From cd93c404a213ba44554b809653ed14d8c563822e Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 11:29:17 +0200
Subject: [PATCH 01/17] rm unused pkgs from ed-rev for #12

---
 DESCRIPTION           | 2 +-
 codemeta.json         | 2 +-
 quarto/ed-reviews.qmd | 5 -----
 3 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9cf099b..b0dcd7a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.024
+Version: 0.1.8.025
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index f1a0a6d..fe64bc9 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.024",
+  "version": "0.1.8.025",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/ed-reviews.qmd b/quarto/ed-reviews.qmd
index 0e6c1fc..cb9adaa 100644
--- a/quarto/ed-reviews.qmd
+++ b/quarto/ed-reviews.qmd
@@ -11,11 +11,6 @@ format:
 
 ```{r load-pkg-ed-rev, echo = FALSE, message = FALSE}
 library (dashboard)
-library (gt)
-library (ggplot2)
-library (tidyr)
-library (dplyr)
-library (viridis)
 ```
 
 ```{r get-ed-dat, echo = FALSE, message = FALSE}

From e61e50274603e557116d029de2a92bab9f173ce7 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 12:08:01 +0200
Subject: [PATCH 02/17] start observable table for reviews page #12

---
 DESCRIPTION               |  2 +-
 codemeta.json             |  2 +-
 quarto/_colorTable_fn.qmd | 72 +++++++++++++++++++++++++++++++++++++++
 quarto/reviews.qmd        | 65 +++++++++++++++++++++++++++++++++++
 4 files changed, 139 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b0dcd7a..305b643 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.025
+Version: 0.1.8.026
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index fe64bc9..cca87ae 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.025",
+  "version": "0.1.8.026",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/_colorTable_fn.qmd b/quarto/_colorTable_fn.qmd
index 5a9be21..7cd2250 100644
--- a/quarto/_colorTable_fn.qmd
+++ b/quarto/_colorTable_fn.qmd
@@ -73,3 +73,75 @@ function colorTable(data, {
   return form;
 }
 ```
+
+```{ojs}
+// And modified verison for open reviews table
+function reviewTable(data, {
+        colorColumn,
+        colorOpacity = 0.5,
+        issueNumColumn,
+        titleColumn,
+        columns = undefined,
+        format = {}, ...options}) {
+  const [row] = data;
+  if(!row) return Inputs.table(data, options);
+  
+  let index = Object.keys(row).indexOf(colorColumn);
+  if(index < 0) throw Error("colorColumn not found in data");
+  if(format[colorColumn]) throw Error("colorColumn is reserved");
+  if(columns && columns.indexOf(colorColumn) < 0) columns.push(colorColumn);
+  if(columns) index = columns.indexOf(colorColumn);
+  const nth = `nth-child(${index + 2})`;
+
+  // Observable Table doesn't know about rows, so need to convert the
+  // "titleColumn" into an array with the title and issue number
+  // so then pass to the `format` call below to construct <a> href
+  // objects:
+  const preprocessedData = data.map(row => ({
+     ...row,
+     [titleColumn]: [row[titleColumn],row[issueNumColumn]]
+  }));``
+
+  const form = Inputs.table(preprocessedData, {
+    format: {
+      ...format,
+      [colorColumn]: d => htl.html`<div style="--row-color:${d}">`,
+      [issueNumColumn]: d => htl.html`<a href="https://github.com/ropensci/software-review/issues/${d}">${d}</a>`,
+      [titleColumn]: d => htl.html`<a href="https://github.com/ropensci/software-review/issues/${d[1]}">${d[0]}</a>`,
+    },
+    columns,
+    ...options
+  });
+
+  const scope = DOM.uid().id;
+  form.classList.add(scope);
+  
+  form.append(htl.html`<style>
+
+    /* Ensure that the sticky header always stays on top */
+    .${scope} thead { position: relative; z-index: 2 }
+
+    /* Hide the last column */
+    .${scope} th:${nth},
+    .${scope} td:${nth} { width: 0; padding: 0 }
+    .${scope} th:${nth} { visibility: hidden }
+
+    /* Inject the background color */
+    .${scope} tr { position: relative }
+    .${scope} td:${nth} div:after {
+      opacity: ${colorOpacity};
+      content: "";
+      display: block;
+      height: 100%;
+      width: 100%;
+      position: absolute;
+      left: 0;
+      top: 0;
+      z-index: -1;
+      background-color: var(--row-color);
+    }
+  `);
+
+  return form;
+}
+```
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index a668cfc..aa4e095 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -1,5 +1,7 @@
 ---
 title: "Software Review Overview"
+execute:
+  echo: false
 format: 
   html:
     fig-width: 8
@@ -119,6 +121,69 @@ gt::gt (udat) |>
     dashboard:::add_urgency_cols (c ("urgency", "importance"))
 ```
 
+```{r}
+ojs_define (submissions = rev_dat)
+```
+```{ojs}
+submissionsIn = {
+    return transpose(submissions).map(row => ({
+        ...row,
+        rowColor: row.submission_type === "Stats" ? "yellow" : "transparent",
+    }));
+}
+```
+```{ojs}
+viewof stage = Inputs.checkbox(
+    ["0/presubmission",
+     "1/editor-checks",
+     "2/seeking-reviewer(s)",
+     "3/reviewer(s)-assigned",
+     "4/review(s)-in-awaiting-changes",
+     "5/awaiting-reviewer(s)-response"
+    ],
+    { value: ["0/presubmission"], label: "Submission Stage:" }
+)
+```
+
+```{ojs}
+filtered = submissionsIn.filter(function(submission) {
+  return stage.includes(submission.stage);
+})
+sortColumn = "elapsed_days"
+
+// This sorts in reverse order:
+filteredSorted = filtered.sort((a, b) => {
+  if (a[sortColumn] < b[sortColumn]) {
+    return 1;
+  }
+  if (a[sortColumn] > b[sortColumn]) {
+    return -1;
+  }
+  return 0;
+});
+```
+
+{{< include _colorTable_fn.qmd >}}
+
+nope
+
+```{ojs}
+// And this uses the 'reviewTable' function defined in the above file to
+// generate an Observable Inputs.table with coloured rows.
+console.log("----filteredSorted: ", filteredSorted)
+columns = ["number", "title", "status", "stage_date", "editor", "inactive_for"]
+reviewTable(filteredSorted,
+  {
+    colorColumn: "rowColor",
+    issueNumColumn: "number",
+    titleColumn: "title",
+    columns: columns,
+    height: 'auto',
+  }
+)
+```
+
+
 
 ## 0\/Pre-submission
 

From e1014ff26fa63df15c904204fc9e3a64e7484e26 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 12:19:43 +0200
Subject: [PATCH 03/17] fix 'inactive_for' col in reviews table for #12

---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 11 +++++++++--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 305b643..7b8d712 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.026
+Version: 0.1.8.027
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index cca87ae..d004978 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.026",
+  "version": "0.1.8.027",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index aa4e095..f1879d6 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -51,7 +51,7 @@ dat <- dashboard:::add_gt_html (dat, u, "number")
 # `gt` code below, so use of any value other than `ncols = 5` requires the
 # subsequent colors to be re-coded.
 ncols <- 5L
-dat$urgency <- 0L
+dat$urgency <- rev_dat$urgency <- 0L
 
 # time scales for each stage, in days
 time_scales <- list (
@@ -66,12 +66,19 @@ for (i in time_scales) {
     index <- grep (paste0 ("^", i [1]), dat$stage)
     dat$urgency [index] <-
         floor (as.numeric (dat$elapsed_days [index]) / i [2])
+    rev_dat$urgency [index] <-
+        floor (as.numeric (rev_dat$elapsed_days [index]) / i [2])
 }
 
 dat$urgency [dat$urgency > ncols] <- ncols
 dat$urgency [grepl ("holding", dat$labels)] <- 0
 dat_holding <- dat [grep ("holding", dat$labels), ] # Done at end
 dat <- dat [which (!grepl ("holding", dat$labels)), ]
+
+rev_dat$urgency [rev_dat$urgency > ncols] <- ncols
+rev_dat$urgency [grepl ("holding", rev_dat$labels)] <- 0
+
+rev_dat <- dplyr::rename (rev_dat, "inactive_for" = elapsed)
 ```
 
 ```{r dat-stages, echo = FALSE}
@@ -171,7 +178,7 @@ nope
 // And this uses the 'reviewTable' function defined in the above file to
 // generate an Observable Inputs.table with coloured rows.
 console.log("----filteredSorted: ", filteredSorted)
-columns = ["number", "title", "status", "stage_date", "editor", "inactive_for"]
+columns = ["stage", "number", "title", "stats", "stage_date", "editor", "inactive_for"]
 reviewTable(filteredSorted,
   {
     colorColumn: "rowColor",

From ce6d9427ed5828afcf866c04bb05f664d3c2f440 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 12:33:18 +0200
Subject: [PATCH 04/17] pre-select all stages for reviews #12

Plus implement proper 2-column sort in js for filtered table
---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 35 ++++++++++++++++++++++++-----------
 3 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7b8d712..9358eb5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.027
+Version: 0.1.8.028
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index d004978..bde8db2 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.027",
+  "version": "0.1.8.028",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index f1879d6..8f21ee5 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -148,7 +148,15 @@ viewof stage = Inputs.checkbox(
      "4/review(s)-in-awaiting-changes",
      "5/awaiting-reviewer(s)-response"
     ],
-    { value: ["0/presubmission"], label: "Submission Stage:" }
+    { value: [
+        "0/presubmission",
+        "1/editor-checks",
+        "2/seeking-reviewer(s)",
+        "3/reviewer(s)-assigned",
+        "4/review(s)-in-awaiting-changes",
+        "5/awaiting-reviewer(s)-response"
+      ],
+      label: "Submission Stage:" }
 )
 ```
 
