Fix CV_Tissue merge loop producing duplicate columns and missing Anatomical_entity_name

[toniecrumley]

Summary

There are several old changes for version numbers and such that I didn't realize were in here. Also, I should have branched off of devel and then merged back to it but I will do that right next time.

Fix CV_Tissue merge loop producing duplicate columns and missing Anatomical_entity_name

The original loop fed the accumulated result back into each merge iteration,
creating a Cartesian product with cascading .x/.y column duplicates and a
broken Anatomical_entity_name column (also contained a typo in the fallback
rename). This was rewritten to join each species independently against the original
id_dataframe and combine on all ID columns + Anatomical_entity_name.

Fixes #71

Author Checklist

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CoSIA

Verify that the modifications to CoSIA work correctly.

Setup

cd $USER_SCRATCH
git clone git@github.com:lasseignelab/CoSIA.git
cd CoSIA
git checkout devel

Test

Run the testthat unit test suite:

./tests/test.sh

Validate that new and old CoSIA produce the same results for functionality that wasn't broken:

./validation/validate.sh

Cleanup

cd $USER_SCRATCH
rm -rf CoSIA

Worthey Lab

Verify that the modifications to CoSIA fix the issues identified by the Worthey Lab in the vignette_script_walkthrough_CPAM_All_Models_Together_Tissues.R script and that the results of that script are correct.

Setup

cd $USER_SCRATCH
git clone git@github.com:toniecrumley/CoSIA-worthey.git
cd CoSIA-worthey
git checkout vignette_walkthroughs_example_plot_creation_scripts

Test

Run the testthat unit test suite:

./tests/test.sh

Validate that new and old CoSIA produce the same results for functionality that wasn't broken:

./validation/validate.sh

Run the analysis scripts created by the Worthey Lab.

./analysis/test.sh

Cleanup

cd $USER_SCRATCH
rm -rf CoSIA-worthey

[lizzyjoan]

Trying to run the testthat unit suite, I run into this, but haven't looked further into it yet

SIF not found: /scratch/lizzyr/CoSIA/bin/container/bioc_cosia_1.10.0.sif
Pulling from docker://lizzyr/bioc_cosia:1.10.0 ...
./tests/test.sh: line 16: singularity: command not found

**EDIT my bad-- did not realize test.sh was not a job, but runs interactively when I tried earlier. 😅 Rerunning on interactive node now!

[tsoelter]

I think everything works as expected. I played around with the reproducible example, with the vignette, and the Shiny app (in addition to what is in the PR instructions) and did not encounter any issues.

[lizzyjoan]

Everything looks good and worked with the different examples, tests, and seems to be as expected results!