Made libsmallrna a submodule.

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "libdeseq"]
 	path = libdeseq
 	url = git@gitlab.pasteur.fr:bli/libdeseq.git
+[submodule "libsmallrna"]
+	path = libsmallrna
+	url = git@gitlab.pasteur.fr:bli/libsmallrna.git

libsmallrna @ af0b5271

+Subproject commit af0b5271e3f1ec2f4bcd4c43e108d3d442e2897b

libsmallrna/.gitignore

-# Compiled python modules.
-*.pyc
-
-# Setuptools distribution folder.
-/dist/
-
-# Python egg metadata, regenerated from source files by setuptools.
-/*.egg-info
-
-# Backups
-*~

libsmallrna/install.sh

-#!/bin/sh
-python3.6 setup.py build_ext
-# .egg-link does not work with PYTHONPATH ?
-python3.6 -m pip install -e .
-python3.6 -m pip install  --no-deps --ignore-installed .

libsmallrna/libsmallrna/__init__.py

-from .libsmallrna import (
-    has_pi_signature, has_endosi_signature, has_26G_signature, has_csr1_endosi_signature,
-    count_small,
-    count_annots, count_pimis, count_sis, count_all_sis, count_nucl, count_first_bases,
-    add_compositions, add_results, Composition, get_read_info,
-    PI_MIN, PI_MAX, SI_MIN, SI_MAX,
-    SI_SUFFIXES, SI_PREFIXES,
-    SMALL_TYPES_TREE,
-    type2RNA,
-    types_under,
-    SMALL_TYPES,
-    SI_TYPES,
-    SIU_TYPES,
-    SISIU_TYPES,
-    RMSK_SISIU_TYPES,
-    JOINED_SMALL_TYPES)

libsmallrna/setup.py

-from setuptools import setup, find_packages
-from Cython.Build import cythonize
-
-setup(
-    name="libsmallrna",
-    version="0.2",
-    description="Miscellaneous things to deal with small RNA",
-    author="Blaise Li",
-    author_email="blaise.li@normalesup.org",
-    license="MIT",
-    # packages=["libsmallrna"],
-    ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
-    install_requires=["cytoolz"],
-    zip_safe=False,
-    packages=find_packages())