@@ -156,17 +164,23 @@ viewof stage = Inputs.checkbox(
 filtered = submissionsIn.filter(function(submission) {
   return stage.includes(submission.stage);
 })
-sortColumn = "elapsed_days"
+sortCol1 = "stage"
+sortCol2 = "elapsed_days"
 
-// This sorts in reverse order:
+// Sorts by both stage and elapsed days:
 filteredSorted = filtered.sort((a, b) => {
-  if (a[sortColumn] < b[sortColumn]) {
-    return 1;
-  }
-  if (a[sortColumn] > b[sortColumn]) {
-    return -1;
-  }
-  return 0;
+    if (a[sortCol1] > b[sortCol1]) {
+        return 1;
+    } else if (a[sortCol1] < b[sortCol1]) {
+        return -1;
+    } else {
+        if (a[sortCol2] < b[sortCol2]) {
+            return 1;
+        } else if (a[sortCol2] > b[sortCol2]) {
+            return -1;
+        }
+    }
+    return 0;
 });
 ```
 
@@ -177,7 +191,6 @@ nope
 ```{ojs}
 // And this uses the 'reviewTable' function defined in the above file to
 // generate an Observable Inputs.table with coloured rows.
-console.log("----filteredSorted: ", filteredSorted)
 columns = ["stage", "number", "title", "stats", "stage_date", "editor", "inactive_for"]
 reviewTable(filteredSorted,
   {

From ac40f6a8ca2e6c2b8a75b65508bba6153916db73 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:16:24 +0200
Subject: [PATCH 05/17] linewrap titles in reviews table for #12

---
 DESCRIPTION               |  2 +-
 codemeta.json             |  2 +-
 quarto/_colorTable_fn.qmd |  2 +-
 quarto/reviews.qmd        | 15 ++++++++++++---
 4 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9358eb5..74f8400 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.028
+Version: 0.1.8.029
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index bde8db2..dbe0ea8 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.028",
+  "version": "0.1.8.029",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/_colorTable_fn.qmd b/quarto/_colorTable_fn.qmd
index 7cd2250..3b36796 100644
--- a/quarto/_colorTable_fn.qmd
+++ b/quarto/_colorTable_fn.qmd
@@ -107,7 +107,7 @@ function reviewTable(data, {
       ...format,
       [colorColumn]: d => htl.html`<div style="--row-color:${d}">`,
       [issueNumColumn]: d => htl.html`<a href="https://github.com/ropensci/software-review/issues/${d}">${d}</a>`,
-      [titleColumn]: d => htl.html`<a href="https://github.com/ropensci/software-review/issues/${d[1]}">${d[0]}</a>`,
+      [titleColumn]: d => htl.html`<span style="white-space:break-spaces;"><a href="https://github.com/ropensci/software-review/issues/${d[1]}">${d[0]}</a></span>`,
     },
     columns,
     ...options
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 8f21ee5..37868af 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -39,6 +39,7 @@ cat (paste0 (
 
 ```{r add-html-to-table, echo = FALSE}
 u <- "https://github.com/ropensci/software-review/issues/"
+rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
 dat <- rev_dat
 # Number has to come last here!!
 dat <- dashboard:::add_gt_html (dat, u, "title")
@@ -128,6 +129,7 @@ gt::gt (udat) |>
     dashboard:::add_urgency_cols (c ("urgency", "importance"))
 ```
 
+
 ```{r}
 ojs_define (submissions = rev_dat)
 ```
@@ -186,12 +188,11 @@ filteredSorted = filtered.sort((a, b) => {
 
