{ "cells": [ { "cell_type": "markdown", "id": "dafb4329-2206-45d5-aa42-ca8e69b4cd3f", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [] }, "source": [ "# Reproducibility \n", "\n", "## Learning Objectives\n", "- Understand the concept of reproducibility and its importance in research\n", "- Identify the benefits of adopting reproducible research practices\n", "- Implement key practices to enhance the reproducibility of your research\n", "- Utilize tools and techniques to ensure the openness, reusability, and transparency of your research outputs\n", "- Apply quality assurance and peer review processes to maintain reproducible standards \n", "\n", "## Overview \n", "\n", "Reproducibility is fundamental for credible, impactful, and collaborative research. It enhances the credibility of research by enabling verification of results and encourages faster progression in the field due to increased accessibility and shared knowledge. Adopting reproducible practices varies with project scope, but generally includes making research open, reusable, and transparent.\n", "\n", "## Benefits \n", "- Improved research credibility through verifiable results.\n", "- Increased citations for open access articles.\n", "- Enhanced rate of research progression.\n", "- Easier identification and engagement with collaborators.\n", "- Broader public access to research findings.\n", "- Potential for alternative research impact metrics.\n", "\n", "## Key Practices\n", "- **Openness**: Ensure that all research elements are publicly available and accessible.\n", "- **Reusability**: Share data, code, and other outputs in usable formats with appropriate licenses.\n", "- **Transparency**: Provide clear documentation on how outputs were produced.\n", "- **Quality Assurance and Peer Review**: Implement checks to ensure adherence to reproducible standards.\n", "- **Use of Tools**:\n", " - Employ open-source software and version control.\n", " - Minimize manual steps in data processing.\n", " - Manage dependencies, code style, and structure.\n", " - Implement testing and continuous integration.\n", "- **Documentation and Access**: Make code and data available on sharing platforms with comprehensive documentation.\n", "\n", "## Summary Quiz" ] }, { "cell_type": "code", "execution_count": 2, "id": "e3805232-1062-43db-b308-bdcafe85fe51", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [ "remove-input" ] }, "outputs": [ { "data": { "text/html": [ "
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "var questionsOZkwrkYGQGGl=[\n", " {\n", " \"question\": \"What is the primary goal of reproducibility in research?\",\n", " \"type\": \"many_choice\",\n", " \"answers\": [\n", " {\n", " \"answer\": \"To increase the length of research papers\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"To ensure that research results can be verfiied and reproduced by others\",\n", " \"correct\": true,\n", " \"feedback\": \"Correct\"\n", " },\n", " {\n", " \"answer\": \"To reduce the complexity of research methods\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"To eliminate the need for peer review\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " }\n", " ]\n", " },\n", " {\n", " \"question\": \"Which of the following is a benefit of reproducible research practices?\",\n", " \"type\": \"many_choice\",\n", " \"answers\": [\n", " {\n", " \"answer\": \"Decreased credibility of research findings.\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"Reduced citations for open access articles.\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"Enhanced rate of research progression.\",\n", " \"correct\": true,\n", " \"feedback\": \"Correct\"\n", " },\n", " {\n", " \"answer\": \"Limited access to research findings\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " }\n", " ]\n", " },\n", " {\n", " \"question\": \"Why is quality assurance and peer review important in reproducible research?\",\n", " \"type\": \"many_choice\",\n", " \"answers\": [\n", " {\n", " \"answer\": \"To lengthen the research process.\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"To ensure adherence to reproducible standards\",\n", " \"correct\": true,\n", " \"feedback\": \"Correct\"\n", " },\n", " {\n", " \"answer\": \"To avoid sharing data and code\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " },\n", " {\n", " \"answer\": \"To minimize the documentation effort\",\n", " \"correct\": false,\n", " \"feedback\": \"Incorrect\"\n", " }\n", " ]\n", " }\n", "];\n", " // Make a random ID\n", "function makeid(length) {\n", " var result = [];\n", " var characters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz';\n", " var charactersLength = characters.length;\n", " for (var i = 0; i < length; i++) {\n", " result.push(characters.charAt(Math.floor(Math.random() * charactersLength)));\n", " }\n", " return result.join('');\n", "}\n", "\n", "// Choose a random subset of an array. Can also be used to shuffle the array\n", "function getRandomSubarray(arr, size) {\n", " var shuffled = arr.slice(0), i = arr.length, temp, index;\n", " while (i--) {\n", " index = Math.floor((i + 1) * Math.random());\n", " temp = shuffled[index];\n", " shuffled[index] = shuffled[i];\n", " shuffled[i] = temp;\n", " }\n", " return shuffled.slice(0, size);\n", "}\n", "\n", "function printResponses(responsesContainer) {\n", " var responses=JSON.parse(responsesContainer.dataset.responses);\n", " var stringResponses='IMPORTANT!To preserve this answer sequence for submission, when you have finalized your answers:
