Merge pull request #47 from 4dn-dcic/versions

Versions

README.md

@@ -17,6 +17,12 @@ The hic parsing code is based off the [straw project](https://github.com/theaide
 $ pip install hic2cool
 ```
 
+You can also download the code directly and run the setup yourself.
+```
+# setuptools >=42 is recommended
+$ python setup.py install
+```
+
 Once the package is installed, the main method is hic2cool_convert. It takes the same parameters as hic2cool.py, described in the next section. Example usage in a Python script is shown below or in test.py.
 ```
 from hic2cool import hic2cool_convert
@@ -31,21 +37,6 @@ The main use of hic2cool is converting between filetypes using `hic2cool convert
 $ hic2cool convert <infile> <outfile> -r <resolution> -p <nproc>
 ```
 
-You can also download the code directly and run the setup yourself. First ensure that dependencies are installed:
-```
-$ pip install -r requirements.txt
-```
-
-You can alternatively build the hic2cool package with:
-```
-$ python setup.py install
-```
-
-Then, execute the Python code from the root directory with:
-```
-$ python -m hic2cool convert <infile> <outfile> -r <resolution> -p <nproc>
-```
-
 ### Arguments for hic2cool convert
 
 **infile** is a .hic input file.
@@ -128,6 +119,8 @@ You may also provide the optional `-e` flag, which will cause the mitchondrial c
 
 
 ## Changelog
+### 0.8.1
+* `setup.py` takes dependencies directly from `requirements.txt` (`requirements.txt` updated to match `setup.py`)
 ### 0.8.0
 * multiprocessing support for convert
 * change in usage of convert API due to the addition of the `nproc` option

hic2cool/_version.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.8.1"

requirements.txt

@@ -1,5 +1,5 @@
-h5py==2.8.0
-pandas==0.24.2
-numpy==1.16.3
-scipy==1.2.1
-cooler==0.8.5
+h5py>=2.8.0
+numpy>=1.10.1,<=1.16.3
+scipy<=1.2.1
+pandas<=0.24.2
+cooler>=0.8.5

setup.py

@@ -13,16 +13,9 @@
 with io.open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
     long_description = f.read()
 
-# dependencies must be handled carefully for py2 and py3 compatibility
-# specifically, scipy==1.3.0
-requires = [
-    'h5py>=2.8.0',
-    'numpy>=1.10.1,<=1.16.3',
-    'scipy<=1.2.1',
-    'pandas<=0.24.2',
-    'cooler>=0.8.5'
-
-]
+with open('requirements.txt') as f:
+    set_parsed = f.read().splitlines()
+requires = [req.strip() for req in set_parsed if 'git+' not in req]
 
 this_version = io.open(path.join(this_directory, "hic2cool/_version.py")).readlines()[-1].split()[-1].strip("\"'")