Merge pull request #6 from genomoncology/isocodes

0.1.0: Refactored to follow PEP 593 standards.

.gitignore

@@ -30,4 +30,5 @@ wheels/
 model_cache/
 .DS_Store
 /training/
-profile.dat
+profile.dat
+notebooks

CHANGELOG.md

@@ -0,0 +1,22 @@
+## v0.1.0 (2023-03-25)
+
+The project's typing system was validated using mypy and refactored to follow
+Annotated types as specified by [PEP 593](https://peps.python.org/pep-0593/).
+
+#### Added
+ - FuzzValidator annotation type created to simplify design
+ - validate_python, validate_json, and validate_entity functions added
+ - Added Language, LanguageName, and LanguageCode usable types
+ - fuzztypes.logger and fuzztypes.utils module for downloading iso codes
+
+#### Changed
+ - Renamed OnDisk to OnDiskValidator
+ - Renamed InMemory to InMemoryValidator
+ - Refactored InMemoryValidator and OnDiskValidator to use FuzzValidator
+ - Refactored Person to use FuzzValidator
+ - Renamed Regex to RegexValidator
+ - Changed error message to more common "did you mean" message format
+
+#### Removed
+ - abstract.py module and AbstractType class, simplified by FuzzValidator
+ - function.py module and Function annotation type, replaced by FuzzValidator

pyproject.toml

@@ -25,12 +25,14 @@ dynamic = ["version"]
 [project.optional-dependencies]
 test = [
     "pytest",
+    "pytest-mock",
     "coverage[toml]",
 ]
 local = [
     "build",
     "jupyter",
     "ipython",
+    "mypy",
     "pip",
     "setuptools",
     "twine",
@@ -59,11 +61,6 @@ ext = [
 path = "src/fuzztypes/__init__.py"
 
 [tool.mypy]
-strict = true
-
-[[tool.mypy.overrides]]
-module = "gpt.tests.*"
-ignore_missing_imports = true
 check_untyped_defs = true
 
 [tool.pytest.ini_options]

requirements-dev.txt

@@ -217,6 +217,9 @@ more-itertools==10.2.0
     # via jaraco-classes
 mpmath==1.3.0
     # via sympy
+mypy==1.9.0
+mypy-extensions==1.0.0
+    # via mypy
 nameparser==1.1.3
 nbclient==0.10.0
     # via nbconvert
@@ -320,6 +323,8 @@ pylance==0.10.2
 pyproject-hooks==1.0.0
     # via build
 pytest==8.0.1
+    # via pytest-mock
+pytest-mock==3.12.0
 python-dateutil==2.9.0.post0
     # via
     #   arrow
@@ -434,6 +439,7 @@ tomli==2.0.1
     #   build
     #   coverage
     #   jupyterlab
+    #   mypy
     #   pyproject-hooks
     #   pytest
 torch==2.2.1
@@ -480,6 +486,7 @@ typing-extensions==4.9.0
     #   async-lru
     #   huggingface-hub
     #   ipython
+    #   mypy
     #   pydantic
     #   pydantic-core
     #   torch