Add new example from JLacey and tidy up repo

Makefile

@@ -1,13 +1,8 @@
-.PHONY : docs
-docs :
-	rm -rf docs/build/
-	sphinx-autobuild -b html --watch convast/ docs/source/ docs/build/
-
-.PHONY : run-checks
-run-checks :
-	black --check .
-	ruff check .
-	pytest -v --color=yes --doctest-modules tests/ convast/
+.PHONY : check 
+check :
+	black convast
+	ruff check convast
+	pytest -v --color=yes tests/ 
 
 .PHONY : build
 build :

README.md

@@ -35,3 +35,7 @@ EMR/LIMs exports?
 - Standardised INSDC AST format dataclass imported from linkML (e.g., [linkML documentation example](https://linkml.io/linkml/intro/tutorial05.html))
 - Input parent class with generic functions for parsing, iterating, write, applying mappings (e.g., [hAMRonizedResultIterator](https://github.com/pha4ge/hAMRonization/blob/master/hAMRonization/Interfaces.py#L15))  
 - For each Vitek/Phoenix/Microtitre etc an iterator subclass that inherits from this input parent class including specific mappings and any adjustments to generic functions needed (e.g., [tool specific hAMRonization classes](https://github.com/pha4ge/hAMRonization/blob/master/hAMRonization/StarAmrIO.py#L14))
+
+Using the linkml runtime - the dataclasses are generated as follows:
+
+    gen-python convast/schema/NCBI_schema.yaml > convast/schema.py

convast/__init__.py

@@ -1,2 +1,3 @@
 """Module init"""
+
 from .version import VERSION, VERSION_SHORT

convast/cli.py

@@ -5,20 +5,18 @@
 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"
+        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("-f", "--format", help="Origin of input file", required=True, choices=["VITEK"])
     parser.add_argument("-o", "--output", help="The output file destination")
     return parser
 

convast/convast.py

@@ -1,3 +1,22 @@
 #!/usr/bin/env python
+import dataclasses
 
-# implement parent convast class including linkml output
+
+@dataclasses.dataclass
+class ConvAST:
+    """
+    Single INSDC compatible AST result entry
+    Should be generated directly from LinkML yaml
+    """
+
+    def to_ena(self):
+        """
+        Export just ENA fields
+        """
+        raise NotImplementedError("ENA export not implemented")
+
+    def to_ncbi(self):
+        """
+        Export just NCBI fields
+        """
+        raise NotImplementedError("NCBI export not implemented")

convast/utils.py

@@ -1,4 +1,5 @@
 """General utility functions for convast"""
+
 from pathlib import Path
 import logging
 import argparse

convast/version.py

@@ -1,4 +1,5 @@
 """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

pyproject.toml

@@ -32,9 +32,7 @@ Changelog = "https://github.com/pha4ge/convast/blob/main/CHANGELOG.md"
 dev = [
     "ruff",
     "black",
-    "pylint",
     "pytest",
-    "pytest-cov",
     "twine>=1.11.0",
     "build",
     "setuptools",
@@ -57,15 +55,13 @@ include-package-data = true
 version = {attr = "convast.version.VERSION"}
 
 [tool.black]
-line-length = 100
+line-length = 115
 include = '\.pyi?$'
 exclude = '''
 (
       __pycache__
     | \.git
-    | \.mypy_cache
     | \.pytest_cache
-    | \.vscode
     | \.venv
     | \bdist\b
     | \bdoc\b
@@ -75,19 +71,8 @@ exclude = '''
 [tool.ruff]
 line-length = 115
 target-version = "py39"
-
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
 
-[tool.pylint.'MESSAGES CONTROL']
-max-line-length = 115
-disable = """
-logging-fstring-interpolation
-"""
-
 [tool.pytest.ini_options]
 testpaths = "tests/"
-python_classes = [
-  "Test*",
-  "*Test"
-]