full setup transfer

Author: TimMonko

.github/workflows/test_and_deploy.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

README.md

@@ -7,7 +7,7 @@
 [![codecov](https://codecov.io/gh/ndev-kit/platemapper/branch/main/graph/badge.svg)](https://codecov.io/gh/ndev-kit/platemapper)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/platemapper)](https://napari-hub.org/plugins/platemapper)
 
-Map microplate treatments to image metadata.
+Map microplate treatments to metadata.
 
 ----------------------------------
 
@@ -27,9 +27,6 @@ You can install `platemapper` via [pip]:
 
     pip install platemapper
 
-
-
-
 ## Contributing
 
 Contributions are very welcome. Tests can be run with [tox], please ensure

pyproject.toml

@@ -21,11 +21,14 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Image Processing",
 ]
 requires-python = ">=3.9"
 dependencies = [
     "numpy",
+    "pandas[output-formatting]",
+    "seaborn",
 ]
 
 [project.optional-dependencies]
@@ -59,7 +62,7 @@ version = {attr = "platemapper.__init__.__version__"}
 
 [tool.black]
 line-length = 79
-target-version = ['py38', 'py39', 'py310']
+target-version = ['py39', 'py310', 'py311', 'py312', 'py313']
 
 [tool.ruff]
 line-length = 79
@@ -104,5 +107,5 @@ exclude = [
     "*_vendor*",
 ]
 
-target-version = "py38"
+target-version = "py310"
 fix = true

src/platemapper/__init__.py

@@ -1,3 +1,5 @@
 __version__ = "0.0.1"
 
-__all__ = ()
+from platemapper.platemapper import PlateMapper
+
+__all__ = ["PlateMapper"]

src/platemapper/_tests/test_plate_mapper.py

@@ -0,0 +1,119 @@
+from __future__ import annotations
+
+import pandas as pd
+import pytest
+
+from platemapper.platemapper import PlateMapper
+
+
+@pytest.fixture
+def plate_mapper():
+    return PlateMapper(96)
+
+
+def test_plate_mapper_init_empty():
+    pm = PlateMapper()
+    plate_map = pm.plate_map
+    assert isinstance(plate_map, pd.DataFrame)
+    assert pm.pivoted_plate_map is None
+    assert pm.styled_plate_map is None
+    assert len(plate_map) == 96
+    assert len(plate_map.columns) == 3
+    assert "row" in plate_map.columns
+    assert "A" in plate_map["row"].values
+    assert "column" in plate_map.columns
+    assert 1 in plate_map["column"].values
+    assert "well_id" in plate_map.columns
+    assert "A1" in plate_map["well_id"].values
+
+
+def test_plate_mapper_init_with_plate_size():
+    pm = PlateMapper(384)
+    plate_map = pm.plate_map
+    assert len(plate_map) == 384
+    assert len(plate_map.columns) == 3
+    assert "P" in plate_map["row"].values  # 16th letter
+    assert 24 in plate_map["column"].values
+
+
+def test_plate_mapper_leading_zeroes():
+    pm = PlateMapper(leading_zeroes=True)
+    assert "A" in pm.plate_map["row"].values
+    assert "01" in pm.plate_map["column"].values
+    assert "12" in pm.plate_map["column"].values
+    assert "A01" in pm.plate_map["well_id"].values
+    assert "H12" in pm.plate_map["well_id"].values
+
+
+@pytest.fixture
+def treatments():
+    return {
+        "Treatment1": {"Condition1": ["A1", "B2"], "Condition2": ["C3"]},
+        "Treatment2": {"Condition3": ["D4:E5"]},
+    }
+
+
+def test_plate_mapper_init_with_treatments(treatments):
+    pm = PlateMapper(96, treatments=treatments)
+    plate_map = pm.plate_map
+    pivoted_pm = pm.pivoted_plate_map
+
+    assert isinstance(plate_map, pd.DataFrame)
+    assert isinstance(pivoted_pm, pd.DataFrame)
+    assert "Treatment1" in plate_map.columns
+    assert "Treatment2" in plate_map.columns
+    assert (
+        plate_map.loc[plate_map["well_id"] == "A1", "Treatment1"].values[0]
+        == "Condition1"
+    )
+    assert (
+        plate_map.loc[plate_map["well_id"] == "B2", "Treatment1"].values[0]
+        == "Condition1"
+    )
+    assert (
+        plate_map.loc[plate_map["well_id"] == "C3", "Treatment1"].values[0]
+        == "Condition2"
+    )
+    assert (
+        plate_map.loc[plate_map["well_id"] == "D4", "Treatment2"].values[0]
+        == "Condition3"
+    )
+    assert (
+        plate_map.loc[plate_map["well_id"] == "E5", "Treatment2"].values[0]
+        == "Condition3"
+    )
+    assert (
+        plate_map.loc[plate_map["well_id"] == "E4", "Treatment2"].values[0]
+        == "Condition3"
+    )
+
+
+def test_plate_mapper_init_with_treatments_and_leading_zeroes(treatments):
+    pm = PlateMapper(96, treatments=treatments, leading_zeroes=True)
+    plate_map = pm.plate_map
+
+    assert plate_map.loc[plate_map["well_id"] == "A01", "Treatment1"].values[0]
+
+
+def test_plate_mapper_get_pivoted_plate_map(
+    plate_mapper: PlateMapper, treatments: dict[str, dict[str, list[str]]]
+):
+    plate_mapper.assign_treatments(treatments)
+    plate_map_pivot = plate_mapper.get_pivoted_plate_map("Treatment1")
+
+    assert isinstance(plate_map_pivot, pd.DataFrame)
+    assert len(plate_map_pivot) == 8
+    assert len(plate_map_pivot.columns) == 12
+    assert "A" in plate_map_pivot.index
+    assert "Condition1" in plate_map_pivot.values
+    assert "Condition2" in plate_map_pivot.values
+
+
+def test_plate_mapper_get_styled_plate_map(
+    plate_mapper: PlateMapper, treatments: dict[str, dict[str, list[str]]]
+):
+    plate_mapper.assign_treatments(treatments)
+    plate_map_styled = plate_mapper.get_styled_plate_map("Treatment1")
+
+    assert isinstance(plate_map_styled, pd.io.formats.style.Styler)
+    assert plate_map_styled.caption == "Treatment1 Plate Map"

src/platemapper/napari.yaml

@@ -1,7 +1,7 @@
 name: platemapper
 display_name: ndev PlateMapper
 # use 'hidden' to remove plugin from napari hub search results
-visibility: public
+visibility: hidden
 # see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
 categories: ["Utilities"]
 contributions: