Metadata-Version: 2.0
Name: dsc
Version: 0.2.7.6
Summary: Implementation of Dynamic Statistical Comparisons
Home-page: https://github.com/stephenslab/dsc
Author: Gao Wang
Author-email: gaow@uchicago.edu
License: MIT
Download-URL: https://pypi.python.org/pypi/dsc/0.2.7.6#downloads
Description-Content-Type: UNKNOWN
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Dist: h5py
Requires-Dist: msgpack-python
Requires-Dist: numexpr
Requires-Dist: numpy
Requires-Dist: pandas (>=0.22.0)
Requires-Dist: pyarrow (>=0.5.0)
Requires-Dist: sos (>=0.9.13.3)
Requires-Dist: sqlalchemy
Requires-Dist: sympy

Dynamic Statistical Comparisons (DSC)
=====================================

|PyPI version| |Codacy Badge|

The `project wiki <https://stephenslab.github.io/dsc-wiki>`__ is the
main source of documentation for both developers and users of the DSC
project. If you are new to the concept of DSC, it may worth reading this
`blog
post <http://stephens999.github.io/blog/2014/10/Data-Driven-Discovery.html>`__
to understand the motivation behind this project.

This work is supported by the the Gordon and Betty Moore Foundation via
an Investigator Award to Matthew Stephens, `Grant
GBMF4559 <https://www.moore.org/grants/list/GBMF4559>`__, as part of the
`Data-Driven Discovery
program <https://www.moore.org/programs/science/data-driven-discovery>`__.
If you have any questions or want to share some information with the
developer / user community, please open a `github
issue <https://github.com/stephenslab/dsc/issues>`__.

Developer notes
---------------

Upgrading DSC to latest development version
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

For most users, we recommend installing the `most recent stable
release <https://stephenslab.github.io/dsc-wiki/installation.html>`__.
If you would like to upgrade your existing installation of DSC to the
most recent (unstable) development version, follow these steps.

DSC is closely developed in parallel with
`SoS <http://github.com/vatlab/sos>`__. Therefore, the development
version of DSC (maintained in the ``master`` branch of the GitHub
repository) typically requires the development version of SoS.

Install the latest SoS
^^^^^^^^^^^^^^^^^^^^^^

::

    git clone https://github.com/vatlab/SoS.git
    cd SoS
    pip install -U --upgrade-strategy only-if-needed . 

Install DSC from source
^^^^^^^^^^^^^^^^^^^^^^^

::

    git clone https://github.com/stephenslab/dsc.git
    cd dsc
    ./setup.sos

Or, if you have downloaded it before,

::

    cd dsc
    git pull
    ./setup.sos

Change Log
----------

Upcoming release
~~~~~~~~~~~~~~~~

Goal for 0.2.8

-  Support for multiple outputs per module, for shell executables
-  Improve command options for scripts

0.2.x
~~~~~

0.2.7.6

-  Add new feature ``dscrutils::shiny_plot`` to display simple benchmark
   results.
-  [minor] Display unused modules with ``-h`` option.

0.2.7.5

-  Add R / Python packages and version display with ``-h`` option.
-  Add ``.gitignore`` for cache folder when a git environment is
   detected.
-  SoS bumped to 0.9.13.3 that now bundles the ``pbs`` module.

0.2.7.4

-  Improved R’s sessionInfo format.
-  Bug fixes #119, #121, #122
-  [minor] Error message improvements.

0.2.7.3

-  More stringent R library and command executable check.
-  [minor] Fix a regression bug on path due to 0.2.7.2.

0.2.7.2

-  Improved Windows path support.
-  [minor] Fix a bug with nested tuple with ``raw()``.

0.2.7.1

-  Dump individual data object with scripts using ``dsc-query *.pkl``
   and ``dsc-query *.rds``.
-  [minor] Improve behavior for length 1 vector in R’s list with ``R()``
   operator.
-  [minor] Various bug fixes.

0.2.7

-  `#92 <https://github.com/stephenslab/dsc/issues/92>`__ paired
   parameter input convention.
-  `#90 <https://github.com/stephenslab/dsc/issues/90>`__ and
   `#93 <https://github.com/stephenslab/dsc/issues/93>`__ use ``Rmd``
   files as module executables.
-  `#94 <https://github.com/stephenslab/dsc/issues/94>`__ and
   `#95 <https://github.com/stephenslab/dsc/issues/95>`__ added
   ``DSC::replicate`` and command option ``--replicate``.
-  Enhance ``R()`` operator due to use of
   `dscrutils <https://github.com/stephenslab/dsc/tree/master/dscrutils>`__
   package. This packages is now required to parse DSC file when ``R``
   modules are involved.
-  Add, by default, a variable ``DSC_DEBUG`` to output files that saves
   various runtime info.
-  SoS bumped to 0.9.13.2

   -  Support R github package force install when version mismatches.
   -  Fix bug with ``--touch`` option.
   -  Force use ``pip`` to install local development version.
   -  `#97 <https://github.com/stephenslab/dsc/issues/97>`__ Improved
      error logging and reporting behavior.

-  [minor] Revert from ``ruamel.yaml`` to ``yaml`` for better
   performance.
-  [minor] `#96 <https://github.com/stephenslab/dsc/issues/96>`__
-  [minor] `#98 <https://github.com/stephenslab/dsc/issues/98>`__
-  [minor] Various bug fixes.

0.2.6.5

-  Bring back partial mixed languages support. **Piplines with mixed R
   and Python code can communicate data of limited types (recursively
   support array, matrix, dataframe), via ``rpy2`` as in versions prior
   to 0.2.5.x**. Support for additional languages will be implemented on
   need basis with ``HDF5`` format
   `#86 <https://github.com/stephenslab/dsc/issues/86>`__.

0.2.6.4

-  Add a ``dsc-io`` command to convert between python ``pickle`` and R
   ``RDS`` files – an internal command for data conversion and a test
   for ``rpy2`` configuration.

0.2.6.3

-  Inline module executable via language interpreters (eg. ``R()``,
   ``Python()``).

0.2.6.2

-  [minor] Ignore leading ``.`` in ``file()``: ``file(.txt)`` and
   ``file(txt)`` are equivalent.
-  [minor] Disallow derivation of modules from ensemble.
-  [minor] Various bug fixes.

0.2.6.1

-  Internally replace ``RDS`` format with ``HDF5`` format for Python
   routines. **Pipeline with mixed languages is now officially broken at
   this point until the next major release that supports ``HDF5`` in
   R**.
-  SoS required version bumped to 0.9.12.7 for relevant upstream bug
   fixes for remote host computing.
-  [minor] Various bug fixes.

0.2.6

-  Bring back ``--host`` option; add a companion option ``--to-host`` to
   facilicate sending resources to remote computer.
-  Add ``--truncate`` switch.
-  SoS required version bumped to 0.9.12.3 for relevant upstream bug
   fixes.
-  [minor] Improved command interface.

0.2.5.2

-  SoS required version bumped to 0.9.12.2 for relevant upstream bug
   fixes.

0.2.5.1

-  Change in ``seed`` behavior: since this release ``seed`` will no
   longer be a DSC keyword. Users are responsible to set seeds on their
   own.
-  [minor] Allow for both lower case and capitalized operator names
   ``File/file, List/list, Dict/dict``.

0.2.5

-  New syntax release, compatible with SoS 0.9.12.1.
-  Removed ``--host`` option due to upstream changes.

.. _x-1:

0.1.x
~~~~~

0.1.0

-  First release, compatible with SoS 0.6.4.

.. |PyPI version| image:: https://badge.fury.io/py/dsc.svg
   :target: https://badge.fury.io/py/dsc
.. |Codacy Badge| image:: https://api.codacy.com/project/badge/Grade/46bb573ea0414f6095f1b7fd4bedbfd3
   :target: https://www.codacy.com/app/gaow/dsc?utm_source=github.com&utm_medium=referral&utm_content=stephenslab/dsc&utm_campaign=Badge_Grade


