improved docs

mfiers · May 30, 2012 · bde341f · bde341f
1 parent 49164ad
commit bde341f
Show file tree

Hide file tree

Showing 38 changed files with 71 additions and 109 deletions.
diff --git a/lib/jinja2/plugin.index.rst.jinja2 b/lib/jinja2/plugin.index.rst.jinja2
@@ -4,6 +4,6 @@ moa.plugin
 .. toctree::
    :maxdepth: 2
 
-   {% for plugin in plugins -%}
-   {{plugin}}
+   {% for category, plugin in plugins -%}
+   {{category}}__{{plugin}}
    {% endfor %}
diff --git a/lib/jinja2/plugin.rst.jinja2 b/lib/jinja2/plugin.rst.jinja2
@@ -1,2 +1,2 @@
-.. automodule:: moa.plugin.{{name}}
+.. automodule:: {{module}}
    :members:
diff --git a/lib/python/moa/backend/ruff/map.py b/lib/python/moa/backend/ruff/map.py
@@ -104,7 +104,7 @@ def generate_data_map():
                            for x in self.job.data.inputs]
 
                 l.debug('pushing job with inputs %s' % ", ".join(inputs[:10]))
-                                
+
                 fsDict = dict([(x, self.job.data.filesets[x]['files'][i])
                                for x in self.job.data.inputs + self.job.data.outputs])
 

diff --git a/sphinx/Makefile b/sphinx/Makefile
@@ -32,13 +32,17 @@ help:
 
 ghpages:
 	cp -r  $(BUILDDIR)/html/* $(GHPAGES)/
-	cd $(GHPAGES) && git commit -m 'rebuild documentation' -a || true && pwd && git push
+	cd $(GHPAGES) && \
+		sh add_all_to_repo.sh && \
+		git commit -m 'rebuild documentation' -a || true && \
+		pwd && \
+		git push
 
 clean:
 	-rm -rf $(BUILDDIR)/*
 
 prepare:
-	cd templates && rm -r *.rst && ./refresh_templates
+	cd templates &&  ( rm -rf *.rst || true ) && ./refresh_templates
 	cd commands && ./update_commands
 
 html: prepare pdf

diff --git a/sphinx/api/plugin/adhoc.rst b/sphinx/api/plugin/adhoc.rst
diff --git a/sphinx/api/plugin/checkversion.rst b/sphinx/api/plugin/checkversion.rst
diff --git a/sphinx/api/plugin/configure.rst b/sphinx/api/plugin/configure.rst
diff --git a/sphinx/api/plugin/doc.rst b/sphinx/api/plugin/doc.rst
diff --git a/sphinx/api/plugin/extraCommands.rst b/sphinx/api/plugin/extraCommands.rst
diff --git a/sphinx/api/plugin/fileset.rst b/sphinx/api/plugin/fileset.rst
diff --git a/sphinx/api/plugin/help.rst b/sphinx/api/plugin/help.rst
diff --git a/sphinx/api/plugin/index.rst b/sphinx/api/plugin/index.rst
@@ -4,31 +4,26 @@ moa.plugin
 .. toctree::
    :maxdepth: 2
 
-   adhoc
-   checkversion
-   configure
-   doc
-   extraCommands
-   fileset
-   help
-   info
-   lock
-   logger
-   logo
-   mail
-   metavar
-   moaGit
-   moautil
-   newjob
-   parameterCheck
-   project
-   prompt
-   report
-   sgeActor
-   status
-   template
-   test
-   twit
-   umask
-   varInject
+   job__metavar
+   system__adhoc
+   system__configure
+   system__doc
+   system__extraCommands
+   system__fileset
+   system__help
+   system__info
+   system__lock
+   system__logger
+   system__moaGit
+   system__moautil
+   system__newjob
+   system__parameterCheck
+   system__project
+   system__remoteLogger
+   system__smw
+   system__status
+   system__template
+   system__test
+   system__umask
+   system__varInject
 
