update readme; logo; pypi

Author: telatin

.github/workflows/publish-pypi.yml

@@ -0,0 +1,75 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # Allow manual trigger
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/votuderep
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/votuderep
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

README.md

@@ -1,5 +1,10 @@
 # votuderep
 
+[![Test](https://github.com/quadram-institute-bioscience/votuderep/actions/workflows/test.yml/badge.svg)](https://github.com/quadram-institute-bioscience/votuderep/actions/workflows/test.yml)
+
+
+![Logo](votuderep.png)
+
 A Python CLI tool for dereplicating and filtering viral contigs (vOTUs - viral Operational Taxonomic Units)
 using the CheckV method.
 
@@ -188,4 +193,4 @@ Contributions are welcome! Please feel free to submit a Pull Request.
 Andrea Telatin & QIB Core Bioinformatics
 
 ©️ Quadram Institute Bioscience 2025
- 
+ 

pyproject.toml

@@ -10,7 +10,7 @@ readme = "README.md"
 requires-python = ">=3.10"
 license = {text = "MIT"}
 authors = [
-    {name = "Your Name", email = "your.email@example.com"}
+    {name = "Andrea Telatin", email = "andrea.telatin@gmail.com"}
 ]
 keywords = ["bioinformatics", "viral", "contigs", "dereplication", "blast"]
 classifiers = [
@@ -44,10 +44,10 @@ dev = [
 votuderep = "votuderep.cli:main"
 
 [project.urls]
-Homepage = "https://github.com/yourusername/votuderep"
-Documentation = "https://github.com/yourusername/votuderep#readme"
-Repository = "https://github.com/yourusername/votuderep"
-Issues = "https://github.com/yourusername/votuderep/issues"
+Homepage = "https://github.com/quadram-institute-bioscience/votuderep"
+Documentation = "https://github.com/quadram-institute-bioscience/votuderep#readme"
+Repository = "https://github.com/quadram-institute-bioscience/votuderep"
+Issues = "https://github.com/quadram-institute-bioscience/votuderep/issues"
 
 [tool.setuptools.packages.find]
 where = ["src"]

requirements.txt

@@ -0,0 +1,38 @@
+#
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
+#
+#    pip-compile pyproject.toml
+#
+click==8.3.0
+    # via rich-click
+markdown-it-py==4.0.0
+    # via rich
+mdurl==0.1.2
+    # via markdown-it-py
+numpy==2.2.6
+    # via
+    #   pandas
+    #   votuderep (pyproject.toml)
+pandas==2.3.3
+    # via votuderep (pyproject.toml)
+pyfastx==2.2.0
+    # via votuderep (pyproject.toml)
+pygments==2.19.2
+    # via rich
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2025.2
+    # via pandas
+rich==14.2.0
+    # via
+    #   rich-click
+    #   votuderep (pyproject.toml)
+rich-click==1.9.3
+    # via votuderep (pyproject.toml)
+six==1.17.0
+    # via python-dateutil
+typing-extensions==4.15.0
+    # via rich-click
+tzdata==2025.2
+    # via pandas