add MANIFEST.in, Merge branch 'release/0.1.2'

MANIFEST.in

@@ -0,0 +1 @@
+include deepsignal/utils/*

README.md

@@ -30,12 +30,17 @@ conda activate deepsignalenv
 The virtual environment can also be created by using [*virtualenv*](https://github.com/pypa/virtualenv/).
 
 #### Install deepsignal
-After creating the environment, download and install deepsignl from github:
+After creating the environment, download and install the **lastest** deepsignl from github:
 ```bash
 git clone https://github.com/bioinfomaticsCSU/deepsignal.git
 cd deepsignal
 python setup.py install
 ```
+or install deepsignal using *pip*:
+```bash
+pip install deepsignal
+```
+
 [tombo](https://github.com/nanoporetech/tombo) is required to be installed in the same environment:
 ```bash
 # install using conda

README.rst

@@ -0,0 +1,15 @@
+deepsignal
+==========
+
+
+Documentation
+-------------
+
+
+v0.1.2
+-------------
+add MANIFEST.in file
+
+v0.1.1
+-------------
+3 modules (extract, call_mods, train) supported

deepsignal/__init__.py

@@ -2,4 +2,4 @@
 DNA methylation state from Nanopore reads."""
 
 
-__version__ = '0.1.1'
+__version__ = '0.1.2'

deepsignal/deepsignal.py

@@ -111,7 +111,8 @@ def main_train(args):
 
 
 def main():
-    parser = argparse.ArgumentParser(description="detecting base modifications from Nanopore sequencing reads, "
+    parser = argparse.ArgumentParser(prog='deepsignal',
+                                     description="detecting base modifications from Nanopore sequencing reads, "
                                                  "deepsignal contains three modules: \n"
                                                  "\t%(prog)s extract: extract features from corrected (tombo) "
                                                  "fast5s for training or testing\n"

setup.cfg

@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md

setup.py

@@ -44,6 +44,7 @@ def run_tests(self):
     keywords=['methylation', 'nanopore', 'neural network'],
     version=find_version('deepsignal', '__init__.py'),
     url='https://github.com/bioinfomaticsCSU/deepsignal',
+    download_url='https://github.com/bioinfomaticsCSU/deepsignal/archive/v0.1.1.tar.gz',
     license='GNU General Public License v3 (GPLv3)',
     author='Peng Ni, Neng Huang',
     # tests_require=['pytest'],
@@ -66,7 +67,7 @@ def run_tests(self):
     # test_suite='test',
     zip_safe=False,
     include_package_data=True,
-    package_data={'deepsignal': ['utils/*']},
+    # package_data={'deepsignal': ['utils/*']},
     classifiers=[
         'Programming Language :: Python :: 3',
         'Development Status :: 4 - Beta',