Big revamp of README and push the info into the setup.py 'long_descri…

…ption' field

- Also moved numpy into the setup dependencies so it is definitely available before trying to install biopython
- Deleting all conda recipe files. It's not currently necessary, so don't worry about it for now.
- Add the pytest-cov and pytest-xdist dependencies
- Swap the order of nexus and embl format guessing, to prevent some uncaught Nexus errors

MANIFEST.in

@@ -4,4 +4,7 @@ include buddysuite/DatabaseBuddy.py
 include buddysuite/PhyloBuddy.py
 include buddysuite/SeqBuddy.py
 include buddysuite/BuddySuite.py
-include buddysuite/__init__.py
+include buddysuite/__init__.py
+include README.md
+include LICENSE.txt
+include privacy

README.md

@@ -10,119 +10,55 @@
 </p>
 <p align="center">Do fun stuff with biological data files. Seriously, biological data is fun stuff :)</p>
 ___
-## Description
-The BuddySuite modules are designed to be 'one-stop-shop' command line tools for common biological data file
- manipulations.
-
-[SeqBuddy](https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy) is the most mature BuddySuite tool, although
- [AlignBuddy](https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy) and
- [PhyloBuddy](https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy) are also functional with a more limited number
- of commands. [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy) is a very different project,
- existing mostly as a 'live shell' for downloading sequences from GenBank, ENSEMBL, and UniProt.
 
-Being pure Python, the BuddySuite should be cross platform. Development and testing have been done on Linux
- and Mac OS X, however, so it is unclear how well the suite will work within Windows. 
+## Description
+The BuddySuite modules are 'one-stop-shop' command line tools for common biological data file
+ manipulations. Formats are detected automatically, conversions are seamless, and you can pipe into
+ or out of the modules, allowing you to spend more time analyzing your sequences, alignments, and phylogenetic
+ trees, instead of wrangling them.
+
+For example, the following command reads in three sequence files (all in different formats), pulls out records with RefSeq identifiers,
+ calls MAFFT to generate an alignment, shifts gaps to force a codon alignment, calls RAxML to infer a phylogeny, and then roots
+ the tree at its midpoint.
 
-If you're new to the command line, or simply want to get a better feel for how BuddySuite works, check out the [Beginners Guide](https://github.com/biologyguy/BuddySuite/wiki/Beginners-Guide).
+`$: seqbuddy seqs1.gb seqs2.embl seqs3.fasta --pull_records "[XN]M" | alignbuddy --generate_alignment mafft | alignbuddy --enforce_triplets | phylobuddy --generate_tree raxmlHPC-SSE3 | phylobuddy --root`
 
-## Installation 
-Clone the repository to your local machine and run setup.py installer (or
- [fork](https://help.github.com/articles/fork-a-repo/) it if planning to develop):
+BuddySuite is a Python3 project, developed and tested on Linux and Mac OS X. It should generally work on Windows as well, but
+ testing on Windows has been extremely limited.
 
-    $: git clone https://github.com/biologyguy/BuddySuite.git
-    $: cd BuddySuite
-    $: python3 setup.py install clean
-
-The project should now be in your Python PATH along with sym-links to the executables. For example:
-
-    $: which seqbuddy
-    >>> /usr/local/anaconda/bin/seqbuddy
+## Getting started
+The simplest way to get up and running is:
 
-And to get started, simply use the 'help' flag
+```bash
+$: pip install buddysuite 
+$: buddysuite -setup
+```
 
-    $: seqbuddy -h
+Further instructions are available in the [installation guide](https://github.com/biologyguy/BuddySuite/wiki/Installation-Guide).
 
-For a detailed breakdown of the tools available within each module, check out the
- [BuddySuite wiki](https://github.com/biologyguy/BuddySuite/wiki).
-
-### Create shortcuts (OPTIONAL)
-We also recommend creating a set of short-form symbolic links or aliases to each program, which are very convenient if
- using the programs on a regular basis. Furthermore, all of the 
- [examples in the wiki](https://github.com/biologyguy/buddysuite/wiki) use the following short forms:
+There is also a short [Beginners' Guide](https://github.com/biologyguy/BuddySuite/wiki/Beginners-Guide) to show you the basics.
 
-*Tool* | *Short-form*
----------- | -------- 
-AlignBuddy | alb
-DatabaseBuddy | db
-PhyloBuddy | pb
-SeqBuddy | sb
-
-First check to make sure the short-form command doesn't already exist; for example, the
- following should not return anything:
+Each tool in the BuddySuite has been extensively documented in the [wiki](https://github.com/biologyguy/BuddySuite/wiki),
+ complete with worked examples and explanations for all arguments/options.
 
-    $: which sb
-    >>>
-
-If there is a conflict, choose something else that seems reasonable (e.g., 'sbd' or 'sqb'). Now either create aliases
- or symbolic links:
-
-**Aliases**
-
-Copy the following into either the `.bashrc`, `.profile`, or `.bash_profile` (system dependent) file in your home directory:
-
-    alias sb="seqbuddy"
-    alias alb="alignbuddy"
-    alias pb="phylobuddy"
-    alias db="databasebuddy"
-
-Then restart your terminal
-
-**Symbolic Links**
+* [SeqBuddy](https://github.com/biologyguy/BuddySuite/wiki/SeqBuddy) 
+* [AlignBuddy](https://github.com/biologyguy/BuddySuite/wiki/AlignBuddy)
+* [PhyloBuddy](https://github.com/biologyguy/BuddySuite/wiki/PhyloBuddy)
+* [DatabaseBuddy](https://github.com/biologyguy/BuddySuite/wiki/DatabaseBuddy). 
 