 {{< include _colorTable_fn.qmd >}}
 
-nope
 
 ```{ojs}
 // And this uses the 'reviewTable' function defined in the above file to
 // generate an Observable Inputs.table with coloured rows.
-columns = ["stage", "number", "title", "stats", "stage_date", "editor", "inactive_for"]
+columns = ["stage_num", "number", "title", "stats", "stage_date", "editor", "inactive_for"]
 reviewTable(filteredSorted,
   {
     colorColumn: "rowColor",
@@ -199,12 +200,20 @@ reviewTable(filteredSorted,
     titleColumn: "title",
     columns: columns,
     height: 'auto',
+    layout: 'auto',
+    header: {
+        stage_num: "Stage",
+        number: "Number",
+        title: "Title",
+        stats: "Stats?",
+        stage_date: "Stage date",
+        inactive_for: "Inactive for",
+    }
   }
 )
 ```
 
 
-
 ## 0\/Pre-submission
 
 ```{r dat0, echo = FALSE}

From 0c59390a126364be2614b432077333b033f61447 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:17:21 +0200
Subject: [PATCH 06/17] pre-select only 1st 2 stages of rev table #12

---
 DESCRIPTION        | 2 +-
 codemeta.json      | 2 +-
 quarto/reviews.qmd | 8 ++++----
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 74f8400..f214b01 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.029
+Version: 0.1.8.030
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index dbe0ea8..c3b1691 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.029",
+  "version": "0.1.8.030",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 37868af..40be6fb 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -153,10 +153,10 @@ viewof stage = Inputs.checkbox(
     { value: [
         "0/presubmission",
         "1/editor-checks",
-        "2/seeking-reviewer(s)",
-        "3/reviewer(s)-assigned",
-        "4/review(s)-in-awaiting-changes",
-        "5/awaiting-reviewer(s)-response"
+        // "2/seeking-reviewer(s)",
+        // "3/reviewer(s)-assigned",
+        // "4/review(s)-in-awaiting-changes",
+        // "5/awaiting-reviewer(s)-response"
       ],
       label: "Submission Stage:" }
 )

From 6677b54bdc20bc7ca92e3616dae276e0d84db588 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:23:57 +0200
Subject: [PATCH 07/17] add urgency cols to review table #12

---
 DESCRIPTION        | 2 +-
 codemeta.json      | 2 +-
 quarto/reviews.qmd | 5 ++++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f214b01..ceca84f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.030
+Version: 0.1.8.031
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index c3b1691..a48cb2d 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.030",
+  "version": "0.1.8.031",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 40be6fb..3e40fba 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -137,7 +137,10 @@ ojs_define (submissions = rev_dat)
 submissionsIn = {
     return transpose(submissions).map(row => ({
         ...row,
-        rowColor: row.submission_type === "Stats" ? "yellow" : "transparent",
+        rowColor: row.urgency === 1 ? "#FFFF8088" :
+            row.urgency === 2 ? "#FFAA8088" :
+            row.urgency === 3 ? "#FF550088" :
+            row.urgency === 4 ? "#FF000088" : "transparent",
     }));
 }
 ```

From 76db42d8fa9272329c555cffe6ec141773e850ad Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:33:27 +0200
Subject: [PATCH 08/17] add .js urgency col code table for #12

