updated docs and requirements

sys-bio · Jan 27, 2016 · 4c907fa · 4c907fa
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Showing 31 changed files with 12 additions and 6 deletions.
diff --git a/docs/README.md b/docs/README.md
@@ -78,4 +78,6 @@ To build the complete API documentation use the build script `make_docs.sh` in t
 * creates the `html` documentation (analoque to minimal build)
 
 ## Open Issues
+* API `.. autofunction::` & `automodule:: create` created locally but not on readthedocs.org
 * links between functions in documentation (i.e. hyperlinks between functions for easy navigation in API)
+
diff --git a/docs/_build/html/.doctrees/API.doctree b/docs/_build/html/.doctrees/API.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.Export.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.Export.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.ParameterScan.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.ParameterScan.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.analysis.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.analysis.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.notebooktools.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.notebooktools.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.optimization.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.optimization.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.tests.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.tests.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.visualization.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.visualization.doctree
diff --git a/docs/_build/html/.doctrees/_apidoc/tellurium.widgets.doctree b/docs/_build/html/.doctrees/_apidoc/tellurium.widgets.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/computeSteadyState.doctree b/docs/_build/html/.doctrees/_notebooks/core/computeSteadyState.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/consecutiveUniUniReactions.doctree b/docs/_build/html/.doctrees/_notebooks/core/consecutiveUniUniReactions.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/feedback_oscillations.doctree b/docs/_build/html/.doctrees/_notebooks/core/feedback_oscillations.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/generatingDifferentWaveforms.doctree b/docs/_build/html/.doctrees/_notebooks/core/generatingDifferentWaveforms.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/introduction.doctree b/docs/_build/html/.doctrees/_notebooks/core/introduction.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/nonUnitStoichiometries.doctree b/docs/_build/html/.doctrees/_notebooks/core/nonUnitStoichiometries.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/parameter_scan.doctree b/docs/_build/html/.doctrees/_notebooks/core/parameter_scan.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/steadystate_scan.doctree b/docs/_build/html/.doctrees/_notebooks/core/steadystate_scan.doctree
diff --git a/docs/_build/html/.doctrees/_notebooks/core/template.doctree b/docs/_build/html/.doctrees/_notebooks/core/template.doctree
diff --git a/docs/_build/html/.doctrees/environment.pickle b/docs/_build/html/.doctrees/environment.pickle
diff --git a/docs/_build/html/.doctrees/index.doctree b/docs/_build/html/.doctrees/index.doctree
diff --git a/docs/_build/html/.doctrees/installation.doctree b/docs/_build/html/.doctrees/installation.doctree
diff --git a/docs/_build/html/.doctrees/introduction.doctree b/docs/_build/html/.doctrees/introduction.doctree
diff --git a/docs/_build/html/.doctrees/notebooks.doctree b/docs/_build/html/.doctrees/notebooks.doctree
diff --git a/docs/_build/html/.doctrees/tellurium_methods.doctree b/docs/_build/html/.doctrees/tellurium_methods.doctree
diff --git a/docs/_build/html/API.html b/docs/_build/html/API.html
@@ -129,8 +129,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="api">
-<h1>API<a class="headerlink" href="#api" title="Permalink to this headline">¶</a></h1>
+  <div class="section" id="module-tellurium">
+<span id="api"></span><h1>API<a class="headerlink" href="#module-tellurium" title="Permalink to this headline">¶</a></h1>
 </div>
 
 

diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
diff --git a/docs/make_docs.sh b/docs/make_docs.sh
@@ -34,7 +34,8 @@ echo "DONE"
 echo "--------------------------------------"
 echo "create html docs"
 echo "--------------------------------------"
-make html
+# make html
+sphinx-build -b html . _build/html
 echo "DONE"
 
 # the new documentation is now in docs/_built

diff --git a/requirements.txt b/requirements.txt
@@ -1,16 +1,19 @@
+# not installable via pip
 roadrunner
 antimony
-libsbml
 libsedml
 phrasedml
 sbml2matlab
+sedml2py        # unzipy used in SedmlToRr but not available
+
+# installable via pip
+python-libsbml
 ipywidgets
 bioservices
 matplotlib
 numpy
 pygraphviz
 ipython
-sedml2py        # unzipy used in SedmlToRr but not available
 
 # for testing
 nose