+ This blog contains posts from the PHUSE working group on The use of Git in Statisical Programming
+Meetings are happening bi-weekly every Tuesday
+
${missingFields[0]} field.`,
+ message: `The items being returned for this search do not include all the required fields. Please ensure that your index items include the ${missingFields[0]} field or use index-fields in your _quarto.yml file to specify the field names.`,
+ };
+ } else if (missingFields.length > 1) {
+ const missingFieldList = missingFields
+ .map((field) => {
+ return `${field}`;
+ })
+ .join(", ");
+
+ throw {
+ name: `Error: Search index is missing the following fields: ${missingFieldList}.`,
+ message: `The items being returned for this search do not include all the required fields. Please ensure that your index items includes the following fields: ${missingFieldList}, or use index-fields in your _quarto.yml file to specify the field names.`,
+ };
+ }
+ }
+}
+
+let lastQuery = null;
+function showCopyLink(query, options) {
+ const language = options.language;
+ lastQuery = query;
+ // Insert share icon
+ const inputSuffixEl = window.document.body.querySelector(
+ ".aa-Form .aa-InputWrapperSuffix"
+ );
+
+ if (inputSuffixEl) {
+ let copyButtonEl = window.document.body.querySelector(
+ ".aa-Form .aa-InputWrapperSuffix .aa-CopyButton"
+ );
+
+ if (copyButtonEl === null) {
+ copyButtonEl = window.document.createElement("button");
+ copyButtonEl.setAttribute("class", "aa-CopyButton");
+ copyButtonEl.setAttribute("type", "button");
+ copyButtonEl.setAttribute("title", language["search-copy-link-title"]);
+ copyButtonEl.onmousedown = (e) => {
+ e.preventDefault();
+ e.stopPropagation();
+ };
+
+ const linkIcon = "bi-clipboard";
+ const checkIcon = "bi-check2";
+
+ const shareIconEl = window.document.createElement("i");
+ shareIconEl.setAttribute("class", `bi ${linkIcon}`);
+ copyButtonEl.appendChild(shareIconEl);
+ inputSuffixEl.prepend(copyButtonEl);
+
+ const clipboard = new window.ClipboardJS(".aa-CopyButton", {
+ text: function (_trigger) {
+ const copyUrl = new URL(window.location);
+ copyUrl.searchParams.set(kQueryArg, lastQuery);
+ copyUrl.searchParams.set(kResultsArg, "1");
+ return copyUrl.toString();
+ },
+ });
+ clipboard.on("success", function (e) {
+ // Focus the input
+
+ // button target
+ const button = e.trigger;
+ const icon = button.querySelector("i.bi");
+
+ // flash "checked"
+ icon.classList.add(checkIcon);
+ icon.classList.remove(linkIcon);
+ setTimeout(function () {
+ icon.classList.remove(checkIcon);
+ icon.classList.add(linkIcon);
+ }, 1000);
+ });
+ }
+
+ // If there is a query, show the link icon
+ if (copyButtonEl) {
+ if (lastQuery && options["copy-button"]) {
+ copyButtonEl.style.display = "flex";
+ } else {
+ copyButtonEl.style.display = "none";
+ }
+ }
+ }
+}
+
+/* Search Index Handling */
+// create the index
+var fuseIndex = undefined;
+var shownWarning = false;
+
+// fuse index options
+const kFuseIndexOptions = {
+ keys: [
+ { name: "title", weight: 20 },
+ { name: "section", weight: 20 },
+ { name: "text", weight: 10 },
+ ],
+ ignoreLocation: true,
+ threshold: 0.1,
+};
+
+async function readSearchData() {
+ // Initialize the search index on demand
+ if (fuseIndex === undefined) {
+ if (window.location.protocol === "file:" && !shownWarning) {
+ window.alert(
+ "Search requires JavaScript features disabled when running in file://... URLs. In order to use search, please run this document in a web server."
