpath, "r").read().strip()
if manual:
version = '"for IMP version ' + version + '"'
doxygen = self.template
if manual:
doxygen = doxygen.replace("@[email protected]", '"IMP Manual"')
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/manual/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/manual_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-tags.xml")
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", ".")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref-tags.xml=../ref")
doxygen = doxygen.replace("@[email protected]", "doxygen/manual/xml/")
doxygen = doxygen.replace("@[email protected]", "")
else:
doxygen = doxygen.replace("@[email protected]", '"IMP Reference Guide"')
doxygen = doxygen.replace("@[email protected]",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@[email protected]", "mainpage.md")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/ref/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]",
"doxygen/ref-tags.xml")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]",
"doc/examples %s/modules/example" % source)
doxygen = doxygen.replace("@[email protected]",
"doxygen/manual-tags.xml=../manual")
doxygen = doxygen.replace("@[email protected]", "doxygen/ref/xml/")
doxygen = doxygen.replace("@[email protected]",
"lib/IMP/kernel lib/IMP/base")
doxygen = doxygen.replace("@[email protected]", "IMP")
doxygen = doxygen.replace("@[email protected]", source) \
.replace("@[email protected]", version)
doxygen = doxygen.replace("@[email protected]", "include")
doxygen = doxygen.replace("@[email protected]",
"*.cpp *.h *.py *.md *.dox")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if is_html:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if manual:
inputsh = [source + "/doc/manual",
source + "/tools/README.md",
source + "/ChangeLog.md"]
else:
inputsh = ["doxygen/generated", source + "/doc/ref",
"include", "doc/examples", "lib/IMP"]
for m, p in tools.get_modules(source):
doc = os.path.join(p, "doc")
if os.path.exists(doc):
inputsh.append(doc + "/")
doxygen = doxygen.replace("@[email protected]", " ".join(inputsh))
return doxygen
def make_doxygen(options, modules):
file = os.path.join("doxygen", options.name, "Doxyfile")
name = options.name
template_file = os.path.join(
options.source,
"tools",
"build",
"doxygen_templates",
"Doxyfile.in")
template = open(template_file, "r").read()
template = template.replace("@[email protected]", options.source)
template = template.replace("@[email protected]", "NONE")
template = template.replace("@[email protected]", name)
template = template.replace("@[email protected]",
'"The Integrative Modeling Platform"')
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "*/tutorial/*")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "IMP." + name)
template = template.replace("@[email protected]", "../../doc/html/" + name)
template = template.replace("@[email protected]", "xml")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "tags")
template = template.replace("@[email protected]",
"%s/doc/doxygen/module_layout.xml" % options.source)
template = template.replace("@[email protected]", "README.md")
template = template.replace("@INCL[email protected]", "include")
template = template.replace("@[email protected]", "*.cpp *.h *.py *.md *.dox")
template = template.replace("@[email protected]", "warnings.txt")
# include lib and doxygen in imput
inputs = []
if options.name == "kernel":
inputs.append("include/IMP/")
exclude = ["include/IMP/%s include/IMP/%s.h" % (m, m)
for m, g in tools.get_modules(options.source) if m != "kernel"]
template = template.replace(
"@[email protected]",
" \\\n ".join(exclude))
else:
template = template.replace("@[email protected]", "")
inputs.append("include/IMP/" + options.name)
inputs.append("lib/IMP/" + options.name)
inputs.append("examples/" + options.name)
# suppress a warning since git removes empty dirs and doxygen gets confused
# if the input path doesn't exist
docpath = os.path.join(options.source, "modules", options.name, "doc")
if os.path.exists(docpath):
inputs.append(docpath)
# overview for module
inputs.append("../generated/IMP_%s.dox" % options.name)
template = template.replace(
"@[email protected]",
" \\\n ".join(inputs))
tags = []
for m in modules:
tags.append(os.path.join("../", m, "tags") + "=" + "../" + m)
template = template.replace(
"@[email protected]",
" \\\n ".join(tags))
if options.name == "example":
template = template.replace("@[email protected]",
"examples/example %s/modules/example" % options.source)