  1. Copy the text in this cell below \"Answer String\"
  2. Double click on the cell directly below the Answer String, labeled \"Replace Me\"
  3. Select the whole \"Replace Me\" text
  4. Paste in your answer string and press shift-Enter.
  5. Save the notebook using the save icon or File->Save Notebook menu item



    6. Answer String:
    ';\n", " console.log(responses);\n", " responses.forEach((response, index) => {\n", " if (response) {\n", " console.log(index + ': ' + response);\n", " stringResponses+= index + ': ' + response +\"
    \";\n", " }\n", " });\n", " responsesContainer.innerHTML=stringResponses;\n", "}\n", "function check_mc() {\n", " var id = this.id.split('-')[0];\n", " //var response = this.id.split('-')[1];\n", " //console.log(response);\n", " //console.log(\"In check_mc(), id=\"+id);\n", " //console.log(event.srcElement.id) \n", " //console.log(event.srcElement.dataset.correct) \n", " //console.log(event.srcElement.dataset.feedback)\n", "\n", " var label = event.srcElement;\n", " //console.log(label, label.nodeName);\n", " var depth = 0;\n", " while ((label.nodeName != \"LABEL\") && (depth < 20)) {\n", " label = label.parentElement;\n", " console.log(depth, label);\n", " depth++;\n", " }\n", "\n", "\n", "\n", " var answers = label.parentElement.children;\n", "\n", " //console.log(answers);\n", "\n", "\n", " // Split behavior based on multiple choice vs many choice:\n", " var fb = document.getElementById(\"fb\" + id);\n", "\n", "\n", "\n", "\n", " if (fb.dataset.numcorrect == 1) {\n", " // What follows is for the saved responses stuff\n", " var outerContainer = fb.parentElement.parentElement;\n", " var responsesContainer = document.getElementById(\"responses\" + outerContainer.id);\n", " if (responsesContainer) {\n", " //console.log(responsesContainer);\n", " var response = label.firstChild.innerText;\n", " if (label.querySelector(\".QuizCode\")){\n", " response+= label.querySelector(\".QuizCode\").firstChild.innerText;\n", " }\n", " console.log(response);\n", " //console.log(document.getElementById(\"quizWrap\"+id));\n", " var qnum = document.getElementById(\"quizWrap\"+id).dataset.qnum;\n", " console.log(\"Question \" + qnum);\n", " //console.log(id, \", got numcorrect=\",fb.dataset.numcorrect);\n", " var responses=JSON.parse(responsesContainer.dataset.responses);\n", " console.log(responses);\n", " responses[qnum]= response;\n", " responsesContainer.setAttribute('data-responses', JSON.stringify(responses));\n", " printResponses(responsesContainer);\n", " }\n", " // End code to preserve responses\n", " \n", " for (var i = 0; i < answers.length; i++) {\n", " var child = answers[i];\n", " //console.log(child);\n", " child.className = \"MCButton\";\n", " }\n", "\n", "\n", "\n", " if (label.dataset.correct == \"true\") {\n", " // console.log(\"Correct action\");\n", " if (\"feedback\" in label.dataset) {\n", " fb.textContent = jaxify(label.dataset.feedback);\n", " } else {\n", " fb.textContent = \"Correct!\";\n", " }\n", " label.classList.add(\"correctButton\");\n", "\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"correct\");\n", "\n", " } else {\n", " if (\"feedback\" in label.dataset) {\n", " fb.textContent = jaxify(label.dataset.feedback);\n", " } else {\n", " fb.textContent = \"Incorrect -- try again.