make our API docstrings more epydoc friendly

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 54659b4ffd65aae40163b15dc630aae14f1710ff..a10c909afc5f8f84f53a91f903289454fa3e58a8 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -1,4 +1,9 @@
+"""
+Extract configuration from Illumina Bustard Directory.
 
+This includes the version number, run date, bustard executable parameters, and 
+phasing estimates. 
+"""
 from datetime import date
 from glob import glob
 import logging
@@ -11,6 +16,9 @@ from htsworkflow.pipelines.runfolder import \
    VERSION_RE, \
    EUROPEAN_STRPTIME
 
+# make epydoc happy
+__docformat__ = "restructuredtext en"
+
 class Phasing(object):
     PHASING = 'Phasing'
     PREPHASING = 'Prephasing'
@@ -124,7 +132,13 @@ class Bustard(object):
 
 def bustard(pathname):
     """
-    Construct a Bustard object from pathname
+    Construct a Bustard object by analyzing an Illumina Bustard directory.
+
+    :Parameters:
+      - `pathname`: A bustard directory
+
+    :Return:
+      Fully initialized Bustard object.
     """
     b = Bustard()
     path, name = os.path.split(pathname)
@@ -143,6 +157,9 @@ def bustard(pathname):
     return b
 
 def fromxml(tree):
+    """
+    Reconstruct a htsworkflow.pipelines.Bustard object from an xml block
+    """
     b = Bustard()
     b.set_elements(tree)
     return b

diff --git a/htsworkflow/pipelines/configure_run.py b/htsworkflow/pipelines/configure_run.py
index ec6da51531058588789b573c8635ace05942ce39..2174de1b31dc084b1cc67930a87184be65fb78d3 100644 (file)
--- a/htsworkflow/pipelines/configure_run.py
+++ b/htsworkflow/pipelines/configure_run.py
@@ -1,4 +1,6 @@
 #!/usr/bin/python
+__docformat__ = "restructuredtext en"
+
 import subprocess
 import logging
 import time

diff --git a/htsworkflow/pipelines/firecrest.py b/htsworkflow/pipelines/firecrest.py
index 4fbde5d517ac661cfecd68ff8ab2fff2472f5d9f..847f608bcb5be87832266037dfc9350d1b61b128 100644 (file)
--- a/htsworkflow/pipelines/firecrest.py
+++ b/htsworkflow/pipelines/firecrest.py
@@ -1,10 +1,13 @@
 """
 Extract information about the Firecrest run
 
-Firecrest - class holding the properties we found
-firecrest - Firecrest factory function initalized from a directory name
-fromxml - Firecrest factory function initalized from an xml dump from
-          the Firecrest object.
+Firecrest 
+  class holding the properties we found
+firecrest 
+  Firecrest factory function initalized from a directory name
+fromxml 
+  Firecrest factory function initalized from an xml dump from
+  the Firecrest object.
 """
 
 from datetime import date
@@ -17,6 +20,8 @@ from htsworkflow.pipelines.runfolder import \
    VERSION_RE, \
    EUROPEAN_STRPTIME
 
+__docformat__ = "restructuredtext en"
+
 class Firecrest(object):
     XML_VERSION=1
 

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index 3d90868910a37d16d4b9b7f70a042294553f0485..9113d6f1717fd6fd2d27fe9c2bd1e848766f2b5d 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -1,11 +1,15 @@
 """
 Extract information about the IPAR run
 
-IPAR - class holding the properties we found
-IPAR - IPAR factory function initalized from a directory name
-fromxml - IPAR factory function initalized from an xml dump from
-          the IPAR object.
+IPAR 
+    class holding the properties we found
+ipar
+    IPAR factory function initalized from a directory name
+fromxml
+    IPAR factory function initalized from an xml dump from
+    the IPAR object.
 """
+__docformat__ = "restructuredtext en"
 
 import datetime
 import logging

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 5c6ec571fb20808a86fdb6633c9f1a2f22610849..13805c9514db7810f6c0c74671ff2c8afa424b6a 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -8,6 +8,8 @@ import os
 import sys
 import urllib2
 
+__docformat__ = "restructredtext en"
+
 CONFIG_SYSTEM = '/etc/hts_frontend/hts_frontend.conf'
 CONFIG_USER = os.path.expanduser('~/.hts_frontend.conf')
 

diff --git a/htsworkflow/pipelines/run_status.py b/htsworkflow/pipelines/run_status.py
index 2f1a695b333d147455f3a9449684742db1fca2ae..e6a3ed8e6b2f41793f1109dac1334900860e8eaf 100644 (file)
--- a/htsworkflow/pipelines/run_status.py
+++ b/htsworkflow/pipelines/run_status.py
@@ -1,3 +1,5 @@
+__docformat__ = "restructuredtext en"
+
 import glob
 import re
 import os
@@ -397,11 +399,12 @@ def _cmdLineStatusMonitorFunc(conf_info):
   You should probably use startCmdLineStatusMonitor()
   instead of ths function.
 
-  Use with:
-    t = threading.Thread(target=_cmdLineStatusMonitorFunc,
-                         args=[conf_info])
-    t.setDaemon(True)
-    t.start()
+  .. python:
+    def example_launch():
+        t = threading.Thread(target=_cmdLineStatusMonitorFunc,
+                             args=[conf_info])
+        t.setDaemon(True)
+        t.start()
   """
   SLEEP_AMOUNT = 30