else:
template = template.replace(
"@[email protected]",
"examples/" + options.name)
tools.rewrite(file, template)
def check_readme():
for module, g in tools.get_modules("."):
if not os.path.exists(os.path.join(g, "README.md")):
sys.stderr.write("Each module must have a file 'README.md' describing what what it does and who wrote it.\n")
sys.stderr.write(module, "does not.\n")
exit(1)
def make_doxygen(options, modules):
file = os.path.join("doxygen", options.name, "Doxyfile")
name = options.name
template_file = os.path.join(options.source, "tools", "build",
"doxygen_templates", "Doxyfile.in")
template = open(template_file, "r").read()
template = template.replace("@[email protected]", options.source)
template = template.replace("@[email protected]", "NONE")
template = template.replace("@[email protected]", name)
template = template.replace("@[email protected]",
'"The Integrative Modeling Platform"')
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "*/tutorial/*")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "IMP." + name)
template = template.replace("@[email protected]", "../../doc/html/" + name)
template = template.replace("@[email protected]", "xml")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "tags")
template = template.replace(
"@[email protected]", "%s/doc/doxygen/module_layout.xml" % options.source)
template = template.replace("@[email protected]", "README.md")
template = template.replace("@[email protected]", "include")
template = template.replace("@[email protected]", "*.cpp *.h *.py *.md *.dox")
template = template.replace("@[email protected]", "warnings.txt")
# include lib and doxygen in imput
inputs = []
if options.name == "kernel":
inputs.append("include/IMP/")
exclude = [
"include/IMP/%s include/IMP/%s.h" % (m, m)
for m, g in tools.get_modules(options.source) if m != "kernel"
]
template = template.replace(
"@[email protected]", " \\\n ".join(exclude))
else:
template = template.replace("@[email protected]", "")
inputs.append("include/IMP/" + options.name)
inputs.append("lib/IMP/" + options.name)
inputs.append("examples/" + options.name)
# suppress a warning since git removes empty dirs and doxygen gets confused
# if the input path doesn't exist
docpath = os.path.join(options.source, "modules", options.name, "doc")
if os.path.exists(docpath):
inputs.append(docpath)
# overview for module
inputs.append("../generated/IMP_%s.dox" % options.name)
template = template.replace("@[email protected]",
" \\\n ".join(inputs))
tags = []
for m in modules:
tags.append(os.path.join("../", m, "tags") + "=" + "../" + m)
template = template.replace("@[email protected]",
" \\\n ".join(tags))
if options.name == "example":
template = template.replace(
"@[email protected]",
"examples/example %s/modules/example" % options.source)
else:
template = template.replace("@[email protected]",
"examples/" + options.name)
tools.rewrite(file, template)
def link_data(source):
target = os.path.join("data")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(os.path.join(g, "data"), os.path.join(target, module))
def link_examples(source):
target = os.path.join("doc", "examples")
tools.mkdir(target)
for module, g in tools.get_modules(source):
tools.link_dir(
os.path.join(g, "examples"), os.path.join(target, module))
def get_output_file_contents(self, options):
template = self.template
name = options.name
modules = self.modules
template = template.replace("@[email protected]", options.source)
template = template.replace("@[email protected]", "NONE")
template = template.replace("@[email protected]", name)
template = template.replace("@[email protected]",
'"The Integrative Modeling Platform"')
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "*/tutorial/*")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "YES")
template = template.replace("@[email protected]", "IMP." + name)
template = template.replace("@[email protected]", "../../doc/html/" + name)
template = template.replace("@[email protected]", "xml")
template = template.replace("@[email protected]", "NO")
template = template.replace("@[email protected]", "tags")
template = template.replace("@[email protected]",
"%s/doc/doxygen/module_layout.xml" % options.source)
template = template.replace("@[email protected]", "README.md")
template = template.replace("@[email protected]", "include")
template = template.replace("@[email protected]",
"*.cpp *.h *.py *.md *.dox")
template = template.replace("@[email protected]", "warnings.txt")
# include lib and doxygen in input
inputs = []