diff --git a/sphinx/api/plugin/info.rst b/sphinx/api/plugin/info.rst
diff --git a/sphinx/api/plugin/lock.rst b/sphinx/api/plugin/lock.rst
diff --git a/sphinx/api/plugin/logger.rst b/sphinx/api/plugin/logger.rst
diff --git a/sphinx/api/plugin/logo.rst b/sphinx/api/plugin/logo.rst
diff --git a/sphinx/api/plugin/mail.rst b/sphinx/api/plugin/mail.rst
diff --git a/sphinx/api/plugin/metavar.rst b/sphinx/api/plugin/metavar.rst
diff --git a/sphinx/api/plugin/moaGit.rst b/sphinx/api/plugin/moaGit.rst
diff --git a/sphinx/api/plugin/moautil.rst b/sphinx/api/plugin/moautil.rst
diff --git a/sphinx/api/plugin/newjob.rst b/sphinx/api/plugin/newjob.rst
diff --git a/sphinx/api/plugin/parameterCheck.rst b/sphinx/api/plugin/parameterCheck.rst
diff --git a/sphinx/api/plugin/project.rst b/sphinx/api/plugin/project.rst
diff --git a/sphinx/api/plugin/prompt.rst b/sphinx/api/plugin/prompt.rst
diff --git a/sphinx/api/plugin/refresh_plugins b/sphinx/api/plugin/refresh_plugins
@@ -1,12 +1,16 @@
 #!/usr/bin/env python
 
 import os
+import sys
 import yaml
 import moa.utils
 import moa.template
 
 import moa.logger as l
 
+
+from moa.sysConf import sysConf
+
 from jinja2 import Template as jTemplate
 
 tPluginFile = os.path.join(
@@ -17,22 +21,20 @@ tIndexFile = os.path.join(
 tPlugin = jTemplate(open(tPluginFile).read())
 tIndex = jTemplate(open(tIndexFile).read())
 
-os.chdir(os.path.join(moa.utils.getMoaBase(), 'sphinx', 'api', 'plugin'))
-
 all_plugs = []
 l.warning("start parsing plugins")
-plugindir = os.path.join(moa.utils.getMoaBase(), 'lib', 'python', 'moa', 'plugin')
-l.warning("in directory %s" % plugindir)
-
-for plugin in os.listdir(plugindir):
-    if not os.path.isdir(os.path.join(plugindir, plugin)):
-        continue
-    pluginfile = os.path.join(plugindir, plugin, '__init__.py')
-    name = plugin
-    print 'Found plugin: ' + name
-    all_plugs.append(name)    
-    with open('%s.rst' % name, 'w') as F:
-        F.write(tPlugin.render({'name' : name}))
+#plugindir = os.path.join(moa.utils.getMoaBase(), 'lib', 'python', 'moa', 'plugin')
+#l.warning("in directory %s" % plugindir)
+
+for category in ['job', 'system']:
+    for plugin in sysConf.plugins[category].keys():
+        plugInfo = sysConf.plugins[category].get(plugin, {})
+        module = plugInfo.module
+        name = plugin
+        print 'Found plugin: ', category, name
+        all_plugs.append((category, name))
+        with open('%s__%s.rst' % (category, name), 'w') as F:
+            F.write(tPlugin.render({'module' : module}))
 
 all_plugs.sort()
 with open("index.rst", 'w') as F:

diff --git a/sphinx/api/plugin/report.rst b/sphinx/api/plugin/report.rst
diff --git a/sphinx/api/plugin/sgeActor.rst b/sphinx/api/plugin/sgeActor.rst
diff --git a/sphinx/api/plugin/status.rst b/sphinx/api/plugin/status.rst
diff --git a/sphinx/api/plugin/template.rst b/sphinx/api/plugin/template.rst
diff --git a/sphinx/api/plugin/test.rst b/sphinx/api/plugin/test.rst
diff --git a/sphinx/api/plugin/twit.rst b/sphinx/api/plugin/twit.rst
diff --git a/sphinx/api/plugin/umask.rst b/sphinx/api/plugin/umask.rst
diff --git a/sphinx/api/plugin/varInject.rst b/sphinx/api/plugin/varInject.rst
diff --git a/sphinx/commands/index.rst b/sphinx/commands/index.rst
@@ -89,8 +89,8 @@ moa **change**
 ~~~~~~~~~~~~~~~~~~
 usage: moa change [-h] [-r] [-v] [--profile]
 
-Add entry to Changelog.md This function allows the user to add an entry to
-Changelog.md (including a timestamp). Use it as follows:: $ moa change Enter
+Add entry to CHANGELOG.md This function allows the user to add an entry to
+CHANGELOG.md (including a timestamp). Use it as follows:: $ moa change Enter
 your changelog message (ctrl-d on an empty line to finish) ... enter your
 message here .. [ctrl-d] Note: the ctrl-d needs to be given on an empty line.
 The text is appended to moa.desciption. In the web interface this is converted
@@ -390,7 +390,7 @@ moa **readme**
 ~~~~~~~~~~~~~~~~~~
 usage: moa readme [-h] [-r] [-v] [--profile]
 
-Edit the Readme.md file for this job You could, obviously, also edit the file
+Edit the README.md file for this job You could, obviously, also edit the file
 yourself - this is a mere shortcut to try to stimulate you in maintaining one
 
 optional arguments:

diff --git a/sphinx/index.rst b/sphinx/index.rst
@@ -34,6 +34,7 @@ Table of contents:
    intro   
    install
    coretemplates
+   sync
    #using
    #configuration
    #filesets

diff --git a/sphinx/install.rst b/sphinx/install.rst
@@ -76,11 +76,13 @@ and many more
 Installing git (from github)
 ----------------------------
 
-Moa is hosted on and can be installed from `github <http://github.com/mfiers/Moa>`_::
+Moa is hosted on, and can be installed from, `github <http://github.com/mfiers/Moa>`_::
 
     cd ~
     git clone git://github.com/mfiers/Moa.git moa
 
+Note - their is also a copy of moa in the python package index - this
+one is almost certainly outdated, and is currently not supported.
 
 Configuration
 -------------
@@ -108,9 +110,9 @@ are a few options that you can pursue:
 Installing the web interface
 ----------------------------
 
-Note - this is experimental - you will probably need to fiddle a
-little with the configuration to get it working. Start with installing
-apache2. 
+Note - this is highly experimental - you will probably need to fiddle
+with the configuration files to get it working. Start with installing
+apache2.
 
 Then - assuming that:
 * Your Moa work directory is under /home/moa/work

diff --git a/sphinx/templates/refresh_templates b/sphinx/templates/refresh_templates
@@ -21,7 +21,10 @@ os.chdir(os.path.join(moa.utils.getMoaBase(), 'sphinx', 'templates'))
 _allTemplates = []
 for tfile in moa.template.templateList():
     print tfile
-    template = moa.template.getMoaFile(tfile)
+    template = moa.template.getMoaFile(tfile)    
+    if not template: 
+        continue
+
     tname = template.moa_id
     assert(template.moa_id == tfile)
 

diff --git a/template2/hagfish.jinja2 b/template2/hagfish.jinja2
@@ -1,13 +1,22 @@
 ### run
 
+echo "Running Hagfish:"
+echo "Input file is {{ input }}"
+echo "Output file is {{ output }}"
+
 mkdir -p touch
+echo hagfish_extract -v --low {{ min_ok }} --high {{ max_ok }} {{ input }}
 hagfish_extract -v --low {{ min_ok }} --high {{ max_ok }} {{ input }}
 echo touch {{ output }}
+touch {{ output }}
 
 ### finish
 
+echo hagfish_gapfinder -v -f {{ fasta }}
 hagfish_gapfinder -v -f {{ fasta }}
+echo hagfish_coverage_combine -v
 hagfish_coverage_combine -v
+echo hagfish_report -v
 hagfish_report -v
 
 ### clean