The js colors are rendered quite differently from the gt equivalents via R,
so it's important to render this rather than gt, to properly match versions
rendered in Observable.
---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 42 +++++++++++++++++++++++++++++++++++++-----
 3 files changed, 39 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ceca84f..0677681 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.031
+Version: 0.1.8.032
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index a48cb2d..b4a6478 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.031",
+  "version": "0.1.8.032",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 3e40fba..bdfd0d5 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -125,22 +125,54 @@ udat <- data.frame (
         "very high"
     )
 )
-gt::gt (udat) |>
-    dashboard:::add_urgency_cols (c ("urgency", "importance"))
 ```
 
 
 ```{r}
 ojs_define (submissions = rev_dat)
+# And define dummy data for urgency color scheme:
+urgency_dat <- data.frame (
+    urgency = 1:5,
+    importance = c (
+        "low",
+        "moderate",
+        "medium",
+        "high",
+        "very high"
+    )
+)
+ojs_define (urgency = urgency_dat)
 ```
+
+```{ojs}
+urgencyDat = transpose(urgency).map(row => ({
+    ...row,
+    rowColor: row.urgency === 1 ? "#FFFF8088" :
+        row.urgency === 2 ? "#FFFF0088" :
+        row.urgency === 3 ? "#FFAA0088" :
+        row.urgency === 4 ? "#FF550088" :
+        row.urgency === 5 ? "#FF000088" : "transparent",
+}));
+```
+
+```{ojs}
+colorTable(urgencyDat, {
+    columns: ["urgency", "importance"],
+    colorColumn: "rowColor",
+})
+```
+
+
+
 ```{ojs}
 submissionsIn = {
     return transpose(submissions).map(row => ({
         ...row,
         rowColor: row.urgency === 1 ? "#FFFF8088" :
-            row.urgency === 2 ? "#FFAA8088" :
-            row.urgency === 3 ? "#FF550088" :
-            row.urgency === 4 ? "#FF000088" : "transparent",
+            row.urgency === 2 ? "#FFFF0088" :
+            row.urgency === 3 ? "#FFAA0088" :
+            row.urgency === 4 ? "#FF550088" :
+            row.urgency === 5 ? "#FF000088" : "transparent",
     }));
 }
 ```

From b2e513d166f7b98f91051c61d122afe06e7ed78d Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:38:03 +0200
Subject: [PATCH 09/17] rm old stage-by-stage rev code for #12

---
 DESCRIPTION        |   2 +-
 codemeta.json      |   2 +-
 quarto/reviews.qmd | 205 ---------------------------------------------
 3 files changed, 2 insertions(+), 207 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0677681..dc7995f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.032
+Version: 0.1.8.033
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index b4a6478..5c8bd1d 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.032",
+  "version": "0.1.8.033",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index bdfd0d5..f31927f 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -247,208 +247,3 @@ reviewTable(filteredSorted,
   }
 )
 ```
-
-
-## 0\/Pre-submission
-
-```{r dat0, echo = FALSE}
-dat0 <- dat [which (dat$submission_type == "Pre-submission"), ]
-n_lab <- length (which (!is.na (dat0$stage)))
-n_nolab <- length (which (is.na (dat0$stage)))
-v_lab <- ifelse (n_lab == 1L, "is", "are")
-v_nolab <- ifelse (n_nolab == 1L, "is", "are")
-i_lab <- ifelse (n_lab == 1L, "issue", "issues")
-i_nolab <- ifelse (n_nolab == 1L, "issue", "issues")
-```
-
-There `r v_lab` `r n_lab` labelled pre-submission `r i_lab`, and `r n_nolab`
-unlabelled `r i_nolab`. Data on the labelled `r i_lab` are:
-
-```{r presub-table-prepro, echo = FALSE}
-keep <- c (
-    "number", "title", "state", "stats", "stage_date", "editor",
-    "elapsed", "elapsed_days", "urgency"
-)
-dat0_lab <- dat0 [which (!is.na (dat0$stage)) [1], keep, drop = FALSE]
-dat0_lab <- dplyr::rename (dat0_lab, "inactive_for" = elapsed) |>
-    dplyr::arrange (dplyr::desc (elapsed_days))
-dat0_lab$editor [which (!nzchar (dat0_lab$editor))] <- "(None)"
-has_presub <- nrow (dat0_lab) > 0
-
-urgency_cols <- c ("number", "title", "state")
-```
-
-
-::: {style="all.initial;"}
-```{r presub-table-lab, echo = FALSE, eval = has_presub}
-gt::gt (dat0_lab) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-presub-lab, echo = FALSE, results = "asis", eval = !has_presub}
-cat ("There are currently no submissions at this stage.")
-```
-
-```{r presub-nolab-prepro, echo = FALSE, results = "asis"}
-dat0_nolab <- dat0 [which (is.na (dat0$stage)), keep, drop = FALSE]
-dat0_nolab <- dplyr::rename (dat0_nolab, "inactive_for" = elapsed) |>
-    dplyr::arrange (dplyr::desc (elapsed_days))
-has_presub_nolab <- nrow (dat0_nolab) > 0
-if (has_presub_nolab) {
-    dat0_nolab$editor [which (!nzchar (dat0_nolab$editor))] <- "(None)"
-    cat ("Data on the unlabelled ", i_nolab, " are:")
-}
-```
-
-
-::: {style="all.initial;"}
-```{r presub-table-nolab, echo = FALSE, eval = has_presub_nolab}
-gt::gt (dat0_nolab) |>
-    gt::cols_hide (c (urgency, state, stage_date, editor, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-## 1\/Editor Checks
-
-```{r ed-check-prepro, echo = FALSE}
-# From that point on, data for all stages can be pre-processed with this
-# generic function.
-preprocess_one_stage <- function (dat, stage = 1) {
-    ptn <- paste0 ("^", stage)
-    dat_stage <- dat [grep (ptn, dat$stage), keep, drop = FALSE]
-    dat_stage <- dplyr::rename (dat_stage, "inactive_for" = elapsed) |>
-        dplyr::arrange (dplyr::desc (elapsed_days))
-    dat_stage$editor [which (!nzchar (dat_stage$editor))] <- "(None)"
-    return (dat_stage)
-}
-dat1 <- preprocess_one_stage (dat, 1)
-has_ed_checks <- nrow (dat1) > 0L
-```
-
-
-::: {style="all.initial;"}
-```{r ed-check-table, echo = FALSE, eval = has_ed_checks}
-gt::gt (dat1) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-ed-checks, echo = FALSE, results = "asis", eval = !has_ed_checks}
-cat ("There are currently no submissions at this stage.")
-```
-
-
-## 2\/Seeking Reviewers
-
-```{r seek-rev-prepro, echo = FALSE}
-dat2 <- preprocess_one_stage (dat, 2)
-has_seek_rev <- nrow (dat2) > 0L
-```
-
-::: {style="all.initial;"}
-```{r seek-rev-table, echo = FALSE, eval = has_seek_rev}
-gt::gt (dat2) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-seek-rev, echo = FALSE, results = "asis", eval = !has_seek_rev}
-cat ("There are currently no submissions at this stage.")
-```
-
-## 3\/Reviewer(s) Assigned
-
-```{r rev-assign-prepro, echo = FALSE}
-dat3 <- preprocess_one_stage (dat, 3)
-has_rev_assign <- nrow (dat3) > 0L
-```
-
-::: {style="all.initial;"}
-```{r rev-assign-table, echo = FALSE, eval = has_rev_assign}
-gt::gt (dat3) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-rev-assign, echo = FALSE, results = "asis", eval = !has_rev_assign}
-cat ("There are currently no submissions at this stage.")
-```
-
-## 4\/Review(s) in Awaiting Changes
-
-```{r revs-in-prepro, echo = FALSE}
-dat4 <- preprocess_one_stage (dat, 4)
-has_rev_in <- nrow (dat4) > 0L
-```
-
-::: {style="all.initial;"}
-```{r revs-in-table, echo = FALSE, eval = has_rev_in}
-gt::gt (dat4) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-revs-in, echo = FALSE, results = "asis", eval = !has_rev_in}
-cat ("There are currently no submissions at this stage.")
-```
-
-## 5\/Awaiting Reviewer(s) Response
-
-```{r await-rev-resp-prepro, echo = FALSE}
-dat5 <- preprocess_one_stage (dat, 5)
-has_rev_in <- nrow (dat5) > 0L
-```
-
-::: {style="all.initial;"}
-```{r await-rev-resp-table, echo = FALSE, eval = has_rev_in}
-gt::gt (dat5) |>
-    gt::cols_hide (c (urgency, state, elapsed_days)) |>
-    dashboard:::add_urgency_cols (urgency_cols) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-await-rev-resp, echo = FALSE, results = "asis", eval = !has_rev_in}
-cat ("There are currently no submissions at this stage.")
-```
-
-## Holding
-
-```{r holding-prepro, echo = FALSE}
-# Change 'elapsed' to time since 'holding' label applied:
-date_vec <- lubridate::ymd_hms (dat_holding$holding_date)
-hold_elapsed <- dashboard:::get_elapsed_time (date_vec)
-
-dat_holding$elapsed <- hold_elapsed$dtime
-dat_holding$elapsed_days <- hold_elapsed$dtime_days
-hold_cols <- c ("number", "title", "stats", "stage", "elapsed", "elapsed_days")
-dat_holding <- dplyr::select (dat_holding, dplyr::all_of (hold_cols)) |>
-    dplyr::rename ("on_hold_for" = elapsed) |>
-    dplyr::arrange (dplyr::desc (elapsed_days))
-has_on_hold <- nrow (dat_holding) > 0L
-```
-
-::: {style="all.initial;"}
-```{r on-hold-table, echo = FALSE, eval = has_on_hold}
-gt::gt (dat_holding) |>
-    gt::cols_hide (c (elapsed_days)) |>
-    dashboard:::add_bg_colours ()
-```
-:::
-
-```{r no-on-hold, echo = FALSE, results = "asis", eval = !has_on_hold}
-cat ("There are currently no submissions on hold.")
-```

