Merge pull request #27 from fabio-t/rel/v1.9.4

Rel/v1.9.4

python/MANIFEST.in

@@ -3,5 +3,5 @@ include readme.MD
 include scripts/example-data/readme.MD
 include scripts/example-data/seq/chr1-5k-55k.fa
 include scripts/example-data/matrices/*
-include scripts/ex-*.py scripts/moods_dna.py
-include COPYING.BIOPYTHON COPYING.GPLv3
+include scripts/ex-*.py scripts/moods-dna.py
+include COPYING.BIOPYTHON COPYING.GPLv3

python/build.sh

@@ -1,6 +1,11 @@
 #!/bin/bash
+
+ln -sf ../core
+
 swig -c++ -python -outdir MOODS/ core/scan.i
 swig -c++ -python -outdir MOODS/ core/tools.i
 swig -c++ -python -outdir MOODS/ core/misc.i
 swig -c++ -python -outdir MOODS/ core/parsers.i
-python setup.py build_ext --inplace
+
+python setup.py build_ext --inplace
+

python/readme.MD

@@ -32,7 +32,7 @@ Alternatively, you can install MOODS from the source package:
 
 (a) Compile the extensions in place and create a symlink under `scripts/`
 (if you just want to test things without installing to Python library path,
-or you are simply planning to use the `moods_dna.py` scripts for basic 
+or you are simply planning to use the `moods-dna.py` scripts for basic 
 analysis):
 
     python setup.py build_ext --inplace
@@ -47,12 +47,12 @@ analysis):
 
     sudo python setup.py install
 
-You can test MOODS by running the `moods_dna.py` script with
+You can test MOODS by running the `moods-dna.py` script with
 the example data provided with the package:
 
     cd scripts/
-    python moods_dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001
-    python moods_dna.py --help
+    python moods-dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001
+    python moods-dna.py --help
 
 
 Documentation

python/setup.py

@@ -46,7 +46,7 @@
 
 
 this_directory = path.abspath(path.dirname(__file__))
-with open(path.join(this_directory, 'readme.MD'), encoding='utf-8') as f:
+with open(path.join(this_directory, 'readme.MD')) as f:
     long_description = f.read()
 
 setup (name = 'MOODS-python',
@@ -61,6 +61,6 @@
        ext_modules = [tools_mod, scan_mod, parsers_mod],
        packages = ["MOODS"],
        scripts=['scripts/moods-dna.py'],
-       classifiers=["Topic :: Scientific/Engineering :: Bio-Informatics"]
+       classifiers=["Topic :: Scientific/Engineering :: Bio-Informatics"],
        keywords="PWM, PSSM, motif scan"
-)
+)