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Bai-Li-NOAA committed Jun 12, 2024
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8 changes: 8 additions & 0 deletions 404.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions code-of-conduct.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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39 changes: 24 additions & 15 deletions contributor-guidelines.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
Expand Down Expand Up @@ -705,25 +713,26 @@ <h2><span class="header-section-number">7.14</span> Code Review<a href="contribu
which allows reviewers to analyze code changes, provide inline comments,
and view change histories.</p>
<p><a href="https://google.github.io/eng-practices/review/">The Google code review developer guide</a> provides a useful set of guidelines for both reviewers and code authors.</p>
<p>Below is a flowchart for the FIMS code review process. The author starts by submitting
a pull request (PR), ensuring documentation, tests, and CI checks are complete,
then propose a reviewer. The reviewer receives the review request and either
executes the review independently or pairs with another team representative
if assistance is needed. Based on the review, changes may be requested, which
the author must address before approval. Once the PR is approved, the author
merges it into the main branch.</p>
<div id="htmlwidget-735c2f0abfb288ba612f" style="width:672px;height:1000px;" class="DiagrammeR html-widget"></div>
<script type="application/json" data-for="htmlwidget-735c2f0abfb288ba612f">{"x":{"diagram":"\n graph TB\n A[Author: Submit a pull request PR<br/><br/>- Documentation included<br/>- Tests implemented<br/>- CI checks passed]\n B[Author: Propose a reviewer<br/><br/>- Default assignee: an OST rep for a quick review]\n \n A-->B\n B-->C[Reviewer: Receive code review request]\n C --> |No assistance needed| E[Reviewer: Execute code review]\n C --> |Help wanted| D[Reviewer: Add an additional reviewer to the PR] \n D --> E\n E --> |Changes needed| F[Reviewer: Request changes] \n F --> G[Author: Make changes]\n G --> H[Reviewer: Approve PR]\n E --> |No changes needed| H\n H --> I[Author: Rebase and merge PR]\n \n style A text-align:left, fill:#FFF\n style B fill:#FFF\n style G fill:#FFF\n style I fill:#FFF\n"},"evals":[],"jsHooks":[]}</script>
<div id="assigning-reviewers" class="section level3 hasAnchor" number="7.14.1">
<h3><span class="header-section-number">7.14.1</span> Assigning Reviewers<a href="contributor-guidelines.html#assigning-reviewers" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Reviewers for the FIMS Project may be assigned in two different ways:</p>
<ol style="list-style-type: decimal">
<li>A specific member of the FIMS Development Team is requested to review
a pull request, based on their specific expertise.</li>
<li>Code review assignments are automatically assigned using the
<a href="https://docs.github.com/en/organizations/organizing-members-into-teams/managing-code-review-settings-for-your-team">GitHub load balance routing algorithm</a>;
this approach tries to ensure that each team member reviews an equal
number of pull request in any 30 day period.</li>
</ol>
<p>Team members should keep their status in Github current
(see <a href="https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-github-profile/customizing-your-profile/personalizing-your-profile#setting-a-status">“Setting a
status”</a>
for more information). Reviews will not be auto-assigned to “Busy” team
members.</p>
<p>Reviewers of PRs for changes to the codebase in FIMS should be
suggested by the author of the PR. For those FIMS Implementation
Team Members that keep their status in Github current (see <a href="https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-github-profile/customizing-your-profile/personalizing-your-profile#setting-a-status">“Setting
a status”</a>
for more information), authors can use the status information to
prevent assigning a reviewer who is known to be “Busy”.</p>
<p>If a review has been assigned to you and you don’t feel like you have
the expertise to address it properly, please respond directly to the
code owner immediately so a different reviewer can be found promptly.</p>
PR so a different reviewer can be found promptly.</p>
</div>
<div id="automated-testing" class="section level3 hasAnchor" number="7.14.2">
<h3><span class="header-section-number">7.14.2</span> Automated Testing<a href="contributor-guidelines.html#automated-testing" class="anchor-section" aria-label="Anchor link to header"></a></h3>
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8 changes: 8 additions & 0 deletions developer-software-guide.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions documentation-template.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions fims-project-management-process.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions glossary.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions hpp-template-for-c-modules.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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8 changes: 8 additions & 0 deletions index.html
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<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
<script src="libs/d3-3.3.8/d3.min.js"></script>
<script src="libs/dagre-0.4.0/dagre-d3.min.js"></script>
<link href="libs/mermaid-0.3.0/dist/mermaid.css" rel="stylesheet" />
<script src="libs/mermaid-0.3.0/dist/mermaid.slim.min.js"></script>
<link href="libs/DiagrammeR-styles-0.2/styles.css" rel="stylesheet" />
<script src="libs/chromatography-0.1/chromatography.js"></script>
<script src="libs/DiagrammeR-binding-1.0.11/DiagrammeR.js"></script>


<style type="text/css">
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205 changes: 205 additions & 0 deletions libs/DiagrammeR-binding-1.0.11/DiagrammeR.js
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HTMLWidgets.widget({

name: 'DiagrammeR',

type: 'output',

initialize: function(el, width, height) {

/* wait to initialize until renderValue
since x not provided until then
and mermaid will try to build the diagram
as soon as class of the div is set to "mermaid"
*/

/* to prevent auto init() by mermaid
not documented but
see lines https://github.com/knsv/mermaid/blob/master/src/main.js#L100-L109
mermaid_config in global with mermaid_config.startOnLoad = false
appears to turn off the auto init behavior
allowing us to callback after manually init and then callback
after complete
*/
window.mermaid.startOnLoad = false;

