Tweak repository for publishing (#18)

* add proper version to pyproject.toml

* update readme

* add pypi-publish action

* add upper limit to python version

.github/workflows/pypi-publish.yml

@@ -0,0 +1,31 @@
+name: publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi_release:
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - uses: snok/install-poetry@v1
+        with:
+          version: 1.3.2
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - run: poetry install
+
+      - run: poetry run pytest
+
+      - run: poetry config pypi-token.pypi "${{ secrets.PYPI_API_KEY }}"
+
+      - name: Publish package
+        run: poetry publish --build

README.md

@@ -1,5 +1,8 @@
 # PRODIGY-cryst
 
+![PyPI - License](https://img.shields.io/pypi/l/prodigy-cryst)
+![PyPI - Status](https://img.shields.io/pypi/status/prodigy-cryst)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/prodigy-cryst)
 [![ci](https://github.com/haddocking/prodigy-cryst/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/prodigy-cryst/actions/workflows/ci.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/4f129d451ec04c4e9529a6eb28457619)](https://www.codacy.com/gh/haddocking/prodigy-cryst/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/prodigy-cryst&utm_campaign=Badge_Grade)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/4f129d451ec04c4e9529a6eb28457619)](https://www.codacy.com/gh/haddocking/prodigy-cryst/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/prodigy-cryst&utm_campaign=Badge_Coverage)
@@ -10,14 +13,69 @@ Collection of scripts to predict whether an interface in a protein-protein compl
 ## Installation
 
 ```bash
-> git clone http://github.com/haddocking/prodigy-cryst
-> python setup.py install
+pip install prodigy-cryst
 ```
 
 ## Usage
 
+Type --help to get a list of all the possible options.
+
+```bash
+$ prodigy_cryst --help
+usage: prodigy_cryst [-h] [--contact_list] [-q] [--selection A B [A,B C ...]] structf
+
+Biological/crystallographic interface classifier based on Intermolecular Contacts (ICs).
+
+positional arguments:
+  structf               Structure to analyse in PDB or mmCIF format
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --contact_list        Output a list of contacts
+  -q, --quiet           Outputs only the predicted interface class
+
+Selection Options:
+
+      By default, all intermolecular contacts are taken into consideration,
+      a molecule being defined as an isolated group of amino acids sharing
+      a common chain identifier. In specific cases, for example
+      antibody-antigen complexes, some chains should be considered as a
+      single molecule.
+
+      Use the --selection option to provide collections of chains that should
+      be considered for the calculation. Separate by a space the chains that
+      are to be considered _different_ molecules. Use commas to include multiple
+      chains as part of a single group:
+
+      --selection A B => Contacts calculated (only) between chains A and B.
+      --selection A,B C => Contacts calculated (only) between chains A and C; and B and C.
+      --selection A B C => Contacts calculated (only) between chains A and B; B and C; and A and C.
+
+
+  --selection A B [A,B C ...]
+```
+
+## Examples
+
+Download PDB file 1ppe from the PDB and run the script on it.
+
 ```bash
-prodigy_cryst <pdb file> [--selection <chain1><chain2>]
+wget https://files.rcsb.org/download/1PPE.pdb
 ```
 
-Type --help to get a list of all the possible options.
+Check how PRODIGY-cryst works on the 1PPE.pdb file. The script will output the number of intermolecular contacts, the number of contacts of each type, the link density, and the predicted interface class.
+
+```bash
+$ prodigy_cryst 1PPE.pdb
+[+] Reading structure file: /home/rodrigo/1PPE.pdb
+[+] Selection: E, I
+[+] No. of intermolecular contacts: 71
+[+] No. of charged-charged contacts: 4
+[+] No. of charged-polar contacts: 8
+[+] No. of charged-apolar contacts: 24
+[+] No. of polar-polar contacts: 0
+[+] No. of apolar-polar contacts: 15
+[+] No. of apolar-apolar contacts: 20
+[+] Link density: 0.14
+[+] Class: BIO 0.804 0.196
+```

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "prodigy-cryst"
-version = "1.0.1"
+version = "1.0.0"
 description = "Predicts if a protein complex interface is biological or crystallographic."
 authors = ["BonvinLab <[email protected]>"]
 readme = "README.md"
@@ -15,7 +15,7 @@ classifiers = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = ">=3.8,<3.9"
 scikit-learn = "0.22"
 biopython = "^1.79"
 numpy = "~1.20"