if options.name == "kernel":
inputs.append("lib/IMP/")
inputs.append("include/IMP/")
exclude = ["include/IMP/%s include/IMP/%s.h lib/IMP/%s" % (m, m, m)
for m, g in tools.get_modules(options.source)]
exclude.append("include/IMP/base include/IMP/base.h lib/IMP/base")
template = template.replace("@[email protected]",
" \\\n ".join(exclude))
else:
template = template.replace("@[email protected]", "")
inputs.append("include/IMP/" + options.name)
inputs.append("lib/IMP/" + options.name)
inputs.append("examples/" + options.name)
# suppress a warning since git removes empty dirs and doxygen
# gets confused if the input path doesn't exist
docpath = os.path.join(options.source, "modules", options.name, "doc")
if os.path.exists(docpath):
inputs.append(docpath)
# overview for module
inputs.append("../generated/IMP_%s.dox" % options.name)
template = template.replace("@[email protected]",
" \\\n ".join(inputs))
tags = [os.path.join(options.source, 'doc', 'doxygen',
'dummy_module_tags.xml')]
for m in modules:
tags.append(os.path.join("../", m, "tags") + "=" + "../" + m)
template = template.replace("@[email protected]",
" \\\n ".join(tags))
if options.name == "example":
template = template.replace("@[email protected]",
"examples/example %s/modules/example" % options.source)
else:
template = template.replace("@[email protected]",
"examples/" + options.name)
return template
def generate_tests(source, scons):
template = """import IMP
import IMP.test
import %(module)s
spelling_exceptions=%(spelling_exceptions)s
class StandardsTest(IMP.test.TestCase):
def test_value_objects(self):
"Test that module classes are either values or objects"
exceptions= %(value_object_exceptions)s
return self.assertValueObjects(%(module)s,exceptions)
def test_classes(self):
"Test that module class names follow the standards"
exceptions=%(value_object_exceptions)s
return self.assertClassNames(%(module)s, exceptions,
spelling_exceptions)
def test_functions(self):
"Test that module function names follow the standards"
exceptions= %(function_name_exceptions)s
return self.assertFunctionNames(%(module)s, exceptions,
spelling_exceptions)
def test_show(self):
"Test all objects have show"
exceptions=%(show_exceptions)s
return self.assertShow(%(module)s, exceptions)
if __name__ == '__main__':
IMP.test.main()
"""
target = os.path.join("test")
tools.mkdir(target)
for module, g in tools.get_modules(source):
targetdir = os.path.join(target, module)
tools.mkdir(targetdir)
exceptions = os.path.join(g, "test", "standards_exceptions")
plural_exceptions = []
show_exceptions = []
function_name_exceptions = []
value_object_exceptions = []
class_name_exceptions = []
spelling_exceptions = []
try:
exec open(exceptions, "r").read()
except:
pass
impmodule = "IMP." + module
test = template % (
{
'module': impmodule,
'plural_exceptions': str(plural_exceptions),
'show_exceptions': str(show_exceptions),
'function_name_exceptions': str(function_name_exceptions),
'value_object_exceptions': str(value_object_exceptions),
'class_name_exceptions': str(class_name_exceptions),
'spelling_exceptions': str(spelling_exceptions)
})
open(os.path.join("test", module, "medium_test_standards.py"),
"w").write(test)
cpptests = tools.get_glob([os.path.join(g, "test", "test_*.cpp")])
ecpptests = tools.get_glob(
[os.path.join(g, "test", "expensive_test_*.cpp")])
cppexamples = tools.get_glob([os.path.join(g, "examples", "*.cpp")])
if len(cpptests) > 0 and scons:
_make_test_driver(os.path.join(targetdir, "test_cpp_tests.py"),
cpptests)
if len(ecpptests) > 0 and scons:
_make_test_driver(
os.path.join(targetdir, "expensive_test_cpp_tests.py"),
cpptests)
if len(cppexamples) > 0 and scons:
_make_test_driver(os.path.join(targetdir, "cpp_examples_test.py"),
cppexamples)
for app, g in tools.get_applications(source):
tools.mkdir(os.path.join(target, app))
def generate_tests(source, scons):
template = """import IMP
import IMP.test
import %(module)s
spelling_exceptions=%(spelling_exceptions)s
class StandardsTest(IMP.test.TestCase):
def test_value_objects(self):
"Test that module classes are either values or objects"
exceptions= %(value_object_exceptions)s
return self.assertValueObjects(%(module)s,exceptions)
def test_classes(self):
"Test that module class names follow the standards"
exceptions=%(value_object_exceptions)s
return self.assertClassNames(%(module)s, exceptions,
spelling_exceptions)
def test_functions(self):
"Test that module function names follow the standards"
exceptions= %(function_name_exceptions)s