// set config options for Gantt
// undocumented but these can be provided
// so from R
// m1 <- mermaid(spec)
// m1$x$config = list(ganttConfig = list( barHeight = 100 ) )
mermaid.ganttConfig = {
titleTopMargin:25,
barHeight:20,
barGap:4,
topPadding:50,
sidePadding:100,
gridLineStartPadding:35,
fontSize:11,
numberSectionStyles:4,
axisFormatter: [
// Within a day
["%I:%M", function (d) {
return d.getHours();
}],
// Monday a week
["w. %U", function (d) {
return d.getDay() == 1;
}],
// Day within a week (not monday)
["%a %d", function (d) {
return d.getDay() && d.getDate() != 1;
}],
// within a month
["%b %d", function (d) {
return d.getDate() != 1;
}],
// Month
["%m-%y", function (d) {
return d.getMonth();
}]
]
};

return {
// TODO: add instance fields as required
}

},

renderValue: function(el, x, instance) {

// if no diagram provided then assume
// that the diagrams are provided through htmltools tags
// and DiagrammeR was just used for dependencies
if ( x.diagram != "" ) {
el.innerHTML = x.diagram;
//if dynamic such as shiny remove data-processed
// so mermaid will reprocess and redraw
el.removeAttribute("data-processed");
el.classList.add('mermaid');
//make sure if shiny that we turn display back on
el.style.display = "";
//again if dynamic such as shiny
// explicitly run mermaid.init()
} else {
// set display to none
// should we remove instead??
el.style.display = "none";
}

// check for undocumented ganttConfig
// to override the defaults manually entered
// in initialize above
// note this is really sloppy and will not
// work well if multiple gantt charts
// with custom configs here
if( typeof x.config !== "undefined" &&
typeof x.config.ganttConfig !== "undefined" ){
Object.keys(x.config.ganttConfig).map(function(k){
window.mermaid.ganttConfig[k] = x.config.ganttConfig[k];
})
}


// use this to sort of make our diagram responsive
// or at a minimum fit within the bounds set by htmlwidgets
// for the parent container
function makeResponsive(el){
var svg = el.getElementsByTagName("svg")[0];
if(svg){
if(svg.width) {svg.removeAttribute("width")};
if(svg.height) {svg.removeAttribute("height")};
svg.style.width = "100%";
svg.style.height = "100%";
}
};


// get all DiagrammeR mermaids widgets
dg = document.getElementsByClassName("DiagrammeR");
// run mermaid.init
// but use try catch block
// to send error to the htmlwidget for display
try{
mermaid.init( el );

// sort of make our diagram responsive
// should we make this an option?
// if so, then could easily add to list of post process tasks
makeResponsive( el );

if (HTMLWidgets.shinyMode) {
// Get widget id
var id = el.id;

$("#" + id + " .node").click(function(e) {
// Build return object *obj* with node-id and node textContent
var obj = {
id: e.currentTarget.id,
nodeValues: e.currentTarget.textContent
};
// Send *obj* to Shiny's inputs (input$[id]+_click e.g.: input$vtree_click))
Shiny.setInputValue(id + "_click", obj, {priority: "event"});
});
}

/*
// change the id of our SVG assigned by mermaid to prevent conflict
// mermaid.init has a counter that will reset to 0
// and cause duplication of SVG id if multiple
d3.select(el).select("svg")
.attr("id", "mermaidChart-" + el.id);
// now we have to change the styling assigned by mermaid
// to point to our new id that we have assigned
// will add if since sequence diagrams do not have stylesheet
if(d3.select(el).select("svg").select("style")[0][0]){
d3.select(el).select("svg").select("style")[0][0].innerHTML = d3.select(el).select("svg")
.select("style")[0][0].innerHTML
*/
/// sep comment for / in regex .replace(/mermaidChart[0-9]*/gi, "mermaidChart-" + el.id);
/*}
*/

// set up a container for tasks to perform after completion
// one example would be add callbacks for event handling
// styling
if (!(typeof x.tasks === "undefined") ){
if ( (typeof x.tasks.length === "undefined") ||
(typeof x.tasks === "function" ) ) {
// handle a function not enclosed in array
// should be able to remove once using jsonlite
x.tasks = [x.tasks];
}
x.tasks.map(function(t){
// for each tasks add it to the mermaid.tasks with el
t.call(el);
})
}

} catch(e) {
// if error look for last processed DiagrammeR
// and send error to the container div
// with pre containing the errors
var processedDg = d3.selectAll(".DiagrammeR[data-processed=true]");
// select the last
processedDg = d3.select(processedDg[0][processedDg[0].length - 1])
// remove the svg
processedDg.select("svg").remove();

//if dynamic such as shiny remove data-processed
// so mermaid will reprocess and redraw
if (HTMLWidgets.shinyMode) {
el.removeAttribute("data-processed")
}

processedDg.append("pre").html( ["parse error with " + x.diagram, e.message].join("\n") )
}

},

resize: function(el, width, height, instance) {

}


});
14 changes: 14 additions & 0 deletions libs/DiagrammeR-styles-0.2/styles.css
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.DiagrammeR,.grViz pre {
white-space: pre-wrap; /* CSS 3 */
white-space: -moz-pre-wrap; /* Mozilla, since 1999 */
white-space: -pre-wrap; /* Opera 4-6 */
white-space: -o-pre-wrap; /* Opera 7 */
word-wrap: break-word; /* Internet Explorer 5.5+ */
}

.DiagrammeR g .label {
font-family: Helvetica;
font-size: 14px;
color: #333333;
}

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