Merge branch 'master' into pendulum.

opencor · Mar 1, 2019 · 0bfa010 · 0bfa010
2 parents 86c8cc0 + adf0517
commit 0bfa010
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Showing 220 changed files with 5,466 additions and 2,061 deletions.
diff --git a/distrib/linux/mesa/CMakeLists.txt b/distrib/linux/mesa/CMakeLists.txt
@@ -3,11 +3,11 @@ project(Mesa)
 # Name and version of our package
 
 set(PACKAGE_NAME Mesa)
-set(PACKAGE_VERSION 18.2.8)
+set(PACKAGE_VERSION 18.3.4)
 
 # Git tag for our library
 
-set(GIT_TAG v18.2.8)
+set(GIT_TAG v18.3.4)
 
 # Specify where our local package will be installed
 
@@ -32,9 +32,9 @@ if(USE_PREBUILT_MESA_PACKAGE)
            RELATIVE_PROJECT_SOURCE_DIR "${PROJECT_SOURCE_DIR}/${REMOTE_EXTERNAL_PACKAGE_DIR}")
 
     retrieve_package_file(${PACKAGE_NAME} ${PACKAGE_VERSION}
-                          ${RELATIVE_PROJECT_SOURCE_DIR} 8caeac7734935529ce880aed1d799e2208a3c856
+                          ${RELATIVE_PROJECT_SOURCE_DIR} febd1f5343d8106b5a1b27fa26022698f0827a95
                           SHA1_FILES ${SHA1_FILES}
-                          SHA1_VALUES 9542db2ad4e6c427d01ee061b01cf2971ea3c50f)
+                          SHA1_VALUES 65ad9049bfe22070ad006d10479686ff57fe2f1f)
 else()
     # Build Mesa as an external project
 

diff --git a/distrib/macos/Info.plist.in b/distrib/macos/Info.plist.in
@@ -48,5 +48,7 @@
         <string>${VERSION}</string>
         <key>CFBundleShortVersionString</key>
         <string>${VERSION}</string>
+        <key>NSRequiresAquaSystemAppearance</key>
+        <string>true</string>
     </dict>
 </plist>
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": 11, "month": 12, "year": 2018, "type": 2, "license": 2,
+                   { "major": 0, "minor": 0, "patch": 0, "day": 1, "month": 2, "year": 2019, "type": 2, "license": 2,
                      "platforms": [
                        { "name": "Windows", "supported": "Windows 7 and later",
                          "files": [
@@ -37,13 +37,9 @@ var jsonData = { "versions": [
                        }
                      ],
                      "changes": [
-                       { "change": "<strong>General:</strong> upgraded to Qt 5.12.0 LTS (see issue <a href=\"https://github.com/opencor/opencor/issues/1910\">#1910</a>)." },
-                       { "change": "<strong>COMBINE support:</strong> now recognise files that have a master attribute of \"1\" rather than \"true\" (see issue <a href=\"https://github.com/opencor/opencor/issues/1912\">#1912</a>)." },
-                       { "change": "<strong>Graph Panel widget:</strong> fixed a small problem with the scale range of an axis in some cases (see issue <a href=\"https://github.com/opencor/opencor/issues/1941\">#1941</a>)." },
-                       { "change": "<strong>CellML Annotation view:</strong> prevent OpenCOR from crashing after a CellML file has been rendered invalid (see issue <a href=\"https://github.com/opencor/opencor/issues/1958\">#1958</a>)." },
-                       { "change": "<strong>CellML Text view:</strong> improved Unicode support (see issue <a href=\"https://github.com/opencor/opencor/issues/1926\">#1926</a>)." },
-                       { "change": "<strong>Simulation Experiment view:</strong> ensure that graph panels are always properly aligned (see issue <a href=\"https://github.com/opencor/opencor/issues/1956\">#1956</a>)." },
-                       { "change": "<strong>Third-party libraries:</strong> upgraded <a href=\"http://www.llvm.org/\">LLVM</a>+<a href=\"http://clang.llvm.org/\">Clang</a> to version 7.0.1 (see issue <a href=\"https://github.com/opencor/opencor/issues/1917\">#1917</a>). Upgraded the <a href=\"http://computation.llnl.gov/projects/sundials\">SUNDIALS</a> library to version 4.0.2 (see issue <a href=\"https://github.com/opencor/opencor/issues/1960\">#1960</a>). Upgraded the <a href=\"http://qwt.sourceforge.net/\">Qwt</a> library to version 6.1.4 (see issue <a href=\"https://github.com/opencor/opencor/issues/1933\">#1933</a>). Upgraded <a href=\"https://www.mesa3d.org/\">Mesa</a> to version 18.2.8 (see issue <a href=\"https://github.com/opencor/opencor/issues/1945\">#1945</a>)." }
+                       { "change": "<strong>General:</strong> enforce the use of Light Mode on <a href=\"https://en.wikipedia.org/wiki/MacOS\">macOS</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/1991\">#1991</a>). Added the <code>importFile</code> and <code>importFiles</code> commands to OpenCOR's <a href=\"https://en.wikipedia.org/wiki/Uniform_Resource_Identifier\">URI scheme</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/2000\">#2000</a>)." },
+                       { "change": "<strong>Simulation Experiment view:</strong> fixed an issue with a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file / <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a> being considered modified after changing languages (see issue <a href=\"https://github.com/opencor/opencor/issues/2001\">#2001</a>)." },
+                       { "change": "<strong>Third-party libraries:</strong> upgraded <a href=\"https://riverbankcomputing.com/software/qscintilla/intro\">QScintilla</a> to version 2.11.1 (see issue <a href=\"https://github.com/opencor/opencor/issues/1983\">#1983</a>). Upgraded <a href=\"https://libgit2.github.com/\">libgit2</a> to version 0.28.1 (see issue <a href=\"https://github.com/opencor/opencor/issues/1993\">#1993</a>). Upgraded <a href=\"https://www.mesa3d.org/\">Mesa</a> to version 18.3.4 (see issue <a href=\"https://github.com/opencor/opencor/issues/1994\">#1994</a>). Upgraded the <a href=\"http://computation.llnl.gov/projects/sundials\">SUNDIALS</a> library to version 4.1.0 (see issue <a href=\"https://github.com/opencor/opencor/issues/1995\">#1995</a>). Upgraded the <a href=\"https://www.openssl.org/\">OpenSSL</a> library to version 1.0.2r (see issue <a href=\"https://github.com/opencor/opencor/issues/2009\">#2009</a>). Upgraded <a href=\"https://katex.org/\">KaTeX</a> to version 0.10.1 (see issue <a href=\"https://github.com/opencor/opencor/issues/2014\">#2014</a>)." }
                      ]
                    },
                    { "major": 0, "minor": 5, "patch": 0, "day": 15, "month": 10, "year": 2016, "type": 0, "license": 1,

