Software Review

Current Reviews

rOpenSci software peer-review is currently handling:

2 pre-submission issues
13 standard issues
9 stats issues

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. Submissions which have not yet been given a ‘Stage’ label are listed below as ‘(No stage)’, and highlighted with the highest urgency level.

urgency_colours = ["#FFFF8088", "#FFFF0088", "#FFAA0088", "#FF550088", "#FF000088"]

submissionsIn = {
    return transpose(submissions).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",
    }));
}

urgency_colours = Array(5) ["#FFFF8088", "#FFFF0088", "#FFAA0088", "#FF550088", "#FF000088"]

submissionsIn = Array(24) [Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, …]

viewof stage = {
    const input =  Inputs.checkbox(
        ["(No stage)",
         "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: [
                "(No stage)",
                "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;
}

stage = Array(7) ["(No stage)", "0/presubmission", "1/editor-checks", "2/seeking-reviewer(s)", "3/reviewer(s)-assigned", "4/review(s)-in-awaiting-changes", "5/awaiting-reviewer(s)-response"]

viewof holding = Inputs.checkbox(
    [true, false],
    {
        value: [false],
        label: htl.html`<b>Holding:</b>`,
    }
)

holding = Array(1) [false]

viewof sortBy = Inputs.radio(
    ["stage", "urgency"],
    {
        value: "stage",
        label: htl.html`<b>Sort by:</b>`,
    }
)

sortBy = "stage"

filtered = submissionsIn.filter(function(submission) {
  return stage.includes(submission.stage) &&
    holding.includes(submission.holding)
})
// 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:
filteredSorted = filtered.sort((a, b) => {
    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;
});

filtered = Array(13) [Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object]

anyUrgent = true

sortCol1 = "stage"

sortCol2 = "elapsed_days"

filteredSorted = Array(13) [Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object]

// Definition of colorTable function, adapted from
// https://observablehq.com/@mootari/colored-table-rows
// This can't be placed in a separate file, because that requires importing
// observable/table, but there is no path here to do that import.
function colorTable(data, {
        colorColumn,
        colorOpacity = 0.5,
        editorColumn,
        lastActiveColumn,
        issueNumColumn,
        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
  // "lastActiveColumn" into an array with the issue number and last active
  // string so then pass to the `format` call below to construct <a> href
  // objects:
  const preprocessedData = data.map(row => ({
     ...row,
     [lastActiveColumn]: [row[issueNumColumn],row[lastActiveColumn]]
  }));``

  const form = Inputs.table(preprocessedData, {
    format: {
      ...format,
      [colorColumn]: d => htl.html`<div style="--row-color:${d}">`,
      [editorColumn]: d => htl.html`<a href="https://github.com/${d}">${d}</a>`,
      [lastActiveColumn]: d => htl.html`<a href="https://github.com/ropensci/software-review/issues/${d[0]}">${d[1]}</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;
}

colorTable = ƒ(…)

// 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}">${d}</a>`,
      [titleColumn]: d => htl.html`<span style="white-space:break-spaces;"><a href="https://github.com/ropensci/software-review/issues/${d[1]}">${d[0]}</a></span>`,
    },
    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;
}

reviewTable = ƒ(…)

columns = ["stage_num", "number", "title", "stats", "stage_date", "editor", "inactive_for"]
reviewTable(filteredSorted,
  {
    colorColumn: "rowColor",
    issueNumColumn: "number",
    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",
    },
    format: {
        stage_num: s => s === -1 ? "(No stage)" : s,
    }
  }
)

columns = Array(7) ["stage_num", "number", "title", "stats", "stage_date", "editor", "inactive_for"]

Stage	Number	Title	Stats?	Stage date	editor	Inactive for
(No stage)	702	[Pre-submission Inquiry]: Athlytics	false			1 day
1	645	Capybara	false	2024-12-16	@rkillick	2 months
2	615	galamm: Generalized Additive Latent and Mixed Models	true	2024-09-22	@noamross	2 months
2	706	rixpress: Reproducible Analytical Pipelines with Nix	false	2025-06-10	@ldecicco-USGS	2 weeks
2	703	partialling.out	true	2025-06-05	@nhejazi	2 days
3	667	read.abares - Provides simple downloading, parsing and importing of Australian Bureau of Agricultural and Resource Economics and Sciences (ABARES) data sources	false	2025-05-03	@obrl-soil	3 weeks
3	673	`sasquatch`: Use SAS, R, and Quarto together	false	2025-05-04	@maurolepore	2 days
3	688	distionary: Create and Evaluate Probability Distributions	false	2025-06-10	@helske	1 day
4	685	SSARP: Easily Create Species- and Speciation- Area Relationships Using Web Databases	false	2025-06-12	@jhollist	2 weeks
4	705	trud: Query the 'NHS TRUD API' (full submission)	false	2025-06-18	@emilyriederer	6 days
4	596	SITS: Satellite Image Time Series Analysis for Earth Observation Data Cubes (submit R package for review)	false	2025-05-09	@mpadge	1 day
4	681	dataset: Create Data Frames that are Easier to Exchange and Reuse	false	2025-05-12	@maurolepore	1 day
5	698	PFW: Tools for Filtering and Processing Data from Project FeederWatch	false	2025-06-23	@maelle	1 day

Urgency of Reviews

Levels of urgency used in the previous table are coloured according to the following scheme:

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",
}));

urgencyDat = Array(5) [Object, Object, Object, Object, Object]

colorTable(urgencyDat, {
    columns: ["urgency", "importance"],
    colorColumn: "rowColor",
})

	urgency	importance	rowColor
	1	low
	2	moderate
	3	medium
	4	high
	5	very high

Levels of urgency are calculated from the following expected times for each review stage:

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 then map on to the colour codes shown above.