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Commits on Jun 27, 2016
  1. @jmuhlich

    Merge branch 'alubbock-docker' (rebased from #202)

    Closes #202 (will this work on a PR?)
    jmuhlich committed Jun 27, 2016
  2. @alubbock @jmuhlich

    Update Docker setup

    * Use jupyter/scipy-notebook base image (previous one was deprecated)
    * Update BioNetGen to 2.2.6-stable
    * Use non-privileged user within container
    alubbock committed with jmuhlich Apr 18, 2016
Commits on Jun 24, 2016
  1. @jmuhlich

    Merge pull request #216 from LoLab-VU/pysbflat_matchonce

    Add MatchOnce to pysb_flat exporter
    jmuhlich committed on GitHub Jun 24, 2016
  2. @jmuhlich

    Merge pull request #220 from jmuhlich/rtd-cleanup

    Sphinx / ReadTheDocs fixes
    jmuhlich committed on GitHub Jun 24, 2016
  3. @jmuhlich

    Fix problems with ReadTheDocs build

    * Use mock.MagicMock rather than home-grown Mock class to mock out 3rd party
      modules.
    * Mock out all 3rd party modules rather than just pygraphviz. This makes the
      RTD build process much simpler as numpy scipy etc. are no longer needed.
    * Rework doc/requirements.txt and improve the comment inside it.
    
    Fixes #215
    jmuhlich committed Jun 10, 2016
Commits on Jun 17, 2016
  1. @jmuhlich

    Merge pull request #218 from gitter-badger/gitter-badge

    Add a Gitter chat badge to README.rst
    jmuhlich committed on GitHub Jun 17, 2016
  2. @gitter-badger

    Add Gitter badge

    gitter-badger committed Jun 17, 2016
Commits on Jun 14, 2016
  1. @alubbock
Commits on Jun 10, 2016
  1. @alubbock
Commits on May 2, 2016
  1. @jmuhlich
Commits on Apr 12, 2016
  1. @johnbachman

    Merge pull request #201 from jmuhlich/doc_req_ver_updates

    Update installation section of docs and sphinx configuration
    johnbachman committed Apr 12, 2016
  2. @jmuhlich

    Update sphinx conf for our new version API

    Now we can just access pysb.__version__ directly and parse it with
    pkg_resources.
    jmuhlich committed Apr 11, 2016
  3. @jmuhlich

    Update requirements section of docs

    * Rephrase summary of hard requirements and listed version numbers
    * Remove excess verbiage describing some version number issues, deferring
      to the summary instead
    * Move matplotlib from required to recommended
    * Mention Python 3 compatibility
    * Update minimum BioNetGen version
    * Add minimum Kappa version
    * Add instructions for installing BioNetGen and Kappa for PySB use
    * Update some URLs
    jmuhlich committed Apr 11, 2016
  4. @johnbachman

    Merge pull request #200 from johnbachman/kappa_path

    Kappa path environment variables and directory search
    johnbachman committed Apr 12, 2016
  5. @jmuhlich @johnbachman

    Clean up the kappa path detection code a bit (#1)

    * Avoid shadowing builtin 'dir'
    * Remove comment text about checking for directory-ness
    * Clean up logical flow in a couple of places
    * Add more information to some exception messages
    jmuhlich committed with johnbachman Apr 12, 2016
Commits on Apr 11, 2016
  1. @jmuhlich

    Merge pull request #197 from jmuhlich/delete_export_hoda

    Remove this one-off exporter from an old project
    jmuhlich committed Apr 11, 2016
Commits on Apr 5, 2016
  1. @johnbachman
  2. @johnbachman
Commits on Apr 4, 2016
  1. @johnbachman
Commits on Apr 1, 2016
  1. @jmuhlich
  2. @jmuhlich

    Merge pull request #196 from jmuhlich/delete_simulator

    Removed simulate.py for future reintroduction
    jmuhlich committed Apr 1, 2016
  3. @jmuhlich
Commits on Mar 31, 2016
  1. @johnbachman

    Merge pull request #195 from jmuhlich/simulator_fixes

    Simulator fixes
    johnbachman committed Mar 31, 2016
  2. @jmuhlich
  3. @jmuhlich

    Clean up integrator tests.

    * Remove unused imports
    * Make test class *not* a subclass of TestCase and rename it so nose sees it
    * Only build the default solver in TestSolver.setUp and also add tearDown
    * Change time range in TestSolver so it actually triggers jacobian evaluation
    * Clean up docstrings
    * Change to numpy.allclose for comparing numeric results to be more explicit
      about what's being done
    * Add vode + analytic_jacobian test
    * Drop analytic_jacobian from earm and robertson general simulation tests as
      generating the jacobian is very slow.
    jmuhlich committed Mar 31, 2016
  4. @JamesPino @jmuhlich

    Small bug fix.

    JamesPino committed with jmuhlich Feb 16, 2016
  5. @JamesPino @jmuhlich
  6. @jmuhlich

    Initialize self.jac_fn even if analytic jacobian is not used

    Thanks to @JamesPino for the original fix.
    jmuhlich committed Mar 31, 2016
Commits on Mar 27, 2016
  1. @alubbock

    Merge pull request #194 from LoLab-VU/kappatests

    Use fixed git SHA for Kappa tests in Travis
    alubbock committed Mar 27, 2016
  2. @alubbock

    Merge pull request #189 from alubbock/bngl_fix

    BNGL fixes: begin/end model declarations; only send "done" when using console
    alubbock committed Mar 27, 2016
  3. @alubbock
Commits on Mar 23, 2016
  1. @alubbock
Commits on Mar 9, 2016
  1. @jmuhlich

    Merge pull request #188 from johnbachman/kappa_fixes

    Kappa updates (ANY/WILD, Expressions, KaSa, tests)
    jmuhlich committed Mar 9, 2016
  2. @johnbachman

    Remove try blocks, optional no ic warning

    Also fix error parsing kappa output files containing no observables and
    only a single timepoint (fixed by loading to a float array and then
    subsequently converting to a recarray).
    
    Also make _parse_kasim_outfile non-public.
    johnbachman committed Mar 9, 2016
  3. @johnbachman
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