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):
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_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_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_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_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 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(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 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 generate_overview_pages(source):
name = os.path.join("doxygen", "generated", "applications.dox")
contents = []
contents.append("/** ")
contents.append("\\page applications All IMP Applications")
contents.append("""
IMP provides a number of applications (command line tools).
These are listed below:""")
for bs, g in tools.get_applications(source):
contents.append("- \subpage imp%s \"IMP.%s\"" % (bs, bs))
p = pickle.load(
open(os.path.join("data", "build_info", "IMP_%s.pck" % 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 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_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("@PROJECT_NAME@", '"IMP Tutorial"')
doxygen = doxygen.replace("@PROJECT_BRIEF@", "")
doxygen = doxygen.replace("@MAINPAGE@", "")
doxygen = doxygen.replace("@RECURSIVE@", "NO")
doxygen = doxygen.replace("@HTML_OUTPUT@", "doc/tutorial/")
doxygen = doxygen.replace("@LAYOUT_FILE@", "")
doxygen = doxygen.replace("@GENERATE_TAGFILE@", "")
doxygen = doxygen.replace("@WARNINGS@", "doxygen/tutorial-warnings.txt")
doxygen = doxygen.replace("@EXCLUDE_PATTERNS@", "")
doxygen = doxygen.replace("@EXAMPLE_PATH@", ".")
doxygen = doxygen.replace("@TAGS@", "doxygen/tags.html=../html")
else:
doxygen = doxygen.replace("@PROJECT_NAME@", "IMP")
doxygen = doxygen.replace("@PROJECT_BRIEF@",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@MAINPAGE@", "mainpage.md")
doxygen = doxygen.replace("@RECURSIVE@", "YES")
doxygen = doxygen.replace("@HTML_OUTPUT@", "doc/html/")
doxygen = doxygen.replace("@LAYOUT_FILE@",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@GENERATE_TAGFILE@", "doxygen/tags.html")
doxygen = doxygen.replace("@WARNINGS@", "doxygen/warnings.txt")
doxygen = doxygen.replace("@EXCLUDE_PATTERNS@", "*/tutorial/*")
doxygen = doxygen.replace("@EXAMPLE_PATH@", "doc/examples %s/modules/example"%source)
doxygen = doxygen.replace("@TAGS@", "")
doxygen = doxygen.replace( "@NAME@", "IMP")
doxygen = doxygen.replace( "@IMP_SOURCE_PATH@", source).replace("@VERSION@", version)
doxygen = doxygen.replace("@EXCLUDE@", "")
doxygen = doxygen.replace("@INCLUDE_PATH@", "include")
doxygen = doxygen.replace("@FILE_PATTERNS@", "*.cpp *.h *.py *.md *.dox")
doxygen = doxygen.replace("@XML_OUTPUT@", "doxygen/xml/")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@IS_XML@", "YES")
else:
doxygen = doxygen.replace("@IS_XML@", "NO")
if is_html:
doxygen = doxygen.replace( "@IS_HTML@", "YES")
else:
doxygen = doxygen.replace( "@IS_HTML@", "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("@INPUT_PATH@", " ".join(inputsh))
open(target, "w").write(doxygen)
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, "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_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("@PROJECT_NAME@", '"IMP Tutorial"')
doxygen = doxygen.replace("@PROJECT_BRIEF@", "")
doxygen = doxygen.replace("@MAINPAGE@", "")
doxygen = doxygen.replace("@RECURSIVE@", "NO")
doxygen = doxygen.replace("@HTML_OUTPUT@", "doc/tutorial/")
doxygen = doxygen.replace("@LAYOUT_FILE@", "")
doxygen = doxygen.replace("@GENERATE_TAGFILE@", "")
doxygen = doxygen.replace("@WARNINGS@",
"doxygen/tutorial-warnings.txt")
doxygen = doxygen.replace("@EXCLUDE_PATTERNS@", "")
doxygen = doxygen.replace("@EXAMPLE_PATH@", ".")
doxygen = doxygen.replace("@TAGS@", "doxygen/tags.html=../html")
else:
doxygen = doxygen.replace("@PROJECT_NAME@", "IMP")
doxygen = doxygen.replace("@PROJECT_BRIEF@",
'"The Integrative Modeling Platform"')
doxygen = doxygen.replace("@MAINPAGE@", "mainpage.md")
doxygen = doxygen.replace("@RECURSIVE@", "YES")
doxygen = doxygen.replace("@HTML_OUTPUT@", "doc/html/")
doxygen = doxygen.replace("@LAYOUT_FILE@",
"%s/doc/doxygen/main_layout.xml" % source)
doxygen = doxygen.replace("@GENERATE_TAGFILE@", "doxygen/tags.html")
doxygen = doxygen.replace("@WARNINGS@", "doxygen/warnings.txt")
doxygen = doxygen.replace("@EXCLUDE_PATTERNS@", "*/tutorial/*")
doxygen = doxygen.replace("@EXAMPLE_PATH@",
"doc/examples %s/modules/example" % source)
doxygen = doxygen.replace("@TAGS@", "")
doxygen = doxygen.replace("@NAME@", "IMP")
doxygen = doxygen.replace("@IMP_SOURCE_PATH@",
source).replace("@VERSION@", version)
doxygen = doxygen.replace("@EXCLUDE@", "")
doxygen = doxygen.replace("@INCLUDE_PATH@", "include")
doxygen = doxygen.replace("@FILE_PATTERNS@", "*.cpp *.h *.py *.md *.dox")
doxygen = doxygen.replace("@XML_OUTPUT@", "doxygen/xml/")
# TAGS, INPUT_PATH
if is_xml:
doxygen = doxygen.replace("@IS_XML@", "YES")
else:
doxygen = doxygen.replace("@IS_XML@", "NO")
if is_html:
doxygen = doxygen.replace("@IS_HTML@", "YES")
else:
doxygen = doxygen.replace("@IS_HTML@", "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("@INPUT_PATH@", " ".join(inputsh))
open(target, "w").write(doxygen)