\";\n", " }\n", " //console.log(\"Error action\");\n", " label.classList.add(\"incorrectButton\");\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"incorrect\");\n", " }\n", " }\n", " else {\n", " var reset = false;\n", " var feedback;\n", " if (label.dataset.correct == \"true\") {\n", " if (\"feedback\" in label.dataset) {\n", " feedback = jaxify(label.dataset.feedback);\n", " } else {\n", " feedback = \"Correct!\";\n", " }\n", " if (label.dataset.answered <= 0) {\n", " if (fb.dataset.answeredcorrect < 0) {\n", " fb.dataset.answeredcorrect = 1;\n", " reset = true;\n", " } else {\n", " fb.dataset.answeredcorrect++;\n", " }\n", " if (reset) {\n", " for (var i = 0; i < answers.length; i++) {\n", " var child = answers[i];\n", " child.className = \"MCButton\";\n", " child.dataset.answered = 0;\n", " }\n", " }\n", " label.classList.add(\"correctButton\");\n", " label.dataset.answered = 1;\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"correct\");\n", "\n", " }\n", " } else {\n", " if (\"feedback\" in label.dataset) {\n", " feedback = jaxify(label.dataset.feedback);\n", " } else {\n", " feedback = \"Incorrect -- try again.\";\n", " }\n", " if (fb.dataset.answeredcorrect > 0) {\n", " fb.dataset.answeredcorrect = -1;\n", " reset = true;\n", " } else {\n", " fb.dataset.answeredcorrect--;\n", " }\n", "\n", " if (reset) {\n", " for (var i = 0; i < answers.length; i++) {\n", " var child = answers[i];\n", " child.className = \"MCButton\";\n", " child.dataset.answered = 0;\n", " }\n", " }\n", " label.classList.add(\"incorrectButton\");\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"incorrect\");\n", " }\n", " // What follows is for the saved responses stuff\n", " var outerContainer = fb.parentElement.parentElement;\n", " var responsesContainer = document.getElementById(\"responses\" + outerContainer.id);\n", " if (responsesContainer) {\n", " //console.log(responsesContainer);\n", " var response = label.firstChild.innerText;\n", " if (label.querySelector(\".QuizCode\")){\n", " response+= label.querySelector(\".QuizCode\").firstChild.innerText;\n", " }\n", " console.log(response);\n", " //console.log(document.getElementById(\"quizWrap\"+id));\n", " var qnum = document.getElementById(\"quizWrap\"+id).dataset.qnum;\n", " console.log(\"Question \" + qnum);\n", " //console.log(id, \", got numcorrect=\",fb.dataset.numcorrect);\n", " var responses=JSON.parse(responsesContainer.dataset.responses);\n", " if (label.dataset.correct == \"true\") {\n", " if (typeof(responses[qnum]) == \"object\"){\n", " if (!responses[qnum].includes(response))\n", " responses[qnum].push(response);\n", " } else{\n", " responses[qnum]= [ response ];\n", " }\n", " } else {\n", " responses[qnum]= response;\n", " }\n", " console.log(responses);\n", " responsesContainer.setAttribute('data-responses', JSON.stringify(responses));\n", " printResponses(responsesContainer);\n", " }\n", " // End save responses stuff\n", "\n", "\n", "\n", " var numcorrect = fb.dataset.numcorrect;\n", " var answeredcorrect = fb.dataset.answeredcorrect;\n", " if (answeredcorrect >= 0) {\n", " fb.textContent = feedback + \" [\" + answeredcorrect + \"/\" + numcorrect + \"]\";\n", " } else {\n", " fb.textContent = feedback + \" [\" + 0 + \"/\" + numcorrect + \"]\";\n", " }\n", "\n", "\n", " }\n", "\n", " if (typeof MathJax != 'undefined') {\n", " var version = MathJax.version;\n", " console.log('MathJax version', version);\n", " if (version[0] == \"2\") {\n", " MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]);\n", " } else