Setup Project

.github/workflows/python-package.yml

@@ -14,16 +14,25 @@ jobs:
         python-version: [3.9]
 
     steps:
+    - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install dependencies for test
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        python -m pip install .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name : Test install successful
+      run: |
+        convertGVFtoVCF.py -h
     - name: Test with pytest
       run: |
         PYTHONPATH=. pytest tests

pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = [
+    "setuptools >= 64",
+    "setuptools_scm[toml] >= 8",
+    "setuptools_scm_git_archive",
+    "wheel >= 0.29.0",
+]
+build-backend = 'setuptools.build_meta'
+
+[project]
+name = 'convertGVFtoVCF'
+description = 'EBI EVA - Tool to convert GVF files from DGVa database into VCF files that can be used by the EVA'
+dynamic = ["version", 'dependencies']
+readme = 'README.md'
+classifiers = [
+    'Development Status :: 2 - Pre-Alpha',
+    'Environment :: Console',
+    'Intended Audience :: Science/Research',
+    'Natural Language :: English',
+    'Operating System :: POSIX :: Linux',
+    'Operating System :: MacOS :: MacOS X',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Topic :: File Formats',
+    'License :: OSI Approved :: Apache Software License',
+]
+
+[project.scripts]
+'convertGVFtoVCF.py'='convert_gvf_to_vcf.convertGVFtoVCF:main'
+
+[tool.setuptools]
+packages = ['convert_gvf_to_vcf']
+
+[tool.setuptools.package-data]
+'convert_gvf_to_vcf'=['etc/*']
+
+[tool.setuptools.dynamic]
+dependencies = {file = 'requirements.txt'}
+
+[tool.setuptools_scm]
+write_to = 'convert_gvf_to_vcf/_version.py'
+

requirements.txt

@@ -0,0 +1 @@
+ebi_eva_common_pyutils >= 0.7.4, == 0.*