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Documentation updates & new installation instructions #232

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alubbock commented Oct 8, 2016

This PR contains new PySB installation instructions for Anaconda and Docker-based installs, which work on Windows, Mac and Linux. Hopefully the new step-by-step approach is clear, but feedback is welcome. I removed the virtual appliance instructions since it's quite out of date now (based on PySB 0.1.9).

I've improved documentation for the Simulation class and SBML/BNGL importers, which are now included in Sphinx output. I also fixed a couple of Sphinx warnings when parsing the bind_complex macro docstring and missing pysb_flat exporter docs.

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coveralls commented Oct 8, 2016

Coverage Status

Coverage increased (+0.004%) to 76.061% when pulling fe9cd9e on LoLab-VU:more_docs into a7c6f2c on pysb:master.

@jmuhlich

Mostly minor stuff.

* `matplotlib`_
This Python package allows you to plot the results of your simulations. It
is not a hard requirement of PySB but many of the example scripts use it.
Installed with :command:`pip install matplotlib`.

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jmuhlich Oct 14, 2016

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Perhaps mention that those who installed Python via Anaconda will already have all of the Python packages listed here and thus don't need to run the pip install commands.

appears, you have succeeded in installing PySB! You can now proceed to
the :doc:`tutorial`.
Those from a programming background may choose to use Python from within

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jmuhlich Oct 14, 2016

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Anyone who would do this does not need this instruction, and it might be a distraction for anyone else...

.. _Python: http://www.python.org/
.. _SciPy: http://www.scipy.org/
.. _NumPy: http://www.numpy.org/
.. _SymPy: http://www.sympy.org/
.. _matplotlib: http://matplotlib.org/
.. _BioNetGen: http://www.bionetgen.org/
.. _Perl: http://www.perl.org/
.. _PyCharm: https://www.jetbrains.com/pycharm/

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jmuhlich Oct 14, 2016

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If you strike the section mentioning these three, then this block can go too.

@@ -314,13 +314,12 @@ def model_from_bngl(filename, force=False):
"""
Convert a BioNetGen .bngl model file into a PySB Model.
Limitations
-----------
**Limitations**

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jmuhlich Oct 14, 2016

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Perhaps this should be a "Notes" section (officially supported by Napoleon: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/#docstring-sections ).

@@ -113,8 +122,7 @@ def model_from_sbml(filename, force=False, cleanup=True, **kwargs):
:class:`BnglBuilder` class converts the BioNetGen language model into a
PySB Model.
Limitations
-----------
**Limitations**

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jmuhlich Oct 14, 2016

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Same as importers.bngl

Please note that the interface for this class is considered
experimental and may change without warning as PySB is updated.
.. note::

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jmuhlich Oct 14, 2016

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Also make this a Note section?

@@ -224,27 +234,72 @@ class SimulationResult(object):
A set of species trajectories from a simulation. Should either be a
list of 2D numpy arrays or a single 3D numpy array.
Attributes

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jmuhlich Oct 14, 2016

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Where did the Attributes section go? Does this somehow get auto-populated from the @property method docstrings?

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@alubbock

alubbock Oct 14, 2016

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@property method docstrings get listed with methods (see base_filename from the BNG interface for an example). Having an Attributes section means they get listed twice and documentation is duplicated. Alternatively, they could all be listed under Attributes, and have a method docstring that says "See Attributes for description". Listing docstrings under each method seems cleaner to me though, and nicer when reading the code directly.

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coveralls commented Oct 14, 2016

Coverage Status

Coverage decreased (-0.01%) to 76.047% when pulling 1a5fbb2 on LoLab-VU:more_docs into a7c6f2c on pysb:master.

@jmuhlich jmuhlich merged commit 8f72353 into pysb:master Nov 1, 2016

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@alubbock alubbock deleted the LoLab-VU:more_docs branch May 1, 2017

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