Move to setup via setup.cfg instead of setup.py (#25)

* Move to setup via setup.cfg instead of setup.py

* Delete unnecessary files, adapt README

* adapt test

.github/workflows/tests.yaml

@@ -13,11 +13,9 @@ jobs:
       with:
         python-version: 3.7
     - name: Install dependencies
-      run: pip install -e .
+      run: pip install -e .[dev]
     - name: Install RDKit
       run: pip install rdkit
-    - name: Install test dependencies
-      run: pip install -r dev_requirements.txt
     - name: Check black
       run: python -m black --check --diff --color .
     - name: Check isort

README.md

@@ -6,13 +6,11 @@ Enable robust atom mapping on valid reaction SMILES. The atom-mapping informatio
 - [Unsupervised attention-guided atom-mapping preprint](http://dx.doi.org/10.26434/chemrxiv.12298559): presented at the ML Interpretability for Scientific Discovery ICML workshop, 2020.
 
 ## Installation
-For all installations, we recommend using `conda` to get the necessary `rdkit` dependency:
 
 ### From pip
 ```console
 conda create -n rxnmapper python=3.6 -y
 conda activate rxnmapper
-conda install -c rdkit rdkit=2020.03.3.0
 pip install rxnmapper
 ```
 
@@ -22,10 +20,24 @@ You can install the package and setup the environment directly from github using
 ```console
 git clone https://github.com/rxn4chemistry/rxnmapper.git 
 cd rxnmapper
-conda env create -f environment.yml
+conda create -n rxnmapper python=3.6 -y
 conda activate rxnmapper
 pip install -e .
-pip install -r requirements.txt
+```
+
+### RDkit
+
+In both installation settings above, the `RDKit` dependency is not installed automatically.
+It can be installed via Conda or Pypi:
+
+```bash
+# Install RDKit from Conda
+conda install -c conda-forge rdkit
+
+# Install RDKit from Pypi
+pip install rdkit
+# for Python<3.7
+# pip install rdkit-pypi
 ```
 
 ## Usage
@@ -52,7 +64,7 @@ The results contain the mapped reactions and confidence scores:
 
 You can run the examples above with the test suite as well:
 
-1. `pip install -r dev_requirements.txt` 
+1. In your Conda environment: `pip install -e .[dev]`
 2. `pytest tests` from the root 
 
 ## Examples

rxnmapper/__init__.py

@@ -1,5 +1,5 @@
 """rxnmapper initialization."""
 __name__ = "rxnmapper"
-__version__ = "0.1.0"
+__version__ = "0.1.4"
 
 from .core import RXNMapper  # noqa

setup.cfg

@@ -1,6 +1,49 @@
-# Inside of setup.cfg
 [metadata]
-description-file = README.md
+name = rxnmapper
+version = attr: rxnmapper.__version__
+description = Reaction atom-mapping from transfomers
+author = IBM RXN team
+author_email = [email protected]
+license = MIT
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers =
+    Operating System :: OS Independent
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Topic :: Software Development :: Libraries :: Python Modules
+url = https://github.com/rxn4chemistry/rxnmapper
+
+[options]
+packages = find:
+python_requires = >= 3.6
+zip_safe = False
+include_package_data = True
+install_requires =
+    pandas>=1.0.3
+    rxn-chem-utils>=1.0.3
+    scipy==1.4.1
+    torch==1.5.0
+    transformers==4.0.0
+
+[options.package_data]
+rxnmapper =
+    models/transformers/albert_heads_8_uspto_all_1310k/*
+
+[options.extras_require]
+dev =
+    black>=22.1.0
+    bump2version>=1.0.1
+    flake8>=3.7.9
+    isort>=5.10.0
+    pytest>=5.4.1
+    sphinx-rtd-theme==0.4.3
+    sphinx==2.2.1
+    twine==3.1.1
 
 [flake8]
 extend-ignore = E203, E501

setup.py

@@ -1,41 +1,5 @@
 #!/usr/bin/env python
 
-import os
+from setuptools import setup
 
-from setuptools import find_packages, setup
-
-if os.path.exists("README.md"):
-    long_description = open("README.md").read()
-else:
-    long_description = """Reaction atom-mapping from transfomers"""
-
-setup(
-    name="rxnmapper",
-    version="0.1.4",
-    author="RXNMapper team",
-    author_email="[email protected], [email protected]",
-    py_modules=["rxnmapper"],
-    description="Reaction atom-mapping from transfomers",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    license="MIT",
-    install_requires=[
-        "transformers==4.0.0",
-        "torch==1.5.0",
-        "scipy==1.4.1",
-        "rxn-chem-utils>=1.0.3",
-    ],
-    packages=find_packages(),
-    package_data={
-        "rxnmapper": ["models/transformers/albert_heads_8_uspto_all_1310k/*"]
-    },
-    url="https://github.com/rxn4chemistry/rxnmapper",
-    classifiers=[
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-    ],
-)
+setup()