Merge branch 'master' of https://github.com/cortex-lab/matlab-ci

Author: k1o0

README.md

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+# MATLAB-ci
+
+A small set of modules written in Node.js for running automated tests of MATLAB code in response to GitHub events.  Also submits code coverage to the Coveralls API.
+
+## Getting Started
+
+Run the install script to install all dependencies, then create your .env file containing your App's tokens, secrets, etc.
+
+### Prerequisites
+
+Requires MATLAB 2017a or later and Node.js.  The following Node.js modules are required:
+
+```
+npm install --save express dotenv @octokit/app @octokit/request ...
+github-webhook-handler smee-client xml2js
+```
+
+### Installing
+
+Make sure runAllTests.m is on your MATLAB paths
+
+## Running the tests
+
+TODO
+
+### Break down into end to end tests
+
+Explain what these tests test and why
+
+```
+Give an example
+```
+
+### And coding style tests
+
+Explain what these tests test and why
+
+```
+Give an example
+```
+
+## Deployment
+
+To work properly you need to create install a Github app on your target repository and download the private key.  Update your .env file like so:
+
+```
+GITHUB_PRIVATE_KEY=path\to\private-key.pem
+GITHUB_APP_IDENTIFIER=1234
+GITHUB_WEBHOOK_SECRET=
+WEBHOOK_PROXY_URL=https://smee.io/abcd
+RIGBOX_REPO_PATH=C:\Path\To\Code\Repo
+COVERALLS_TOKEN=
+```
+
+To run at startup create a batch file with the following command:
+
+```batch
+cmd /k node -r dotenv/config dotenv_config_path=/Path/To/Env/Vars ./Path/To/index.js 
+```
+
+Create a shortcut in your startup folder ([Windows-logo] + [R] in Windows-10 and enter the command `shell:startup`)
+
+## Built With
+
+* [Coveralls](coveralls.io) - Code coverage
+
+## Contributing
+
+Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c63ec426) for details on our code of conduct, and the process for submitting pull requests to us.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/your/project/tags). 
+
+## Authors
+
+* **Miles Wells**
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details

coverage.js

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+/**
+ * Coverage module loads a Cobertura Format XML file containing code coverage information and reformats it into an
+ * object for POSTing to the Coveralls API.
+ * @module ./coverage
+ * @example
+ * // create queue
+ * const queue = new require(./queue.js).Queue()
+ * queue.process((job, done) => {
+ *   console.log('Job with id ' + job.id + ' is being processed');
+ *   setTimeout(done, 3000);
+ * });
+ * var data = {key: 'value'};
+ * queue.add(data);
+ * @requires module:dotenv For loading in API token
+ * @requires module:xml2js For converting XML to object
+ * @version 0.9.0
+ * @author Miles Wells [<k1o0@3tk.co>]
+ * @license Apache-2.0
+ */
+
+var fs = require('fs'),
+    xml2js = require('xml2js'),
+    crypto = require('crypto'),
+    assert = require('assert').strict,
+    parser = new xml2js.Parser(),
+    timestamp, md5;
+var timestamp;
+var token = process.env.COVERALLS_TOKEN;
+
+/**
+ * Formates list of classes from XML file and return object formatted for the Coveralls API.
+ * @see {@link https://docs.coveralls.io/api-reference|Coveralls API docs}
+ * @param {Array} classList - An array of class objects from the loaded XML file.
+ * @param {String} path - The root path of the code repository.
+ * @param {String} sha - The commit SHA for this coverage test.
+ * @returns {Object} Object containing array of source code files and their code coverage
+ * @todo Generalize path default
+ */
+const formatCoverage = function(classList, path, sha) {
+  var job = {};
+  var sourceFiles = [];
+  typeof path != "undefined" ? 'C:\\Users\\User\\' : path; // default FIXME
+  // For each class, create file object containing array of lines covered and add to sourceFile array
+  classList.forEach( async c => {
+    let file = {}; // Initialize file object
+    var digest = md5(path + c.$.filename); // Create digest and line count for file
+    let lines = new Array(digest.count).fill(null); // Initialize line array the size of source code file
+    c.lines[0].line.forEach(ln => {
+      let n = Number(ln.$.number);
+      if (n <= digest.count) {lines[n] = Number(ln.$.hits) }
+    });
+    // create source file object
+    file.name = c.$.filename;
+    file.source_digest = digest.hash;
+    file.coverage = lines; // file.coverage[0] == line 1
+    sourceFiles.push(file);
+  });
+
+  job.repo_token = token; // env secret token?
+  job.service_name = 'continuous-integration/ZTEST';
+  // The associated pull request ID of the build. Used for updating the status and/or commenting.
+  job.service_pull_request = '';
+  job.source_files = sourceFiles;
+  job.commit_sha = sha;
+  job.run_at = timestamp; // "2013-02-18 00:52:48 -0800"
+  return job;
+}
+
+/**
+ * Loads a code coverage XML file in Cobertura Format and returns payload object for Coveralls API
+ * @see {@link https://docs.coveralls.io/api-reference|Coveralls API docs}
+ * @param {String} path - Path to the XML file containing coverage information.
+ * @param {String} sha - The commit SHA for this coverage test
+ * @returns {Object} Object containing array of source code files and their code coverage
+ * @todo Remove assert
+ * @todo Generalize ignoring of submodules
+ * @see {@link https://github.com/cobertura/cobertura/wiki|Cobertura Wiki}
+ */
+const coverage = function(path, sha) {
+  fs.readFile(path, function(err, data) { // Read in XML file
+     parser.parseString(data, function (err, result) { // Parse XML
+        const rigboxPath = result.coverage.sources[0].source[0]; // Extract root code path
+        assert(rigboxPath.endsWith('Rigbox\\'), 'Incorrect source code repository')
+        timestamp = new Date(result.coverage.$.timestamp*1000); // Convert UNIX timestamp to Date object
+        let classes = []; // Initialize classes array
+
+        const packages = result.coverage.packages[0].package;
+        packages.forEach(package => { classes.push(package.classes[0].class) }); // Get all classes
+        classes = classes.reduce((acc, val) => acc.concat(val), []); // Flatten
+        //console.log(classes.length);
+
+        // The submodules
+        var alyx_matlab = [];
+        var signals = [];
+        var npy_matlab = [];
+        var wheelAnalysis = [];
+        // Sort into piles
+        classes = classes.filter(function (e) {
+            if (e.$.filename.search(/(tests\\|_.*test|docs\\)/i) != -1) {return false;} // Filter out tests and docs
+            if (!Array.isArray(e.lines[0].line)) {return false;} // Filter out files with no functional lines
+            if (e.$.filename.startsWith('alyx-matlab\\')) {alyx_matlab.push(e); return false;}
+            if (e.$.filename.startsWith('signals\\')) {signals.push(e); return false;}
+            if (e.$.filename.startsWith('npy-matlab\\')) {npy_matlab.push(e); return false;}
+            if (e.$.filename.startsWith('wheelAnalysis\\')) {wheelAnalysis.push(e); return false;}
+            else {return true};
+        });
+        //console.log(obj.source_files[0].coverage.length);
+        return obj = formatCoverage(classes, rigboxPath);
+     });
+  });
+};
+
+/**
+ * Loads file containing source code, returns a hash and line count
+ * @param {String} path - Path to the source code file.
+ * @returns {Object} key `Hash` contains MD5 digest string of file; `count` contains number of lines in source file
+ */
+const md5 = function(path) {
+  var hash = crypto.createHash('md5'); // Creating hash object
+  var buf = fs.readFileSync(path, 'utf-8'); // Read in file
+  var count = buf.split(/\r\n|\r|\n/).length; // Count the number of lines
+  hash.update(buf, 'utf-8'); // Update hash
+  return {hash: hash.digest('hex'), count: count};
+};
+
+// Export Coverage
+module.exports = coverage;