def generate_api_doc(self):
"""
This generates API doc in HTML format and include this into distribution.
"""
# Create a TMP folder where to store generated RST files.
temp_folder = tempfile.mktemp(prefix='tvb_sphinx_rst_')
try:
os.makedirs(temp_folder)
opts = GenOptions(None, 'rst', temp_folder, 'Project', 10, True, None)
import tvb
# Start to create RST files needed for Sphinx to generate final HTML
process_sources(opts, tvb.__path__, self.EXCLUDES)
# Now generate HTML doc
conf_folder = os.path.dirname(tvb_documentor.api_doc.generate_modules.__file__)
args = ['anything', # Ignored but must be there
'-b', 'html', # Specify builder: html, dirhtml, singlehtml, txt, latex, pdf,
'-a', # Use option "-a" : build all
'-q', # Log only Warn and Error
'-c', conf_folder, # Specify path where to find conf.py
'-d', temp_folder,
temp_folder, # Source folder
self._dist_api_folder, # Output folder
]
# This include should stay here, otherwise generation of PDFs will crash
from sphinx.cmdline import main as sphinx_build
sphinx_build(args)
finally:
# Delete temp folder
if os.path.exists(temp_folder):
shutil.rmtree(temp_folder)
def make_rest(core_path, settings, gene_symbols, scandb_results, direct_ints):
# Directory path to write ReST and HTML files.
dir_path = settings.outdir
# Create directory for rst files.
rst_path = os.path.join(dir_path, "rst")
html_path = os.path.join(dir_path, "html")
os.mkdir(rst_path)
os.mkdir(html_path)
# Write ReST formatted output.
index = os.path.join(rst_path, "index.rst")
with open(index, 'w') as f:
write_rest_index(f)
input = os.path.join(rst_path, "input.rst")
with open(input, 'w') as f:
write_rest_input(settings, f)
genes = os.path.join(rst_path, "genes.rst")
with open(genes, 'w') as f:
Gene.writeReST(gene_symbols, settings.db_file, settings.terms, f)
terms = os.path.join(rst_path, "terms.rst")
with open(terms, 'w') as f:
write_rest_terms(gene_symbols, f)
eqtls = os.path.join(rst_path, "eqtls.rst")
with open(eqtls, 'w') as f:
write_rest_eqtls(scandb_results, f)
inters = os.path.join(rst_path, "interactions.rst")
with open(inters, 'w') as f:
write_rest_ints(direct_ints, f)
# Write README file.
write_readme(os.path.join(dir_path, "README.txt"))
# Run sphinx build process.
try:
from sphinx.cmdline import main as sphinx_build
except:
raise Exception("Error: sphinx is not installed.")
args = [
core_path, "-Q", "-b", "html", "-c", core_path, rst_path, html_path
]
try:
sphinx_build(args)
report_index = os.path.join(html_path, "index.html")
print "HTML report created: %s." % report_index
except:
raise
def generate_api_doc(self):
"""
This generates API doc in HTML format and include this into distribution.
"""
# Create a TMP folder where to store generated RST files.
temp_folder = tempfile.mktemp(prefix='tvb_sphinx_rst_')
try:
os.makedirs(temp_folder)
opts = GenOptions(None, 'rst', temp_folder, 'Project', 10, True,
None)
import tvb
# Start to create RST files needed for Sphinx to generate final HTML
process_sources(opts, tvb.__path__, self.EXCLUDES)
# Now generate HTML doc
conf_folder = os.path.dirname(
tvb_documentor.api_doc.generate_modules.__file__)
args = [
'anything', # Ignored but must be there
'-b',
'html', # Specify builder: html, dirhtml, singlehtml, txt, latex, pdf,
'-a', # Use option "-a" : build all
'-q', # Log only Warn and Error
'-c',
conf_folder, # Specify path where to find conf.py
'-d',
temp_folder,
temp_folder, # Source folder
self._dist_api_folder, # Output folder
]
# This include should stay here, otherwise generation of PDFs will crash
from sphinx.cmdline import main as sphinx_build
sphinx_build(args)
finally:
# Delete temp folder
if os.path.exists(temp_folder):
shutil.rmtree(temp_folder)
def _run_sphinx(self, builder, src_folder, dest_folder, args=None):
if args is None:
args = []
sphinx_args = [
'anything', # Ignored but must be there
'-b',
builder, # Specify builder: html, dirhtml, singlehtml, txt, latex, pdf,
'-a', # Use option "-a" : build all
'-q', # Log only Warn and Error
] + args + [src_folder, dest_folder]
status = sphinx_build(sphinx_args)
if status != 0:
raise Exception('sphinx build failure')
def make_rest(core_path,settings,gene_symbols,scandb_results,direct_ints):
# Directory path to write ReST and HTML files.
dir_path = settings.outdir;
# Create directory for rst files.
rst_path = os.path.join(dir_path,"rst");
html_path = os.path.join(dir_path,"html");
os.mkdir(rst_path);
os.mkdir(html_path);
# Write ReST formatted output.
index = os.path.join(rst_path,"index.rst");
with open(index,'w') as f:
write_rest_index(f);
input = os.path.join(rst_path,"input.rst");
with open(input,'w') as f:
write_rest_input(settings,f);
genes = os.path.join(rst_path,"genes.rst");
with open(genes,'w') as f:
Gene.writeReST(gene_symbols,settings.db_file,settings.terms,f);
terms = os.path.join(rst_path,"terms.rst");
with open(terms,'w') as f:
write_rest_terms(gene_symbols,f);
eqtls = os.path.join(rst_path,"eqtls.rst");
with open(eqtls,'w') as f:
write_rest_eqtls(scandb_results,f);
inters = os.path.join(rst_path,"interactions.rst");
with open(inters,'w') as f:
write_rest_ints(direct_ints,f);
# Write README file.
write_readme(os.path.join(dir_path,"README.txt"));
# Run sphinx build process.
try:
from sphinx.cmdline import main as sphinx_build
except:
raise Exception("Error: sphinx is not installed.");
args = [
core_path,
"-Q",
"-b",
"html",
"-c",
core_path,
rst_path,
html_path
];
try:
sphinx_build(args);
report_index = os.path.join(html_path,"index.html");
print "HTML report created: %s." % report_index;
except:
raise;