+ );
+ shownWarning = true;
+ return;
+ }
+ const fuse = new window.Fuse([], kFuseIndexOptions);
+
+ // fetch the main search.json
+ const response = await fetch(offsetURL("search.json"));
+ if (response.status == 200) {
+ return response.json().then(function (searchDocs) {
+ searchDocs.forEach(function (searchDoc) {
+ fuse.add(searchDoc);
+ });
+ fuseIndex = fuse;
+ return fuseIndex;
+ });
+ } else {
+ return Promise.reject(
+ new Error(
+ "Unexpected status from search index request: " + response.status
+ )
+ );
+ }
+ }
+
+ return fuseIndex;
+}
+
+function inputElement() {
+ return window.document.body.querySelector(".aa-Form .aa-Input");
+}
+
+function focusSearchInput() {
+ setTimeout(() => {
+ const inputEl = inputElement();
+ if (inputEl) {
+ inputEl.focus();
+ }
+ }, 50);
+}
+
+/* Panels */
+const kItemTypeDoc = "document";
+const kItemTypeMore = "document-more";
+const kItemTypeItem = "document-item";
+const kItemTypeError = "error";
+
+function renderItem(
+ item,
+ createElement,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh,
+ quartoSearchOptions
+) {
+ switch (item.type) {
+ case kItemTypeDoc:
+ return createDocumentCard(
+ createElement,
+ "file-richtext",
+ item.title,
+ item.section,
+ item.text,
+ item.href,
+ item.crumbs,
+ quartoSearchOptions
+ );
+ case kItemTypeMore:
+ return createMoreCard(
+ createElement,
+ item,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh
+ );
+ case kItemTypeItem:
+ return createSectionCard(
+ createElement,
+ item.section,
+ item.text,
+ item.href
+ );
+ case kItemTypeError:
+ return createErrorCard(createElement, item.title, item.text);
+ default:
+ return undefined;
+ }
+}
+
+function createDocumentCard(
+ createElement,
+ icon,
+ title,
+ section,
+ text,
+ href,
+ crumbs,
+ quartoSearchOptions
+) {
+ const iconEl = createElement("i", {
+ class: `bi bi-${icon} search-result-icon`,
+ });
+ const titleEl = createElement("p", { class: "search-result-title" }, title);
+ const titleContents = [iconEl, titleEl];
+ const showParent = quartoSearchOptions["show-item-context"];
+ if (crumbs && showParent) {
+ let crumbsOut = undefined;
+ const crumbClz = ["search-result-crumbs"];
+ if (showParent === "root") {
+ crumbsOut = crumbs.length > 1 ? crumbs[0] : undefined;
+ } else if (showParent === "parent") {
+ crumbsOut = crumbs.length > 1 ? crumbs[crumbs.length - 2] : undefined;
+ } else {
+ crumbsOut = crumbs.length > 1 ? crumbs.join(" > ") : undefined;
+ crumbClz.push("search-result-crumbs-wrap");
+ }
+
+ const crumbEl = createElement(
+ "p",
+ { class: crumbClz.join(" ") },
+ crumbsOut
+ );
+ titleContents.push(crumbEl);
+ }
+
+ const titleContainerEl = createElement(
+ "div",
+ { class: "search-result-title-container" },
+ titleContents
+ );
+
+ const textEls = [];
+ if (section) {
+ const sectionEl = createElement(
+ "p",
+ { class: "search-result-section" },
+ section
+ );
+ textEls.push(sectionEl);
+ }
+ const descEl = createElement("p", {
+ class: "search-result-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+ textEls.push(descEl);
+
+ const textContainerEl = createElement(
+ "div",
+ { class: "search-result-text-container" },
+ textEls
+ );
+
+ const containerEl = createElement(
+ "div",
+ {
+ class: "search-result-container",
+ },
+ [titleContainerEl, textContainerEl]
+ );
+
+ const linkEl = createElement(
+ "a",
+ {
+ href: offsetURL(href),
+ class: "search-result-link",
+ },
+ containerEl
+ );
+
+ const classes = ["search-result-doc", "search-item"];
+ if (!section) {
+ classes.push("document-selectable");
+ }
+
+ return createElement(
+ "div",
+ {
+ class: classes.join(" "),
+ },
+ linkEl
+ );
+}
+
+function createMoreCard(
+ createElement,
+ item,
+ state,
+ setActiveItemId,
+ setContext,
+ refresh
+) {
+ const moreCardEl = createElement(
+ "div",
+ {
+ class: "search-result-more search-item",
+ onClick: (e) => {
+ // Handle expanding the sections by adding the expanded
+ // section to the list of expanded sections
+ toggleExpanded(item, state, setContext, setActiveItemId, refresh);
+ e.stopPropagation();
+ },
+ },
+ item.title
