Develop core project structure

convAST/__init__.py → convast/__init__.py

@@ -1 +1,2 @@
+"""Module init"""
 from .version import VERSION, VERSION_SHORT

convast/cli.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+"""Defines CLI and main execution entrypoint to enable easier import
+of key classes directly into other scripts"""
+
+import argparse
+from .utils import check_file_exists, initialise_logger
+
+def generate_cli():
+    """
+    Create the CLI interface for the AST entrypoint
+    """
+    parser = argparse.ArgumentParser(
+        description="Converts antibiotic susceptibility "
+        "testing data to INSDC standardised format"
+    )
+
+    # takes input file and confirms it exists
+    parser.add_argument("input_file", help="The input file to convert", type=check_file_exists)
+    parser.add_argument(
+        "-f", "--format", help="Origin of input file", required=True, choices=["VITEK"]
+    )
+    parser.add_argument("-o", "--output", help="The output file destination")
+    return parser
+
+
+def main():
+    """
+    CLI entrypoint
+    """
+    parser = generate_cli()
+    args = parser.parse_args()
+
+    if not args.output:
+        args.output = args.input_file.with_suffix(".insdc.csv")
+
+    logger = initialise_logger()
+
+    logger.info(f"Converting {args.input_file} as {args.format} to INSDC {args.output}")

convast/convast.py

@@ -0,0 +1,3 @@
+#!/usr/bin/env python
+
+# implement parent convast class including linkml output

convast/utils.py

@@ -0,0 +1,27 @@
+"""General utility functions for convast"""
+from pathlib import Path
+import logging
+import argparse
+
+
+def check_file_exists(file_path):
+    """
+    Check if a given filepath exists
+    """
+    file_path = Path(file_path)
+    if not file_path.exists():
+        raise argparse.ArgumentTypeError(f"{file_path} does not exist")
+    return file_path
+
+
+def initialise_logger():
+    """
+    Initialise the logger to stderr
+    """
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s-%(levelname)s: %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    logger = logging.getLogger(__name__)
+    return logger

convAST/version.py → convast/version.py

@@ -1,3 +1,4 @@
+"""Version information for the package"""
 _MAJOR = "0"
 _MINOR = "1"
 # On main and in a nightly release the patch should be one ahead of the last
@@ -7,5 +8,5 @@
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""
 
-VERSION_SHORT = "{0}.{1}".format(_MAJOR, _MINOR)
-VERSION = "{0}.{1}.{2}{3}".format(_MAJOR, _MINOR, _PATCH, _SUFFIX)
+VERSION_SHORT = f"{_MAJOR}.{_MINOR}"
+VERSION = "{_MAJOR}.{_MINOR}.{_PATCH}{_SUFFIX}"

pyproject.toml

@@ -3,51 +3,41 @@ requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-# See https://setuptools.pypa.io/en/latest/userguide/quickstart.html for more project configuration options.
-name = "my-package"
+name = "convast"
 dynamic = ["version"]
 readme = "README.md"
 classifiers = [
     "Intended Audience :: Science/Research",
     "Development Status :: 3 - Alpha",
-    "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering :: Artificial Intelligence",
 ]
 authors = [
-    {name = "Allen Institute for Artificial Intelligence", email = "[email protected]"}
-]
+    {name = "Finlay Maguire", email = "[email protected]"},
+    {name = "Amos Raphenya", email = "[email protected]"},]
 requires-python = ">=3.8"
 dependencies = [
   # Add your own dependencies here
 ]
 license = {file = "LICENSE"}
 
+[project.scripts]
+convast = "convast.cli:main"
+
 [project.urls]
-Homepage = "https://github.com/allenai/python-package-template"
-Repository = "https://github.com/allenai/python-package-template"
-Changelog = "https://github.com/allenai/python-package-template/blob/main/CHANGELOG.md"
+Homepage = "https://github.com/pha4ge/convast"
+Repository = "https://github.com/pha4ge/convast"
+Changelog = "https://github.com/pha4ge/convast/blob/main/CHANGELOG.md"
 # Documentation = "https://my-package.readthedocs.io/"
 
 [project.optional-dependencies]
 dev = [
     "ruff",
-    "mypy>=1.0,<1.5",
     "black>=23.0,<24.0",
-    "isort>=5.12,<5.13",
     "pytest",
-    "pytest-sphinx",
     "pytest-cov",
     "twine>=1.11.0",
     "build",
     "setuptools",
     "wheel",
-    "Sphinx>=4.3.0,<7.1.0",
-    "furo==2023.7.26",
-    "myst-parser>=1.0,<2.1",
-    "sphinx-copybutton==0.5.2",
-    "sphinx-autobuild==2021.3.14",
-    "sphinx-autodoc-typehints==1.23.3",
     "packaging"
 ]
 
@@ -57,18 +47,13 @@ exclude = [
     "*.tests.*",
     "tests.*",
     "tests",
-    "docs*",
-    "scripts*"
 ]
 
 [tool.setuptools]
 include-package-data = true
 
-[tool.setuptools.package-data]
-my_package = ["py.typed"]
-
 [tool.setuptools.dynamic]
-version = {attr = "my_package.version.VERSION"}
+version = {attr = "convast.version.VERSION"}
 
 [tool.black]
 line-length = 100
@@ -86,35 +71,22 @@ exclude = '''
 )
 '''
 
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-
-# You can override these pyright settings by adding a personal pyrightconfig.json file.
-[tool.pyright]
-reportPrivateImportUsage = false
-
 [tool.ruff]
 line-length = 115
 target-version = "py39"
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401"]
 
-[tool.mypy]
-ignore_missing_imports = true
-no_site_packages = true
-check_untyped_defs = true
-
-[[tool.mypy.overrides]]
-module = "tests.*"
-strict_optional = false
+[tool.pylint.'MESSAGES CONTROL']
+max-line-length = 115
+disable = """
+logging-fstring-interpolation
+"""
 
 [tool.pytest.ini_options]
 testpaths = "tests/"
 python_classes = [
   "Test*",
   "*Test"
 ]
-log_format = "%(asctime)s - %(levelname)s - %(name)s - %(message)s"
-log_level = "DEBUG"