From dc0fa235925d96506c5c44aed1acf5181d4b3efb Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:42:49 +0200
Subject: [PATCH 10/17] rm old R code from rev table #12

---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 37 +++++--------------------------------
 3 files changed, 7 insertions(+), 34 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index dc7995f..d935ff7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.033
+Version: 0.1.8.034
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 5c8bd1d..c64e877 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.033",
+  "version": "0.1.8.034",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index f31927f..fedfba7 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -37,22 +37,14 @@ cat (paste0 (
 ```
 
 
-```{r add-html-to-table, echo = FALSE}
-u <- "https://github.com/ropensci/software-review/issues/"
-rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
-dat <- rev_dat
-# Number has to come last here!!
-dat <- dashboard:::add_gt_html (dat, u, "title")
-dat <- dashboard:::add_gt_html (dat, u, "number")
-```
-
 ```{r add-urgency-column, echo = FALSE}
+rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
 # Then create an "urgency" column used to highlight rows needing urgent
 # attention. Note that colours have to be individually hand-coded in the
 # `gt` code below, so use of any value other than `ncols = 5` requires the
 # subsequent colors to be re-coded.
 ncols <- 5L
-dat$urgency <- rev_dat$urgency <- 0L
+rev_dat$urgency <- 0L
 
 # time scales for each stage, in days
 time_scales <- list (
@@ -64,17 +56,12 @@ time_scales <- list (
     c (5, 21) # reviewer responses
 )
 for (i in time_scales) {
-    index <- grep (paste0 ("^", i [1]), dat$stage)
-    dat$urgency [index] <-
-        floor (as.numeric (dat$elapsed_days [index]) / i [2])
+    index <- grep (paste0 ("^", i [1]), rev_dat$stage)
     rev_dat$urgency [index] <-
         floor (as.numeric (rev_dat$elapsed_days [index]) / i [2])
 }
 
-dat$urgency [dat$urgency > ncols] <- ncols
-dat$urgency [grepl ("holding", dat$labels)] <- 0
-dat_holding <- dat [grep ("holding", dat$labels), ] # Done at end
-dat <- dat [which (!grepl ("holding", dat$labels)), ]
+dat_holding <- rev_dat [grep ("holding", rev_dat$labels), ] # TODO: Include these
 
 rev_dat$urgency [rev_dat$urgency > ncols] <- ncols
 rev_dat$urgency [grepl ("holding", rev_dat$labels)] <- 0
@@ -83,7 +70,7 @@ rev_dat <- dplyr::rename (rev_dat, "inactive_for" = elapsed)
 ```
 
 ```{r dat-stages, echo = FALSE}
-sub_types <- table (dat$submission_type)
+sub_types <- table (rev_dat$submission_type)
 ```
 
 There are currently:<br>
@@ -113,20 +100,6 @@ under review (stage `3\/Reviewer(s) Assigned`) for 12 weeks would have an
 urgency of `floor(12 * 7 / 21) = 4`. The colour codes for these urgency levels
 are shown in the following table.
 
-```{r colour-scheme, echo = FALSE}
-cols <- dashboard:::define_urgency_colours ()
-udat <- data.frame (
-    urgency = seq_along (cols),
-    importance = c (
-        "low",
-        "moderate",
-        "medium",
-        "high",
-        "very high"
-    )
-)
-```
-
 
 ```{r}
 ojs_define (submissions = rev_dat)

From 2c323faa46fbd785ceb803de0e2ae50f24ceb401 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 14:47:01 +0200
Subject: [PATCH 11/17] mv explanation of urgency to end of reviews #12

---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 46 ++++++++++++++++++++++++++--------------------
 3 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d935ff7..ed51ff6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.034
+Version: 0.1.8.035
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index c64e877..2b30f95 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.034",
+  "version": "0.1.8.035",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index fedfba7..d2f62b2 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -79,26 +79,8 @@ There are currently:<br>
 - `r sub_types [["Standard"]]` standard issues<br>
 - `r sub_types [["Stats"]]` stats issues
 
-Some cells in the following tables are highlighted to visually indicate the
-following degrees of urgency. Levels of urgency depend on the review stage.
-Approximate expected times required to complete each stage are:
-
-stage | time (days)
---- | ---
-0\/Pre-submission | 7
-1\/Editor Checks | 7
-2\/Seeking Reviewers | 14
-3\/Reviewer(s) Assigned | 21
-4\/Review(s) in Awaiting Changes | 21
-5\/Awaiting Reviewer(s) Response | 21
-
-Levels of urgency for each review are times taken for current stage as
-a multiple of those base times, with values rounded *down* to nearest integer.
-For example, a submission which has been undergoing `1\/Editor Checks` for 17
-days would have an urgency of `floor(17/7) = 2`. A submission which has been
-under review (stage `3\/Reviewer(s) Assigned`) for 12 weeks would have an
-urgency of `floor(12 * 7 / 21) = 4`. The colour codes for these urgency levels
-are shown in the following table.
+Some cells in the following table are highlighted to visually indicate the
+following degrees of urgency:
 
 
 ```{r}
@@ -135,6 +117,7 @@ colorTable(urgencyDat, {
 })
 ```
 
+The levels of urgency used in this table are explained at the end.
 
 
 ```{ojs}
@@ -220,3 +203,26 @@ reviewTable(filteredSorted,
   }
 )
 ```
+
+## Urgency of Reviews
+
+
+Levels of urgency depend on the review stage. Approximate expected times
+required to complete each stage are:
+
+stage | time (days)
+--- | ---
+0\/Pre-submission | 7
+1\/Editor Checks | 7
+2\/Seeking Reviewers | 14
+3\/Reviewer(s) Assigned | 21
+4\/Review(s) in Awaiting Changes | 21
+5\/Awaiting Reviewer(s) Response | 21
+
+Levels of urgency for each review are times taken for current stage as
+a multiple of those base times, with values rounded *down* to nearest integer.
+For example, a submission which has been undergoing `1\/Editor Checks` for 17
+days would have an urgency of `floor(17/7) = 2`. A submission which has been
+under review (stage `3\/Reviewer(s) Assigned`) for 12 weeks would have an
+urgency of `floor(12 * 7 / 21) = 4`. These urgency levels define the colour
+codes shown at the top of this page.