if (version[0] == \"3\") {\n", " MathJax.typeset([fb]);\n", " }\n", " } else {\n", " console.log('MathJax not detected');\n", " }\n", "\n", "}\n", "\n", "function make_mc(qa, shuffle_answers, outerqDiv, qDiv, aDiv, id) {\n", " var shuffled;\n", " if (shuffle_answers == \"True\") {\n", " //console.log(shuffle_answers+\" read as true\");\n", " shuffled = getRandomSubarray(qa.answers, qa.answers.length);\n", " } else {\n", " //console.log(shuffle_answers+\" read as false\");\n", " shuffled = qa.answers;\n", " }\n", "\n", "\n", " var num_correct = 0;\n", "\n", "\n", "\n", " shuffled.forEach((item, index, ans_array) => {\n", " //console.log(answer);\n", "\n", " // Make input element\n", " var inp = document.createElement(\"input\");\n", " inp.type = \"radio\";\n", " inp.id = \"quizo\" + id + index;\n", " inp.style = \"display:none;\";\n", " aDiv.append(inp);\n", "\n", " //Make label for input element\n", " var lab = document.createElement(\"label\");\n", " lab.className = \"MCButton\";\n", " lab.id = id + '-' + index;\n", " lab.onclick = check_mc;\n", " var aSpan = document.createElement('span');\n", " aSpan.classsName = \"\";\n", " //qDiv.id=\"quizQn\"+id+index;\n", " if (\"answer\" in item) {\n", " aSpan.innerHTML = jaxify(item.answer);\n", " //aSpan.innerHTML=item.answer;\n", " }\n", " lab.append(aSpan);\n", "\n", " // Create div for code inside question\n", " var codeSpan;\n", " if (\"code\" in item) {\n", " codeSpan = document.createElement('span');\n", " codeSpan.id = \"code\" + id + index;\n", " codeSpan.className = \"QuizCode\";\n", " var codePre = document.createElement('pre');\n", " codeSpan.append(codePre);\n", " var codeCode = document.createElement('code');\n", " codePre.append(codeCode);\n", " codeCode.innerHTML = item.code;\n", " lab.append(codeSpan);\n", " //console.log(codeSpan);\n", " }\n", "\n", " //lab.textContent=item.answer;\n", "\n", " // Set the data attributes for the answer\n", " lab.setAttribute('data-correct', item.correct);\n", " if (item.correct) {\n", " num_correct++;\n", " }\n", " if (\"feedback\" in item) {\n", " lab.setAttribute('data-feedback', item.feedback);\n", " }\n", " lab.setAttribute('data-answered', 0);\n", "\n", " aDiv.append(lab);\n", "\n", " });\n", "\n", " if (num_correct > 1) {\n", " outerqDiv.className = \"ManyChoiceQn\";\n", " } else {\n", " outerqDiv.className = \"MultipleChoiceQn\";\n", " }\n", "\n", " return num_correct;\n", "\n", "}\n", "function check_numeric(ths, event) {\n", "\n", " if (event.keyCode === 13) {\n", " ths.blur();\n", "\n", " var id = ths.id.split('-')[0];\n", "\n", " var submission = ths.value;\n", " if (submission.indexOf('/') != -1) {\n", " var sub_parts = submission.split('/');\n", " //console.log(sub_parts);\n", " submission = sub_parts[0] / sub_parts[1];\n", " }\n", " //console.log(\"Reader entered\", submission);\n", "\n", " if (\"precision\" in ths.dataset) {\n", " var precision = ths.dataset.precision;\n", " // console.log(\"1:\", submission)\n", " submission = Math.round((1 * submission + Number.EPSILON) * 10 ** precision) / 10 ** precision;\n", " // console.log(\"Rounded to \", submission, \" precision=\", precision );\n", " }\n", "\n", "\n", " //console.log(\"In check_numeric(), id=\"+id);\n", " //console.log(event.srcElement.id) \n", " //console.log(event.srcElement.dataset.feedback)\n", "\n", " var fb = document.getElementById(\"fb\" + id);\n", " fb.style.display = \"none\";\n", " fb.textContent = \"Incorrect -- try again.