return self.assertFunctionNames(%(module)s, exceptions,
spelling_exceptions)
def test_show(self):
"Test all objects have show"
exceptions=%(show_exceptions)s
return self.assertShow(%(module)s, exceptions)
if __name__ == '__main__':
IMP.test.main()
"""
target = os.path.join("test")
tools.mkdir(target)
for module, g in tools.get_modules(source):
targetdir = os.path.join(target, module)
tools.mkdir(targetdir)
exceptions = os.path.join(g, "test", "standards_exceptions")
d = {'plural_exceptions': [],
'show_exceptions': [],
'function_name_exceptions': [],
'value_object_exceptions': [],
'class_name_exceptions': [],
'spelling_exceptions': []}
try:
exec(open(exceptions, "r").read(), d)
except IOError:
pass
impmodule = "IMP." + module
test = template % ({'module': impmodule,
'plural_exceptions': str(d['plural_exceptions']),
'show_exceptions': str(d['show_exceptions']),
'function_name_exceptions':
str(d['function_name_exceptions']),
'value_object_exceptions':
str(d['value_object_exceptions']),
'class_name_exceptions':
str(d['class_name_exceptions']),
'spelling_exceptions':
str(d['spelling_exceptions'])})
open(
os.path.join("test",
module,
"medium_test_standards.py"),
"w").write(test)
cpptests = tools.get_glob([os.path.join(g, "test", "test_*.cpp")])
ecpptests = tools.get_glob(
[os.path.join(g, "test", "expensive_test_*.cpp")])
cppexamples = tools.get_glob([os.path.join(g, "examples", "*.cpp")])
if len(cpptests) > 0 and scons:
_make_test_driver(
os.path.join(
targetdir,
"test_cpp_tests.py"),
cpptests)
if len(ecpptests) > 0 and scons:
_make_test_driver(
os.path.join(targetdir,
"expensive_test_cpp_tests.py"),
cpptests)
if len(cppexamples) > 0 and scons:
_make_test_driver(
os.path.join(targetdir,
"cpp_examples_test.py"),
cppexamples)
def generate_doxyfile(source, target, is_xml = False, is_html = False, tutorial=False):
doxyin=os.path.join(source, "tools", "build", "doxygen_templates", "Doxyfile.in")
version="develop"
versionpath=os.path.join("VERSION")
if os.path.exists(versionpath):
version= open(versionpath, "r").read().strip()
if tutorial:
version = '"for IMP version ' + version + '"'
doxygen = open(doxyin, "r").read()
if tutorial:
doxygen = doxygen.replace("@[email protected]", '"IMP Tutorial"')
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "NO")
doxygen = doxygen.replace("@[email protected]", "doc/tutorial/")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "doxygen/tutorial-warnings.txt")
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", ".")
doxygen = doxygen.replace("@[email protected]", "doxygen/tags.html=../html")
else:
doxygen = doxygen.replace("@[email protected]", "IMP")
doxygen = doxygen.replace("@[email protected]",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@[email protected]", "mainpage.md")
doxygen = doxygen.replace("@[email protected]", "YES")
doxygen = doxygen.replace("@[email protected]", "doc/html/")
doxygen = doxygen.replace("@[email protected]",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@[email protected]", "doxygen/tags.html")
doxygen = doxygen.replace("@[email protected]", "doxygen/warnings.txt")
doxygen = doxygen.replace("@[email protected]", "*/tutorial/*")
doxygen = doxygen.replace("@[email protected]", "doc/examples %s/modules/example"%source)
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace( "@[email protected]", "IMP")
doxygen = doxygen.replace( "@[email protected]", source).replace("@[email protected]", version)
doxygen = doxygen.replace("@[email protected]", "")
doxygen = doxygen.replace("@[email protected]", "include")
doxygen = doxygen.replace("@[email protected]", "*.cpp *.h *.py *.md *.dox")
doxygen = doxygen.replace("@[email protected]", "doxygen/xml/")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@[email protected]", "YES")
else:
doxygen = doxygen.replace("@[email protected]", "NO")
if is_html:
doxygen = doxygen.replace( "@[email protected]", "YES")
else:
doxygen = doxygen.replace( "@[email protected]", "NO")
# skip linking later
inputsh = ["doxygen/generated", source + "/doc", source + "/ChangeLog.md",
source + "/tools/README.md", "include", "doc/examples"]
for m, p in tools.get_modules(source):
doc = os.path.join(p, "doc")
inputsh.append(os.path.join("lib", "IMP", m))
if os.path.exists(doc):
inputsh.append(doc + "/")
for m, p in tools.get_applications(source):
doc = os.path.join(p, "doc")
if os.path.exists(doc):
inputsh.append(doc + "/")
if not tutorial:
doxygen = doxygen.replace("@[email protected]", " ".join(inputsh))
open(target, "w").write(doxygen)