+ );
+
+ return moreCardEl;
+}
+
+function toggleExpanded(item, state, setContext, setActiveItemId, refresh) {
+ const expanded = state.context.expanded || [];
+ if (expanded.includes(item.target)) {
+ setContext({
+ expanded: expanded.filter((target) => target !== item.target),
+ });
+ } else {
+ setContext({ expanded: [...expanded, item.target] });
+ }
+
+ refresh();
+ setActiveItemId(item.__autocomplete_id);
+}
+
+function createSectionCard(createElement, section, text, href) {
+ const sectionEl = createSection(createElement, section, text, href);
+ return createElement(
+ "div",
+ {
+ class: "search-result-doc-section search-item",
+ },
+ sectionEl
+ );
+}
+
+function createSection(createElement, title, text, href) {
+ const descEl = createElement("p", {
+ class: "search-result-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+
+ const titleEl = createElement("p", { class: "search-result-section" }, title);
+ const linkEl = createElement(
+ "a",
+ {
+ href: offsetURL(href),
+ class: "search-result-link",
+ },
+ [titleEl, descEl]
+ );
+ return linkEl;
+}
+
+function createErrorCard(createElement, title, text) {
+ const descEl = createElement("p", {
+ class: "search-error-text",
+ dangerouslySetInnerHTML: {
+ __html: text,
+ },
+ });
+
+ const titleEl = createElement("p", {
+ class: "search-error-title",
+ dangerouslySetInnerHTML: {
+ __html: ` ${title}`,
+ },
+ });
+ const errorEl = createElement("div", { class: "search-error" }, [
+ titleEl,
+ descEl,
+ ]);
+ return errorEl;
+}
+
+function positionPanel(pos) {
+ const panelEl = window.document.querySelector(
+ "#quarto-search-results .aa-Panel"
+ );
+ const inputEl = window.document.querySelector(
+ "#quarto-search .aa-Autocomplete"
+ );
+
+ if (panelEl && inputEl) {
+ panelEl.style.top = `${Math.round(panelEl.offsetTop)}px`;
+ if (pos === "start") {
+ panelEl.style.left = `${Math.round(inputEl.left)}px`;
+ } else {
+ panelEl.style.right = `${Math.round(inputEl.offsetRight)}px`;
+ }
+ }
+}
+
+/* Highlighting */
+// highlighting functions
+function highlightMatch(query, text) {
+ if (text) {
+ const start = text.toLowerCase().indexOf(query.toLowerCase());
+ if (start !== -1) {
+ const startMark = "";
+ const endMark = "";
+
+ const end = start + query.length;
+ text =
+ text.slice(0, start) +
+ startMark +
+ text.slice(start, end) +
+ endMark +
+ text.slice(end);
+ const startInfo = clipStart(text, start);
+ const endInfo = clipEnd(
+ text,
+ startInfo.position + startMark.length + endMark.length
+ );
+ text =
+ startInfo.prefix +
+ text.slice(startInfo.position, endInfo.position) +
+ endInfo.suffix;
+
+ return text;
+ } else {
+ return text;
+ }
+ } else {
+ return text;
+ }
+}
+
+function clipStart(text, pos) {
+ const clipStart = pos - 50;
+ if (clipStart < 0) {
+ // This will just return the start of the string
+ return {
+ position: 0,
+ prefix: "",
+ };
+ } else {
+ // We're clipping before the start of the string, walk backwards to the first space.
+ const spacePos = findSpace(text, pos, -1);
+ return {
+ position: spacePos.position,
+ prefix: "",
+ };
+ }
+}
+
+function clipEnd(text, pos) {
+ const clipEnd = pos + 200;
+ if (clipEnd > text.length) {
+ return {
+ position: text.length,
+ suffix: "",
+ };
+ } else {
+ const spacePos = findSpace(text, clipEnd, 1);
+ return {
+ position: spacePos.position,
+ suffix: spacePos.clipped ? "…" : "",
+ };
+ }
+}
+
+function findSpace(text, start, step) {
+ let stepPos = start;
+ while (stepPos > -1 && stepPos < text.length) {
+ const char = text[stepPos];
+ if (char === " " || char === "," || char === ":") {
+ return {
+ position: step === 1 ? stepPos : stepPos - step,
+ clipped: stepPos > 1 && stepPos < text.length,
+ };
+ }
+ stepPos = stepPos + step;
+ }
+
+ return {
+ position: stepPos - step,
+ clipped: false,
+ };
+}
+
+// removes highlighting as implemented by the mark tag
+function clearHighlight(searchterm, el) {
+ const childNodes = el.childNodes;
+ for (let i = childNodes.length - 1; i >= 0; i--) {
+ const node = childNodes[i];
+ if (node.nodeType === Node.ELEMENT_NODE) {
+ if (
