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cogent

PyCogent: Official repository for software and unit tests

https://github.com/pycogent/pycogent

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    15 of 39 committers (38.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.9%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

PyCogent: Official repository for software and unit tests

Basic Info
Statistics
  • Stars: 91
  • Watchers: 18
  • Forks: 51
  • Open Issues: 0
  • Releases: 0
Created over 13 years ago · Last pushed over 5 years ago
Metadata Files
Readme Changelog

README 

The Readme
==========

:Download: `From github `_ or follow the :ref:`quick-install` instructions.

Dependencies
------------

The toolkit requires Python 2.5.1 or greater, and Numpy 1.3 or greater. Aside from these the dependencies below are optional and the code will work as is. A C compiler, however, will allow external C module's responsible for the likelihood and matrix exponentiation calculations to be compiled, resulting in significantly improved performance.

.. _required:

Required
^^^^^^^^

- Python_: the language the toolkit is primarily written in, and in which the user writes control scripts.
- Numpy_: This is a python module used for speeding up matrix computations. It is available as source code for \*nix.
- zlib_: This is a compression library which is available for all platforms and comes pre-installed on most too. If, by chance, your platform doesn't have this installed then download the source from the zlib_ site and follow the install instructions, or refer to the instructions for `compiling matplotlib`_.

.. note:: On some linux platforms (like Ubuntu), you must specifically install a ``python-dev`` package so that the Python_ header files required for building some external dependencies are available.

Optional
^^^^^^^^

- C compiler: This is standard on most \*nix platforms. On Macos X this is available for free in the Developer tools which, if you don't already have them, can be obtained from Apple_.
- Matplotlib_: used to plot several kinds of graphs related to codon usage. For installation, see these instructions for `compiling matplotlib`_.
- Cython_: This module is only necessary if you are a developer who wants to modify the \*.pyx files.
- mpi4py_: Message Passing Interface interface, required for parallel computation.
- SQLAlchemy_ and a mysql connector such as `PyMySQL `_: These are required for the Ensembl querying code.

See the :ref:`quick-install` approach for how these can be grabbed using the ``all`` option..

Installation
------------

See the :ref:`quick-install`.

Testing
-------

``PyCogent/tests`` contains all the tests. You can most readily run the tests using the ``PyCogent/run_tests`` shell script. This is done by typing:

.. code-block:: guess
    
    $ sh run_tests

which will automatically build extensions in place, set up the PYTHONPATH and run ``PyCogent/tests/alltests.py``. Note that if certain optional applications are not installed this will be indicated in the output as "can't find" or "not installed". A "`.`" will be printed to screen for each test and if they all pass, you'll see output like:

.. code-block:: guess
    
    Ran 3299 tests in 58.128s
    
    OK

Tips for usage
--------------

A good IDE can greatly simplify writing control scripts. Features such as code completion and definition look-up are extremely useful. For a complete list of `editors go here`_.

To get help on attributes of an object in python, use

.. code-block:: python
    
    >>> dir(myalign)

to list the attributes of ``myalign`` or 

.. code-block:: python
    
    >>> help(myalign.writeToFile)

to figure out how to use the ``myalign.writeToFile`` method. Also note that the directory structure of the package is similar to the import statements required to use a module -- to see the contents of ``alignment.py`` or ``sequence.py`` you need to look in the directory ``cogent/core`` path, to use the classes in those files you specify ``cogent.core`` for importing.

.. _Python: http://www.python.org
.. _Cython: http://www.cython.org/
.. _Numpy: http://numpy.scipy.org/
.. _Matplotlib: http://matplotlib.sourceforge.net
.. _Apple: http://www.apple.com
.. _Pyrex: http://www.cosc.canterbury.ac.nz/~greg/python/Pyrex/
.. _`editors go here`: http://www.python.org/cgi-bin/moinmoin/PythonEditors
.. _mpi4py: http://code.google.com/p/mpi4py
.. _`restructured text`: http://docutils.sourceforge.net/rst.html
.. _gcc: http://gcc.gnu.org/
.. _SQLAlchemy: http://www.sqlalchemy.org
.. _`mysql-connector-python`: https://pypi.python.org/pypi/mysql-connector-python
.. _zlib: http://www.zlib.net/
.. _`compiling matplotlib`: http://sourceforge.net/projects/pycogent/forums/forum/651121/topic/5635916