From c1c4da39f0f8b44cf8a5e44ebbe0081fc6a6dec4 Mon Sep 17 00:00:00 2001
From: mark padgham <mark.padgham@email.com>
Date: Mon, 22 Apr 2024 21:53:12 +0200
Subject: [PATCH 12/17] no, do not run publish workflow on PR

---
 .github/workflows/publish.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index a433f64..0ca1416 100644
--- a/.github/workflows/publish.yaml
+++ b/.github/workflows/publish.yaml
@@ -2,8 +2,6 @@ on:
   workflow_dispatch:
   push:
     branches: main
-  pull_request:
-    branches: main
   schedule:
     - cron: 0 0 * * *
 

From 42c3b346cf46e30c66aa183d05f08fbc86c37979 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Tue, 23 Apr 2024 11:39:07 +0200
Subject: [PATCH 13/17] rm 'gt' pkg dep from reviews page for #12

---
 DESCRIPTION        | 2 +-
 codemeta.json      | 2 +-
 quarto/reviews.qmd | 7 +++----
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ed51ff6..db3114c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.035
+Version: 0.1.8.036
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 2b30f95..444f6a1 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.035",
+  "version": "0.1.8.036",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index d2f62b2..9fa8083 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -11,7 +11,6 @@ format:
 
 ```{r load-pkg-rev, echo = FALSE, message = FALSE}
 library (dashboard)
-library (gt)
 ```
 
 ```{r get-rev-dat, echo = FALSE}
@@ -40,9 +39,9 @@ cat (paste0 (
 ```{r add-urgency-column, echo = FALSE}
 rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
 # Then create an "urgency" column used to highlight rows needing urgent
-# attention. Note that colours have to be individually hand-coded in the
-# `gt` code below, so use of any value other than `ncols = 5` requires the
-# subsequent colors to be re-coded.
+# attention. Note that colours have to be individually hand-coded below, so
+# use of any value other than `ncols = 5` requires the subsequent colors to
+# be re-coded.
 ncols <- 5L
 rev_dat$urgency <- 0L
 

From d479b073b95cef56ec19e47ab886a4cfed5ed999 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Tue, 23 Apr 2024 11:42:01 +0200
Subject: [PATCH 14/17] fix final 'issue(s)' word on initial review summary #12

---
 DESCRIPTION        | 2 +-
 codemeta.json      | 2 +-
 quarto/reviews.qmd | 9 ++++++---
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index db3114c..d3bff64 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.036
+Version: 0.1.8.037
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 444f6a1..7cf05a2 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.036",
+  "version": "0.1.8.037",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 9fa8083..cbc5cdb 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -70,13 +70,16 @@ rev_dat <- dplyr::rename (rev_dat, "inactive_for" = elapsed)
 
 ```{r dat-stages, echo = FALSE}
 sub_types <- table (rev_dat$submission_type)
+sub_type_end <- rep ("issue", length (sub_types))
+sub_type_end [sub_types > 1] <- "issues"
+names (sub_type_end) <- names (sub_types)
 ```
 
 There are currently:<br>
 
-- `r sub_types [["Pre-submission"]]` pre-submission issues<br>
-- `r sub_types [["Standard"]]` standard issues<br>
-- `r sub_types [["Stats"]]` stats issues
+- `r sub_types [["Pre-submission"]]` pre-submission `r sub_type_end [["Pre-submission"]]`<br>
+- `r sub_types [["Standard"]]` standard `r sub_type_end [["Standard"]]`<br>
+- `r sub_types [["Stats"]]` stats `r sub_type_end [["Stats"]]`
 
 Some cells in the following table are highlighted to visually indicate the
 following degrees of urgency:

From b7985c3540380a0efc9bbf8bf82a7a028176aad6 Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Tue, 23 Apr 2024 12:31:05 +0200
Subject: [PATCH 15/17] style checkboxes in review page for #12

---
 DESCRIPTION        |   2 +-
 codemeta.json      |   2 +-
 quarto/reviews.qmd | 111 +++++++++++++++++++++++++++------------------
 3 files changed, 68 insertions(+), 47 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d3bff64..7373cbe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.037
+Version: 0.1.8.038
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 7cf05a2..73be9f3 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.037",
+  "version": "0.1.8.038",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index cbc5cdb..c40cf66 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -75,14 +75,16 @@ sub_type_end [sub_types > 1] <- "issues"
 names (sub_type_end) <- names (sub_types)
 ```
 
-There are currently:<br>
+rOpenSci software peer-review is currently handling:<br>
 
 - `r sub_types [["Pre-submission"]]` pre-submission `r sub_type_end [["Pre-submission"]]`<br>
 - `r sub_types [["Standard"]]` standard `r sub_type_end [["Standard"]]`<br>
 - `r sub_types [["Stats"]]` stats `r sub_type_end [["Stats"]]`
 
-Some cells in the following table are highlighted to visually indicate the
-following degrees of urgency:
+The following table provides details of each issue, defined by the "Submission
+Stage" listed in the check-boxes. Some rows in the table are highlighted to
+visually indicate the following degrees of urgency according to the scheme
+defined below.
 
 
 ```{r}
@@ -101,60 +103,59 @@ urgency_dat <- data.frame (
 ojs_define (urgency = urgency_dat)
 ```
 
-```{ojs}
-urgencyDat = transpose(urgency).map(row => ({
-    ...row,
-    rowColor: row.urgency === 1 ? "#FFFF8088" :
-        row.urgency === 2 ? "#FFFF0088" :
-        row.urgency === 3 ? "#FFAA0088" :
-        row.urgency === 4 ? "#FF550088" :
-        row.urgency === 5 ? "#FF000088" : "transparent",
-}));
-```
 
 ```{ojs}
-colorTable(urgencyDat, {
-    columns: ["urgency", "importance"],
-    colorColumn: "rowColor",
-})
-```
-
-The levels of urgency used in this table are explained at the end.
+urgency_colours = ["#FFFF8088", "#FFFF0088", "#FFAA0088", "#FF550088", "#FF000088"]
 