+ node.tagName === "MARK" &&
+ node.innerText.toLowerCase() === searchterm.toLowerCase()
+ ) {
+ el.replaceChild(document.createTextNode(node.innerText), node);
+ } else {
+ clearHighlight(searchterm, node);
+ }
+ }
+ }
+}
+
+function escapeRegExp(string) {
+ return string.replace(/[.*+?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
+}
+
+// highlight matches
+function highlight(term, el) {
+ const termRegex = new RegExp(term, "ig");
+ const childNodes = el.childNodes;
+
+ // walk back to front avoid mutating elements in front of us
+ for (let i = childNodes.length - 1; i >= 0; i--) {
+ const node = childNodes[i];
+
+ if (node.nodeType === Node.TEXT_NODE) {
+ // Search text nodes for text to highlight
+ const text = node.nodeValue;
+
+ let startIndex = 0;
+ let matchIndex = text.search(termRegex);
+ if (matchIndex > -1) {
+ const markFragment = document.createDocumentFragment();
+ while (matchIndex > -1) {
+ const prefix = text.slice(startIndex, matchIndex);
+ markFragment.appendChild(document.createTextNode(prefix));
+
+ const mark = document.createElement("mark");
+ mark.appendChild(
+ document.createTextNode(
+ text.slice(matchIndex, matchIndex + term.length)
+ )
+ );
+ markFragment.appendChild(mark);
+
+ startIndex = matchIndex + term.length;
+ matchIndex = text.slice(startIndex).search(new RegExp(term, "ig"));
+ if (matchIndex > -1) {
+ matchIndex = startIndex + matchIndex;
+ }
+ }
+ if (startIndex < text.length) {
+ markFragment.appendChild(
+ document.createTextNode(text.slice(startIndex, text.length))
+ );
+ }
+
+ el.replaceChild(markFragment, node);
+ }
+ } else if (node.nodeType === Node.ELEMENT_NODE) {
+ // recurse through elements
+ highlight(term, node);
+ }
+ }
+}
+
+/* Link Handling */
+// get the offset from this page for a given site root relative url
+function offsetURL(url) {
+ var offset = getMeta("quarto:offset");
+ return offset ? offset + url : url;
+}
+
+// read a meta tag value
+function getMeta(metaName) {
+ var metas = window.document.getElementsByTagName("meta");
+ for (let i = 0; i < metas.length; i++) {
+ if (metas[i].getAttribute("name") === metaName) {
+ return metas[i].getAttribute("content");
+ }
+ }
+ return "";
+}
+
+function algoliaSearch(query, limit, algoliaOptions) {
+ const { getAlgoliaResults } = window["@algolia/autocomplete-preset-algolia"];
+
+ const applicationId = algoliaOptions["application-id"];
+ const searchOnlyApiKey = algoliaOptions["search-only-api-key"];
+ const indexName = algoliaOptions["index-name"];
+ const indexFields = algoliaOptions["index-fields"];
+ const searchClient = window.algoliasearch(applicationId, searchOnlyApiKey);
+ const searchParams = algoliaOptions["params"];
+ const searchAnalytics = !!algoliaOptions["analytics-events"];
+
+ return getAlgoliaResults({
+ searchClient,
+ queries: [
+ {
+ indexName: indexName,
+ query,
+ params: {
+ hitsPerPage: limit,
+ clickAnalytics: searchAnalytics,
+ ...searchParams,
+ },
+ },
+ ],
+ transformResponse: (response) => {
+ if (!indexFields) {
+ return response.hits.map((hit) => {
+ return hit.map((item) => {
+ return {
+ ...item,
+ text: highlightMatch(query, item.text),
+ };
+ });
+ });
+ } else {
+ const remappedHits = response.hits.map((hit) => {
+ return hit.map((item) => {
+ const newItem = { ...item };
+ ["href", "section", "title", "text", "crumbs"].forEach(
+ (keyName) => {
+ const mappedName = indexFields[keyName];
+ if (
+ mappedName &&
+ item[mappedName] !== undefined &&
+ mappedName !== keyName
+ ) {
+ newItem[keyName] = item[mappedName];
+ delete newItem[mappedName];
+ }
+ }
+ );
+ newItem.text = highlightMatch(query, newItem.text);
+ return newItem;
+ });
+ });
+ return remappedHits;
+ }
+ },
+ });
+}
+
+let subSearchTerm = undefined;
+let subSearchFuse = undefined;
+const kFuseMaxWait = 125;
+
+async function fuseSearch(query, fuse, fuseOptions) {
+ let index = fuse;
+ // Fuse.js using the Bitap algorithm for text matching which runs in
+ // O(nm) time (no matter the structure of the text). In our case this
+ // means that long search terms mixed with large index gets very slow
