[MNT] Additions for Project Documentation and Code Quality Workflows

.github/workflows/coverage.yml

@@ -26,20 +26,24 @@ jobs:
 
       - name: Build coverage file
         run: |
-          mkdir coverage
-          pytest --cov=pyKVFinder --cov-report=term-missing | tee coverage/coverage.txt
+          pytest --cov=pyKVFinder --cov-report=term-missing | tee coverage.txt
 
       - name: Pytest coverage comment
         uses: MishaKav/pytest-coverage-comment@main
         with:
-          pytest-coverage-path: coverage/coverage.txt
+          pytest-coverage-path: coverage.txt
           default-branch: master
           remove-link-from-badge: true
 
       - name: Coverage Bagdge
         uses: tj-actions/coverage-badge-py@v2
         with:
-          output: coverage/coverage.svg
+          output: coverage.svg
+
+      - name: Move report to coverage directory
+        run: |
+          mkdir coverage
+          mv coverage.txt coverage.svg coverage/
 
       - name: Publish coverage report to coverage branch
         uses: JamesIves/github-pages-deploy-action@v4

.github/workflows/pylint.yml

@@ -0,0 +1,33 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files 'pyKVFinder/*.py') --output=pylint.txt || true
+
+    - name: Upload pylint report
+      uses: actions/upload-artifact@v3
+      with:
+        name: artifacts
+        path: ./pylint.txt

MANIFEST.in

@@ -10,10 +10,10 @@ include pyKVFinder/data/tests/*.pdb
 include pyKVFinder/data/tests/*.xyz
 
 # Include the license file
-include LICENSE.txt
+include LICENSE
 
 # Include README
-include README.rst
+include README.md
 
 # Include Python requirements
 include requirements.txt

README.md

@@ -0,0 +1,53 @@
+# pyKVFinder
+
+[![PyPI - Version](https://img.shields.io/pypi/v/pyKVFinder)](https://pypi.org/project/pyKVFinder/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyKVFinder)](https://pypi.org/project/pyKVFinder/)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/pyKVFinder)](https://pypi.org/project/pyKVFinder/)
+[![Unit testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/unit-testing.yml?label=unit-testing)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/unit-testing.yml)
+[![Integration testing](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/integration-testing.yml?label=integration-testing)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/integration-testing.yml)
+[![Build](https://img.shields.io/github/actions/workflow/status/LBC-LNBio/pyKVFinder/deploy.yml?label=build)](https://github.com/LBC-LNBio/pyKVFinder/actions/workflows/deploy.yml)
+[![Coverage](https://raw.githubusercontent.com/LBC-LNBio/pyKVFinder/coverage/coverage.svg)](https://github.com/LBC-LNBio/pyKVFinder/blob/coverage/coverage.txt)
+
+A Python package for detecting and characterizing biomolecular cavities.
+
+See also:
+
+- [GitHub repository](https://github.com/LBC-LNBio/pyKVFinder/)
+- [Documentation and tutorial](https://lbc-lnbio.github.io/pyKVFinder/)
+
+## Installation
+
+To install the latest release on
+[PyPI](https://pypi.org/project/pyKVFinder), run:
+
+    pip install pyKVFinder
+
+Or to install the latest developmental version, run:
+
+    git clone https://github.com/LBC-LNBio/pyKVFinder.git
+    pip install pyKVFinder
+
+## Citation
+
+If you use *pyKVFinder* package, please cite:
+
+Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O.,
+Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an
+efficient and integrable Python package for biomolecular cavity
+detection and characterization in data science. BMC bioinformatics,
+22(1), 607. <https://doi.org/10.1186/s12859-021-04519-4>.
+
+If you use *pyKVFinder.Molecule*, please also cite:
+
+Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P.
+S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular
+Cages. Journal of chemical information and modeling, 63(12), 3772-3785.
+<https://doi.org/10.1021/acs.jcim.3c00328>.
+
+## License
+
+The software is licensed under the terms of the GNU General Public
+License version 3 (GPL3) and is distributed in the hope that it will be
+useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+Public License for more details.

pyproject.toml

@@ -11,26 +11,26 @@ build-backend = "setuptools.build_meta"
 name = "pyKVFinder"
 description = "Python package to detect and characterize cavities in biomolecular structures"
 authors = [
-    { name = "João Victor da Silva Guerra", email = "[email protected]" },
-    { name = "Helder Veras Ribeiro Filho" },
-    { name = "Luiz Fernando Giolo Alves" },
-    { name = "Gabriel Ernesto Jara" },    
-    { name = "Leandro Oliveira Bortot" },
-    { name = "José Geraldo de Carvalho Pereira" },
-    { name = "Paulo Sergio Lopes-de-Oliveira" },
+    { name = "João V. S. Guerra", email = "[email protected]" },
+    { name = "Helder V. Ribeiro-Filho" },
+    { name = "Luiz F. G. Alves" },
+    { name = "Pablo W. A. Silva" },
+    { name = "Gabriel E. Jara" },
+    { name = "Leandro O. Bortot" },
+    { name = "José G. C. Pereira" },
+    { name = "Paulo S. Lopes-de-Oliveira" },
 ]
-maintainers = [
-    { name = "João Victor da Silva Guerra", email = "[email protected]" },
-]
-license = { file = "LICENSE.txt" }
-readme = { file = "README.rst", content-type = "text/x-rst" }
+maintainers = [{ name = "João V. S. Guerra", email = "[email protected]" }]
+license = { file = "LICENSE" }
+readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.9"
 keywords = [
     "structural biology",
     "proteins",
     "biomolecules",
     "cavity detection",
     "cavity characterization",
+    "binding sites",
 ]
 classifiers = [
     "Development Status :: 4 - Beta",