Basic packaging details

bio2zarr/vcf.py

@@ -1564,7 +1564,7 @@ def validate(vcf_path, zarr_path, show_progress):
                 elif vcf_type == "String":
                     assert np.all(zarr_val == ".")
                 elif vcf_type == "Flag":
-                    assert zarr_val == False
+                    assert zarr_val == False  # noqa 712
                 elif vcf_type == "Float":
                     assert_all_missing_float(zarr_val)
                 else:
@@ -1576,7 +1576,7 @@ def validate(vcf_path, zarr_path, show_progress):
                 elif vcf_type == "Float":
                     assert_prefix_float_equal_1d(vcf_val, zarr_val)
                 elif vcf_type == "Flag":
-                    assert zarr_val == True
+                    assert zarr_val == True  # noqa 712
                 elif vcf_type == "String":
                     assert np.all(zarr_val == vcf_val)
                 else:

setup.cfg

@@ -0,0 +1,59 @@
+[metadata]
+name = bio2zarr
+author = sgkit Developers
+author_email = [email protected]
+license = Apache
+description = FIXME
+long_description_content_type=text/x-rst
+long_description =
+    FIXME
+url = https://github.com/pystatgen/bio2zarr
+classifiers =
+    Development Status :: 3 - Alpha
+    License :: OSI Approved :: Apache Software License
+    Operating System :: OS Independent
+    Intended Audience :: Science/Research
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Topic :: Scientific/Engineering
+
+[options]
+packages = bio2zarr
+zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
+include_package_data = True
+python_requires = >=3.8
+install_requires =
+    numpy
+    zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2
+    cyvcf2
+    bed_reader 
+setup_requires =
+    setuptools >= 41.2
+    setuptools_scm
+
+[flake8]
+ignore =
+    # whitespace before ':' - doesn't work well with black
+    E203
+    E402
+    # line too long - let black worry about that
+    E501
+    # do not assign a lambda expression, use a def
+    E731
+    # line break before binary operator
+    W503
+
+[isort]
+profile = black
+default_section = THIRDPARTY
+known_first_party = sgkit
+known_third_party = hypothesis,msprime,numpy,pandas,pytest,setuptools,sgkit,zarr
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88

setup.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+from setuptools import setup
+
+setup(
+    # The package name along with all the other metadata is specified in setup.cfg
+    # However, GitHub's dependency graph can't see the package unless we put this here.
+    name="bio2zarr",
+    use_scm_version=True,
+)