Merge pull request #68 from cortex-lab/dev

v3.0.0

CHANGELOG.md

@@ -1,6 +1,33 @@
 # Changelog
 
-## [Latest](https://github.com/cortex-lab/matlab-ci/commits/master) [2.2.0]
+## [Latest](https://github.com/cortex-lab/matlab-ci/commits/master) [3.0.0]
+
+## Added
+
+ - any number of tasks may be added for a job, which are then executed in series 
+ - now serves a Webpage that shows the log in realtime
+ - added a jobs endpoint to see which jobs are on the pile
+ - stderr is piped to log file
+ - flake8 errors are neatly captured in GitHub status description
+ - param to skip checks when only ignored files changed
+ - param to skip draft PR event checks 
+
+ ## Modified
+
+ - renamed MATLAB-CI to labCI
+ - records endpoint can return pending jobs
+ - tests badge endpoint returns 'error' on errored tests instead of 'unknown'
+ - job waits for coverage calculation and updating of records before finishing
+ - On successful completion of tests the duration is appended to the description
+
+## [2.2.1]
+
+## Modified
+
+ - fix error where github event incorrectly rejected
+ - fix bug incorrect log name when endpoint called with branch name
+
+## [2.2.0]
 
 ## Added
  - nyc dependency for manual coverage of matlab-ci

README.md

@@ -1,8 +1,8 @@
-# MATLAB-ci
+# LabCI
 [![Build Status](https://travis-ci.com/cortex-lab/matlab-ci.svg?branch=master)](https://travis-ci.com/cortex-lab/matlab-ci)
-[![Coverage](https://img.shields.io/badge/coverage-81.07-green)](https://img.shields.io/badge/coverage-72.35-yellowgreen)
+[![Coverage](https://img.shields.io/badge/coverage-92.13-brightgreen)](https://img.shields.io/badge/coverage-72.35-yellowgreen)
 
-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.
+A small set of modules written in Node.js for running automated tests of MATLAB and Python code in response to GitHub events.  Also submits code coverage to the Coveralls API.
 
 Currently unsupported:
 * Running tests on forked repositories
@@ -26,11 +26,8 @@ Create a shell/batch script for preparing your environment, and one for running
 Add these to the settings.json file in config:
 ```
 {
-  "setup_function": "./prep_env.BAT",
-  "test_function": "./run_tests.BAT",
   "listen_port": 3000,
   "timeout": 480000,
-  "program": "python",
   "strict_coverage": false,
   "events": {
     "push": {
@@ -40,15 +37,23 @@ Add these to the settings.json file in config:
     "pull_request": {
       "checks": ["continuous-integration", "coverage"],
       "actions": ["opened", "synchronize", "reopened"],
-      "ref_ignore": ["documentation", "gh-pages"]
+      "ref_ignore": ["documentation", "gh-pages"],
+      "files_ignore": [".*\\.yml", ".*\\.md", "LICEN[SC]E"]
     }
   }
+  "routines": {
+    "*": ["prep_env.BAT", "run_tests.BAT"]
+  }
 }
 ``` 
 Some extra optional settings:
 
 - `shell` - optional shell to use when calling scripts (see `child_process.execFile` options).
 - `events:event:ref_include` - same as `ref_ignore`, but a pass list instead of block list.
+- `events:event:files_ignore` - list of files whose changes can be ignored.  If only ignored files
+are changed checks are skipped.
+- `events:pull_request:ignore_drafts` - if true draft pull request actions are skipped (NB: Be
+sure to add 'ready_for_review' to the actions list when ignoring drafts).
 - `kill_children` - if present and true, `tree-kill` is used to kill the child processes, required 
 if shell/batch script forks test process (e.g. a batch script calls python).
 - `repos` - an array of submodules or map of modules to their corresponding paths.

config/config.js

@@ -2,78 +2,78 @@ const userSettings = require('./settings.json') || {};  // User settings
 const path = require('path');
 env = process.env.NODE_ENV || 'production';
 const appdata = process.env.APPDATA || process.env.HOME;
-const dataPath = process.env.APPDATA? path.join(appdata, 'CI') : path.join(appdata, '.ci');
+const dataPath = process.env.APPDATA ? path.join(appdata, 'CI') : path.join(appdata, '.ci');
 const fixtureDir = path.resolve(__dirname, '..', 'test', 'fixtures');
 const dbFilename = '.db.json';
 let settings;
 
 // Defaults for when there's no user file; will almost certainly fail
-defaults = {
-    setup_function: null,
-    test_function: null,
+const defaults = {
+    max_description_len: 140,  // GitHub status API has a description char limit
     listen_port: 3000,
-    timeout: 8*60000,
-    program: "python",
+    timeout: 8 * 60000,
     strict_coverage: false,
     events: {
         push: {
             checks: null,
-            ref_ignore: ["documentation", "gh-pages"]
+            ref_ignore: ['documentation', 'gh-pages']
         },
         pull_request: {
-            checks: ["continuous-integration", "coverage"],
-            actions: ["opened", "synchronize", "reopen"],
-            ref_ignore: ["documentation", "gh-pages"]
+            checks: ['continuous-integration', 'coverage'],
+            actions: ['opened', 'synchronize', 'reopen'],
+            ref_ignore: ['documentation', 'gh-pages']
         }
     },
     dataPath: dataPath,
     dbFile: path.join(dataPath, dbFilename)
-}
+};
 
 // Settings for the tests
-testing = {
+const testing = {
     listen_port: 3000,
     timeout: 60000,
-    setup_function: 'prep_env.BAT',
-    test_function: "run_tests.BAT",
     events: {
         push: {
-            checks: "continuous-integration",
-            ref_ignore: "documentation"
+            checks: 'continuous-integration',
+            ref_ignore: 'documentation'
         },
         pull_request: {
-            checks: ["coverage", "continuous-integration"],
-            actions: ["opened", "synchronize"],
-            ref_ignore: ["documentation", "gh-pages"]
+            checks: ['coverage', 'continuous-integration'],
+            actions: ['opened', 'synchronize'],
+            ref_ignore: ['documentation', 'gh-pages']
         }
     },
+    routines: {
+        '*': ['prep_env.BAT', 'run_tests.BAT']
+    },
     dataPath: fixtureDir,
     dbFile: path.join(fixtureDir, dbFilename)  // cache of test results
-}
+};
 
 // Pick the settings to return
 if (env.startsWith('test')) {
-  settings = testing;
+    settings = testing;
 } else if (userSettings) {
-  settings = userSettings;
-  if (!('dbFile' in settings)) {
-    settings.dbFile = path.join(dataPath, dbFilename)
-  }
-  if (!('dataPath' in settings)) {
-      settings.dataPath = dataPath;
-  }
+    settings = userSettings;
 } else {
-  settings = defaults;
+    settings = defaults;
+}
+
+// Ensure defaults for absent fields
+for (let field in defaults) {
+    if (!(field in settings)) settings[field] = defaults[field];
 }
 
 // Check ENV set up correctly
 required = ['GITHUB_PRIVATE_KEY', 'GITHUB_APP_IDENTIFIER', 'GITHUB_WEBHOOK_SECRET',
-            'WEBHOOK_PROXY_URL', 'REPO_PATH', 'REPO_NAME', 'REPO_OWNER', 'TUNNEL_HOST',
-            'TUNNEL_SUBDOMAIN'];
-missing = required.filter(o => { return !process.env[o] });
+    'WEBHOOK_PROXY_URL', 'REPO_PATH', 'REPO_NAME', 'REPO_OWNER', 'TUNNEL_HOST',
+    'TUNNEL_SUBDOMAIN'];
+missing = required.filter(o => {
+    return !process.env[o];
+});
 if (missing.length > 0) {
-    errMsg = `Env not set correctly; the following variables not found: \n${missing.join(', ')}`
-    throw ReferenceError(errMsg)
+    errMsg = `Env not set correctly; the following variables not found: \n${missing.join(', ')}`;
+    throw ReferenceError(errMsg);
 }
 
