Simplify installation

pyproject.toml

@@ -1,3 +1,8 @@
+# See https://setuptools.readthedocs.io/en/latest/build_meta.html
+[build-system]
+requires = ["setuptools", "wheel", "torch"]
+build-backend = "setuptools.build_meta:__legacy__"
+
 [tool.black]
 line-length = 120
 target-version = ["py37", "py38", "py39"]
@@ -6,4 +11,4 @@ target-version = ["py37", "py38", "py39"]
 profile = "black"
 multi_line_output = 3
 include_trailing_comma = true
-reverse_relative = true
+reverse_relative = true

readthedocs.yaml

@@ -13,9 +13,8 @@ formats:
 
 python:
    version: "3.7"
-   system_packages: "True"
    install:
       - requirements: docs/requirements_1.txt
-      - method: setuptools
+      - method: pip
         path: .
    system_packages: true

setup.cfg

@@ -2,5 +2,88 @@
 # Setup.py Configuration #
 ##########################
 [metadata]
+name = chemicalx
+version = 0.0.8
+description = A Deep Learning Library for Drug Pair Scoring
 long_description = file: README.md
 long_description_content_type = text/markdown
+
+# Links
+url = https://github.com/AstraZeneca/chemicalx
+download_url = https://github.com/AstraZeneca/chemicalx/archive/v0.0.8.tar.gz
+project_urls =
+    Bug Tracker = https://github.com/AstraZeneca/chemicalx/issues
+
+
+# Author information
+author = Benedek Rozemberczki and Charles Tapley Hoyt
+author_email = [email protected]
+maintainer = Benedek Rozemberczki
+maintainer_email = [email protected]
+
+# License information
+license = Apache-2.0
+license_file = LICENSE
+
+# Search tags
+classifiers =
+    Development Status :: 3 - Alpha
+    Intended Audience :: Developers
+    Topic :: Software Development :: Build Tools
+    License :: OSI Approved :: Apache Software License
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+keywords =
+    drug
+    deep-learning
+    deep-chemistry
+    deep-ai
+    torch-drug
+    synergy-prediction
+    synergy
+    drug-combination
+    deep-synergy
+    drug-interaction
+    chemistry
+    pharma
+
+[options]
+install_requires =
+    numpy
+    torch>=1.10.0
+    torchdrug
+    torch-scatter>=2.0.8
+    pandas<=1.3.5
+    tqdm
+    scikit-learn
+    class-resolver>=0.2.1
+    tabulate
+    pystow
+    pytdc
+
+zip_safe = false
+include_package_data = True
+python_requires = >=3.7
+
+# Where is my code
+packages = find:
+package_dir =
+    = src
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+tests =
+    pytest
+    pytest-cov
+    coverage
+docs =
+    sphinx
+    sphinx-rtd-theme
+    sphinx-click
+    sphinx-autodoc-typehints
+    sphinx_automodapi
+    nbsphinx_link
+    jupyter-sphinx

tox.ini

@@ -4,6 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
+isolated_build = true
 envlist =
     lint
     flake8
@@ -16,10 +17,8 @@ envlist =
 [testenv]
 commands =
     coverage run -m pytest
-deps =
-    torch
-    pytest
-    coverage
+extras =
+    tests
 
 [testenv:coverage]
 commands =
@@ -99,7 +98,7 @@ skip_install = true
 deps =
     docstr-coverage
 commands =
-    docstr-coverage chemicalx/ examples/ tests/ data_cleaning/ --skip-private --skip-magic
+    docstr-coverage src/chemicalx examples/ tests/ data_cleaning/ --skip-private --skip-magic
 description = Run the docstr-coverage tool to check documentation coverage
 
 [testenv:pyroma]