Merge pull request #197 from alexismhill3/release-0.1.0

Release 0.1.0

.gitignore

@@ -1,17 +1,16 @@
 # virtual environments
 env/
 env_test/
+env-dist/
 
-# distribution stuff
+# distribution artifacts
 dist/
 .eggs/
-
-# build stuff
-__pycache__/
 opfi.egg-info/
-.eggs/
-*.o
 build/
+
+# don't include compiled pilercr
+*.o
 lib/pilercr1.06/pilercr
 
 # dev tools
@@ -25,3 +24,5 @@ docs/_build
 
 # python notebook checkpoints
 .ipynb_checkpoints
+
+__pycache__/

NEWS.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## Opfi 0.1.0
+
+Initial release.

README.md

@@ -15,12 +15,17 @@ sudo make install
 
 ## Installation
 
-To install Opfi, clone the repository and run pip from the project root directory:
+You can install Opfi with Pip:
+
+```
+pip3 install opfi
+```
+
+Alternatively, you can install the latest version on Github:
 
 ```
 git clone https://github.com/wilkelab/Opfi.git
 cd Opfi
-pip3 install -r requirements.txt
 pip3 install .
 ```
 

docs/installation.rst

@@ -19,7 +19,6 @@ Alternatively, you can install the latest version on Github:
     git clone https://github.com/alexismhill3/Opfi.git
     cd Opfi
     pip3 install .
-    pip3 install -r requirements.txt
 
 Dependencies
 ------------

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx==4.0.1
+sphinx-rtd-theme==0.5.2
+docutils==0.16

requirements.txt

@@ -6,6 +6,3 @@ PyYAML==5.4
 dna-features-viewer==3.0.1
 more-itertools==8.4.0
 parasail==1.2
-sphinx==4.0.1
-sphinx-rtd-theme==0.5.2
-docutils==0.16

setup.py

@@ -1,17 +1,14 @@
 import setuptools
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
 setuptools.setup(
     name="opfi", 
     version="0.1.0",
     author="Alexis M Hill, James Rybarski",
     author_email="[email protected]",
-    description="A suite of tools for finding and analyzing genomic systems of interest.",
-    # long_description=long_description,
-    # long_description_content_type="text/markdown",
-    url="https://github.com/alexismhill3/CRISPR-Transposons",
+    description="A package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics datasets.",
+    long_description=open('README.md').read(),
+    long_description_content_type="text/markdown",
+    url="https://github.com/wilkelab/Opfi",
     packages=setuptools.find_packages('src'),
     package_dir={'': 'src'},
     classifiers=[
@@ -20,5 +17,14 @@
         "Operating System :: OS Independent",
     ],
     python_requires='>=3.6',
-    setup_requires=['wheel'],
+    install_requires=[
+        "biopython==1.76", 
+        "pytest==5.3.2",
+        "hypothesis==5.1.1", 
+        "matplotlib==3.2.1", 
+        "PyYAML==5.4", 
+        "dna-features-viewer==3.0.1", 
+        "more-itertools==8.4.0", 
+        "parasail==1.2", 
+        ]
 )