diff --git a/doc/downloads/previousSnapshots.js b/doc/downloads/previousSnapshots.js
diff --git a/doc/whatIsNew.js b/doc/whatIsNew.js
@@ -1,5 +1,5 @@
 var jsonData = { "versions": [
-                   { "anchor": "latest", "description": "Latest snapshot", "day": 11, "month": 12, "year": 2018,
+                   { "anchor": "latest", "description": "Latest snapshot", "day": 1, "month": 2, "year": 2019,
                      "categories": [
                        { "name": "Editing",
                          "entries": [
@@ -19,8 +19,11 @@ var jsonData = { "versions": [
                          "entries": [
                            { "type": "subCategory", "name": "Simulation Experiment view",
                              "entries": [
+                               { "type": "added", "description": "Basic support for the import of external data." },
                                { "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
-                               { "type": "improved", "description": "Plotting of simulations." }
+                               { "type": "improved", "description": "Plotting of simulations." },
+                               { "type": "fixed", "description": "Various issues with saving a file under a new name." },
+                               { "type": "fixed", "description": "Issue with a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file / <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a> being considered modified after changing languages." }
                              ]
                            }
                          ]
@@ -33,6 +36,15 @@ var jsonData = { "versions": [
                              ]
                            }
                          ]
+                       },
+                       { "name": "Tools",
+                         "entries": [
+                           { "type": "subCategory", "name": "CellML tools",
+                             "entries": [
+                               { "type": "added", "description": "Validation of a <a href=\"https://www.cellml.org/\">CellML</a> file from the <a href=\"https://en.wikipedia.org/wiki/Command-line_interface\">CLI</a>." }
+                             ]
+                           }
+                         ]
                        }
                      ]
                    },

diff --git a/src/checkforupdatesdialog.cpp b/src/checkforupdatesdialog.cpp
@@ -164,16 +164,19 @@ bool CheckForUpdatesEngine::hasNewerOfficialVersion() const
 
 //==============================================================================
 
-CheckForUpdatesDialog::CheckForUpdatesDialog(QSettings *pSettings,
-                                             const QString &pApplicationDate,
+CheckForUpdatesDialog::CheckForUpdatesDialog(const QString &pApplicationDate,
                                              CheckForUpdatesEngine *pEngine,
                                              QWidget *pParent) :
-    Dialog(pSettings, pParent)
+    Dialog(pParent)
 {
     // We are not yet initialised
 
     mInitialized = false;
 
+    // Customise our settings
+
+    mSettings.beginGroup(SettingsCheckForUpdatesDialog);
+
     // Set up the GUI
 
     mGui = new Ui::CheckForUpdatesDialog;
@@ -203,8 +206,8 @@ CheckForUpdatesDialog::CheckForUpdatesDialog(QSettings *pSettings,
 