+ //
+ // This injects a subIndex that will be used once the terms get long enough
+ // Usually making this subindex is cheap since there will typically be
+ // a subset of results matching the existing query
+ if (subSearchFuse !== undefined && query.startsWith(subSearchTerm)) {
+ // Use the existing subSearchFuse
+ index = subSearchFuse;
+ } else if (subSearchFuse !== undefined) {
+ // The term changed, discard the existing fuse
+ subSearchFuse = undefined;
+ subSearchTerm = undefined;
+ }
+
+ // Search using the active fuse
+ const then = performance.now();
+ const resultsRaw = await index.search(query, fuseOptions);
+ const now = performance.now();
+
+ const results = resultsRaw.map((result) => {
+ const addParam = (url, name, value) => {
+ const anchorParts = url.split("#");
+ const baseUrl = anchorParts[0];
+ const sep = baseUrl.search("\\?") > 0 ? "&" : "?";
+ anchorParts[0] = baseUrl + sep + name + "=" + value;
+ return anchorParts.join("#");
+ };
+
+ return {
+ title: result.item.title,
+ section: result.item.section,
+ href: addParam(result.item.href, kQueryArg, query),
+ text: highlightMatch(query, result.item.text),
+ crumbs: result.item.crumbs,
+ };
+ });
+
+ // If we don't have a subfuse and the query is long enough, go ahead
+ // and create a subfuse to use for subsequent queries
+ if (
+ now - then > kFuseMaxWait &&
+ subSearchFuse === undefined &&
+ resultsRaw.length < fuseOptions.limit
+ ) {
+ subSearchTerm = query;
+ subSearchFuse = new window.Fuse([], kFuseIndexOptions);
+ resultsRaw.forEach((rr) => {
+ subSearchFuse.add(rr.item);
+ });
+ }
+ return results;
+}
diff --git a/docs/styles.css b/docs/styles.css
new file mode 100644
index 0000000..2ddf50c
--- /dev/null
+++ b/docs/styles.css
@@ -0,0 +1 @@
+/* css styles */
diff --git a/git-in-statistical-programming.Rproj b/git-in-statistical-programming.Rproj
index 8e3c2eb..0c0d9b6 100644
--- a/git-in-statistical-programming.Rproj
+++ b/git-in-statistical-programming.Rproj
@@ -1,4 +1,5 @@
Version: 1.0
+ProjectId: f88a3db9-ec2d-4fb9-81d1-af2d80e1823a
RestoreWorkspace: Default
SaveWorkspace: Default
diff --git a/site/.nojekyll b/site/.nojekyll
new file mode 100644
index 0000000..e69de29
diff --git a/site/32743PHUSE.jpg b/site/32743PHUSE.jpg
new file mode 100644
index 0000000..7101c27
Binary files /dev/null and b/site/32743PHUSE.jpg differ
diff --git a/site/_quarto.yml b/site/_quarto.yml
index ffc296e..fb1b2e1 100644
--- a/site/_quarto.yml
+++ b/site/_quarto.yml
@@ -9,8 +9,7 @@ website:
- about.qmd
- icon: github
href: https://github.com/
- - icon: twitter
- href: https://twitter.com
+
format:
html:
theme: cosmo
diff --git a/site/about.qmd b/site/about.qmd
index 5440eb0..f34b1f9 100644
--- a/site/about.qmd
+++ b/site/about.qmd
@@ -1,13 +1,23 @@
---
title: "About"
-image: profile.jpg
+image: phuselogo.png
about:
template: jolla
links:
- icon: github
text: Github
href: https://github.com/phuse-org/git-in-statistical-programming
-
+
---
-This blog contains posts from the PHUSE working group on The use of Git in Statisical Programming
\ No newline at end of file
+This blog contains posts from the PHUSE working group on The use of Git in Statisical Programming
+
+# Meetings
+
+Meetings are happening bi-weekly every Tuesday
+
+# Goal
+
+- White paper about Git in pharma for statisticians : Guidelines
+- Poster for Europe PHUSE 2025
+
diff --git a/site/myblog.Rproj b/site/myblog.Rproj
index 9930d80..8ca8d77 100644
--- a/site/myblog.Rproj
+++ b/site/myblog.Rproj
@@ -1,4 +1,5 @@
Version: 1.0
+ProjectId: 8e193641-009b-47a2-8e08-b2bb3cdb7cd5
RestoreWorkspace: Default
SaveWorkspace: Default
@@ -10,4 +11,4 @@ NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Knitr
-LaTeX: pdfLaTeX
\ No newline at end of file
+LaTeX: pdfLaTeX
diff --git a/site/phuselogo.png b/site/phuselogo.png
new file mode 100644
index 0000000..8ac0038
Binary files /dev/null and b/site/phuselogo.png differ
diff --git a/site/phuselogoETI.webp b/site/phuselogoETI.webp
new file mode 100644
index 0000000..9a9e918
Binary files /dev/null and b/site/phuselogoETI.webp differ