GitHub - jrfaeder/cellblender_tutorials: CellBlender Tutorials

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blends		blends
images		images
organelle_images		organelle_images
project_files		project_files
.gitignore		.gitignore
CellOrganelle12.rst		CellOrganelle12.rst
FAQ.rst		FAQ.rst
Makefile		Makefile
README		README
advanced_features.rst		advanced_features.rst
advanced_models.rst		advanced_models.rst
analyze.rst		analyze.rst
checkpointing.rst		checkpointing.rst
clamp.rst		clamp.rst
conf.py		conf.py
examine_mdls.rst		examine_mdls.rst
ficks_laws.rst		ficks_laws.rst
getting_started.rst		getting_started.rst
index.rst		index.rst
installs.rst		installs.rst
irrev_rev_uni_bi.rst		irrev_rev_uni_bi.rst
lotka_volterra.rst		lotka_volterra.rst
make.bat		make.bat
mapk.rst		mapk.rst
mdl_editing.rst		mdl_editing.rst
mesh_repair.rst		mesh_repair.rst
optimize.rst		optimize.rst
rat.rst		rat.rst
rel_pattern.rst		rel_pattern.rst
seed.rst		seed.rst
software.rst		software.rst
surf_class_surf_mol.rst		surf_class_surf_mol.rst
surface_classes.rst		surface_classes.rst
variable_rxn_rates.rst		variable_rxn_rates.rst
visualize_plot.rst		visualize_plot.rst

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README for CellBlender and MCell Tutorials

The CellBlender and MCell tutorials located at
http://www.mcell.psc.edu/tutorials/ are generated using Sphinx
(http://sphinx-doc.org/index.html). If Sphinx is installed, the html files can
be generated by using the command "make html" in this directory.

Some of the binary files are not stored in the repo to keep the size of it
small, but that policy will likely change if more collaborators need to
contribute images, blend files, etc.

Here are some basic steps to begin contributing to the "CellBlender and MCell
Tutorials" repository:

* Read this page to develop a basic understanding of ReST syntax:
  http://sphinx-doc.org/rest.html
    * The official "quick start" guide:
      http://docutils.sourceforge.net/docs/user/rst/quickstart.html
    * The official reference guide:
      http://docutils.sourceforge.net/docs/user/rst/quickref.html
    * Sphinx specific syntax: http://sphinx-doc.org/markup/index.html
* Install sphinx on your local machine.
* Follow this tutorial, which will briefly explain how Sphinx projects work:
  http://sphinx-doc.org/tutorial.html
* Once you finish the previous tutorial, you are free to delete the project
  directory that they have you create (if you want).
* Pull the CellBlender tutorial from the github repository
  (https://github.com/jczech/cellblender_tutorials.git).
    * The repostiory itself is a Sphinx project made up of various ReST files
      and Sphinx configuration files (e.g conf.py).
    * You shouldn't have to do another "sphinx-quickstart".
    * Simply edit the ReST files locally as needed.
    * Each ReST file will create a corresponding HTML file.
    * If you add a completely new ReST file, make sure you add it to
      the table of content tree (toctree) in "index.rst"
    * When you're ready to see your changes, type "make html".
    * A status message will tell you if creating the html was successful.
    * From the repo directory, change into "./_build/html/" and open index.html
      with your browser of choice.
    * If you're satisfied with how the new html looks, push it to the github
      repository (assuming you have permissions).
        * The "_build" directory will not be pushed, since it is in the
          ".gitignore" file.