Fix requirements (#284)

* Fix pandas dependency, pinned to `pandas>=1.0.0,<=1.1.4` to prevent 'pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects'. 
* Add min version for numpy<=1.16.5 to match pandas requirement. 
* Remove unused cython requirement.
* Add README.md and requirements.txt to package MANIFEST.in
* Bump package version and add short description to setup.py

MANIFEST.in

@@ -1,4 +1,7 @@
 include ppi-resources.md
+include README.md
+include LICENSE
+include requirements.txt
 include cellphonedb/src/core/cellphone.db
 include cellphonedb/src/app/config/*.yml
 include cellphonedb/src/core/data/*.csv

requirements.txt

@@ -1,6 +1,6 @@
 click>=6.7,<6.7.99
-pandas
-numpy
+pandas>=1.0.0,<=1.1.4
+numpy>=1.16.5
 scikit-learn==0.22
 flask>=1.0,<1.0.99
 Flask-RESTful>=0.3,<0.3.99
@@ -13,6 +13,5 @@ boto3>=1.7,<1.7.99
 geosketch==0.3
 rpy2>=3.0.4,<3.0.99
 tqdm>=4.32,<4.32.99
-cython>=0.29,<0.29.9
 h5py<3.0.0
 anndata>=0.7,<=0.75

setup.py

@@ -10,7 +10,8 @@
     name='CellPhoneDB',
     author='TeichLab',
     author_email='[email protected]',
-    version='2.1.6',
+    version='2.1.7',
+    description='Inferring cell-cell communication',
     long_description=long_description_readme_md,
     long_description_content_type='text/markdown',
     packages=find_packages(),

win-requirements.txt

@@ -1,6 +1,6 @@
 click>=6.7,<6.7.99
-pandas
-numpy
+pandas>=1.0.0,<=1.1.4
+numpy>=1.16.5
 scikit-learn==0.22
 flask>=1.0,<1.0.99
 Flask-RESTful>=0.3,<0.3.99
@@ -13,6 +13,5 @@ boto3>=1.7,<1.7.99
 geosketch==0.3
 rpy2==3.0.3
 tqdm>=4.32,<4.32.99
-cython>=0.29,<0.29.9
 h5py<3.0.0
 anndata>=0.7,<=0.75