     // Retrieve and set some properties
 
-    mGui->checkForUpdatesAtStartupCheckBox->setChecked(mSettings->value(SettingsCheckForUpdatesAtStartup, true).toBool());
-    mGui->includeSnapshotsCheckBox->setChecked(mSettings->value(SettingsIncludeSnapshots, false).toBool());
+    mGui->checkForUpdatesAtStartupCheckBox->setChecked(mSettings.value(SettingsCheckForUpdatesAtStartup, true).toBool());
+    mGui->includeSnapshotsCheckBox->setChecked(mSettings.value(SettingsIncludeSnapshots, false).toBool());
 
     // Update our GUI
 
@@ -215,18 +218,16 @@ CheckForUpdatesDialog::CheckForUpdatesDialog(QSettings *pSettings,
 
 //==============================================================================
 
-CheckForUpdatesDialog::CheckForUpdatesDialog(QSettings *pSettings,
-                                             const QString &pApplicationDate,
+CheckForUpdatesDialog::CheckForUpdatesDialog(const QString &pApplicationDate,
                                              QWidget *pParent) :
-    CheckForUpdatesDialog(pSettings, pApplicationDate, nullptr, pParent)
+    CheckForUpdatesDialog(pApplicationDate, nullptr, pParent)
 {
 }
 
 //==============================================================================
 
-CheckForUpdatesDialog::CheckForUpdatesDialog(QSettings *pSettings,
-                                             CheckForUpdatesEngine *pEngine) :
-    CheckForUpdatesDialog(pSettings, QString(), pEngine, nullptr)
+CheckForUpdatesDialog::CheckForUpdatesDialog(CheckForUpdatesEngine *pEngine) :
+    CheckForUpdatesDialog(QString(), pEngine, nullptr)
 {
 }
 
@@ -338,8 +339,8 @@ void CheckForUpdatesDialog::checkForUpdatesAtStartupCheckBoxToggled(bool pChecke
 
     // Keep track of our property
 
-    mSettings->setValue(SettingsCheckForUpdatesAtStartup,
-                        mGui->checkForUpdatesAtStartupCheckBox->isChecked());
+    mSettings.setValue(SettingsCheckForUpdatesAtStartup,
+                       mGui->checkForUpdatesAtStartupCheckBox->isChecked());
 }
 
 //==============================================================================
@@ -350,8 +351,8 @@ void CheckForUpdatesDialog::includeSnapshotsCheckBoxToggled(bool pChecked)
 
     // Keep track of our property
 
-    mSettings->setValue(SettingsIncludeSnapshots,
-                        mGui->includeSnapshotsCheckBox->isChecked());
+    mSettings.setValue(SettingsIncludeSnapshots,
+                       mGui->includeSnapshotsCheckBox->isChecked());
 
     updateGui();
 }

diff --git a/src/checkforupdatesdialog.h b/src/checkforupdatesdialog.h
@@ -84,11 +84,9 @@ class CheckForUpdatesDialog : public Dialog
     Q_OBJECT
 
 public:
-    explicit CheckForUpdatesDialog(QSettings *pSettings,
-                                   const QString &pApplicationDate,
+    explicit CheckForUpdatesDialog(const QString &pApplicationDate,
                                    QWidget *pParent);
-    explicit CheckForUpdatesDialog(QSettings *pSettings,
-                                   CheckForUpdatesEngine *pEngine);
+    explicit CheckForUpdatesDialog(CheckForUpdatesEngine *pEngine);
     ~CheckForUpdatesDialog() override;
 
 private:
@@ -98,8 +96,7 @@ class CheckForUpdatesDialog : public Dialog
 
     bool mInitialized;
 
-    explicit CheckForUpdatesDialog(QSettings *pSettings,
-                                   const QString &pApplicationDate,
+    explicit CheckForUpdatesDialog(const QString &pApplicationDate,
                                    CheckForUpdatesEngine *pEngine,
                                    QWidget *pParent);
 

diff --git a/src/generalpreferenceswidget.cpp b/src/generalpreferenceswidget.cpp
@@ -53,7 +53,7 @@ GeneralPreferencesWidget::GeneralPreferencesWidget(QWidget *pParent) :
 
     mGui->styleValue->addItems(styles);
 
-    mStyle = mSettings->value(SettingsPreferencesStyle, SettingsPreferencesStyleDefault).toString();
+    mStyle = mSettings.value(SettingsPreferencesStyle, SettingsPreferencesStyleDefault).toString();
 
     mGui->styleValue->setCurrentText(mStyle);
 
@@ -95,7 +95,7 @@ void GeneralPreferencesWidget::savePreferences()
 
     QString style = mGui->styleValue->currentText();
 
-    mSettings->setValue(SettingsPreferencesStyle, style);
+    mSettings.setValue(SettingsPreferencesStyle, style);
 
     // Update our style