diff --git a/.gitignore b/.gitignore index 96664a9..3ae4313 100644 --- a/.gitignore +++ b/.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__/ \ No newline at end of file diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..fc71207 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,5 @@ +# Changelog + +## Opfi 0.1.0 + +Initial release. \ No newline at end of file diff --git a/README.md b/README.md index 87deb12..a0fbd34 100644 --- a/README.md +++ b/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 . ``` diff --git a/docs/installation.rst b/docs/installation.rst index d62ba97..101b46f 100644 --- a/docs/installation.rst +++ b/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 ------------ diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..3bf76c6 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,3 @@ +sphinx==4.0.1 +sphinx-rtd-theme==0.5.2 +docutils==0.16 diff --git a/requirements.txt b/requirements.txt index 015ed03..a741e3b 100644 --- a/requirements.txt +++ b/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 diff --git a/setup.py b/setup.py index 8af8e1f..580e6bb 100644 --- a/setup.py +++ b/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="alexismhill3@gmail.com", - 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", + ] )