ci: incorporate more style check and package build elements from Bioc…

…ommons template (#58)

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/python-package.yml

@@ -0,0 +1,34 @@
+name: Python package
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e .[dev]
+
+    - name: Lint with Ruff
+      run: python3 -m ruff check src/
+
+    - name: Format check with black
+      run: black --check src
+
+    - name: Security check with bandit
+      run: bandit -ll -r src
+

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+    - id: black
+      language_version: python3.11
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.244
+  rev: v0.0.290
   hooks:
     - id: ruff
-- repo: https://github.com/pycqa/isort
-  rev: 5.6.4
-  hooks:
-    - id: isort
-      args: ["--check"]

Makefile

@@ -64,6 +64,12 @@ bdist bdist_egg bdist_wheel build sdist install: %:
 #= TESTING
 # see test configuration in setup.cfg
 
+#=> cqa: execute code quality tests
+cqa:
+	ruff check src
+	black --check src
+	bandit -ll -r src
+
 #=> test: execute tests
 .PHONY: test
 test:

pyproject.toml

@@ -1,3 +1,65 @@
+[project]
+name = "biocommons.anyvar"
+authors = [
+  { name="biocommons contributors", email="[email protected]" },
+]
+description = "AnyVar provides Python and REST interfaces to validate, normalize, generate identifiers, and register biological sequence variation according to the GA4GH Variation Representation standards."
+readme = "README.md"
+license = { file="LICENSE" }
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dynamic = ["version"]
+
+[project.urls]
+"Homepage" = "https://github.com/biocommons/anyvar"
+"Bug Tracker" = "https://github.com/biocommons/anyvar/issues"
+
+
+[build-system]
+requires = [
+    "setuptools >= 65.3",
+    "setuptools_scm[toml] ~= 7.0"
+]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools_scm]
+
+
+[tool.coverage.run]
+branch = true
+source = ["biocommons.example"]
+omit = ["*_test.py", "*/test/*", "*/tests/*"]
+
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+    # Have to re-enable the standard pragma
+    "pragma: no cover",
+
+    # Don't complain about missing debug-only code:
+    "def __repr__",
+    "if self.debug",
+
+    # Don't complain if tests don't hit defensive assertion code:
+    "raise AssertionError",
+    "raise NotImplementedError",
+
+    # Don't complain if non-runnable code isn't run:
+    "if __name__ == .__main__.:",
+]
+
+[tool.black]
+line-length = 100
+
 [tool.ruff]
 exclude = [
     "venv",
@@ -6,11 +68,7 @@ exclude = [
     "tests"
 ]
 
-line-length = 88
+line-length = 100
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401", "E402"]
-"uidoc.py" = ["E501"]
-
-[tool.isort]
-group_by_package = true

setup.cfg

@@ -1,12 +1,7 @@
-[metadata]
-name = anyvar
-author = Reece Hart
-author-email = [email protected]
-description-file = README.rst
-description-content-type = text/x-rst; charset=UTF-8
-
 [options]
-zip_safe = false
+packages = find_namespace:
+package_dir =
+    = src
 install_requires =
     canonicaljson
     fastapi >= 0.95.0
@@ -15,11 +10,6 @@ install_requires =
     ga4gh.vrs[extras] ~= 0.8.4
     ga4gh.vrsatile.pydantic ~= 0.0.11
     psycopg[binary]
-setup_requires =
-    setuptools_scm
-packages = find:
-package_dir =
-    = src
 
 [options.package_data]
 * =
@@ -35,24 +25,15 @@ exclude =
 
 [options.extras_require]
 dev =
-	ruff
-        pre-commit
-        isort
+    black
+    ruff
+    pre-commit
+    bandit~=1.7
 test =
-	pytest
-        pytest-cov
-        pytest-mock
-        httpx
-
-
-[aliases]
-test = pytest
-
-[bdist_wheel]
-universal = 1
-
-[build_sphinx]
-all_files  = 1
+    pytest
+    pytest-cov
+    pytest-mock
+    httpx
 