\";\n", "\n", " var answers = JSON.parse(ths.dataset.answers);\n", " //console.log(answers);\n", "\n", " var defaultFB = \"\";\n", " var correct;\n", " var done = false;\n", " answers.every(answer => {\n", " //console.log(answer.type);\n", "\n", " correct = false;\n", " // if (answer.type==\"value\"){\n", " if ('value' in answer) {\n", " if (submission == answer.value) {\n", " if (\"feedback\" in answer) {\n", " fb.textContent = jaxify(answer.feedback);\n", " } else {\n", " fb.textContent = jaxify(\"Correct\");\n", " }\n", " correct = answer.correct;\n", " //console.log(answer.correct);\n", " done = true;\n", " }\n", " // } else if (answer.type==\"range\") {\n", " } else if ('range' in answer) {\n", " //console.log(answer.range);\n", " if ((submission >= answer.range[0]) && (submission < answer.range[1])) {\n", " fb.textContent = jaxify(answer.feedback);\n", " correct = answer.correct;\n", " //console.log(answer.correct);\n", " done = true;\n", " }\n", " } else if (answer.type == \"default\") {\n", " defaultFB = answer.feedback;\n", " }\n", " if (done) {\n", " return false; // Break out of loop if this has been marked correct\n", " } else {\n", " return true; // Keep looking for case that includes this as a correct answer\n", " }\n", " });\n", "\n", " if ((!done) && (defaultFB != \"\")) {\n", " fb.innerHTML = jaxify(defaultFB);\n", " //console.log(\"Default feedback\", defaultFB);\n", " }\n", "\n", " fb.style.display = \"block\";\n", " if (correct) {\n", " ths.className = \"Input-text\";\n", " ths.classList.add(\"correctButton\");\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"correct\");\n", " } else {\n", " ths.className = \"Input-text\";\n", " ths.classList.add(\"incorrectButton\");\n", " fb.className = \"Feedback\";\n", " fb.classList.add(\"incorrect\");\n", " }\n", "\n", " // What follows is for the saved responses stuff\n", " var outerContainer = fb.parentElement.parentElement;\n", " var responsesContainer = document.getElementById(\"responses\" + outerContainer.id);\n", " if (responsesContainer) {\n", " console.log(submission);\n", " var qnum = document.getElementById(\"quizWrap\"+id).dataset.qnum;\n", " //console.log(\"Question \" + qnum);\n", " //console.log(id, \", got numcorrect=\",fb.dataset.numcorrect);\n", " var responses=JSON.parse(responsesContainer.dataset.responses);\n", " console.log(responses);\n", " if (submission == ths.value){\n", " responses[qnum]= submission;\n", " } else {\n", " responses[qnum]= ths.value + \"(\" + submission +\")\";\n", " }\n", " responsesContainer.setAttribute('data-responses', JSON.stringify(responses));\n", " printResponses(responsesContainer);\n", " }\n", " // End code to preserve responses\n", "\n", " if (typeof MathJax != 'undefined') {\n", " var version = MathJax.version;\n", " console.log('MathJax version', version);\n", " if (version[0] == \"2\") {\n", " MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]);\n", " } else if (version[0] == \"3\") {\n", " MathJax.typeset([fb]);\n", " }\n", " } else {\n", " console.log('MathJax not detected');\n", " }\n", " return false;\n", " }\n", "\n", "}\n", "\n", "function isValid(el, charC) {\n", " //console.log(\"Input char: \", charC);\n", " if (charC == 46) {\n", " if (el.value.indexOf('.') === -1) {\n", " return true;\n", " } else if (el.value.indexOf('/') != -1) {\n", " var parts = el.value.split('/');\n", " if (parts[1].indexOf('.') === -1) {\n", " return true;\n", " }\n", " }\n", " else {\n", " return false;\n", " }\n", " } else if (charC == 47) {\n", " if (el.value.indexOf('/') === -1) {\n", " if ((el.value != \"\") && (el.value != \".