Warren/packaging

README.md

@@ -4,7 +4,7 @@
 [![codecov](https://codecov.io/gh/codonlibrary/codonPython/branch/master/graph/badge.svg)](https://codecov.io/gh/codonlibrary/codonPython)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-## What is `codon`?   
+## What is `codon`?
 
 The `codon` project was created to increase code sharing, code consistency, coding standards, and encourage collaboration.  Package documentation is available on the [GitHub pages](https://codonlibrary.github.io/codonPython/). `codonPython` aims to reduce the barrier for entry for analysis and provide software development experience for those at a higher level of technical ability. 
 

pyproject.toml

@@ -0,0 +1,27 @@
+[tool.poetry]
+name = "codonpython"
+version = "0.2.1"
+description = "This is a first attempt at how our package will work."
+authors = ["NHS Digital DIS Team"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.10"
+pandas = ">=2.2.3"
+numpy = ">=2.1.3"
+scipy = ">=1.14.1"
+sqlalchemy = ">=2.0.36"
+scikit-learn = ">=1.5.2"
+statsmodels = ">=0.14.4"
+seaborn = ">=0.13.2"
+sphinx = ">=8.1.3"
+sphinx-rtd-theme = ">=3.0.1"
+flake8 = ">=7.1.1"
+m2r = ">=0.3.1"
+pytest = ">=8.3.3"
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

codonPython/check_nat_val.py → src/codonpython/check_nat_val.py

@@ -86,7 +86,7 @@ def check_nat_val(
         raise KeyError("Check column names correspond to the DataFrame.")
     # aggregate values by measure and breakdown
     grouped = (
-        df.groupby([measure_col, breakdown_col]).agg({value_col: sum}).reset_index()
+        df.groupby([measure_col, breakdown_col]).agg({value_col: "sum"}).reset_index()
     )
     national = grouped.loc[grouped[breakdown_col] == nat_val].reset_index()
     non_national = grouped.loc[grouped[breakdown_col] != nat_val].reset_index()

codonPython/tolerance.py → src/codonpython/tolerance.py

@@ -122,18 +122,17 @@ def check_tolerance(
         _, yhat_l, yhat_u = wls_prediction_std(model, t_predict, alpha=alpha)
 
         # Store model results in master frame
-        results = results.append(
-            pd.DataFrame(
-                {
-                    "t": t_orig,
-                    "yhat_u": yhat_u,
-                    "yobs": y_predict,
-                    "yhat": yhat,
-                    "yhat_l": yhat_l,
-                    "polynomial": degree,
-                }
-            ),
-            ignore_index=True,
+        degree_results = pd.DataFrame(
+            {
+                "t": t_orig,
+                "yhat_u": yhat_u,
+                "yobs": y_predict,
+                "yhat": yhat,
+                "yhat_l": yhat_l,
+                "polynomial": degree,
+            }
         )
 
+        results = pd.concat([results, degree_results], ignore_index=True)
+
     return results

codonPython/tests/age_bands_test.py → tests/age_bands_test.py

@@ -1,4 +1,4 @@
-from codonPython import age_bands
+from codonpython import age_bands
 import numpy as np
 import math
 import pytest

codonPython/tests/check_consistent_measures_test.py → tests/check_consistent_measures_test.py

@@ -1,4 +1,4 @@
-from codonPython.check_consistent_measures import check_consistent_measures
+from codonpython.check_consistent_measures import check_consistent_measures
 import pandas as pd
 import numpy as np
 import pytest

codonPython/tests/check_consistent_submissions_test.py → tests/check_consistent_submissions_test.py

@@ -1,4 +1,4 @@
-from codonPython.check_consistent_submissions import check_consistent_submissions
+from codonpython.check_consistent_submissions import check_consistent_submissions
 import pandas as pd
 import numpy as np
 import pytest

codonPython/tests/check_nat_val_test.py → tests/check_nat_val_test.py

@@ -1,4 +1,4 @@
-from codonPython.check_nat_val import check_nat_val
+from codonpython.check_nat_val import check_nat_val
 import pytest
 import pandas as pd
 

codonPython/tests/check_null_test.py → tests/check_null_test.py

@@ -1,4 +1,4 @@
-from codonPython.check_null import check_null
+from codonpython.check_null import check_null
 import numpy as np
 import pandas as pd
 import pytest

codonPython/tests/dateValidator_test.py → tests/dateValidator_test.py

@@ -1,4 +1,4 @@
-from codonPython import dateValidator
+from codonpython import dateValidator
 import pytest
 
 

codonPython/tests/file_utils_test.py → tests/file_utils_test.py

@@ -1,6 +1,6 @@
-from codonPython.file_utils import compare
-from codonPython.file_utils import file_search
-from codonPython.file_utils import import_files
+from codonpython.file_utils import compare
+from codonpython.file_utils import file_search
+from codonpython.file_utils import import_files
 import numpy as np
 import pytest
 import pandas as pd
@@ -90,26 +90,27 @@ def test_compare_BAU(x, y, names, dups, same, expected):
                 assert list_test1 == list_exp
 
 
+
 @pytest.mark.parametrize(
     "doctype, like, strict, expected", [("md", ["README"], True, ["README.md"])]
 )
 def test_file_search_BAU(doctype, like, strict, expected):
     assert file_search(doctype=doctype, like=like, strict=strict) == expected
 
+file_import_path = './tests'
 
 @pytest.mark.parametrize("expected", [({})])
 def test_import_files_BAU(expected):
-    assert import_files() == expected
-
+    assert import_files(file_import_path) == expected
 
 @pytest.mark.parametrize("subdir, expected", [(True, {})])
 def test_import_files_BAU_2(subdir, expected):
-    assert import_files(subdir=subdir) == expected
+    assert import_files(file_import_path, subdir=subdir) == expected
 
 
 @pytest.mark.parametrize("strict,subdir, expected", [(True, True, {})])
 def test_import_files_BAU_3(strict, subdir, expected):
-    assert import_files(strict=strict, subdir=subdir) == expected
+    assert import_files(file_import_path, strict=strict, subdir=subdir) == expected
 
 
 # ----------------Console output-------------------------

codonPython/tests/nhsNumber_test.py → tests/nhsNumber_test.py

@@ -1,4 +1,4 @@
-from codonPython.nhsNumber import nhsNumberGenerator, nhsNumberValidator
+from codonpython.nhsNumber import nhsNumberGenerator, nhsNumberValidator
 import pytest
 import random
 

codonPython/tests/suppression_test.py → tests/suppression_test.py

@@ -1,4 +1,4 @@
-from codonPython.suppression import suppress_value
+from codonpython.suppression import suppress_value
 import pytest
 
 

codonPython/tests/tolerance_test.py → tests/tolerance_test.py

@@ -1,7 +1,7 @@
-from codonPython.tolerance import check_tolerance
+from codonpython.tolerance import check_tolerance
 import numpy as np
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 import pytest
 
 testdata = [