 [tool:pytest]
 addopts = --cov=anyvar --cov-report term-missing

src/anyvar/anyvar.py

@@ -35,6 +35,7 @@ def create_storage(uri: Optional[str] = None) -> _Storage:
 
     if parsed_uri.scheme == "postgresql":
         from anyvar.storage.postgres import PostgresObjectStore
+
         storage = PostgresObjectStore(uri)  # type: ignore
 
     else:
@@ -64,9 +65,7 @@ def __init__(self, /, translator: _Translator, object_store: _Storage):
         :param object_store: Object storage instance
         """
         if not isinstance(object_store, MutableMapping):
-            _logger.warning(
-                "AnyVar(object_store=) should be a mutable mapping; you're on your own"
-            )
+            _logger.warning("AnyVar(object_store=) should be a mutable mapping; you're on your own")
 
         self.object_store = object_store
         self.translator = translator
@@ -84,9 +83,7 @@ def put_object(self, variation_object: VrsPythonObject) -> Optional[str]:
         _id = ga4gh_identify(v)
         return _id
 
-    def get_object(
-        self, object_id: str, deref: bool = False
-    ) -> Optional[VrsPythonObject]:
+    def get_object(self, object_id: str, deref: bool = False) -> Optional[VrsPythonObject]:
         """Retrieve registered variation.
 
         :param object_id: object identifier

src/anyvar/extras/clinvarparser.py

@@ -8,8 +8,7 @@
 
 class VariationArchive:
     def __init__(self, element):
-        assert element.tag == "VariationArchive", \
-            "Expected node type `VariationArchive`"
+        assert element.tag == "VariationArchive", "Expected node type `VariationArchive`"
         self._element = element
 
     @property
@@ -62,17 +61,20 @@ def __init__(self, fp, current_only=True):
         self.current_only = current_only
 
     def __iter__(self):
-        yield from (va for va in (VariationArchive(e) for _, e in self._xp)
-                    if not self.current_only or va.is_current)
+        yield from (
+            va
+            for va in (VariationArchive(e) for _, e in self._xp)
+            if not self.current_only or va.is_current
+        )
 
 
 def clinvar_open(fp):
     yield from ClinvarParser(fp)
 
 
-
 if __name__ == "__main__":
     import sys
+
     fn = sys.argv[1]
     for va in clinvar_open(fn):
         print(

src/anyvar/extras/vcf.py

@@ -23,8 +23,11 @@ def __init__(self, av: AnyVar) -> None:
         self.av = av
 
     def annotate(
-        self, vcf_in: str, vcf_out: Optional[str] = None,
-        vrs_pickle_out: Optional[str] = None, assembly: str = "GRCh38",
+        self,
+        vcf_in: str,
+        vcf_out: Optional[str] = None,
+        vrs_pickle_out: Optional[str] = None,
+        assembly: str = "GRCh38",
     ) -> None:
         """Annotates an input VCF file with VRS Allele IDs & creates a pickle file
         containing the vrs object information.
@@ -42,9 +45,14 @@ def annotate(
             super().annotate(vcf_in, vcf_out, vrs_pickle_out, assembly)
 
     def _get_vrs_object(
-        self, vcf_coords: str, vrs_data: Dict, vrs_allele_ids: List[str], assembly: str,
-        vrs_data_key: Optional[str] = None, output_pickle: bool = True,
-        output_vcf: bool = False
+        self,
+        vcf_coords: str,
+        vrs_data: Dict,
+        vrs_allele_ids: List[str],
+        assembly: str,
+        vrs_data_key: Optional[str] = None,
+        output_pickle: bool = True,
+        output_vcf: bool = False,
     ) -> None:
         """Get VRS Object given `vcf_coords`. `vrs_data` and `vrs_allele_ids` will
         be mutated. Generally, we expect AnyVar to use the output_vcf option rather than