PyPI setup refactored and fixed

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+bert_model/
+.pypirc

CHANGELOG.md

@@ -2,25 +2,16 @@
 All notable changes to this project will be documented in this file.
 
 
-## [0.3.0] - 21.08.2020
-### Added
-* `embedding` module with BERT pre-trained embedding model for proteins with support for single protein vectorization as well as for proteins sets which are averagend to bacteriophage level;
-
+## [0.0.2] - 24.08.2020
 ### Changed
-* `requirements.txt` with bio-embedding and fake-useragent;
+* Improved setup for Python Index Packages;
 
 
-## [0.2.0] - 20.08.2020
+## [0.0.1] - 10.08.2020 - 21.08.2020
 ### Added
+* `embedding` module with BERT pre-trained embedding model for proteins with support for single protein vectorization as well as for proteins sets which are averagend to bacteriophage level;
 * `features` module with protein-based (amino-acid) feature extractor for single protein sequence as well as for multifasta;
-
-### Changed
-* `requirements.txt` with biopython;
-
-
-## [0.1.0] - 10.08.2020
-### Added
 * `crawlers` module with MillardLab website support;
 
 ### Changed
-* `requirements.txt` with lxml, python-requests and pandas;
+* `requirements.txt` with bio-embedding, fake-useragent, biopython, lxml, python-requests and pandas;

MANIFEST.in

@@ -0,0 +1,6 @@
+include requirements.txt
+include LICENSE
+include CHANGELOG.md
+include README.md
+include setup.py
+recursive-include examples .ipynb

examples/embeddings/Bacteriophage-proteins-embedding.ipynb

@@ -0,0 +1,34 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pha"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

setup.cfg

@@ -1,3 +1,4 @@
 [metadata]
 description-file = README.md
-
+long_description = file: README.md
+long_description_content_type = text/markdown

setup.py

@@ -1,44 +1,64 @@
-from distutils.core import setup
+from setuptools import setup
+from glob import glob
+from pathlib import Path
 
 
-long_description = (
+CURRENT_DIR = Path(__file__).parent
+
+long_description = (CURRENT_DIR / "README.md").read_text(encoding="utf8")
+
+description = (
     "PHAGES2050 is a novel Python 3.6+ programming language framework"
-    " to boost bacteriophage research & therapy and infrastructure in"
-    " order to achieve the full potential to fight against antimicrobial"
-    " resistant bacteria within **Natural Language Processing (NLP)** and **Deep Learning**."
+    " to boost bacteriophage research & therapy"
 )
 
+# Read requirements and process as list of strings
+dependencies = (CURRENT_DIR / "requirements.txt").read_text()
+dependencies = list(map(str.strip, filter(None, dependencies.split('\n'))))
+
 
-with open("requirements.txt") as requirements:
-    # Read requirements and process as list of strings
-    packages = list(map(str.strip, requirements.readlines()))
-    version = '0.3.0'
-
-    setup(
-        name="phages2050",
-        version=version,
-        license="MIT",
-        description=long_description,
-        long_description=long_description,
-        long_description_content_type="text/markdown",
-        author="Piotr Tynecki",
-        author_email="[email protected]",
-        url="https://github.com/ptynecki/PHAGES2050",
-        download_url=f"https://github.com/ptynecki/PHAGES2050/archive/v{version}.tar.gz",
-        install_requires=packages,
-        keywords=[
-            "bacteriophages",
-            "phages",
-            "phage therapy",
-            "phage research",
-            "amr",
-            "genome embedding",
-            "protein embedding",
-        ],
-        classifiers=[
-            "Development Status :: 3 - Alpha",
-            "License :: OSI Approved :: MIT License",
-            "Programming Language :: Python :: 3.6",
-        ],
-        python_requires=">=3.6",
-    )
+version = "0.0.2"
+
+setup(
+    name="phages2050",
+    version=version,
+    license="MIT",
+    description=description,
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Piotr Tynecki",
+    author_email="[email protected]",
+    url="https://github.com/ptynecki/PHAGES2050",
+    download_url=f"https://github.com/ptynecki/PHAGES2050/archive/v{version}.tar.gz",
+    setup_requires=[
+        'setuptools>=49.6.0',
+        'wheel>=0.35.1'
+    ],
+    install_requires=dependencies,
+    packages=[
+        "crawlers",
+        "crawlers.ncbi",
+        "crawlers.millardlab",
+        "features",
+        "features.extractors",
+        "embeddings",
+        "embeddings.proteins",
+    ],
+    data_files=glob('examples/*/**'),
+    include_package_data=True,
+    keywords=[
+        "bacteriophages",
+        "phages",
+        "phage therapy",
+        "phage research",
+        "amr",
+        "genome embedding",
+        "protein embedding",
+    ],
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python :: 3.6",
+    ],
+    python_requires=">=3.6",
+)