-For each program, replace the necessary path components in the command below and run from the shell
-
-    $: ln -s /<your>/<path>/<to>/BuddySuite/buddysuite/SeqBuddy.py /usr/local/bin/sb
-
-You should now be able to see the short form commands in your PATH, e.g.,:
-
-    $: which sb
-    >>> /usr/local/bin/sb
-
-## Dependencies
-This project has been written in Python3 and is not backwards compatible with Python2. If Python3 is not currently
- installed on your system, we highly recommend using the free [Anaconda manager](http://continuum.io/downloads#py34)
- from Continuum Analytics (if you experience any difficulty, 
- [click here](https://github.com/biologyguy/BuddySuite/wiki/anaconda)). Alternatively, the software can be downloaded 
- directly from the [Python Software Foundation](https://www.python.org/downloads/).
-
-AlignBuddy and PhyloBuddy can be used to launch a number of third party alignment and tree building programs, but
- installation of these optional programs is up to you. For example, if you wish to use PhyloBuddy to build a 
- phylogenetic tree with RAxML, you will first need to get RAxML into your system PATH. 
-
-The SeqBuddy blast, bl2seq, and purge functions require access to the blastp, blastn, and blastdbcmd binaries from the
- [NCBI C++ toolkit](http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/).
-
-See the [Dependencies](https://github.com/biologyguy/BuddySuite/wiki/Dependencies) page for a full list of all
- third-party packages and software that BuddySuite requires or wraps.
-
 ## Developers
 All of the individual Buddy toolkits are located in the 'buddysuite' directory and the 
  ['develop' branch](https://github.com/biologyguy/BuddySuite/tree/develop) is where all new features have been
  implemented. If you're interested in contributing, please refer to the
  [developer page](https://github.com/biologyguy/BuddySuite/wiki/Developers) for further information on dependencies
  and instructions.
 
-## Unit tests
-We are striving for high unit test coverage with py.test. To run the tests:
-
-    $: cd BuddySuite/buddysuite
-    $: bash run_tests.sh
-
 ## Citation
-There is a very short application note on bioRxiv that can be cited if you use BuddySuite in your work.
+We are currently working on a [peer reviewed manuscript](https://github.com/biologyguy/BuddySuite/tree/develop/manuscript), but until then
+ there is a very short application note on bioRxiv that can be cited if you use BuddySuite in your work.
 
 [DOI: 10.1101/040675](http://dx.doi.org/10.1101/040675)
 
 ## Contact
-Any comments you may have would be really appreciated. Please feel free to add issues in the GitHub issue tracker or
- contact Steve Bond (lead developer) directly at [steve.bond@nih.gov](mailto:steve.bond@nih.gov)
+Any comments you have would be really appreciated. Please feel free to add issues in the GitHub issue tracker or
+ contact Steve Bond (lead developer) directly at [steve.bond@nih.gov](mailto:steve.bond@nih.gov).

buddysuite/SeqBuddy.py

@@ -605,7 +605,7 @@ def _guess_format(_input):
         _input.seek(0)
 
         possible_formats = ["stockholm", "fasta", "gb", "phylipss", "phylipsr", "phylip", "phylip-relaxed",
-                            "fastq", "nexus", "embl", "seqxml", "clustal", "swiss"]
+                            "fastq", "embl", "nexus", "seqxml", "clustal", "swiss"]
         for next_format in possible_formats:
             try:
                 _input.seek(0)

setup.py

@@ -27,15 +27,17 @@ def run():
 ]
 
 DEPENDENCIES = [
-    'biopython',
-    'ete3',
-    'six',
-    'dendropy',
     'pytest',
-    'scipy',
+    'pytest-xdist',
+    'pytest-cov',
     'numpy',
+    'scipy',
+    'six',
     'dill',
-    'suds-py3'
+    'suds-py3',
+    'biopython',
+    'dendropy',
+    'ete3',
 ]
 
 CLASSIFIERS = [
@@ -58,7 +60,8 @@ def run():
     'genetics',
     'genome',
     'phylogenetics',
-    'biology'
+    'biology',
+    'bioinformatics'
 ]
 
 ENTRY_POINTS = {
@@ -72,13 +75,15 @@ def run():
 }
 
 setup(name='buddysuite',
-      version='1.2b.12',
+      version='1.2b.3',
       description='BuddySuite is a collection of command line utilities written in Python for '
                   'working with biological data.',
+      long_description=open(os.path.join(os.path.dirname(__file__), 'README.md')).read(),
       author='Stephen Bond',
       author_email='steve.bond@gmail.com',
       url='https://github.com/biologyguy/BuddySuite',
       packages=PACKAGES,
+      setup_requires=['numpy'],
       install_requires=DEPENDENCIES,
       entry_points=ENTRY_POINTS,
       license='Public Domain',