Converted README to RST and removed pypandoc dependency on installer …

…(issue #49)

README.rst

@@ -0,0 +1,182 @@
+Overview
+========
+
+This is a collection of bioinformatics scripts many have found useful
+and code modules which make writing new ones a lot faster.
+
+Over the years most bioinformatics people amass a collection of small
+utility scripts which make their lives easier. Too often they are kept
+either in private repositories or as part of a public collection to
+which noone else can contribute. Biocode is a curated repository of
+general-use utility scripts my colleagues and I have found useful and
+want to share with others. I have also developed some code
+libraries/modules which have made my scripting work a lot easier. Some
+have found these to be more useful than the scripts themselves.
+
+Look below if you want to learn more, contribute code yourself, or just
+get the scripts.
+
+-- Joshua Orvis
+
+The scripts
+===========
+
+The scope here is intentionally very open. I want to include anything
+that developers find generally useful. There are no limitations on
+language choice, though the majority are Python. For now, the following
+directories make up the initial groupings but will be expanded as
+needed:
+
+-  blast - It if uses, massages, or just reformats BLAST output, it goes
+   here.
+-  chado - Scripts that are tied into the chado schema (gmod.org) should
+   be found here.
+-  fasta - Filtering, converting, size distribution plots, etc.
+-  fastq - Utilities for fasta's newer sister format.
+-  genbank - Anything related to the GenBank? Flat File Format.
+-  general - Utility scripts that may not fit in any other existing
+   directory or don't warrant creation of their own. We should be
+   selective about what we put here and create or use other directories
+   whenever appropriate.
+-  gff - Extractions, conversions and manipulations of files in the
+   `Generic Feature Format <http://sequenceontology.org/gff3.shtml>`__
+-  gtf - From Ensembl/WashU, the GTF format is the focus of scripts
+   here.
+-  hmm - Merging, manipulating or reading HMM libraries.
+-  sam\_bam - Analysis of and parsing SAM/BAM files.
+-  sandbox - Each committer gets their own personal directory here to
+   add anything they want while testing or waiting to be moved to the
+   production directories.
+-  sysadmin - While not specifically bioinformatics, our work tends to
+   be on Unix machines, and utility scripts are often needed to support
+   our work. From file system manipulation to database backup scripts,
+   put your generic sysadmin utilities here.
+-  taxonomy - Anything related to taxonomic analysis.
+
+The modules
+===========
+
+If you're a developer these modules can save a lot of time. Yes, there
+is some duplicate functionality you'll find in modules like
+`Biopython <http://biopython.org/wiki/Main_Page>`__, but these were
+written to add features I always wanted and with a more
+biologically-focused API.
+
+Three of the primary Python modules:
+
+`biocode.things <https://github.com/jorvis/biocode/blob/master/lib/biocode/things.py>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Classes here represent biological things (as defined by the `Sequence
+Ontology <http://sequenceontology.org/>`__) in a way that makes more
+sense biologically and hiding some of the CS abstraction. What does this
+mean? This is a simple example, but compare these syntax approaches:
+
+::
+
+    # This way is typical of other libraries
+    genes = assembly.get_subfeatures_by_type( 'type': 'genes' )
+    mRNAs = assembly.get_subfeatures_by_type( 'type': 'mRNA' )
+
+    # And instead, in biothings:
+    genes = assembly.genes()
+    for gene in genes:
+        mRNAs = gene.mRNAs()
+
+This more direct approach is held throughout these libraries. It also
+adds some shortcuts for tasks that always annoyed me when working with
+things that had coordinates. Consider if you wanted to determine if one
+gene is before another one on a molecule:
+
+::
+
+    if gene1 < gene2:
+        return True
+
+In the background, biocode checks if the two gene objects are located on
+the same molecule and, if so, compares their coordinates. There are many
+other methods for coordinate comparison, such as:
+
+-  thing1 <= thing2 : The thing1 overlaps thing2 on the 5' end
+-  thing1.contained\_within( thing2 )
+-  thing1.overlaps( thing2 )
+-  thing1.overlap\_size\_with( thing2 )
+
+This module also contains readable and detailed documention within the
+`source
+code <https://github.com/jorvis/biocode/blob/master/lib/biocode/things.py>`__.
+
+`biocode.annotation <https://github.com/jorvis/biocode/blob/master/lib/biocode/annotation.py>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This set of classes allows formal definition of functional annotation
+which can be attached to various biothings. These include gene product
+names, gene symbols, EC numbers, GO terms, etc. Once annotated, the
+biothings can be written out in common formats such as GFF3, GenBank,
+NCBI tbl, etc.
+
+`biocode.gff <https://github.com/jorvis/biocode/blob/master/lib/biocode/gff.py>`__
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Much of biocode was written while working with genomic data and
+annotation, and one of the more common formats for storing these is
+`GFF3 <http://sequenceontology.org/resources/gff3.html>`__. Using this
+module, you can parse a GFF3 file of annotations into a set of biothings
+with a single line of code. For example:
+
+::
+
+    import biocode.gff
+
+    (assemblies, features) = biocode.gff.get_gff3_features( input_file_path )
+
+That's it. You can then iterate over the assemblies and their children,
+or access the 'features' dict, which is keyed on each feature's ID.
+
+Getting the code (pip, latest release)
+======================================
+
+You can install biocode using pip (requires Python3) like this:
+
+::
+
+    pip3 install biocode
+
+Getting the code (github, current trunk)
+========================================
+
+If you want the latest developer version:
+
+::
+
+    git clone https://github.com/jorvis/biocode.git
+
+**Important**: Many of these scripts use the modules in the biocode/lib
+directory, so you'll need to point Python to them. Full setup example:
+
+::
+
+    cd /opt
+    git clone https://github.com/jorvis/biocode.git
+
+    # You probably want to add this line to your $HOME/.bashrc file
+    export PYTHONPATH=/opt/biocode/lib:$PYTHONPATH
+
+Problems / Suggestions?
+=======================
+
+If you encounter any issues with the existing code, or would like to
+request new features or scripts please submit to the `Issue tracking
+system <https://github.com/jorvis/biocode/issues>`__.
+
+Contributing
+============
+
+If you'd like to contribute code to this collection have a look at the
+`Requirements And Convention
+Guide <https://github.com/jorvis/biocode/blob/master/RequirementsAndConventionGuide.md>`__
+and then submit a pull request once your code is ready. We'll check your
+script and pull it into the production directories. If you're not that
+confident yet we'll happily pull in your sandbox directory if you'd like
+to add your code to the project but aren't sure if it's ready to be in
+the production directories yet.