-
-```{ojs}
 submissionsIn = {
     return transpose(submissions).map(row => ({
         ...row,
-        rowColor: row.urgency === 1 ? "#FFFF8088" :
-            row.urgency === 2 ? "#FFFF0088" :
-            row.urgency === 3 ? "#FFAA0088" :
-            row.urgency === 4 ? "#FF550088" :
-            row.urgency === 5 ? "#FF000088" : "transparent",
+        rowColor: row.urgency === 1 ? urgency_colours[0] :
+            row.urgency === 2 ? urgency_colours[1] :
+            row.urgency === 3 ? urgency_colours[2] :
+            row.urgency === 4 ? urgency_colours[3] :
+            row.urgency === 5 ? urgency_colours[4] : "transparent",
     }));
 }
 ```
 ```{ojs}
-viewof stage = Inputs.checkbox(
-    ["0/presubmission",
-     "1/editor-checks",
-     "2/seeking-reviewer(s)",
-     "3/reviewer(s)-assigned",
-     "4/review(s)-in-awaiting-changes",
-     "5/awaiting-reviewer(s)-response"
-    ],
-    { value: [
-        "0/presubmission",
-        "1/editor-checks",
-        // "2/seeking-reviewer(s)",
-        // "3/reviewer(s)-assigned",
-        // "4/review(s)-in-awaiting-changes",
-        // "5/awaiting-reviewer(s)-response"
-      ],
-      label: "Submission Stage:" }
-)
+viewof stage = {
+    const input =  Inputs.checkbox(
+        ["0/presubmission",
+         "1/editor-checks",
+         "2/seeking-reviewer(s)",
+         "3/reviewer(s)-assigned",
+         "4/review(s)-in-awaiting-changes",
+         "5/awaiting-reviewer(s)-response"
+        ],
+        {
+            value: [
+                "0/presubmission",
+                "1/editor-checks",
+                // "2/seeking-reviewer(s)",
+                // "3/reviewer(s)-assigned",
+                // "4/review(s)-in-awaiting-changes",
+                // "5/awaiting-reviewer(s)-response"
+            ],
+            label: htl.html`<b>Submission Stage:<b>`,
+        }
+    );
+
+    // Modification ideas from
+    // https://talk.observablehq.com/t/what-is-the-best-way-to-style-an-input-checkbox/7690/2
+    const scope = DOM.uid().id;
+    input.classList.add(scope);
+
+    input.append(htl.html`<style>
+    .${scope} > div, .${scope} > div label { display: flex; flex-wrap: wrap; gap: 10px; width: 300px }
+    `)
+
+    return input;
+}
 ```
 
+<br>
+
 ```{ojs}
 filtered = submissionsIn.filter(function(submission) {
   return stage.includes(submission.stage);
@@ -208,6 +209,26 @@ reviewTable(filteredSorted,
 
 ## Urgency of Reviews
 
+```{ojs}
+urgencyDat = transpose(urgency).map(row => ({
+    ...row,
+    rowColor: row.urgency === 1 ? urgency_colours[0] :
+        row.urgency === 2 ? urgency_colours[1] :
+        row.urgency === 3 ? urgency_colours[2] :
+        row.urgency === 4 ? urgency_colours[3] :
+        row.urgency === 5 ? urgency_colours[4] : "transparent",
+}));
+```
+
+```{ojs}
+colorTable(urgencyDat, {
+    columns: ["urgency", "importance"],
+    colorColumn: "rowColor",
+})
+```
+
+The levels of urgency used in this table are explained at the end. Rows with no
+highlight may be considered up-to-date, and require no action.
 
 Levels of urgency depend on the review stage. Approximate expected times
 required to complete each stage are:

From 29d0e8a0fe35a09d2f743fe5385cd008ba405add Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Tue, 23 Apr 2024 13:10:42 +0200
Subject: [PATCH 16/17] implement 'holding' filter for reviews page #12

---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 57 +++++++++++++++++++++++++++++++++++-----------
 3 files changed, 46 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7373cbe..6c5222a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.038
+Version: 0.1.8.039
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 73be9f3..8a0d9ad 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.038",
+  "version": "0.1.8.039",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index c40cf66..4927cd0 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -19,7 +19,11 @@ rev_dat <- review_status (open_only = TRUE, browse = FALSE, quiet = TRUE)
 has_multiple_stages <- !is.null (attr (rev_dat, "multiple_stages"))
 ```
 
+## Current Reviews
+
 ```{r multiple-stages, eval = has_multiple_stages, echo = FALSE, results = "asis"}
+# Chunk to print details of any reviews which have multiple stage labels.
+# If there are none, this chunk has no effect.
 stages <- attr (rev_dat, "multiple_stages")
 u <- "https://github.com/ropensci/software-review/issues/"
 stages <- paste0 ("[", stages, "](", u, stages, ")")
@@ -37,11 +41,11 @@ cat (paste0 (
 
 
 ```{r add-urgency-column, echo = FALSE}
-rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
-# Then create an "urgency" column used to highlight rows needing urgent
+# This chunk creates an "urgency" column used to highlight rows needing urgent
 # attention. Note that colours have to be individually hand-coded below, so
 # use of any value other than `ncols = 5` requires the subsequent colors to
 # be re-coded.
+rev_dat$stage_num <- as.integer (substr (rev_dat$stage, 1, 1))
 ncols <- 5L
 rev_dat$urgency <- 0L
 
@@ -69,6 +73,7 @@ rev_dat <- dplyr::rename (rev_dat, "inactive_for" = elapsed)
 ```
 
 ```{r dat-stages, echo = FALSE}
+# Chunk to derive values to be printed in the text strings that follow:
 sub_types <- table (rev_dat$submission_type)
 sub_type_end <- rep ("issue", length (sub_types))
 sub_type_end [sub_types > 1] <- "issues"
@@ -82,9 +87,17 @@ rOpenSci software peer-review is currently handling:<br>
 - `r sub_types [["Stats"]]` stats `r sub_type_end [["Stats"]]`
 
 The following table provides details of each issue, defined by the "Submission
-Stage" listed in the check-boxes. Some rows in the table are highlighted to
-visually indicate the following degrees of urgency according to the scheme
-defined below.
+Stage" listed in the check-boxes. There is also a "Holding" check box which can
+be used to inspect reviews which are currently on hold. Some rows in the table
+are highlighted to visually indicate degrees of urgency according to the scheme
+defined in the following sub-section. Rows with no highlight may be considered
+up-to-date, and require no action.
+
+```{r rev-dat-prepro}
+# Final pre-processing to add 'holding' column
+rev_dat$holding <- grepl ("holding", rev_dat$labels)
+```
+
 
 
 ```{r}
@@ -137,7 +150,7 @@ viewof stage = {
                 // "4/review(s)-in-awaiting-changes",
                 // "5/awaiting-reviewer(s)-response"
             ],
-            label: htl.html`<b>Submission Stage:<b>`,
+            label: htl.html`<b>Submission Stage:</b>`,
         }
     );
 
