diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 00000000..66f16af3 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,53 @@ +# This configuration does the following: + +# It triggers the CI pipeline when code is pushed to the master branch. +# It sets up a Python environment, installs project dependencies, and runs pytest. +# Test results are uploaded as artifacts for later examination. + +name: CI + +on: + push: + branches: + # - master + - 147_CI-pipeline +jobs: + build: + runs-on: ubuntu-latest + steps: + - name: Checkout Repository + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: 3.10.13 + + - name: Install Dependencies + run: | + pip install -r requirements.txt + pip install pytest pytest-html pytest-cov + + - name: Run Tests with coverage and save report + run: | + coverage run -m pytest pytest/ --junitxml=report.xml --html=report.html + coverage xml -o coverage.xml + continue-on-error: true # Continue to the next step even if tests fail + + - name: Upload HTML Report + uses: actions/upload-artifact@v2 + with: + name: test-report-html + path: report.html + + - name: Upload XML Report + uses: actions/upload-artifact@v2 + with: + name: test-report-xml + path: report.xml + + - name: Upload Coverage Report + uses: actions/upload-artifact@v2 + with: + name: coverage-report + path: coverage.xml \ No newline at end of file diff --git a/.gitignore b/.gitignore index 8fa439c4..ea6f81b1 100644 --- a/.gitignore +++ b/.gitignore @@ -76,4 +76,10 @@ ssh_error_log.txt HBR_demo/* dist/pcntoolkit-0.27-py3.11.egg + +# Overrule for github folder +!.github + +# Basic test functions for SHASH tests/test_SHASH.ipynb + diff --git a/CHANGES b/CHANGES index 93e0fa36..169180f0 100644 --- a/CHANGES +++ b/CHANGES @@ -75,6 +75,15 @@ version 0.27 - Added configuration files for containerisation with Docker version 0.28 -- Updated to PyMC5 (including migrating back-end to PyTensor +- Updated to PyMC5 (including migrating back-end to PyTensor) - Added support for longitudinal normative modelling with BLR (see Buckova-Rehak et al 2023) - Changed default optimiser for trend surface models (for scalability) + +version 0.29 +- Bug fixes (e.g. HBR predict crash, normative_paralell support for .txt input) +- Added docstrings for most functions +- Fixed some problems with exception handling +- Formatted whole project with autopep8 +- Addedd functionality to compute SHASH z-scores from normative.py +- Updated requirements +- Basic pytest continuous integration framework implemented diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..cf078cde --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,71 @@ +# Contributing to PCNtoolkit + +First off, thanks for taking the time to contribute! 🎉👍 + +The following is a set of guidelines for contributing to PCNtoolkit. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request. + +## How Can I Contribute? + +### Reporting Bugs + +This section guides you through submitting a bug report. Following these guidelines helps maintainers and the community understand your report, reproduce the behavior, and find related reports. + +**Before Submitting A Bug Report** + +- Check the debugging guide. +- Check the FAQs on the forum for a list of common questions and problems. +- Ensure the bug is not already reported by searching on GitHub under [Issues](https://github.com/amarquand/PCNtoolkit/issues). + +**How Do I Submit A Good Bug Report?** + +Bugs are tracked as [GitHub issues](https://github.com/amarquand/PCNtoolkit/issues). Create an issue and provide the following information: + +- **Use a clear and descriptive title** for the issue to identify the problem. +- **Describe the exact steps which reproduce the problem** in as much detail as possible. +- **Provide specific examples to demonstrate the steps**. Include links to files or GitHub projects, or copy/pasteable snippets, which you use in those examples. + +### Suggesting Enhancements + +This section guides you through submitting an enhancement suggestion, including completely new features and minor improvements to existing functionality. Following these guidelines helps maintainers and the community understand your suggestion and find related suggestions. + +**How Do I Submit A Good Enhancement Suggestion?