Merge pull request #18 from ebolyen/release

Release

LICENSE

@@ -11,7 +11,7 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of Barcode-pdf-generator nor the names of its
+* Neither the name of cual-id nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 
@@ -25,4 +25,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

MANIFEST.in

@@ -0,0 +1,5 @@
+include README.rst
+include LICENSE
+include .coveragerc
+
+graft examples

README.rst

@@ -0,0 +1,97 @@
+=======
+cual-id
+=======
+|Build Status| |Coverage Status|
+
+Install
+=======
+
+.. code:: bash
+
+   pip install cual-id
+
+Usage
+=====
+
+Getting help
+------------
+
+.. code:: bash
+
+   cual-id --help
+
+
+Creating a list of IDs
+----------------------
+
+.. code:: bash
+
+   cual-id create ids 42 # writes 42 ids to stdout
+   cual-id create ids 42 > my-ids.txt # writes 42 ids to my-ids.txt
+
+
+
+Creating a PDF of ID labels
+---------------------------
+
+If you need to label sample containers with stickers, you can create a
+printable PDF for those stickers. Currently the only sticker sheet format
+supported is a 4 by 9 sheet. We designed this printout for
+`Electronic Imaging Materials #80402 label sheets
+<http://barcode-labels.com/?s=80402&submit=Search>`_. When printing PDFs make
+sure to check `Actual Size` in the print dialog box.
+
+.. code:: bash
+
+   cual-id create labels my-ids.txt --output-pdf my-labels.pdf
+   cual-id create labels my-ids.txt --output-pdf my-labels.pdf --suppress-ids # don't print the ids, only the barcodes
+   cual-id create labels my-ids.txt --output-pdf my-labels.pdf --barcode none # don't print barcodes, just the ids
+
+
+Correcting a list of ids
+------------------------
+
+.. code:: bash
+
+   cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt # report fixed, unfixable and duplicates, the default
+   cual-id fix examples/modified-ids.txt --correct-ids examples/ids.txt --show FN # report only fixed and unfixable IDs
+
+Result code definitions
+~~~~~~~~~~~~~~~~~~~~~~~
+* D: duplicate
+* F: fixed
+* N: not fixable
+* V: valid (didn't need correction)
+
+Output Format
+~~~~~~~~~~~~~
+
+::
+
+   input-id <tab> output-id <tab> result-codes
+
+
+For example:
+
+::
+
+   1a529f8b	1a529f88	F
+   d60d0e2b	d60d0c2b	F
+   439628o9	43962809	F
+   439628o9	43962809	DF
+   df47deb4	df47deba	F
+
+
+Python API
+----------
+
+.. code:: python
+
+   from cualid import create_ids
+   create_ids(10) # Creates a list of tuples containing a UUID and a cualid
+
+
+.. |Build Status| image:: https://travis-ci.org/johnchase/cual-id.svg?branch=master
+   :target:  https://travis-ci.org/johnchase/cual-id
+.. |Coverage Status| image:: https://coveralls.io/repos/johnchase/cual-id/badge.svg?branch=master&service=github
+   :target:  https://coveralls.io/github/johnchase/cual-id?branch=master

setup.py

@@ -2,15 +2,35 @@
 # copied and modified from https://github.com/biocore/scikit-bio
 from setuptools import find_packages, setup
 from glob import glob
-__version__ = "0.0.1-dev"
+__version__ = "0.9.0"
 
+classes = """
+    Development Status :: 4 - Beta
+    License :: OSI Approved :: BSD License
+    Intended Audience :: Science/Research
+    Topic :: Utilities
+    Topic :: Scientific/Engineering
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.3
+    Programming Language :: Python :: 3.4
+    Operating System :: Unix
+    Operating System :: POSIX
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft :: Windows
+"""
+classifiers = [s.strip() for s in classes.split('\n') if s]
 
-description = ('Make a pdf out of barcodes')
+description = ('A package for creating and managing sample identifiers in'
+               ' comparative -omics datasets.')
 
-with open('README.md') as f:
+with open('README.rst') as f:
     long_description = f.read()
 
-setup(name='Cual-ID',
+setup(name='cual-id',
+      author="John Chase",
+      author_email="[email protected]",
+      url="https://github.com/johnchase/cual-id",
+      classifiers=classifiers,
       version=__version__,
       description=description,
       long_description=long_description,