\")) {\n", " return true;\n", " } else {\n", " return false;\n", " }\n", " } else {\n", " return false;\n", " }\n", " } else if (charC == 45) {\n", " var edex = el.value.indexOf('e');\n", " if (edex == -1) {\n", " edex = el.value.indexOf('E');\n", " }\n", "\n", " if (el.value == \"\") {\n", " return true;\n", " } else if (edex == (el.value.length - 1)) { // If just after e or E\n", " return true;\n", " } else {\n", " return false;\n", " }\n", " } else if (charC == 101) { // \"e\"\n", " if ((el.value.indexOf('e') === -1) && (el.value.indexOf('E') === -1) && (el.value.indexOf('/') == -1)) {\n", " // Prev symbol must be digit or decimal point:\n", " if (el.value.slice(-1).search(/\\d/) >= 0) {\n", " return true;\n", " } else if (el.value.slice(-1).search(/\\./) >= 0) {\n", " return true;\n", " } else {\n", " return false;\n", " }\n", " } else {\n", " return false;\n", " }\n", " } else {\n", " if (charC > 31 && (charC < 48 || charC > 57))\n", " return false;\n", " }\n", " return true;\n", "}\n", "\n", "function numeric_keypress(evnt) {\n", " var charC = (evnt.which) ? evnt.which : evnt.keyCode;\n", "\n", " if (charC == 13) {\n", " check_numeric(this, evnt);\n", " } else {\n", " return isValid(this, charC);\n", " }\n", "}\n", "\n", "\n", "\n", "\n", "\n", "function make_numeric(qa, outerqDiv, qDiv, aDiv, id) {\n", "\n", "\n", "\n", " //console.log(answer);\n", "\n", "\n", " outerqDiv.className = \"NumericQn\";\n", " aDiv.style.display = 'block';\n", "\n", " var lab = document.createElement(\"label\");\n", " lab.className = \"InpLabel\";\n", " lab.textContent = \"Type numeric answer here:\";\n", " aDiv.append(lab);\n", "\n", " var inp = document.createElement(\"input\");\n", " inp.type = \"text\";\n", " //inp.id=\"input-\"+id;\n", " inp.id = id + \"-0\";\n", " inp.className = \"Input-text\";\n", " inp.setAttribute('data-answers', JSON.stringify(qa.answers));\n", " if (\"precision\" in qa) {\n", " inp.setAttribute('data-precision', qa.precision);\n", " }\n", " aDiv.append(inp);\n", " //console.log(inp);\n", "\n", " //inp.addEventListener(\"keypress\", check_numeric);\n", " //inp.addEventListener(\"keypress\", numeric_keypress);\n", " /*\n", " inp.addEventListener(\"keypress\", function(event) {\n", " return numeric_keypress(this, event);\n", " }\n", " );\n", " */\n", " //inp.onkeypress=\"return numeric_keypress(this, event)\";\n", " inp.onkeypress = numeric_keypress;\n", " inp.onpaste = event => false;\n", "\n", " inp.addEventListener(\"focus\", function (event) {\n", " this.value = \"\";\n", " return false;\n", " }\n", " );\n", "\n", "\n", "}\n", "function jaxify(string) {\n", " var mystring = string;\n", "\n", " var count = 0;\n", " var loc = mystring.search(/([^\\\\]|^)(\\$)/);\n", "\n", " var count2 = 0;\n", " var loc2 = mystring.search(/([^\\\\]|^)(\\$\\$)/);\n", "\n", " //console.log(loc);\n", "\n", " while ((loc >= 0) || (loc2 >= 0)) {\n", "\n", " /* Have to replace all the double $$ first with current implementation */\n", " if (loc2 >= 0) {\n", " if (count2 % 2 == 0) {\n", " mystring = mystring.replace(/([^\\\\]|^)(\\$\\$)/, \"$1\\\\[\");\n", " } else {\n", " mystring = mystring.replace(/([^\\\\]|^)(\\$\\$)/, \"$1\\\\]\");\n", " }\n", " count2++;\n", " } else {\n", " if (count % 2 == 0) {\n", " mystring = mystring.replace(/([^\\\\]|^)(\\$)/, \"$1\\\\(\");\n", " } else {\n", " mystring = mystring.replace(/([^\\\\]|^)(\\$)/, \"$1\\\\)\");\n", " }\n", " count++;\n", " }\n", " loc = mystring.search(/([^\\\\]|^)(\\$)/);\n", " loc2 = mystring.search(/([^\\\\]|^)(\\$\\$)/);\n", " //console.log(mystring,\", loc:\",loc,\", loc2:\",loc2);\n", " }\n", "\n", " //console.log(mystring);\n", " return mystring;\n", "}\n", "\n", "\n", "function show_questions(json, mydiv) {\n", " console.log('show_questions');\n", " //var mydiv=document.getElementById(myid);\n", " var shuffle_questions = mydiv.dataset.shufflequestions;\n", " var num_questions = mydiv.dataset.numquestions;\n", " var shuffle_answers = mydiv.dataset.shuffleanswers;\n", " var max_width = mydiv.dataset.maxwidth;\n", "\n", " if (num_questions > json.length) {\n", " num_questions = json.length;\n", " }\n", "\n", " var questions;\n", " if ((num_questions < json.length) || (shuffle_questions == \"True\")) {\n", " //console.log(num_questions+\",\"+json.length);\n", " questions = getRandomSubarray(json, num_questions);\n", " } else {\n", " questions = json;\n", " }\n", "\n", " //console.log(\"SQ: \"+shuffle_questions+\", NQ: \" + num_questions + \", SA: \", shuffle_answers);\n", "\n", " // Iterate over questions\n", " questions.forEach((qa, index, array) => {\n", " //console.log(qa.question); \n", "\n", " var id = makeid(8);\n", " //console.log(id);\n", "\n", "\n", " // Create Div to contain question and answers\n", " var iDiv = document.createElement('div');\n", " //iDiv.id = 'quizWrap' + id + index;\n", " iDiv.id = 'quizWrap' + id;\n", " iDiv.className = 'Quiz';\n", " iDiv.setAttribute('data-qnum', index);\n", " iDiv.style.maxWidth =max_width+\"px\";\n", " mydiv.appendChild(iDiv);\n", " // iDiv.innerHTML=qa.question;\n", " \n", " var outerqDiv = document.createElement('div');\n", " outerqDiv.id = \"OuterquizQn\" + id + index;\n", " // Create div to contain question part\n", " var qDiv = document.createElement('div');\n", " qDiv.id = \"quizQn\" + id + index;\n", " \n", " if (qa.question) {\n", " iDiv.append(outerqDiv);\n", "\n", " //qDiv.textContent=qa.question;\n", " qDiv.innerHTML = jaxify(qa.question);\n", " outerqDiv.append(qDiv);\n", " }\n", "\n", " // Create div for code inside question\n", " var codeDiv;\n", " if (\"code\" in qa) {\n", " codeDiv = document.createElement('div');\n", " codeDiv.id = \"code\" + id + index;\n", " codeDiv.className = \"QuizCode\";\n", " var codePre = document.createElement('pre');\n", " codeDiv.append(codePre);\n", " var codeCode = document.createElement('code');\n", " codePre.append(codeCode);\n", " codeCode.innerHTML = qa.code;\n", " outerqDiv.append(codeDiv);\n", " //console.log(codeDiv);\n", " }\n", "\n", "\n", " // Create div to contain answer part\n", " var aDiv = document.createElement('div');\n", " aDiv.id = \"quizAns\" + id + index;\n", " aDiv.className = 'Answer';\n", " iDiv.append(aDiv);\n", "\n", " //console.log(qa.type);\n", "\n", " var num_correct;\n", " if ((qa.type == \"multiple_choice\") || (qa.type == \"many_choice\") ) {\n", " num_correct = make_mc(qa, shuffle_answers, outerqDiv, qDiv, aDiv, id);\n", " if (\"answer_cols\" in qa) {\n", " //aDiv.style.gridTemplateColumns = 'auto '.repeat(qa.answer_cols);\n", " aDiv.style.gridTemplateColumns = 'repeat(' + qa.answer_cols + ', 1fr)';\n", " }\n", " } else if (qa.type == \"numeric\") {\n", " //console.log(\"numeric\");\n", " make_numeric(qa, outerqDiv, qDiv, aDiv, id);\n", " }\n", "\n", "\n", " //Make div for feedback\n", " var fb = document.createElement(\"div\");\n", " fb.id = \"fb\" + id;\n", " //fb.style=\"font-size: 20px;text-align:center;\";\n", " fb.className = \"Feedback\";\n", " fb.setAttribute(\"data-answeredcorrect\", 0);\n", " fb.setAttribute(\"data-numcorrect\", num_correct);\n", " iDiv.append(fb);\n", "\n", "\n", " });\n", " var preserveResponses = mydiv.dataset.preserveresponses;\n", " console.log(preserveResponses);\n", " console.log(preserveResponses == \"true\");\n", " if (preserveResponses == \"true\") {\n", " console.log(preserveResponses);\n", " // Create Div to contain record of answers\n", " var iDiv = document.createElement('div');\n", " iDiv.id = 'responses' + mydiv.id;\n", " iDiv.className = 'JCResponses';\n", " // Create a place to store responses as an empty array\n", " iDiv.setAttribute('data-responses', '[]');\n", "\n", " // Dummy Text\n", " iDiv.innerHTML=\"Select your answers and then follow the directions that will appear here.\"\n", " //iDiv.className = 'Quiz';\n", " mydiv.appendChild(iDiv);\n", " }\n", "//console.log(\"At end of show_questions\");\n", " if (typeof MathJax != 'undefined') {\n", " console.log(\"MathJax version\", MathJax.version);\n", " var version = MathJax.version;\n", " setTimeout(function(){\n", " var version = MathJax.version;\n", " console.log('After sleep, MathJax version', version);\n", " if (version[0] == \"2\") {\n", " MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]);\n", " } else if (version[0] == \"3\") {\n", " MathJax.typeset([mydiv]);\n", " }\n", " }, 500);\n", "if (typeof version == 'undefined') {\n", " } else\n", " {\n", " if (version[0] == \"2\") {\n", " MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]);\n", " } else if (version[0] == \"3\") {\n", " MathJax.typeset([mydiv]);\n", " } else {\n", " console.log(\"MathJax not found\");\n", " }\n", " }\n", " }\n", " return false;\n", "}\n", "/* This is to handle asynchrony issues in loading Jupyter notebooks\n", " where the quiz has been previously run. The Javascript was generally\n", " being run before the div was added to the DOM. I tried to do this\n", " more elegantly using Mutation Observer, but I didn't get it to work.\n", "\n", " Someone more knowledgeable could make this better ;-) */\n", "\n", " function try_show() {\n", " if(document.getElementById(\"OZkwrkYGQGGl\")) {\n", " show_questions(questionsOZkwrkYGQGGl, OZkwrkYGQGGl); \n", " } else {\n", " setTimeout(try_show, 200);\n", " }\n", " };\n", " \n", " {\n", " // console.log(element);\n", "\n", " //console.log(\"OZkwrkYGQGGl\");\n", " // console.log(document.getElementById(\"OZkwrkYGQGGl\"));\n", "\n", " try_show();\n", " }\n", " " ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from jupyterquiz import display_quiz\n", "display_quiz(\"questions/summary_reproducibility.json\")" ] }, { "cell_type": "code", "execution_count": null, "id": "1db69e2d-399b-41c0-a479-886691ae60f6", "metadata": { "editable": true, "slideshow": { "slide_type": "" }, "tags": [] }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.19" } }, "nbformat": 4, "nbformat_minor": 5 }