Get passing all tests again

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,52 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## 1. Bug description
+
+(A clear and concise description of what the bug is.)
+
+### Console output 
+
+```
+# Paste console output here (e.g. from R/python/command line)
+
+```
+
+### Expected behaviour   
+
+(A clear and concise description of what you expected to happen.)
+
+
+## 2. Reproducible example   
+
+### Code 
+
+(Please add the steps to reproduce the bug here. See [here](https://www.r-bloggers.com/2020/10/how-to-make-a-reprex/) for an intro to making a reproducible example (i.e. reprex) and why they're important! __This will help us to help you much faster.__)
+
+```R
+# Paste example here
+
+```
+
+### Data
+
+(If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)
+
+
+## 3. Session info
+
+(Add output of the R function `utils::sessionInfo()` below. This helps us assess version/OS conflicts which could be causing bugs.)
+
+<details>
+
+```
+# Paste utils::sessionInfo() output 
+
+```
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [---]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: HPOExplorer
 Title: Analysis and Visualisation of the Human Phenotype Ontology
-Version: 1.0.0
+Version: 1.0.1
 Authors@R:
     c(
     person(given = "Brian",

NEWS.md

@@ -1,3 +1,16 @@
+# HPOExplorer 1.0.1
+
+## New features
+
+- Add Issues templates
+
+## Bug fixes
+
+* Fix tests: 
+  - `gpt_annot_check`
+  - `add_hpo_id`
+* Fix functions: `gpt_annot_plot`
+
 # HPOExplorer 1.0.0
 
 ## New features

R/0docs.R

@@ -116,6 +116,7 @@ NULL
 #' returns the entirely ontology.
 #' @family make_
 #' @inheritParams main
+#' @inheritParams KGExplorer::map_colors
 #' @returns R object.
 #' @name make_
 NULL

R/gpt_annot_check_plot.R

@@ -7,7 +7,8 @@ gpt_annot_check_plot <- function(checks,
                                  scales = "free"){
   requireNamespace("ggplot2")
 
-  annotation <- metric <- metric_category <- metric_type <- NULL;
+  annotation <- metric <- metric_category <- metric_type <- n <-
+    value <- label <-NULL;
   check_df <- lapply(checks[items],
                      data.table::as.data.table, keep.rownames = TRUE) |>
     data.table::rbindlist(idcol = "metric") |>

R/gpt_annot_melt.R

@@ -5,7 +5,8 @@ gpt_annot_melt <- function(res_coded){
                   value = TRUE)
   dat <- data.table::melt.data.table(
     data = res_coded$annot[
-      res_coded$annot_weighted[,c("hpo_id","severity_score_gpt")],on="hpo_id"],
+      unique(res_coded$annot_weighted[,c("hpo_id","severity_score_gpt")]),
+      on="hpo_id"],
     id.vars = c(id.vars,"severity_score_gpt"),
     variable.factor = TRUE,
     value.factor = TRUE)

tests/testthat/test-add_hpo_id.R

@@ -2,15 +2,6 @@ test_that("add_hpo_id works", {
 
   phenotype_to_genes <- load_phenotype_to_genes()
   phenos <- unique(phenotype_to_genes[,-c("hpo_id")])
-  phenos2 <- add_hpo_id(phenos=phenos)
-
-  ## Several terms were omitted from later versions of the HPO
-  ## due to becoming obsolete.
-  testthat::expect_lte(sum(phenos2$hpo_id!=phenos2$hpo_id), 4)
-  mismatched_phenos <- map_phenotypes(
-    terms = phenos2$ID[phenos2$hpo_id!=phenos2$hpo_id]
-  )
-  testthat::expect_true(
-    all(grepl("^obsolete",mismatched_phenos, ignore.case = TRUE))
-  )
+  phenos <- add_hpo_id(phenos=phenos)
+  testthat::expect_equal(sum(is.na(phenos$hpo_id)),0)
 })

tests/testthat/test-gpt_annot_check.R

@@ -2,7 +2,7 @@ test_that("gpt_annot_check works", {
 
   checks <- gpt_annot_check()
   testthat::expect_true(all(
-    c("annot","annot_mean","annot_consist","annot_check","checkable_rate",
+    c("annot","annot_mean","consistency_count","annot_check","checkable_rate",
       "checkable_count","true_pos_rate","false_neg_rate") %in% names(checks)
   ))
 })