Made libhts a submodule.

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "libworkflows"]
 	path = libworkflows
 	url = git@gitlab.pasteur.fr:bli/libworkflows.git
+[submodule "libhts"]
+	path = libhts
+	url = git@gitlab.pasteur.fr:bli/libhts.git

libhts @ 7e25a230

+Subproject commit 7e25a230845896610a1a11a8ba91a51c824e9d0f

libhts/.gitignore

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

libhts/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 .

libhts/libhts/__init__.py

-from .libhts import (
-    aligner2min_mapq,
-    gtf_2_genes_exon_lengths,
-    id_list_gtf2bed,
-    make_empty_bigwig,
-    make_seeding_function,
-    median_ratio_to_pseudo_ref_size_factors,
-    plot_boxplots, plot_counts_distribution, plot_histo,
-    plot_lfc_distribution, plot_MA,
-    plot_norm_correlations, plot_paired_scatters, plot_scatter,
-    repeat_bed_2_lengths, size_factor_correlations,
-    spikein_gtf_2_lengths, status_setter)

libhts/setup.py

-from setuptools import setup, find_packages
-#from Cython.Build import cythonize
-
-name = "libhts"
-
-# Adapted from Biopython
-__version__ = "Undefined"
-for line in open("%s/__init__.py" % name):
-    if (line.startswith('__version__')):
-        exec(line.strip())
-
-
-setup(
-    name=name,
-    version=__version__,
-    description="Miscellaneous things to process high throughput sequencing data.",
-    author="Blaise Li",
-    author_email="blaise.li@normalesup.org",
-    license="MIT",
-    packages=find_packages(),
-    install_requires=[
-        # "libworkflows",
-        "matplotlib",
-        "networkx",
-        "numpy",
-        "pandas",
-        "pyBigWig",
-        "pybedtools",
-        "scipy",
-        "seaborn"])
-    #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
-    #install_requires=["cytoolz"],
-    #zip_safe=False