refactor: remove versioneer, update release-please (#519)

.github/workflows/release-please.yml

@@ -3,39 +3,19 @@ on:
     branches:
       - main
 
+permissions:
+  contents: write
+  pull-requests: write
+
 name: release-please
 
 jobs:
   release-please:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: GoogleCloudPlatform/release-please-action@v2
-        id: release
+      - uses: googleapis/release-please-action@v4
         with:
           release-type: python
-          package-name: clinvar-this
-
-      - uses: actions/checkout@v2
-        if: ${{ steps.release.outputs.release_created }}
-        with:
-          fetch-depth: 0
+          token: ${{ secrets.SNAPPY_RELEASE_PLEASE_TOKEN }}
 
-      - name: Set up Python
-        if: ${{ steps.release.outputs.release_created }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.x'
-
-      - name: Build package
-        if: ${{ steps.release.outputs.release_created }}
-        run: |
-          python -m pip install --upgrade pip
-          python setup.py sdist
-
-      - name: Publish to PyPI
-        if: ${{ steps.release.outputs.release_created }}
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}

MANIFEST.in

@@ -14,7 +14,6 @@ recursive-include snappy_pipeline *.py Snakefile *.rules *.sh *.tpl *.xml
 recursive-include snappy_wrappers *.py *.sh *.txt *.R *.yaml
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
-include versioneer.py
 include snappy_pipeline/_version.py
 
 include requirements.txt requirements/*.txt

setup.cfg

@@ -6,16 +6,6 @@ universal = 1
 [wheel]
 universal = 1
 
-# Package Versioning with Versioneer ----------------------------------------
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = snappy_pipeline/_version.py
-versionfile_build = snappy_pipeline/_version.py
-tag_prefix = v
-parentdir_prefix = snappy_pipeline-
-
 # Style Checking and Linting ------------------------------------------------
 [isort]
 profile = "black"
@@ -36,7 +26,6 @@ exclude =
     splitMNPsAndComplex.py
     wrapper.py
     snappy_pipeline/__init__.py
-    versioneer.py
 max-complexity = 18
 select = B,C,E,F,W,T4,B9
 ignore = E203, E266, E501, W503

setup.py

@@ -9,8 +9,6 @@
 
 from setuptools import find_packages, setup
 
-import versioneer
-
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"
 
 
@@ -85,10 +83,16 @@ def bash_scripts(names):
     return (os.path.join("scripts", name) for name in names)
 
 
+package_root = os.path.abspath(os.path.dirname(__file__))
+
+version = {}
+with open(os.path.join(package_root, "snappy_pipeline/_version.py")) as fp:
+    exec(fp.read(), version)
+version = version["__version__"]
+
 setup(
     name="snappy-pipeline",
-    version=versioneer.get_version(),
-    cmdclass=versioneer.get_cmdclass(),
+    version=version,
     description="SNAPPY Nucleic Acid Processing in Python (by CUBI)",
     long_description=readme + "\n\n" + history,
     long_description_content_type="text/markdown",

snappy_pipeline/__init__.py

@@ -2,13 +2,9 @@
 
 from .base import expand_ref, merge_dicts, print_config, print_sample_sheets
 
-# from ._version import get_versions
-
 __author__ = """Manuel Holtgrewe"""
 __email__ = "manuel.holtgrewe@bih-charite.de"
-__version__ = "master"
-# del get_versions
 
-from . import _version
+from snappy_pipeline._version import __version__
 
-__version__ = _version.get_versions()["version"]
+__all__ = ["__version__", "expand_ref", "merge_dicts", "print_config", "print_sample_sheets"]