Merge pull request #35 from MIDRC/feature/pip_support

Feature/pip support

Author: rtomek

MANIFEST.in

@@ -0,0 +1,5 @@
+include README.md
+include LICENSE
+recursive-include src *
+include jsdconfig-example.yaml
+recursive-include data *.xls *.xlsx

setup.py

@@ -1,20 +1,51 @@
 from setuptools import find_packages, setup
+from pathlib import Path
+
+here = Path(__file__).parent
+long_description = (here / "README.md").read_text(encoding="utf-8")
 
 setup(
-    name='midrc_react',
-    version='0.1.0',
-    packages=find_packages(where='src'),
-    package_dir={'': 'src'},
+    name="midrc_react",
+    version="0.1.0",
+    description="The MIDRC Representativeness Exploration and Comparison Tool (REACT) is a tool designed to compare the representativeness of biomedical data.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Robert Tomek",
+    author_email="rtomek@uchicago.edu",
+    url="https://github.com/MIDRC/MIDRC-REACT",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.10",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    packages=find_packages(where="src"),
+    package_dir={"": "src"},
     include_package_data=True,
     install_requires=[
-        # list additional dependencies here, for example:
-        # 'numpy',
-        # 'pandas',
+        "numpy>=1.26.0",
+        "pandas>=2.2.0",
+        "PySide6>=6.6.0",
+        "scipy>=1.12.0",
+        "openpyxl>=3.1.0",
+        "pytest>=8.1.0",
+        "PyYAML>=6.0.0",
+        "prince>=0.15.0",
+        "dash>=2.18.2",
+        "plotly>=5.24.1",
+        "matplotlib>=3.9.0",
+        "seaborn>=0.13.2",
+        "ipywidgets>=8.1.5",
+        "ipython>=8.28.0",
+        "python-dateutil>=2.9.0.post0",
+        "tabulate>=0.9.0",
+        "scikit-learn>=1.6.1",
     ],
+    python_requires=">=3.10",
     entry_points={
-        'console_scripts': [
-            'midrc-react=midrc_react.gui.pyside6.launch_react:launch_react',
-            'MIDRC-REACT=midrc_react.gui.pyside6.launch_react:launch_react',
+        "console_scripts": [
+            "midrc-react=midrc_react.gui.pyside6.launch_react:launch_react",
+            "MIDRC-REACT=midrc_react.gui.pyside6.launch_react:launch_react",
         ],
     },
 )

src/midrc_react/gui/pyside6/jsdview.py

@@ -304,6 +304,17 @@ def update_pie_chart_dock(self, sheet_dict: Dict[Any, Any]) -> None:
         clear_layout(self.pie_chart_layout)
         categorybox = self.dataselectiongroupbox.category_combobox
         categories: List[str] = [categorybox.itemText(i) for i in range(categorybox.count())]
+
+        # Create a mapping for a fixed ordering per category using the first sheet encountered that has it.
+        common_order: Dict[str, List[str]] = {}
+        for category in categories:
+            common_order[category] = []
+            for sheets in sheet_dict.values():
+                if category in sheets:
+                    for col in sheets[category].data_columns:
+                        if col not in common_order[category]:
+                            common_order[category].append(col)
+
         timepoint: int = -1
         file_comboboxes = self.dataselectiongroupbox.file_comboboxes
         labels: List[QLabel] = JsdWindow._create_pie_chart_labels(sheet_dict, file_comboboxes)
@@ -317,9 +328,17 @@ def update_pie_chart_dock(self, sheet_dict: Dict[Any, Any]) -> None:
                 if category not in sheets:
                     continue
                 df = sheets[category].df
-                cols_to_use = sheets[category].data_columns
+                sheet_order = sheets[category].data_columns
+                # Use common order, but include only columns that exist in the current sheet.
+                final_order = [col for col in common_order.get(category, []) if col in sheet_order]
+                # Append any extra columns from the sheet that are not already in final_order.
+                final_order += [col for col in sheet_order if col not in final_order]
+                # Ensure 'Not Reported' is always the last column.
+                if "Not Reported" in final_order:
+                    final_order = [col for col in final_order if col != "Not Reported"] + ["Not Reported"]
+
                 series = QPieSeries()
-                for col in cols_to_use:
+                for col in final_order:
                     value = df[col].iloc[timepoint]
                     if value > 0:
                         series.append(col, value)