** + +Enhancement suggestions are tracked as [GitHub issues](https://github.com/amarquand/PCNtoolkit/issues). Create an issue and provide the following information: + +- **Use a clear and descriptive title** for the issue to identify the suggestion. +- **Provide a step-by-step description of the suggested enhancement** in as much detail as possible. +- **Provide specific examples to demonstrate the steps**. Include copy/pasteable snippets which you use in those examples, as Markdown code blocks. + + + +## Styleguides + +### Git Commit Messages + +- Use the present tense ("Add feature" not "Added feature") +- Use the imperative mood ("Move cursor to..." not "Moves cursor to...") +- Limit the first line to 72 characters or less +- Reference issues and pull requests liberally after the first line + +### Python Styleguide + +All Python code must adhere to [PEP 8](https://www.python.org/dev/peps/pep-0008/), and we use `autopep8` for automatic code formatting. Please see the [autopep8 documentation](https://github.com/hhatto/autopep8) for more details. The autopep8 settings can be found in setup.cfg. + + +## Additional Notes + +Feel free to propose changes to this document in a pull request. diff --git a/PCNtoolkit.drawio b/PCNtoolkit.drawio new file mode 100644 index 00000000..5bf3ed1d --- /dev/null +++ b/PCNtoolkit.drawio @@ -0,0 +1,909 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/README.md b/README.md index 2c7eb533..fa37c7d4 100644 --- a/README.md +++ b/README.md @@ -49,7 +49,7 @@ conda install -y pandas scipy Install pip dependencies ``` -pip --no-cache-dir install nibabel sklearn torch glob3 +pip --no-cache-dir install nibabel scikit-learn torch glob3 ``` Clone the repo diff --git a/doc/build/doctrees/environment.pickle b/doc/build/doctrees/environment.pickle index 4b4534f8..ed234a5f 100644 Binary files a/doc/build/doctrees/environment.pickle and b/doc/build/doctrees/environment.pickle differ diff --git a/doc/build/doctrees/index.doctree b/doc/build/doctrees/index.doctree index dce80dcc..6b3b646b 100644 Binary files a/doc/build/doctrees/index.doctree and b/doc/build/doctrees/index.doctree differ diff --git a/doc/build/doctrees/pages/BLR_normativemodel_protocol.doctree b/doc/build/doctrees/pages/BLR_normativemodel_protocol.doctree index 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a/doc/build/html/_static/doctools.js +++ b/doc/build/html/_static/doctools.js @@ -10,13 +10,6 @@ */ "use strict"; -const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ - "TEXTAREA", - "INPUT", - "SELECT", - "BUTTON", -]); - const _ready = (callback) => { if (document.readyState !== "loading") { callback(); @@ -25,11 +18,73 @@ const _ready = (callback) => { } }; +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + /** * Small JavaScript module for the documentation. */ const Documentation = { init: () => { + Documentation.highlightSearchWords(); Documentation.initDomainIndexTable(); Documentation.initOnKeyListeners(); }, @@ -71,6 +126,51 @@ const Documentation = { Documentation.LOCALE = catalog.locale; }, + /** + * highlight the search words provided in the url in the text + */ + highlightSearchWords: () => { + const highlight = + new URLSearchParams(window.location.search).get("highlight") || ""; + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + const url = new URL(window.location); + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + }, + /** * helper function to focus on search bar */ @@ -110,11 +210,15 @@ const Documentation = { ) return; + const blacklistedElements = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", + ]); document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.altKey || event.ctrlKey || event.metaKey) return; + if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements + if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys if (!event.shiftKey) { switch (event.key) { @@ -136,6 +240,10 @@ const Documentation = { event.preventDefault(); } break; + case "Escape": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.hideSearchWords(); + event.preventDefault(); } } diff --git a/doc/build/html/_static/documentation_options.js b/doc/build/html/_static/documentation_options.js index be87342d..908cd41f 100644 --- a/doc/build/html/_static/documentation_options.js +++ b/doc/build/html/_static/documentation_options.js @@ -10,5 +10,5 @@ var DOCUMENTATION_OPTIONS = { SOURCELINK_SUFFIX: '.txt', 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// $& means the whole matched string -const _displayItem = (item, searchTerms) => { +const _displayItem = (item, highlightTerms, searchTerms) => { const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const [docName, title, anchor, descr, score, _filename] = item; + const [docName, title, anchor, descr] = item; let listItem = document.createElement("li"); let requestUrl; @@ -82,12 +82,13 @@ const _displayItem = (item, searchTerms) => { requestUrl = docUrlRoot + docName + docFileSuffix; linkUrl = docName + docLinkSuffix; } + const params = new URLSearchParams(); + params.set("highlight", [...highlightTerms].join(" ")); let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; + linkEl.href = linkUrl + "?" + params.toString() + anchor; linkEl.innerHTML = title; if (descr) - listItem.appendChild(document.createElement("span")).innerHTML = + listItem.appendChild(document.createElement("span")).innerText = " (" + descr + ")"; else if (showSearchSummary) fetch(requestUrl) @@ -95,7 +96,7 @@ const _displayItem = (item, searchTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, highlightTerms) ); }); Search.output.appendChild(listItem); @@ -115,14 +116,15 @@ const _finishSearch = (resultCount) => { const _displayNextItem = ( results, resultCount, + highlightTerms, searchTerms ) => { // results left, load the summary and display it // this is intended to be dynamic (don't sub resultsCount) if (results.length) { - _displayItem(results.pop(), searchTerms); + _displayItem(results.pop(), highlightTerms, searchTerms); setTimeout( - () => _displayNextItem(results, resultCount, searchTerms), + () => _displayNextItem(results, resultCount, highlightTerms, searchTerms), 5 ); } @@ -153,8 +155,10 @@ const Search = { _pulse_status: -1, htmlToText: (htmlString) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const htmlElement = document + .createRange() + .createContextualFragment(htmlString); + _removeChildren(htmlElement.querySelectorAll(".headerlink")); const docContent = htmlElement.querySelector('[role="main"]'); if (docContent !== undefined) return docContent.textContent; console.warn( @@ -235,12 +239,6 @@ const Search = { * execute search (requires search index to be loaded) */ query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -268,10 +266,6 @@ const Search = { } }); - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - // console.debug("SEARCH: searching for:"); // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); @@ -280,40 +274,6 @@ const Search = { let results = []; _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - // lookup as object objectTerms.forEach((term) => results.push(...Search.performObjectSearch(term, objectTerms)) @@ -360,7 +320,7 @@ const Search = { // console.info("search results:", Search.lastresults); // print the results - _displayNextItem(results, results.length, searchTerms); + _displayNextItem(results, results.length, highlightTerms, searchTerms); }, /** @@ -441,8 +401,8 @@ const Search = { // prepare search const terms = Search._index.terms; const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; const docNames = Search._index.docnames; + const filenames = Search._index.filenames; const titles = Search._index.titles; const scoreMap = new Map(); @@ -539,15 +499,16 @@ const Search = { /** * helper function to return a node containing the * search summary for a given text. keywords is a list - * of stemmed words. + * of stemmed words, highlightWords is the list of normal, unstemmed + * words. the first one is used to find the occurrence, the + * latter for highlighting it. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, highlightWords) => { + const text = Search.htmlToText(htmlText).toLowerCase(); if (text === "") return null; - const textLower = text.toLowerCase(); const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) + .map((k) => text.indexOf(k.toLowerCase())) .filter((i) => i > -1) .slice(-1)[0]; const startWithContext = Math.max(actualStartPosition - 120, 0); @@ -555,9 +516,13 @@ const Search = { const top = startWithContext === 0 ? "" : "..."; const tail = startWithContext + 240 < text.length ? "..." : ""; - let summary = document.createElement("p"); + let summary = document.createElement("div"); summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + summary.innerText = top + text.substr(startWithContext, 240).trim() + tail; + + highlightWords.forEach((highlightWord) => + _highlightText(summary, highlightWord, "highlighted") + ); return summary; }, diff --git a/doc/build/html/genindex.html b/doc/build/html/genindex.html index 96a1dc53..1509fff9 100644 --- a/doc/build/html/genindex.html +++ b/doc/build/html/genindex.html @@ -1,93 +1,53 @@ - - - - + - - - - + + Index — Predictive Clinical Neuroscience Toolkit 0.20 documentation - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - - - - + - - - +
- -
- - -
- - - - - - - - - + \ No newline at end of file diff --git a/doc/build/html/index.html b/doc/build/html/index.html index 7296db39..680db572 100644 --- a/doc/build/html/index.html +++ b/doc/build/html/index.html @@ -1,94 +1,54 @@ - - - - + - - + - - + Predictive Clinical Neuroscience toolkit — Predictive Clinical Neuroscience Toolkit 0.20 documentation - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - - - - + - - - +
- -
- - -
- - - - - - - - - + \ No newline at end of file diff --git a/doc/build/html/pages/BLR_normativemodel_protocol.html b/doc/build/html/pages/BLR_normativemodel_protocol.html index 6e457f4b..1849646d 100644 --- a/doc/build/html/pages/BLR_normativemodel_protocol.html +++ b/doc/build/html/pages/BLR_normativemodel_protocol.html @@ -1,95 +1,55 @@ - - - - + - - + - - + BLR tutorial — Predictive Clinical Neuroscience Toolkit 0.20 documentation - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - - - - + - - - +
- -
- - -
-

Algorithm & Modeling

+

Algorithm & Modeling

-

Basis expansion using B-Splines

+

Basis expansion using B-Splines

Now, set up a B-spline basis set that allows us to perform nonlinear regression using a linear model, using the following commands. This basis is deliberately chosen to not to be too flexible so that it can @@ -747,7 +669,7 @@

Basis expansion using B-Splines -

Estimate normative model

+

Estimate normative model

Set up a variable (data_dir) that specifies the path to the ROI directories that were created in Step 7. Initiate two empty pandas data frames where the evaluation metrics are the column names, as follows; @@ -922,9 +844,9 @@

Estimate normative model -

Evaluation & Interpretation

+

Evaluation & Interpretation

-

Describe the normative model performance

+

Describe the normative model performance

In step 11, when we looped over each region of interest in the roi_ids list (created in step 4) and evaluated the normative model on the independent test set, it also computed the evaluation metrics @@ -987,10 +909,10 @@

Describe the normative model performance -

Visualize normative model outputs

+

Visualize normative model outputs

-

Figure 4A viz

+

Figure 4A viz

pd.set_option('display.max_rows', 500)
 pd.set_option('display.max_columns', 500)
 pd.set_option('display.width', 1000)
@@ -1023,7 +945,7 @@ 

Figure 4A viznotebook.

-

Post-Hoc analysis ideas

+

Post-Hoc analysis ideas

The code for running SVM classification and classical case vs. control t-testing on the outputs of normative modeling can be found in this notebook.

@@ -1040,51 +962,33 @@

Post-Hoc analysis ideas -

- - - - - - - - - - - - + \ No newline at end of file diff --git a/doc/build/html/pages/FAQs.html b/doc/build/html/pages/FAQs.html index b0ac81f0..430d3036 100644 --- a/doc/build/html/pages/FAQs.html +++ b/doc/build/html/pages/FAQs.html @@ -1,95 +1,55 @@ - - - - + - - + - - + FAQs — Predictive Clinical Neuroscience Toolkit 0.20 documentation - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - - - - + - - - +
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- - - - - - - - - + \ No newline at end of file diff --git a/doc/build/html/pages/HBR_NormativeModel_FCONdata_Tutorial.html b/doc/build/html/pages/HBR_NormativeModel_FCONdata_Tutorial.html index 2e1a829a..ed46b8dc 100644 --- a/doc/build/html/pages/HBR_NormativeModel_FCONdata_Tutorial.html +++ b/doc/build/html/pages/HBR_NormativeModel_FCONdata_Tutorial.html @@ -1,95 +1,55 @@ - - - - + - - + - - + HBR tutorial — Predictive Clinical Neuroscience Toolkit 0.20 documentation - - - - - - + + + + + + + - + - - - - - - - - - - - - - - - - - - + - - - +
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