Merge pull request #16 from EBI-Metagenomics/feature/bioconda_package

Prepared repo for publication as bioconda package

.github/workflows/publish_python.yml

@@ -0,0 +1,51 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/genomeuploader
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pytest_workflow.yml

@@ -0,0 +1,75 @@
+name: Run pytest
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pytest_38:
+    name: Run pytest 3.8
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: pip install .[test]
+      - uses: pavelzw/pytest-action@v2
+        env:
+          ENA_WEBIN: ${{ secrets.ENA_WEBIN }}
+          ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }}
+        with:
+          emoji: false
+          verbose: true
+          job-summary: true
+
+  pytest_39:
+    name: Run pytest 3.9
+    needs:
+    - pytest_38
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+      - name: Install dependencies
+        run: pip install .[test]
+      - uses: pavelzw/pytest-action@v2
+        env:
+          ENA_WEBIN: ${{ secrets.ENA_WEBIN }}
+          ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }}
+        with:
+          emoji: false
+          verbose: true
+          job-summary: true
+
+  pytest_310:
+    name: Run pytest 3.10
+    needs:
+    - pytest_39
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install .[test]
+      - uses: pavelzw/pytest-action@v2
+        env:
+          ENA_WEBIN: ${{ secrets.ENA_WEBIN }}
+          ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }}
+        with:
+          emoji: false
+          verbose: true
+          job-summary: true

genomeuploader/__init__.py

@@ -1 +1 @@
-__version__ = "2.0.0"
+__version__ = '2.1.0'

pyproject.toml

@@ -1,12 +1,12 @@
 [project]
-name = "genomeuploader"
+name = "genome_uploader"
+version = "2.1.0"
 readme = "README.md"
 authors = [
   {name = "MGnify team", email = "[email protected]"},
 ]
 license = {text = "Apache Software License 2.0"}
 keywords = ["bioinformatics", "tool", "metagenomics"]
-dynamic = ["version"]
 description = "Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This script generates xmls and manifests necessary for submission with webin-cli."
 requires-python = ">=3.8"
 classifiers = [
@@ -26,6 +26,10 @@ dependencies = [
     "python-dotenv==1.0.1"
 ]
 
+[project.urls]
+Homepage = "https://github.com/EBI-Metagenomics/genome_uploader"
+Issues = "https://github.com/EBI-Metagenomics/genome_uploader/issues"
+
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = "-ra -q"
@@ -43,7 +47,9 @@ dev = [
     "bump-my-version==0.9.2",
 ]
 test = [
-    "pytest==7.1.2",
+    "pytest==7.4.0",
+    "pytest-md==0.2.0",
+    "pytest-workflow==2.0.1",
     "pytest-cov==3.0.0",
 ]
 
@@ -54,9 +60,6 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools]
 packages = ["genomeuploader"]
 
-[tool.setuptools.dynamic]
-version = {attr = "genomeuploader.__version__"}
-
 [project.scripts]
 genome_upload = "genomeuploader.genome_upload:main"
 

pytest.ini

@@ -1,3 +1,3 @@
 [pytest]
 python_files = tests/*.py
-pythonpath = .
+testpaths = tests