build/make_pypi_release.py

@@ -29,7 +29,6 @@
 
 import argparse
 import os
-import pypandoc
 import shutil
 
 def main():
@@ -74,7 +73,7 @@ def main():
         pass
 
     # place the README
-    shutil.copyfile('README.md', "{0}/README.md".format(lib_path))
+    shutil.copyfile('README.md', "{0}/README.rst".format(lib_path))
 
     # creates the biocode/setup.py file
     setup_fh = open("{0}/setup.py".format(args.output_directory), 'wt')
@@ -191,19 +190,14 @@ def populate_setup_file(fh, version, script_paths):
         'email': '[email protected]',
         'version': version,
         'packages': ['biocode'],
-        'dependencies': ['pypandoc', 'igraph', 'jinja2', 'matplotlib'],
+        'dependencies': ['igraph', 'jinja2', 'matplotlib'],
         'scripts': script_paths
     }
 
     fh.write("""
 from setuptools import setup
 
-try:
-    from pypandoc import convert
-    read_md = lambda f: convert(f, 'rst', 'md')
-except ImportError:
-    raise Exception("Error: pypandoc module not found, could not convert Markdown to RST")
-    read_md = lambda f: open(f, 'r').read()
+read = lambda f: open(f, 'r').read()
 
 setup(name='biocode',
       author='{author}',
@@ -222,7 +216,7 @@ def populate_setup_file(fh, version, script_paths):
       install_requires={dependencies},
       keywords='bioinformatics scripts modules gff3 fasta fastq bam sam',
       license='MIT',
-      long=read_md('biocode/README.md'),
+      long_description=read('biocode/README.rst'),
       packages={packages},
       scripts={scripts},
       url='http://github.com/jorvis/biocode',