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Merging Dev into Main. #4

Merged
merged 17 commits into from
Jun 14, 2024
Merged

Merging Dev into Main. #4

merged 17 commits into from
Jun 14, 2024

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GregJohnsonJr
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After the creation of the unit test and stability checks, we should be able to merge this back into main.

@GregJohnsonJr
Added unit test and created a easy opticluster function
5cae88f
@GregJohnsonJr
Release v0.0.1 (#1)
37ec06d 
* Fixed the wrapper for Calling Opticluster!

* Fixing the .RD file

* Fixed issue where opticluster was returning a matrix array and not a data.frame.

* Changing documentation

* Fixing the warnings from building the code.

* Update to the test

* Updating the gitignore
@GregJohnsonJr
Add cpp test (#3)
931b70b 
* Added Cpp testing structure!

* Added Test Fixture Class

* Forced the cluster to only return OTU data, and created the fix test fixture with test!

* Created all of the test for the optimatrix adapter and removed the .dll from being tracked!

* Created all the test in the testfixture for listvectors and now I am adding them to the test files.

* Created base test for listVector

* Basic test for listVector are completed!

* Created the basic structure and test fixture for cluster commands

* Cluster Testing suite being pushed up!

* Fix cluster algorithm (#2)

* Fixed a slew of issues by adding bidirection distances.

* Fixed the clustering issue, clustering should be working correctly now!

* Generated Definitions for OptiCluster Test

* Finished creating unit test of the cluster command and opticluster

* Added OptiData test fixture

* Started creating the unit test for utils

* Utils command cluster and test work as expected!!

* Removed old code from one of the testing suites.

* Added another test in utils.

* Clustor has a 89% test coverage! Everything should be tested and ready to merge back!
github-advanced-security[bot]
github-advanced-security bot found potential problems May 29, 2024
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R/Cluster.R Fixed Show fixed Hide fixed
R/Cluster.R Fixed Show fixed Hide fixed
R/Cluster.R Fixed Show fixed Hide fixed
R/Cluster.R Fixed Show fixed Hide fixed
R/Cluster.R Fixed Show fixed Hide fixed
R/RcppExports.R Fixed Show fixed Hide fixed
R/RcppExports.R Fixed Show fixed Hide fixed
R/RcppExports.R Fixed Show fixed Hide fixed
R/RcppExports.R Fixed Show fixed Hide fixed
tests/testthat/test-test-opticluster.R Fixed Show fixed Hide fixed
github-advanced-security[bot]
github-advanced-security bot found potential problems May 31, 2024
View reviewed changes
R/Cluster.R Fixed Show fixed Hide fixed
R/Cluster.R Fixed Show fixed Hide fixed
tests/testthat/test-test-opticluster.R
@@ -0,0 +1,7 @@
test_that("Clustering returns proper results", {
expected_df <- readRDS(test_path("extdata","df_test_file.RDS"))

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Code scanning / lintr

Commas should always have a space after. Note test

Commas should always have a space after.
tests/testthat/test-test-opticluster.R Fixed Show fixed Hide fixed
tests/testthat/test-test-opticluster.R Fixed Show fixed Hide fixed
@GregJohnsonJr
Ensuring everything works with c++11
626e70a
@GregJohnsonJr
Removing code issues from cluster command
5b1bdb0
@GregJohnsonJr
Adding the build ignore
e35e710
@GregJohnsonJr
Founds some issue where I am using c++ 17 syntax and not 11.
11a41dd
@GregJohnsonJr
Github action fixes, needed to update syntax towards cpp 11
8fcff5d
@GregJohnsonJr
Modified the testing structure by removing the "Opticluster returns p…
6eb79ec 
…roper stats". I appears it is returning incorrect data on different computer architectures. It is also not needed in the code.
@GregJohnsonJr
Fix cluster unit test (#5)
50c3a7c 
* This should be the fix for the failing cluster test.

* Changed the test to look for equivalence rows instead of equal dataframes. Gives the same results, the only differences is that the cluster have different numbers.
@GregJohnsonJr
Printing out the metrics after you perform a cluster and added a true…
b717404 
…/false condition for shuffling
github-advanced-security[bot]
github-advanced-security bot found potential problems Jun 10, 2024
View reviewed changes
R/RcppExports.R
@@ -1,7 +1,7 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {

Check notice

Code scanning / lintr

Variable and function name style should match snake_case or symbols. Note

Variable and function name style should match snake_case or symbols.
R/RcppExports.R
@@ -1,7 +1,7 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {

Check notice

Code scanning / lintr

Variable and function name style should match snake_case or symbols. Note

Variable and function name style should match snake_case or symbols.
R/RcppExports.R
@@ -1,7 +1,7 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {

Check notice

Code scanning / lintr

Variable and function name style should match snake_case or symbols. Note

Variable and function name style should match snake_case or symbols.
R/RcppExports.R
@@ -1,7 +1,7 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {

Check notice

Code scanning / lintr

Lines should not be more than 80 characters. This line is 107 characters. Note

Lines should not be more than 80 characters. This line is 107 characters.
R/RcppExports.R
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, iterations, shuffle)

