Merge pull request #19 from I-TECH-UW/pip-package-initial-clean

Initial clean to get cli commands to work

pyproject.toml

@@ -16,13 +16,13 @@ fhirpy = ">=1.4"
 Faker = ">=25.0"
 inflect = "^7.3.0"
 python-slugify = ">=8.0.4"
+stringcase = ">=1.2"
 jinja2 = "^3.1.4"
 
 [tool.poetry.group.dev.dependencies]
 pytest = ">=6"
 flake8 = ">=3.8"
 Sphinx = ">=3.2"
-stringcase = ">=1.2"
 pyright = "^1.1.367"
 pre-commit = "^3.7.1"
 pylint = "^3.2.5"
@@ -35,6 +35,10 @@ venv = ".venv"
 [tool.poetry.scripts]
 lint = "scripts.lint:main"
 format = "scripts.format:main"
+logical_model_gen = "who_l3_smart_tools.cli.logical_model_gen:main"
+indicator_testing = "who_l3_smart_tools.cli.indicator_testing:main"
+terminology = "who_l3_smart_tools.cli.terminology:main"
+
 
 [build-system]
 requires = ["poetry-core"]

setup.py

@@ -1,5 +1,4 @@
-from setuptools import setup, find_packages
-
+from setuptools import find_packages, setup
 
 setup(
     name="who_l3_smart_tools",

tests/test_cql_tools.py

@@ -1,17 +1,18 @@
 # Generated by CodiumAI
 import datetime
 import os
-import re
+import unittest
+
+import pandas as pd
+import stringcase
+
 from who_l3_smart_tools.core.cql_tools.cql_file_generator import CqlFileGenerator
 from who_l3_smart_tools.core.cql_tools.cql_resource_generator import (
     CqlResourceGenerator,
 )
 from who_l3_smart_tools.core.cql_tools.cql_template_generator import (
     CqlTemplateGenerator,
 )
-import pandas as pd
-import unittest
-import stringcase
 
 
 class TestCqlTools(unittest.TestCase):
@@ -100,7 +101,7 @@ def test_generate_library_fsh(self):
         with open(output_file, "w") as f:
             f.write(library_fsh)
 
-        expected_lib_file = f"tests/data/example_fsh/HIV27_library.fsh"
+        expected_lib_file = "tests/data/example_fsh/HIV27_library.fsh"
         with open(expected_lib_file, "r") as expected_lib_fsh_file:
             expected_library_fsh = expected_lib_fsh_file.read().rstrip()
 
@@ -116,7 +117,6 @@ def test_generate_measure_fsh(self):
         output_file = (
             f"tests/output/fsh/{stringcase.alphanumcase(p["library_name"])}_measure.fsh"
         )
-
         if os.path.exists(output_file):
             os.remove(output_file)
         with open(output_file, "w") as f:

who_l3_smart_tools/core/terminology/terminology.py

@@ -268,7 +268,7 @@ def _convert_rows(self) -> None:
             sheet = workbook[sheet_name]
             header: Optional[list[str]] = None
             for row in sheet.iter_rows(values_only=True):
-                # if header is set the current raw as the header and skip to the next row.
+                # if header is None. Set the current row as the header and skip to the next row.
                 if header is None:
                     header = row
                     continue