@@ -154,11 +167,24 @@ viewof stage = {
 }
 ```
 
-<br>
+<div style="margin-top: 20px; margin-bottom: 20px;"></div>
+
+```{ojs}
+viewof holding = Inputs.checkbox(
+    [true, false],
+    {
+        value: [false],
+        label: htl.html`<b>Holding:</b>`,
+    }
+)
+```
+
+<div style="margin-top: 20px; margin-bottom: 20px;"></div>
 
 ```{ojs}
 filtered = submissionsIn.filter(function(submission) {
-  return stage.includes(submission.stage);
+  return stage.includes(submission.stage) &&
+    holding.includes(submission.holding)
 })
 sortCol1 = "stage"
 sortCol2 = "elapsed_days"
@@ -207,8 +233,14 @@ reviewTable(filteredSorted,
 )
 ```
 
+<br>
+
+
 ## Urgency of Reviews
 
+Levels of urgency used in the previous table are coloured according to the
+following scheme:
+
 ```{ojs}
 urgencyDat = transpose(urgency).map(row => ({
     ...row,
@@ -227,9 +259,6 @@ colorTable(urgencyDat, {
 })
 ```
 
-The levels of urgency used in this table are explained at the end. Rows with no
-highlight may be considered up-to-date, and require no action.
-
 Levels of urgency depend on the review stage. Approximate expected times
 required to complete each stage are:
 
@@ -242,10 +271,12 @@ stage | time (days)
 4\/Review(s) in Awaiting Changes | 21
 5\/Awaiting Reviewer(s) Response | 21
 
+<div style="margin-top: 20px; margin-bottom: 20px;"></div>
+
 Levels of urgency for each review are times taken for current stage as
 a multiple of those base times, with values rounded *down* to nearest integer.
 For example, a submission which has been undergoing `1\/Editor Checks` for 17
 days would have an urgency of `floor(17/7) = 2`. A submission which has been
 under review (stage `3\/Reviewer(s) Assigned`) for 12 weeks would have an
-urgency of `floor(12 * 7 / 21) = 4`. These urgency levels define the colour
-codes shown at the top of this page.
+urgency of `floor(12 * 7 / 21) = 4`. These urgency levels then map on to the
+colour codes shown above.

From 6657b0282c60133bdd6f17fdee5f105301bfe93d Mon Sep 17 00:00:00 2001
From: mpadge <mark.padgham@email.com>
Date: Tue, 23 Apr 2024 13:27:43 +0200
Subject: [PATCH 17/17] add 'sortBy' radio button stage/urgency for #12

---
 DESCRIPTION        |  2 +-
 codemeta.json      |  2 +-
 quarto/reviews.qmd | 45 +++++++++++++++++++++++++++++++++------------
 3 files changed, 35 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6c5222a..1fe24d0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dashboard
 Title: What the Package Does (One Line, Title Case)
-Version: 0.1.8.039
+Version: 0.1.8.040
 Authors@R: 
   person(given = "First",
          family = "Last",
diff --git a/codemeta.json b/codemeta.json
index 8a0d9ad..f3b5ab4 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -6,7 +6,7 @@
   "name": "dashboard: What the Package Does (One Line, Title Case)",
   "codeRepository": "https://github.com/ropensci-review-tools/dashboard",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.1.8.039",
+  "version": "0.1.8.040",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
diff --git a/quarto/reviews.qmd b/quarto/reviews.qmd
index 4927cd0..0208ad4 100644
--- a/quarto/reviews.qmd
+++ b/quarto/reviews.qmd
@@ -86,16 +86,23 @@ rOpenSci software peer-review is currently handling:<br>
 - `r sub_types [["Standard"]]` standard `r sub_type_end [["Standard"]]`<br>
 - `r sub_types [["Stats"]]` stats `r sub_type_end [["Stats"]]`
 
-The following table provides details of each issue, defined by the "Submission
-Stage" listed in the check-boxes. There is also a "Holding" check box which can
-be used to inspect reviews which are currently on hold. Some rows in the table
-are highlighted to visually indicate degrees of urgency according to the scheme
-defined in the following sub-section. Rows with no highlight may be considered
-up-to-date, and require no action.
+The following table provides details of each issue, with results filtered by
+the following controls:
+
+- "Submission Stage" to list issues with the specified stage.
+- "Holding" to list issues which are on hold (true) or not (false).
+- "Sort By" to sort results either by the Submission Stage ("stage", 0-5), or
+  "urgency", as described below.
+
+Some rows in the table are highlighted to visually indicate degrees of urgency
+according to the scheme defined in the following sub-section. Rows with no
+highlight may be considered up-to-date, and require no action.
 
 ```{r rev-dat-prepro}
-# Final pre-processing to add 'holding' column
+# Final pre-processing to add 'holding' column, and an 'urgency_rev' column so
+# urgency can be sorted via same code as stage.
 rev_dat$holding <- grepl ("holding", rev_dat$labels)
+rev_dat$urgency_rev <- max (rev_dat$urgency) - rev_dat$urgency
 ```
 
 
@@ -145,10 +152,10 @@ viewof stage = {
             value: [
                 "0/presubmission",
                 "1/editor-checks",
-                // "2/seeking-reviewer(s)",
-                // "3/reviewer(s)-assigned",
-                // "4/review(s)-in-awaiting-changes",
-                // "5/awaiting-reviewer(s)-response"
+                "2/seeking-reviewer(s)",
+                "3/reviewer(s)-assigned",
+                "4/review(s)-in-awaiting-changes",
+                "5/awaiting-reviewer(s)-response"
             ],
             label: htl.html`<b>Submission Stage:</b>`,
         }
@@ -181,12 +188,26 @@ viewof holding = Inputs.checkbox(
 
 <div style="margin-top: 20px; margin-bottom: 20px;"></div>
 
+```{ojs}
+viewof sortBy = Inputs.radio(
+    ["stage", "urgency"],
+    {
+        value: "stage",
+        label: htl.html`<b>Sort by:</b>`,
+    }
+)
+```
+
+<div style="margin-top: 20px; margin-bottom: 20px;"></div>
+
 ```{ojs}
 filtered = submissionsIn.filter(function(submission) {
   return stage.includes(submission.stage) &&
     holding.includes(submission.holding)
 })
-sortCol1 = "stage"
+// Only sort by urgency if there are any:
+anyUrgent = filtered.some(submission => submission.urgency > 0)
+sortCol1 = sortBy === "stage" ? "stage" : anyUrgent ? "urgency_rev" : "stage"
 sortCol2 = "elapsed_days"
 
 // Sorts by both stage and elapsed days: