Metadata-Version: 2.0
Name: dsc
Version: 0.2.7.8
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/0.2.7.8#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: PTable
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 (>=0.9.13.7)
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

Install dscrutils from source
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Assuming the working directory in your R environment is the ``dsc``
repository, run the following code in R to install the latest
development version of the dscrutils R package:

.. code:: r

    getwd() # Should be ... /dsc
    install.packages("dscrutils",repos = NULL,type = "source")

Project maintenance
^^^^^^^^^^^^^^^^^^^

Although relatively stable and usable in practice, DSC is still actively
being developed. Occasionally upgrades to the most recent version will
lead to changes of file signatures that triggers rerun of existing
benchmark even if they have not been changed. When this happens we will
indicate in bold in our release note below that “a file signature clean
up is recommended” (see release note 0.2.7.7 for example). That means
after such DSC upgrades you should rerun your benchmark with ``--touch``
option to update file signatures. If possible, it is recommended that
you rerun your benchmark from scratch (if resources can afford) with
``-s none`` instead of ``--touch`` to skip all existing files. We
apologize for the inconveniences it incurs.

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

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

Goal for 0.2.8

-  Support for multiple output per modules.
-  Improve scripts command options.

0.2.x
~~~~~

0.2.7.8

-  Implement a preliminary ``%include`` feature to provide alternative
   code organization style.
-  Allow for ``!`` operator in ``List()`` and ``Dict()``.
-  SoS bumped to version 0.9.13.7 for improved remote job support.
-  [minor] Various bug fixes.

0.2.7.7

-  Improvements for module with shell executables and command options.
-  Improvements for remote execution #131.
-  Improved logging.
-  Bug fixes #126, #127.
-  SoS bumped to version 0.9.13.4 for #128 and related.

**A file signature clean up is recommended after this upgrade.**

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.
   -  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


