Test actions branch

.github/workflows/python-app.yml

@@ -18,7 +18,8 @@ jobs:
 
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout code with submodules
+      uses: actions/checkout@v4
 
     - name: Set up Python
       uses: actions/setup-python@v5
@@ -36,4 +37,5 @@ jobs:
 
     - name: Test with pytest
       run: |
-        poetry run pytest
+        poetry run pytest -s
+      working-directory: ${{ github.workspace }}

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "data/nf1_schwann_cell_painting_data"]
+	path = data/nf1_schwann_cell_painting_data
+	url = git@github.com:WayScience/nf1_schwann_cell_painting_data.git

README.md

@@ -1 +1,28 @@
-# pairwise_compare
+# Pairwise Compare
+This tool allows the user to compare groups of data specified in a tidy-wide pandas dataframe with ease.
+In this repo the capabilities of the PairwiseCompareManger are shown through an example using the nuclear speckle data (`example_pairwise_comparisons.ipynb`).
+Although, most of the development efforts can be found in the `src` folder.
+Users should almost exclusively interact with the PairwiseCompareManager, however, there may be rare exceptions.
+If you choose to interact with another component of the tool, then there will be less input validation safeguards available.
+
+## Data Formats
+When passing arguments to the `PairwiseCompareManager` you can specify the columns that remain the same in each group-to-group comparison, and the columns that will be different in these comparisons.
+These columns are parameterized by `_same_columns` and `_different_columns`, respectively.
+The column values in these columns uniquely define each group.
+During pairwise comparisons of groups, all of the column values of the columns specified in `_same_columns` will be the same between both groups compared for all paired combinations of groups.
+Likewise, all of the column values of the columns specified in `_different_columns` will be different between both groups compared for all paired combinations of groups.
+
+One of the following column arguments conditions must be satisified when using the `PairwiseCompareManager`:
+1. `_same_columns` must include at least one list element if `_different_columns` has less than two list elements.
+2. `_different_columns` must contain one or more list elements.
+3. `_same_columns` and `_different_columns` should not contain any of the same columns.
+
+## Limitations
+1. Input validation is enforced in the `PairwiseCompareManager` and `PairwiseCompare` classes.
+2. Additional column values are not tracked aside from columns used to compare groups (_same_columns, _different_columns).
+3. Output and input python data structures are limited.
+4. All of the data, in the supplied pandas dataframe, is used to compute comparisons.
+
+## Extensibility
+This tool compares features between any two groups of a tidy-wide pandas dataframe.
+To incorporate additional comparators for making comparisons, you must introduce the functionality as a class and inherit from the `Comparator` class (See `Comparator.py` for details).