Merge commit '2b65c99' into pythonplugin

opencor · Apr 5, 2018 · 130836e · 130836e
1 parent e010c71
commit 130836e
Show file tree

Hide file tree

Showing 87 changed files with 1,909 additions and 1,382 deletions.
diff --git a/doc/3rdparty/jQuery/jquery.js b/doc/3rdparty/jQuery/jquery.js
diff --git a/doc/developer/develop/res/stylesheet.css b/doc/developer/develop/res/stylesheet.css
@@ -15,12 +15,12 @@ span.label {
 }
 
 span.bug {
-    background: rgb(225, 29, 33);
+    background: rgb(182, 2, 5);
     color: rgb(255, 255, 255);
 }
 
 span.feature {
-    background: rgb(0, 152, 0);
+    background: rgb(14, 138, 22);
     color: rgb(255, 255, 255);
 }
 
@@ -29,11 +29,11 @@ span.improvement {
 }
 
 span.linux {
-    background: rgb(250, 216, 199);
+    background: rgb(249, 208, 196);
 }
 
 span.macos {
-    background: rgb(199, 222, 248);
+    background: rgb(197, 222, 245);
 }
 
 span.regression {
@@ -45,5 +45,5 @@ span.task {
 }
 
 span.windows {
-    background: rgb(191, 229, 191);
+    background: rgb(194, 224, 198);
 }
diff --git a/doc/developer/prerequisites.html b/doc/developer/prerequisites.html
@@ -40,7 +40,7 @@
                 </ul>
             </li>
             <li>
-                <a href="https://www.qt.io/">Qt</a> 5.9.3 LTS: a cross-platform application and UI framework (<a href="https://www.qt.io/ide/">Qt Creator</a> is its supporting IDE):
+                <a href="https://www.qt.io/">Qt</a> 5.9.4 LTS: a cross-platform application and UI framework (<a href="https://www.qt.io/ide/">Qt Creator</a> is its supporting IDE):
 
                 <ul>
                     <li><strong><a href="https://download.qt.io/official_releases/online_installers/qt-unified-windows-x86-online.exe">Windows</a></strong>;</li>
@@ -57,9 +57,9 @@
         </p>
 
         <ul>
-            <li><strong>Windows:</strong> <code>C:\Program Files\Git\bin</code>, <code>C:\Program Files\CMake\bin</code>, <code>C:\Qt\5.9.3\msvc2015_64\bin</code> and <code>C:\Qt\Tools\QtCreator\bin</code>;</li>
-            <li><strong>Linux:</strong> <code>/opt/Qt/5.9.3/gcc_64/bin</code> in <code>/etc/environment</code> on Ubuntu; and</li>
-            <li><strong>macOS:</strong> <code>/Applications/Qt/5.9.3/clang_64/bin</code> in <code>/etc/profile</code>.</li>
+            <li><strong>Windows:</strong> <code>C:\Program Files\Git\bin</code>, <code>C:\Program Files\CMake\bin</code>, <code>C:\Qt\5.9.4\msvc2015_64\bin</code> and <code>C:\Qt\Tools\QtCreator\bin</code>;</li>
+            <li><strong>Linux:</strong> <code>/opt/Qt/5.9.4/gcc_64/bin</code> in <code>/etc/environment</code> on Ubuntu; and</li>
+            <li><strong>macOS:</strong> <code>/Applications/Qt/5.9.4/clang_64/bin</code> in <code>/etc/profile</code>.</li>
         </ul>
 
         <script type="text/javascript">

diff --git a/doc/developer/thirdPartyLibraries.html b/doc/developer/thirdPartyLibraries.html
@@ -89,7 +89,7 @@
                 </ul>
             </li>
             <li>
-                <a href="https://jquery.com/">jQuery</a> 3.2.1: a fast and concise <a href="https://en.wikipedia.org/wiki/JavaScript">JavaScript</a> library that simplifies <a href="https://www.w3.org/html/">HTML</a> document traversing, event handling, animating, and <a href="https://en.wikipedia.org/wiki/Ajax_(programming)">Ajax</a> interactions for rapid web development.
+                <a href="https://jquery.com/">jQuery</a> 3.3.1: a fast and concise <a href="https://en.wikipedia.org/wiki/JavaScript">JavaScript</a> library that simplifies <a href="https://www.w3.org/html/">HTML</a> document traversing, event handling, animating, and <a href="https://en.wikipedia.org/wiki/Ajax_(programming)">Ajax</a> interactions for rapid web development.
                 <ul>
                     <li>Location: <a href="https://github.com/opencor/opencor/tree/master/doc/3rdparty/jQuery"><code>[OpenCOR]/doc/3rdparty/jQuery</code></a>.</li>
                     <li>Licensing: <a href="https://opensource.org/licenses/MIT">MIT</a>.</li>
@@ -103,7 +103,7 @@
                 </ul>
             </li>
             <li>
-                <a href="https://libgit2.github.com/">libgit2</a> 0.26: a portable, pure C implementation of the <a href="https://git-scm.com/">Git</a> core methods provided as a re-entrant linkable library with a solid API.
+                <a href="https://libgit2.github.com/">libgit2</a> 0.26.0: a portable, pure C implementation of the <a href="https://git-scm.com/">Git</a> core methods provided as a re-entrant linkable library with a solid API.
                 <ul>
                     <li>Location: <a href="https://github.com/opencor/opencor/tree/master/src/plugins/thirdParty/libgit2"><code>[OpenCOR]/src/plugins/thirdParty/libgit2</code></a>.</li>
                     <li>Licensing: <a href="https://opensource.org/licenses/GPL-2.0">GPL v2.0</a> with linking exception.</li>
@@ -197,7 +197,7 @@
                 </ul>
             </li>
             <li>
-                <a href="https://github.com/OpenCMISS/zinc">Zinc</a> 3.1.2: a library for creating software to interact with and visualise complex finite element models and image-based fields.
+                <a href="https://github.com/OpenCMISS/zinc">Zinc</a> 3.1.2: a library for creating software to interact with and visualise complex finite element models and image-based fields.
                 <ul>
                     <li>Location: <a href="https://github.com/opencor/opencor/tree/master/src/plugins/thirdParty/Zinc"><code>[OpenCOR]/src/plugins/thirdParty/Zinc</code></a>.</li>
                     <li>Licensing: <a href="https://opensource.org/licenses/MPL-2.0">MPL v2.0</a>.</li>

diff --git a/doc/downloads/index.js b/doc/downloads/index.js
@@ -18,7 +18,7 @@ var jsonData = { "versions": [
                        }
                      ]
                    },
-                   { "major": 0, "minor": 0, "patch": 0, "day": 12, "month": 1, "year": 2018, "type": 2,
+                   { "major": 0, "minor": 0, "patch": 0, "day": 31, "month": 1, "year": 2018, "type": 2,
                      "platforms": [
                        { "name": "Windows", "supported": "Windows 7 and later",
                          "files": [
@@ -37,10 +37,10 @@ var jsonData = { "versions": [
                        }
                      ],
                      "changes": [
-                       { "change": "<strong>General:</strong> improved our support for <a href=\"https://en.wikipedia.org/wiki/Differential_algebraic_equation\">DAE</a> models (see issues <a href=\"https://github.com/opencor/opencor/issues/188\">#188</a> and <a href=\"https://github.com/opencor/opencor/issues/536\">#536</a>)." },
-                       { "change": "<strong>Solvers:</strong> can now parameterise the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1510\">#1510</a>). Don't reset the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver on consecutive runs and improved its implementation (see issue <a href=\"https://github.com/opencor/opencor/issues/1512\">#1512</a>). Removed the <a href=\"https://computation.llnl.gov/projects/sundials/idas\">IDAS</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1515\">#1515</a>)." },
-                       { "change": "<strong>Simulation Experiment view:</strong> don’t incorrectly mark a CellML file as modified (see issue <a href=\"https://github.com/opencor/opencor/issues/1513\">#1513</a>)." },
-                       { "change": "<strong>Third-party libraries:</strong> upgraded the <a href=\"http://computation.llnl.gov/projects/sundials\">SUNDIALS</a> library to version 3.1.0 (see issue <a href=\"https://github.com/opencor/opencor/issues/1507\">#1507</a>)." }
+                       { "change": "<strong>General:</strong> upgraded to Qt 5.9.4 LTS (see issue <a href=\"https://github.com/opencor/opencor/issues/1526\">#1526</a>). A new file (with no specific type) is not wrongly considered to be a COMBINE archive anymore (see issue <a href=\"https://github.com/opencor/opencor/issues/1530\">#1530</a>)." },
+                       { "change": "<strong>PMR window:</strong> properly refresh the list of public exposures when changing the PMR instance (see issue <a href=\"https://github.com/opencor/opencor/issues/1521\">#1521</a>)." },
+                       { "change": "<strong>Simulation support:</strong> addressed a problem with fixing and then saving a previously invalid simulation (see issue <a href=\"https://github.com/opencor/opencor/issues/1533\">#1533</a>)." },
+                       { "change": "<strong>Simulation Experiment view:</strong> added support for multiple runs (see issue <a href=\"https://github.com/opencor/opencor/issues/1523\">#1523</a>)." }
                      ]
                    },
                    { "major": 0, "minor": 4, "patch": 1, "day": 20, "month": 5, "year": 2015, "type": 0,

diff --git a/doc/downloads/previousSnapshots.js b/doc/downloads/previousSnapshots.js
@@ -1,4 +1,29 @@
 var jsonData = { "versions": [
+                   { "major": 0, "minor": 0, "patch": 0, "day": 12, "month": 1, "year": 2018, "type": 2,
+                     "platforms": [
+                       { "name": "Windows", "supported": "Windows 7 and later",
+                         "files": [
+                           { "extension": ".exe" }, { "extension": ".zip" }
+                         ]
+                       },
+                       { "name": "Linux", "supported": "Ubuntu 16.04 LTS (Xenial Xerus) and later",
+                         "files": [
+                           { "extension": ".tar.gz" }
+                         ]
+                       },
+                       { "name": "macOS", "supported": "OS X 10.10 (Yosemite) and later",
+                         "files": [
+                           { "extension": ".dmg" }, { "extension": ".zip" }
+                         ]
+                       }
+                     ],
+                     "changes": [
+                       { "change": "<strong>General:</strong> improved our support for <a href=\"https://en.wikipedia.org/wiki/Differential_algebraic_equation\">DAE</a> models (see issues <a href=\"https://github.com/opencor/opencor/issues/188\">#188</a> and <a href=\"https://github.com/opencor/opencor/issues/536\">#536</a>)." },
+                       { "change": "<strong>Solvers:</strong> can now parameterise the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1510\">#1510</a>). Don't reset the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver on consecutive runs and improved its implementation (see issue <a href=\"https://github.com/opencor/opencor/issues/1512\">#1512</a>). Removed the <a href=\"https://computation.llnl.gov/projects/sundials/idas\">IDAS</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1515\">#1515</a>)." },
+                       { "change": "<strong>Simulation Experiment view:</strong> don’t incorrectly mark a CellML file as modified (see issue <a href=\"https://github.com/opencor/opencor/issues/1513\">#1513</a>)." },
+                       { "change": "<strong>Third-party libraries:</strong> upgraded the <a href=\"http://computation.llnl.gov/projects/sundials\">SUNDIALS</a> library to version 3.1.0 (see issue <a href=\"https://github.com/opencor/opencor/issues/1507\">#1507</a>)." }
+                     ]
+                   },
                    { "major": 0, "minor": 0, "patch": 0, "day": 23, "month": 12, "year": 2017, "type": 2,
                      "platforms": [
                        { "name": "Windows", "supported": "Windows 7 and later",

diff --git a/doc/user/whatIsNew.js b/doc/user/whatIsNew.js
@@ -1,5 +1,5 @@
 var jsonData = { "versions": [
-                   { "anchor": "latest", "description": "Latest snapshot", "day": 12, "month": 1, "year": 2018,
+                   { "anchor": "latest", "description": "Latest snapshot", "day": 31, "month": 1, "year": 2018,
                      "categories": [
                        { "name": "General",
                          "entries": [
@@ -76,6 +76,7 @@ var jsonData = { "versions": [
                            { "type": "subCategory", "name": "Simulation Experiment view (formerly known as the Single Cell view)",
                              "entries": [
                                { "type": "added", "description": "Support for log scales." },
+                               { "type": "added", "description": "Support for multiple runs." },
                                { "type": "added", "description": "Ability to customise a graph." },
                                { "type": "added", "description": "Ability to customise a graph panel." },
                                { "type": "added", "description": "Ability to show the legend of a graph panel." },

diff --git a/src/mainwindow.cpp b/src/mainwindow.cpp
@@ -587,8 +587,8 @@ void MainWindow::initializeGuiPlugin(Plugin *pPlugin)
 
         // Also keep track of GUI updates in our central widget
 
-        connect(static_cast<Core::CentralWidget *>(centralWidget()), SIGNAL(guiUpdated(Plugin *, const QString &)),
-                this, SLOT(updateGui(Plugin *, const QString &)));
+        connect(static_cast<Core::CentralWidget *>(centralWidget()), SIGNAL(guiUpdated(OpenCOR::Plugin *, const QString &)),
+                this, SLOT(updateGui(OpenCOR::Plugin *, const QString &)));
     }
 
     // Add the plugin's window, in case we are dealing with a window plugin
@@ -1295,7 +1295,8 @@ void MainWindow::showEnableActions(const QList<QAction *> &pActions)
 
 //==============================================================================
 
-void MainWindow::updateGui(Plugin *pViewPlugin, const QString &pFileName)
+void MainWindow::updateGui(OpenCOR::Plugin *pViewPlugin,
+                           const QString &pFileName)
 {
     // We come here as a result of our central widget having updated its GUI,
     // meaning that a new view or file has been selected, so we may need to

diff --git a/src/mainwindow.h b/src/mainwindow.h
@@ -153,7 +153,7 @@ private slots:
     void on_actionCheckForUpdates_triggered();
     void on_actionAbout_triggered();
 
-    void updateGui(Plugin *pViewPlugin, const QString &pFileName);
+    void updateGui(OpenCOR::Plugin *pViewPlugin, const QString &pFileName);
 
     void showDockedWindows(const bool &pShow,
                            const bool &pInitialisation = false);

diff --git a/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredata.cpp b/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredata.cpp
@@ -35,8 +35,9 @@ BiosignalmlDataStoreData::BiosignalmlDataStoreData(const QString &pFileName,
                                                    const QString &pAuthor,
                                                    const QString &pDescription,
                                                    const QString &pComment,
-                                                   const DataStore::DataStoreVariables &pSelectedVariables) :
-    DataStore::DataStoreData(pFileName, pSelectedVariables),
+                                                   DataStore::DataStore *pDataStore,
+                                                   const DataStore::DataStoreVariables &pVariables) :
+    DataStore::DataStoreData(pFileName, pDataStore, pVariables),
     mName(pName),
     mAuthor(pAuthor),
     mDescription(pDescription),

diff --git a/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredata.h b/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredata.h
@@ -42,7 +42,8 @@ class BiosignalmlDataStoreData : public DataStore::DataStoreData
                                       const QString &pAuthor,
                                       const QString &pDescription,
                                       const QString &pComment,
-                                      const DataStore::DataStoreVariables &pSelectedVariables);
+                                      DataStore::DataStore *pDataStore,
+                                      const DataStore::DataStoreVariables &pVariables);
 
     QString name() const;
     QString author() const;

diff --git a/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredialog.cpp b/src/plugins/dataStore/BioSignalMLDataStore/src/biosignalmldatastoredialog.cpp
@@ -40,7 +40,8 @@ namespace BioSignalMLDataStore {
 
 //==============================================================================
 
-BiosignalmlDataStoreDialog::BiosignalmlDataStoreDialog(DataStore::DataStore *pDataStore, QWidget *pParent) :
+BiosignalmlDataStoreDialog::BiosignalmlDataStoreDialog(DataStore::DataStore *pDataStore,
+                                                       QWidget *pParent) :
     DataStore::DataStoreDialog(pDataStore, false, pParent)
 {
     // Customise our GUI