From 17b2b929e5f36eded1ba6352452d6b816e299b45 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 21 Nov 2024 13:00:47 -0700 Subject: [PATCH 1/4] Updated readme by adding links to referenced files and added testing status badge. --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a320dfd..d28f757 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,10 @@ +[![Test Pairwise Compare](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml/badge.svg)](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml) # 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 examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data). These examples can be found in the docs. 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. +Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), 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 @@ -19,11 +20,11 @@ One of the following column arguments conditions must be satisified when using t 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. +1. Input validation is enforced in the `PairwiseCompareManager` and [PairwiseCompare](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompare.py) 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). +To incorporate additional comparators for making comparisons, you must introduce the functionality as a class and inherit from the `Comparator` class (See [Comparator.py](https://github.com/WayScience/pairwise_compare/blob/main/src/comparators/Comparator.py) for details). From 0eaf67db561ce5541231bbb87bbb16bef084d6e5 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 21 Nov 2024 13:25:50 -0700 Subject: [PATCH 2/4] Added docs link in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d28f757..500246b 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # 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 examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data). -These examples can be found in the docs. +These examples can be found in the [docs](https://github.com/WayScience/pairwise_compare/tree/main/docs). Although, most of the development efforts can be found in the `src` folder. Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), 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. From 1ac51ccc07909622d3bb4749e47b622a0263d94e Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 21 Nov 2024 13:31:23 -0700 Subject: [PATCH 3/4] Added line breaks in README --- README.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 500246b..0ca157f 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ [![Test Pairwise Compare](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml/badge.svg)](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml) # 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 examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data). -These examples can be found in the [docs](https://github.com/WayScience/pairwise_compare/tree/main/docs). -Although, most of the development efforts can be found in the `src` folder. -Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), however, there may be rare exceptions. +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 examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data).
+These examples can be found in the [docs](https://github.com/WayScience/pairwise_compare/tree/main/docs).
+Although, most of the development efforts can be found in the `src` folder.
+Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), 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. +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`: @@ -26,5 +26,5 @@ One of the following column arguments conditions must be satisified when using t 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. +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](https://github.com/WayScience/pairwise_compare/blob/main/src/comparators/Comparator.py) for details). From e28e9334e4b72f1125a015df7f8ddc0d8c5664a9 Mon Sep 17 00:00:00 2001 From: Cameron Mattson Date: Thu, 21 Nov 2024 15:48:38 -0700 Subject: [PATCH 4/4] Updated README using pr comments. --- README.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 0ca157f..b115837 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ -[![Test Pairwise Compare](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml/badge.svg)](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml) +[![Tests](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml/badge.svg)](https://github.com/WayScience/pairwise_compare/actions/workflows/python-app.yml) # 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 examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data).
-These examples can be found in the [docs](https://github.com/WayScience/pairwise_compare/tree/main/docs).
-Although, most of the development efforts can be found in the `src` folder.
-Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), however, there may be rare exceptions.
+This tool allows the user to compare groups of data specified in a [tidy](https://tidyr.tidyverse.org/articles/tidy-data.html) pandas dataframe with ease. +In this repo the capabilities of the PairwiseCompareManager are shown through examples using a dataset from the [nf1_schwann_cell_painting_data](https://github.com/WayScience/nf1_schwann_cell_painting_data). +These examples can be found in the [docs](https://github.com/WayScience/pairwise_compare/tree/main/docs). +Although, most of the development efforts can be found in the `src` folder. +Users should almost exclusively interact with the [PairwiseCompareManager](https://github.com/WayScience/pairwise_compare/blob/main/src/comparison_tools/PairwiseCompareManager.py), 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.
+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`: @@ -26,5 +26,5 @@ One of the following column arguments conditions must be satisified when using t 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.
+This tool compares features between any two groups of a tidy 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](https://github.com/WayScience/pairwise_compare/blob/main/src/comparators/Comparator.py) for details).