-module.exports = { settings }
+module.exports = { settings };

config/settings.json

@@ -1,9 +1,6 @@
 {
-  "setup_function": "prep_env.BAT",
-  "test_function": "run_tests.BAT",
   "listen_port": 3000,
   "timeout": 480000,
-  "program": "python",
   "strict_coverage": false,
   "events": {
     "push": {
@@ -15,5 +12,8 @@
       "actions": ["opened", "synchronize", "reopened"],
       "ref_ignore": ["documentation", "gh-pages"]
     }
+  },
+  "routines": {
+    "*": ["prep_env.BAT", "run_tests.BAT"]
   }
 }

coverage.js

@@ -21,10 +21,9 @@
 const fs = require('fs'),
     xml2js = require('xml2js'),
     crypto = require('crypto'),
-    assert = require('assert').strict,
     parser = new xml2js.Parser(),
     path = require('path');
-var timestamp, cb;
+var timestamp;
 
 var token = process.env.COVERALLS_TOKEN;
 
@@ -33,14 +32,14 @@ var token = process.env.COVERALLS_TOKEN;
  * 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
- * @todo Make asynchronous
  */
 function md5(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};
+    const hash = crypto.createHash('md5'); // Creating hash object
+    const buf = fs.readFileSync(path, 'utf-8'); // Read in file
+    const 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};
 }
 
 
@@ -50,42 +49,41 @@ function md5(path) {
  * @param {Array} classList - An array of class objects from the loaded XML file.
  * @param {String} srcPath - The root path of the code repository.
  * @param {String} sha - The commit SHA for this coverage test.
- * @param {function} callback - The callback function to run when complete.  Takes object containing array of source
- * code files and their code coverage
  * @returns {Object}
  * @todo Generalize path default
- * @fixme Doesn't work with python's coverage
  */
-function formatCoverage(classList, srcPath, sha) {
-  var job = {};
-  var sourceFiles = [];
-  var digest;
-  srcPath = typeof srcPath != "undefined" ? srcPath : process.env.HOMEPATH; // default to home dir
-  // 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
-    let fullPath = c.$.filename.startsWith(srcPath)? c.$.filename : path.join(srcPath, c.$.filename);
-    digest = md5(fullPath); // Create digest and line count for file
-    let lines = new Array(digest.count).fill(null); // Initialize line array the size of source code file
-    c.lines[0].line.forEach(ln => {
-      let n = Number(ln.$.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);
-  });
+async function formatCoverage(classList, srcPath, sha) {
+    var job = {};
+    var sourceFiles = [];
+    var digest;
+    srcPath = typeof srcPath != 'undefined' ? srcPath : process.env.REPO_PATH; // default to home dir
+    // For each class, create file object containing array of lines covered and add to sourceFile array
+    await Promise.all(classList.map(async c => {
+        let file = {}; // Initialize file object
+        let fullPath = c.$.filename.startsWith(srcPath) ? c.$.filename : path.join(srcPath, c.$.filename);
+        digest = md5(fullPath); // Create digest and line count for file
+        let lines = new Array(digest.count).fill(null); // Initialize line array the size of source code file
+        c.lines[0].line.forEach(ln => {
+            let n = Number(ln.$.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 = `coverage/${process.env.USERDOMAIN}`;
-  // The associated pull request ID of the build. Used for updating the status and/or commenting.
-  job.service_pull_request = '';
-  job.source_files = sourceFiles;
-  job.commit_sha = sha;
-  job.run_at = timestamp; // "2013-02-18 00:52:48 -0800"
-  cb(job);
+    job.repo_token = token; // env secret token
+    job.service_name = `coverage/${process.env.USERDOMAIN}`;
+    // 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;
 }
 
 /**
@@ -95,44 +93,42 @@ function formatCoverage(classList, srcPath, sha) {
  * @param {String} sha - The commit SHA for this coverage test
  * @param {String} repo - The repo to which the commit belongs
  * @param {Array} submodules - A list of submodules for separating coverage into
- * @param {function} callback - The callback function to run when complete
  * @see {@link https://github.com/cobertura/cobertura/wiki|Cobertura Wiki}
  */
-function coverage(path, repo, sha, submodules, callback) {
-  cb = callback; // @fixme Making callback global feels hacky
-  fs.readFile(path, function(err, data) { // Read in XML file
-    if (err) {throw err}  // @fixme deal with file not found errors
-    parser.parseString(data, function (err, result) { // Parse XML
-        // Extract root code path
-        const rootPath = (result.coverage.sources[0].source[0] || process.env.REPO_PATH).replace(/[\/|\\]+$/, '')
-        assert(rootPath.endsWith(process.env.REPO_NAME), 'Incorrect source code repository')
-        timestamp = new Date(result.coverage.$.timestamp*1000); // Convert UNIX timestamp to Date object
-        let classes = []; // Initialize classes array
+function coverage(path, repo, sha, submodules) {
+    return fs.promises.readFile(path)  // Read in XML file
+        .then(parser.parseStringPromise) // Parse XML
+        .then(result => {
+            // Extract root code path
+            const rootPath = (result.coverage.sources[0].source[0] || process.env.REPO_PATH)
+                .replace(/[\/|\\]+$/, '');
+            timestamp = new Date(result.coverage.$.timestamp * 1000); // Convert UNIX timestamp to Date object
+            let classes = []; // Initialize classes array
 
-        const packages = result.coverage.packages[0].package;
-        packages.forEach(pkg => { classes.push(pkg.classes[0].class) }); // Get all classes
-        classes = classes.reduce((acc, val) => acc.concat(val), []); // Flatten
+            const packages = result.coverage.packages[0].package;
+            packages.forEach(pkg => { classes.push(pkg.classes[0].class); }); // Get all classes
+            classes = classes.reduce((acc, val) => acc.concat(val), []); // Flatten
 
-        // The submodules
-        const byModule = {'main' : []};
-        submodules.forEach((x) => { byModule[x] = []; });  // initialize submodules
+            // The submodules
+            const byModule = {'main': []};
+            submodules.forEach((x) => { byModule[x] = []; });  // initialize submodules
 
-        // Sort into piles
-        byModule['main'] = classes.filter(function (e) {
-            if (e.$.filename.search(/(tests\\|_.*test|docs\\)/i) !== -1) {return false;} // Filter out tests and docs
-            if (!Array.isArray(e.lines[0].line)) {return false;} // Filter out files with no functional lines
-            for (let submodule of submodules) {
-               if (e.$.filename.startsWith(submodule)) {
-                  byModule[submodule].push(e); return false;
-               }
-            }
-            return true;
+            // Sort into piles
+            byModule['main'] = classes.filter(function (e) {
+                if (e.$.filename.search(/(tests\\|_.*test|docs\\)/i) !== -1) return false; // Filter out tests and docs
+                if (!Array.isArray(e.lines[0].line)) return false; // Filter out files with no functional lines
+                for (let submodule of submodules) {
+                    if (e.$.filename.startsWith(submodule)) {
+                        byModule[submodule].push(e);
+                        return false;
+                    }
+                }
+                return true;
+            });
+            // Select module
+            let modules = byModule[repo] || byModule['main'];
+            return formatCoverage(modules, rootPath, sha);
         });
-        // Select module
-        let modules = byModule[repo] || byModule['main'];
-        formatCoverage(modules, rootPath, callback);
-     });
-  });
 }