Add and document pip installation path

BioinfoMachineLearning · Aug 12, 2024 · 2461915 · 2461915
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diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
@@ -0,0 +1,35 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.9.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@
 
 [![Paper](http://img.shields.io/badge/arXiv-2405.14108-B31B1B.svg)](https://arxiv.org/abs/2405.14108)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11477766.svg)](https://doi.org/10.5281/zenodo.11477766)
+[![PyPI version](https://badge.fury.io/py/posebench.svg)](https://badge.fury.io/py/posebench)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Docs](https://assets.readthedocs.org/static/projects/badges/passing-flat.svg)](https://bioinfomachinelearning.github.io/PoseBench/)
 <a href="https://hydra.cc/"><img alt="Config: Hydra" src="https://img.shields.io/badge/config-hydra-89b8cd"></a>
@@ -38,7 +39,19 @@ Comprehensive benchmarking of protein-ligand structure generation methods
 
 <details>
 
-Install `mamba` for dependency management (as a fast alternative to Anaconda)
+### Portable installation
+
+To reuse modules and utilities within `PoseBench` in other projects, one can simply use `pip`
+
+```bash
+pip install posebench
+```
+
+### Full installation
+
+To reproduce, customize, or extend the `PoseBench` benchmark, we recommend fully installing `PoseBench` using `mamba` as follows:
+
+First, install `mamba` for dependency management (as a fast alternative to Anaconda)
 
 ```bash
 wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"

diff --git a/docs/source/acknowledgements.rst b/docs/source/acknowledgements.rst
@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 862
-    :end-line: 879
+    :start-line: 875
+    :end-line: 892
diff --git a/docs/source/available_methods.rst b/docs/source/available_methods.rst
@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 273
-    :end-line: 310
+    :start-line: 286
+    :end-line: 323
 
 .. note::
     Have a new method to add? Please let us know by creating a pull request. We would be happy to work with you to integrate new methodology into this benchmark!
diff --git a/docs/source/bonus.rst b/docs/source/bonus.rst
@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 897
-    :end-line: 899
+    :start-line: 910
+    :end-line: 912
 
 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench

diff --git a/docs/source/citing_this_work.rst b/docs/source/citing_this_work.rst
@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 881
-    :end-line: 893
+    :start-line: 894
+    :end-line: 906
diff --git a/docs/source/comparative_plots.rst b/docs/source/comparative_plots.rst
@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 809
-    :end-line: 818
+    :start-line: 822
+    :end-line: 831
diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst
@@ -2,5 +2,5 @@ How to prepare `PoseBench` data
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 134
-    :end-line: 267
+    :start-line: 147
+    :end-line: 280
diff --git a/docs/source/ensemble_inference.rst b/docs/source/ensemble_inference.rst
@@ -2,8 +2,8 @@ How to run inference with a method ensemble
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 750
-    :end-line: 801
+    :start-line: 763
+    :end-line: 814
 
 .. note::
     In addition to having `consensus` as an available value for `ensemble_ranking_method`, one can also set `ensemble_ranking_method=ff` to have the method ensemble's top-ranked predictions selected using the criterion of "minimum (molecular dynamics) force field energy" (albeit while incurring a very large runtime complexity).
diff --git a/docs/source/for_developers.rst b/docs/source/for_developers.rst
@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 824
-    :end-line: 858
+    :start-line: 837
+    :end-line: 871
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -9,16 +9,16 @@ Welcome to PoseBench's documentation!
 
 .. mdinclude:: ../../README.md
     :start-line: 4
-    :end-line: 12
+    :end-line: 13
 
 .. image:: ./_static/PoseBench.png
   :alt: Overview of PoseBench
   :align: center
   :width: 600
 
 .. mdinclude:: ../../README.md
-    :start-line: 18
-    :end-line: 20
+    :start-line: 19
+    :end-line: 21
 
 
 .. toctree::

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -2,5 +2,5 @@ Installation
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 40
-    :end-line: 116
+    :start-line: 41
+    :end-line: 129
diff --git a/docs/source/method_inference.rst b/docs/source/method_inference.rst
@@ -2,5 +2,5 @@ How to run inference with individual methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 318
-    :end-line: 744
+    :start-line: 331
+    :end-line: 757
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -2,5 +2,5 @@ Tutorials
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 122
-    :end-line: 128
+    :start-line: 135
+    :end-line: 141
diff --git a/posebench/data/neuralplexer_input_preparation.py b/posebench/data/neuralplexer_input_preparation.py
@@ -14,7 +14,9 @@
 rootutils.setup_root(__file__, indicator=".project-root", pythonpath=True)
 
 from posebench import register_custom_omegaconf_resolvers
-from posebench.models.ensemble_generation import LIGAND_ONLY_RECEPTOR_PLACEHOLDER_SEQUENCE
+from posebench.models.ensemble_generation import (
+    LIGAND_ONLY_RECEPTOR_PLACEHOLDER_SEQUENCE,
+)
 from posebench.utils.data_utils import parse_inference_inputs_from_dir
 
 logging.basicConfig(format="[%(asctime)s] {%(filename)s:%(lineno)d} %(levelname)s - %(message)s")

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,96 @@
+[project]
+name = "posebench"
+version = "0.3.0"
+description = "Comprehensive benchmarking of protein-ligand structure generation methods"
+authors = [
+    { name = "Alex Morehead", email = "acmwhb@umsystem.edu" }
+]
+readme = "README.md"
+requires-python = ">= 3.10"
+license = { file = "LICENSE" }
+keywords = [
+    'artificial intelligence',
+    'deep learning',
+    'protein-ligand structure generation',
+    'benchmarking',
+    'molecular docking',
+    'protein-ligand docking',
+    'protein-ligand interaction',
+    'protein-ligand binding',
+    'protein-ligand scoring',
+    'protein-ligand pose prediction',
+    'protein-ligand pose refinement',
+]
+
+classifiers=[
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Developers',
+    'Topic :: Scientific/Engineering :: Artificial Intelligence',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python :: 3.10',
+]
+
+dependencies = [
+    # --------- pytorch --------- #
+    "lightning>=2.1.3",
+    "torch==2.3.0",
+    "torchmetrics>=1.2.0",
+    "torchvision>=0.18.0",
+
+    # --------- hydra --------- #
+    "hydra-core==1.3.2",
+    "hydra-colorlog==1.2.0",
+    "hydra-optuna-sweeper==1.2.0",
+    "omegaconf",
+    "pydantic>=2.18.3",
+    "pyyaml",
+
+    # --------- others --------- #
+    "beartype",        # runtime type checking
+    "biopandas",       # for biological dataframe parsing
+    "biopython==1.79", # for biological data parsing
+    "ipykernel",       # for running Jupyter notebooks
+    "jaxtyping>=0.2.21",  # tensor type checking
+    "joblib",          # for parallel processing
+    "lovely-numpy",    # for fancy numpy debugging
+    "lovely-tensors",  # for fancy pytorch debugging
+    "meeko",           # for molecular docking preparation
+    "numpy",           # for numerical operations
+    "pandas>=1.5.0",   # for data parsing and analysis
+    "plotly",          # for plotting
+    "pre-commit",      # hooks for applying linters on commit
+    "prody",           # for protein data parsing
+    "prolif",          # for protein-ligand data parsing
+    "rdkit>=2023.3.3", # for parsing small molecule data files
+    "rich",            # beautiful text formatting in terminal
+    "rootutils",       # standardizing the project root setup
+    "scikit-learn>=1.1.2", # for basic machine learning utilities
+    "seaborn",         # for plotting
+    "setuptools",      # for packaging
+    "spyrmsd",         # for RMSD calculations
+    "timeout_decorator>=0.5.0", # for preventing certain functions from executing indefinitely
+    "tqdm",            # progress bars
+    "loguru",          # for cleaner logging
+]
+
+[project.urls]
+Homepage = "https://pypi.org/project/posebench/"
+Repository = "https://github.com/BioinfoMachineLearning/PoseBench"
+
+[project.optional-dependencies]
+examples = []
+test = [
+    "pytest",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
 [tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
 addopts = [
   "--color=yes",
   "--durations=0",
@@ -16,6 +108,15 @@ markers = [
 minversion = "6.0"
 testpaths = "tests/"
 
+# Assuming you're developing for Python 3.10
+target-version = "py310"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["posebench"]
+
 [tool.coverage.report]
 exclude_lines = [
     "pragma: nocover",

diff --git a/setup.py b/setup.py