Owner

  • Name: pycogent
  • Login: pycogent
  • Kind: organization

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,312
  • Total Committers: 39
  • Avg Commits per committer: 33.641
  • Development Distribution Score (DDS): 0.71
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Gavin Huttley g****y@a****u 381
Daniel McDonald m****t@c****u 122
Peter Maxwell p****z@g****m 122
Greg Caporaso g****o@g****m 110
mikerobeson s****d@g****m 98
Gavin Huttley G****y@a****u 79
Jai Ram Rideout j****t@g****m 51
Justin Kuczynski j****k@g****m 46
Jeremy Widmann j****n@c****u 45
Kyle Bittinger k****r@g****m 41
Rob Knight r****t@c****u 32
Jesse Stombaugh j****h@g****m 20
Micah Hamady h****y@c****u 18
Sandra Smit S****t@f****l 18
Jesse Zaneveld z****d@g****m 16
Catherine Lozupone l****e@c****u 15
Antonio Gonzalez a****a@g****m 14
Marcin Cieślik m****k@g****m 11
Jens Reeder j****r@g****m 10
Dan Knights d****s@u****u 9
Mike Robeson m****n@c****u 9
Tony Walters w****s@g****m 8
Kristian Rother k****r@r****e 7
gawbul g****l@g****m 5
Zongzhi Liu z****u@g****m 3
Shinya SUZUKI m****u@g****m 2
Skyler Sun s****r@a****g 2
Hua Ying h****g@a****u 2
Jose Carlos Clemente Litran j****e@g****m 2
Meg Pirrung m****p@g****m 2
and 9 more...
Committer Domains (Top 20 + Academic)
colorado.edu: 7 anu.edu.au: 3 little-beast.gateway.2wire.net: 1 atlasantibodies.com: 1 mac92855.ornl.gov: 1 wehi.edu.au: 1 cornell.edu: 1 acm.org: 1 rubor.de: 1 umn.edu: 1 few.vu.nl: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 72
  • Total pull requests: 28
  • Average time to close issues: almost 3 years
  • Average time to close pull requests: over 2 years
  • Total issue authors: 44
  • Total pull request authors: 16
  • Average comments per issue: 2.06
  • Average comments per pull request: 4.64
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gregcaporaso (7)
  • tillea (5)
  • jairideout (5)
  • guillermomarco (4)
  • boxiangliu (3)
  • jergosh (3)
  • mbiokyle29 (2)
  • finswimmer (2)
  • RNAer (2)
  • vladie0 (2)
  • BenKaehler (2)
  • nieder (2)
  • ropermpv (1)
  • wasade (1)
  • JensTimmerman (1)
Pull Request Authors
  • gregcaporaso (5)
  • mikerobeson (5)
  • wasade (3)
  • ctSkennerton (2)
  • adamrp (2)
  • gawbul (1)
  • ggonnella (1)
  • skylersun (1)
  • jonatanfan (1)
  • blankenberg (1)
  • TaskeHAMANO (1)
  • davidsoergel (1)
  • zachcp (1)
  • pm67nz (1)
  • grandynguyen (1)
Top Labels
Issue Labels
bug (5) question (4) enhancement (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 420 last-month
  • Total docker downloads: 220
  • Total dependent packages: 0
  • Total dependent repositories: 24
  • Total versions: 12
  • Total maintainers: 4
pypi.org: cogent

COmparative GENomics Toolkit

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 24
  • Downloads: 420 Last month
  • Docker Downloads: 220
Rankings
Docker downloads count: 1.4%
Dependent repos count: 3.0%
Forks count: 5.6%
Average: 6.9%
Stargazers count: 7.6%
Dependent packages count: 10.1%
Downloads: 13.8%
Maintainers (4)
mcdonald GavinHuttley hamady rdknight
Last synced: 11 months ago

Dependencies

setup.py pypi
  • numpy >=1.3.0