Repo glow-up

.github/workflows/cibuild.yml

@@ -25,8 +25,7 @@ jobs:
       run: |
         sudo apt-get install tabix
         python -m pip install --upgrade pip
-        pip install .
-        make devdeps
+        pip install .[dev,test]
     - name: Test with pytest
       run: make test
     - name: Style check

.gitignore

@@ -2,3 +2,4 @@ __pycache__/
 rsidx.egg-info/
 .coverage
 scratch/
+.vscode/

Makefile

@@ -8,23 +8,16 @@ help: Makefile
 test:
 	pytest --cov=rsidx --doctest-modules rsidx/*/test_*.py
 
-## devdeps:   install development dependencies
-devdeps:
-	pip install --upgrade pip setuptools
-	pip install wheel twine
-	pip install pycodestyle pytest-cov pytest-sugar
+## style:     check code style
+style:
+	black --line-length=99 --check rsidx/*.py rsidx/*/*.py
 
+## format:    autoformat Python code
+format:
+	black --line-length=99 rsidx/*.py rsidx/*/*.py
 
-## devhooks:  install development hooks
-devhooks:
+## hooks:     install development hooks
+hooks:
 	echo 'set -eo pipefail' > .git/hooks/pre-commit
 	echo 'make style' >> .git/hooks/pre-commit
 	chmod 755 .git/hooks/pre-commit
-
-## clean:     remove development artifacts
-clean:
-	rm -rf __pycache__/ rsidx/__pycache__/ rsidx/*/__pycache__ build/ dist/ *.egg-info/
-
-## style:     check code style against PEP8
-style:
-	pycodestyle --max-line-length=99 rsidx/*.py rsidx/*/*.py

pyproject.toml

@@ -0,0 +1,33 @@
+[project]
+name = "rsidx"
+version = "0.3.2.dev"
+description = "Library for indexing VCF files for random access searches by rsID"
+readme = "README.md"
+requires-python = ">=3.8"
+authors = [
+    {name = "Daniel Standage", email = "daniel.standage@st.dhs.gov"},
+]
+
+
+[project.optional-dependencies]
+dev = ["black==24.10", "build", "twine"]
+test = ["pytest", "pytest-cov"]
+
+
+[project.scripts]
+rsidx = "rsidx.__main__:main"
+
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools]
+include-package-data = true
+package-data = { rsidx = ["tests/data/**/*"] }
+
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["rsidx*"]

rsidx/__init__.py

@@ -17,21 +17,18 @@
 from rsidx import __main__
 from rsidx import cli
 
-from . import _version
-__version__ = _version.get_versions()['version']
-
 
 @contextmanager
 def open(filename, mode):
-    if mode not in ('r', 'w'):
+    if mode not in ("r", "w"):
         raise ValueError('invalid mode "{}"'.format(mode))
-    if filename in ['-', None]:
-        filehandle = sys.stdin if mode == 'r' else sys.stdout
+    if filename in ["-", None]:
+        filehandle = sys.stdin if mode == "r" else sys.stdout
         yield filehandle
     else:
         openfunc = builtins.open
-        if filename.endswith('.gz'):
+        if filename.endswith(".gz"):
             openfunc = gzopen
-            mode += 't'
+            mode += "t"
         with openfunc(filename, mode) as filehandle:
             yield filehandle

rsidx/__main__.py

@@ -7,13 +7,13 @@
 # and is licensed under the BSD license: see LICENSE.txt.
 # -----------------------------------------------------------------------------
 
-import argparse
-import rsidx
+from . import cli
+from importlib.metadata import version
 import sys
 
 
 def main(args=None):
-    """Entry point for the happer CLI.
+    """Entry point for the rsidx CLI.
 
     Isolated as a method so that the CLI can be called by other Python code
     (e.g. for testing), in which case the arguments are passed to the function.
@@ -22,10 +22,10 @@ def main(args=None):
     """
     if args is None:  # pragma: no cover
         if len(sys.argv) == 1:
-            rsidx.cli.get_parser().parse_args(['-h'])
-        args = rsidx.cli.get_parser().parse_args()
+            cli.get_parser().parse_args(["-h"])
+        args = cli.get_parser().parse_args()
 
-    versionmessage = '[rsidx] running version {}'.format(rsidx.__version__)
+    versionmessage = "[rsidx] running version {}".format(version("rsidx"))
     print(versionmessage, file=sys.stderr)
-    mainmethod = rsidx.cli.mains[args.subcmd]
+    mainmethod = cli.mains[args.subcmd]
     mainmethod(args)