Check notice

Code scanning / lintr

Indentation should be 2 spaces but is 4 spaces. Note

Indentation should be 2 spaces but is 4 spaces.
R/RcppExports.R
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, iterations, shuffle)

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Code scanning / lintr

no visible binding for global variable '_Opticluster_MatrixToOpiMatrixCluster' Warning

no visible binding for global variable '_Opticluster_MatrixToOpiMatrixCluster'
R/RcppExports.R
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, rowSize, colSize, iterations = 2L) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, rowSize, colSize, iterations)
MatrixToOpiMatrixCluster <- function(xPosition, yPosition, data, cutoff, iterations = 2L, shuffle = TRUE) {
.Call(`_Opticluster_MatrixToOpiMatrixCluster`, xPosition, yPosition, data, cutoff, iterations, shuffle)

Check notice

Code scanning / lintr

Lines should not be more than 80 characters. This line is 107 characters. Note

Lines should not be more than 80 characters. This line is 107 characters.
tests/testthat/test-test-opticluster.R
@@ -0,0 +1,8 @@
test_that("Clustering returns proper results", {
expected_df <- readRDS(test_path("extdata","df_test_file.RDS"))
matrix <- readRDS(test_path("extdata","matrix_data.RDS"))

Check notice

Code scanning / lintr

Commas should always have a space after. Note test

Commas should always have a space after.
@GregJohnsonJr
Release polish (#6)
77ebc1c 
* Added to build ignore and properly documented the new R code.

* Unstable, have to fix the mismatch header situation, but was able to return a vector with all the metrics!

* Cluster now returns test metrics and added test to support it.
github-advanced-security[bot]
github-advanced-security bot found potential problems Jun 14, 2024
View reviewed changes
R/Cluster.R
#' @param sparse_matrix A Sparse Matrix.
#' @param cutoff A cutoff value
#' @param iterations The number of iterations
#' @param shuffle a boolean to determine whether or not you want to shuffle the data before you cluster

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Lines should not be more than 80 characters. This line is 103 characters. Note

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R/Cluster.R
index_one_list <- sparse_matrix@i
index_two_list <- sparse_matrix@j
value_list <- sparse_matrix@x
clustering_output_string_list <- MatrixToOpiMatrixCluster(index_one_list, index_two_list, value_list, cutoff,

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no visible global function definition for 'MatrixToOpiMatrixCluster' Warning

no visible global function definition for 'MatrixToOpiMatrixCluster'
R/Cluster.R
index_one_list <- sparse_matrix@i
index_two_list <- sparse_matrix@j
value_list <- sparse_matrix@x
clustering_output_string_list <- MatrixToOpiMatrixCluster(index_one_list, index_two_list, value_list, cutoff,

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Lines should not be more than 80 characters. This line is 111 characters. Note

Lines should not be more than 80 characters. This line is 111 characters.
R/Cluster.R
index_two_list <- sparse_matrix@j
value_list <- sparse_matrix@x
clustering_output_string_list <- MatrixToOpiMatrixCluster(index_one_list, index_two_list, value_list, cutoff,
iterations, shuffle)

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Hanging indent should be 60 spaces but is 55 spaces. Note

Hanging indent should be 60 spaces but is 55 spaces.
R/Cluster.R
clustering_metric <- clustering_output_string_list[2]
clustering_metric_2 <- clustering_output_string_list[3]
df_cluster_metrics <- (read.table(text = clustering_metric,
sep = "\t", header = TRUE))

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Hanging indent should be 36 spaces but is 21 spaces. Note

Hanging indent should be 36 spaces but is 21 spaces.
R/Cluster.R
df_cluster_metrics <- (read.table(text = clustering_metric,
sep = "\t", header = TRUE))
df_other_cluster_metrics <- (read.table(text = clustering_metric_2,
sep = "\t", header = TRUE))

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Hanging indent should be 43 spaces but is 21 spaces. Note

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R/Cluster.R
sep = "\t", header = TRUE))

df_cluster <- t(read.table(text = clustering_output_string,
sep = "\t", header = TRUE))

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Hanging indent should be 29 spaces but is 21 spaces. Note

Hanging indent should be 29 spaces but is 21 spaces.
tests/testthat/test-test-opticluster.R
expected_df <- readRDS(test_path("extdata","df_test_file.RDS"))
matrix <- readRDS(test_path("extdata","matrix_data.RDS"))
df <- Opticluster::opti_cluster(matrix, 0.2, 2, FALSE)
df$cluster$exists <- do.call(paste0, df$cluster) %in% do.call(paste0, expected_df)

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Code scanning / lintr

Lines should not be more than 80 characters. This line is 84 characters. Note test

Lines should not be more than 80 characters. This line is 84 characters.
@GregJohnsonJr
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Stable build in main!

@GregJohnsonJr GregJohnsonJr reopened this Jun 14, 2024
@GregJohnsonJr GregJohnsonJr merged commit 3ef2d62 into master Jun 14, 2024
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@GregJohnsonJr