chore: update includes with include-what-you-use

avogadro/core/elements.cpp

@@ -3,15 +3,18 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
-#include "elements.h"
+// IWYU pragma: no_include <ext/alloc_traits.h>
 
-#include "avogadrocore.h"
-#include "elementdata.h"
-#include "utilities.h"
+#include "elements.h"
 
 #include <algorithm>
 #include <cctype>
 #include <vector>
+#include <memory>
+
+#include "avogadrocore.h"
+#include "elementdata.h"
+#include "utilities.h"
 
 using Avogadro::Core::isCustomElement;
 

avogadro/core/elements.h

@@ -6,12 +6,11 @@
 #ifndef AVOGADRO_CORE_ELEMENTS_H
 #define AVOGADRO_CORE_ELEMENTS_H
 
-#include "avogadrocoreexport.h"
+#include <string>
 
+#include "avogadrocoreexport.h"
 #include "avogadrocore.h"
 
-#include <string>
-
 namespace Avogadro {
 namespace Core {
 

avogadro/core/graph.cpp

@@ -3,13 +3,18 @@
   This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
+// IWYU pragma: no_include <ext/alloc_traits.h>
+
 #include "graph.h"
 
 #include <algorithm>
 #include <array>
 #include <cassert>
 #include <set>
 #include <stack>
+#include <memory>
+
+#include "avogadro/core/array.h"
 
 namespace Avogadro::Core {
 

avogadro/core/graph.h

@@ -6,14 +6,14 @@
 #ifndef AVOGADRO_CORE_GRAPH_H
 #define AVOGADRO_CORE_GRAPH_H
 
-#include "avogadrocoreexport.h"
-
-#include "avogadrocore.h"
-#include "array.h"
-
 #include <cstddef>
 #include <set>
 #include <vector>
+#include <utility>
+
+#include "avogadrocoreexport.h"
+#include "avogadrocore.h"
+#include "array.h"
 
 namespace Avogadro {
 namespace Core {

avogadro/core/layer.cpp

@@ -4,7 +4,13 @@
 ******************************************************************************/
 
 #include "layer.h"
+
 #include <cassert>
+#include <utility>
+#include <vector>
+
+#include "avogadro/core/array.h"
+#include "avogadro/core/avogadrocore.h"
 
 namespace Avogadro::Core {
 

avogadro/core/layer.h

@@ -6,12 +6,12 @@
 #ifndef AVOGADRO_CORE_LAYER_H
 #define AVOGADRO_CORE_LAYER_H
 
-#include "avogadrocoreexport.h"
+#include <avogadro/core/array.h>
+#include <cstddef>
 
+#include "avogadrocoreexport.h"
 #include "avogadrocore.h"
 
-#include <avogadro/core/array.h>
-
 namespace Avogadro {
 namespace Core {
 

avogadro/core/layermanager.cpp

@@ -4,7 +4,12 @@
 ******************************************************************************/
 
 #include "layermanager.h"
+
 #include <cassert>
+#include <utility>
+
+#include "avogadro/core/array.h"
+#include "avogadro/core/layer.h"
 
 namespace Avogadro::Core {
 

avogadro/core/layermanager.h

@@ -6,19 +6,19 @@
 #ifndef AVOGADRO_CORE_LAYERMANAGER_H
 #define AVOGADRO_CORE_LAYERMANAGER_H
 
-#include "avogadrocoreexport.h"
-
-#include "avogadrocore.h"
-
-#include "array.h"
-#include "layer.h"
-
 #include <cassert>
 #include <map>
 #include <memory>
 #include <set>
 #include <string>
 #include <vector>
+#include <algorithm>
+#include <cstddef>
+
+#include "avogadrocoreexport.h"
+#include "avogadrocore.h"
+#include "array.h"
+#include "layer.h"
 
 namespace Avogadro {
 namespace Core {

avogadro/io/fileformat.cpp

@@ -6,9 +6,9 @@
 #include "fileformat.h"
 
 #include <algorithm>
-#include <fstream>
+#include <fstream> // IWYU pragma: keep
 #include <locale>
-#include <sstream>
+#include <sstream> // IWYU pragma: keep
 
 namespace Avogadro::Io {
 

avogadro/io/fileformat.h

@@ -6,14 +6,14 @@
 #ifndef AVOGADRO_IO_FILEFORMAT_H
 #define AVOGADRO_IO_FILEFORMAT_H
 
-#include "avogadroioexport.h"
 #include <avogadro/core/avogadrocore.h>
-
 #include <istream>
 #include <ostream>
 #include <string>
 #include <vector>
 
+#include "avogadroioexport.h"
+
 namespace Avogadro {
 
 namespace Core {

avogadro/io/fileformatmanager.cpp

@@ -6,7 +6,6 @@
 #include "fileformatmanager.h"
 
 #include "fileformat.h"
-
 #include "cjsonformat.h"
 #include "cmlformat.h"
 #include "dcdformat.h"
@@ -25,6 +24,7 @@
 
 #include <algorithm>
 #include <memory>
+#include <utility>
 
 using std::unique_ptr;
 

avogadro/io/fileformatmanager.h

@@ -6,13 +6,15 @@
 #ifndef AVOGADRO_IO_FILEFORMATMANAGER_H
 #define AVOGADRO_IO_FILEFORMATMANAGER_H
 
-#include "avogadroioexport.h"
-
-#include "fileformat.h" // For FileFormat::Operation enum.
-
+#include <ctype.h>
+#include <stddef.h>
 #include <map>
 #include <string>
 #include <vector>
+#include <algorithm>
+
+#include "avogadroioexport.h"
+#include "fileformat.h" // For FileFormat::Operation enum.
 
 namespace Avogadro {
 namespace Core {

avogadro/molequeue/batchjob.cpp

@@ -4,12 +4,18 @@
 ******************************************************************************/
 
 #include "batchjob.h"
-#include "molequeuemanager.h"
-
-#include <QtCore/QDebug>
 
+#include <qdebug.h>
+#include <qglobal.h>
+#include <qmetatype.h>
+#include <qstringlist.h>
 #include <limits>
 
+#include "molequeuemanager.h"
+#include "avogadro/molequeue/client/client.h"
+#include "avogadro/molequeue/client/jobobject.h"
+#include "avogadro/molequeue/inputgenerator.h"
+
 namespace Avogadro::MoleQueue {
 
 // initialize statics

avogadro/molequeue/batchjob.h

@@ -6,18 +6,25 @@
 #ifndef AVOGADRO_QTGUI_BATCHJOB_H
 #define AVOGADRO_QTGUI_BATCHJOB_H
 
-#include <QtCore/QObject>
-
-#include "inputgenerator.h"
-
 #include <avogadro/core/avogadrocore.h>
-
-#include "client/jobobject.h"
-
+#include <qjsonobject.h>
+#include <qjsonvalue.h>
+#include <qlist.h>
+#include <qmap.h>
+#include <qobject.h>
+#include <qobjectdefs.h>
+#include <qstring.h>
+#include <qvariant.h>
+#include <qvector.h>
+#include <QtCore/QObject>
 #include <QtCore/QJsonObject>
 #include <QtCore/QMap>
 #include <QtCore/QVector>
 
+#include "inputgenerator.h"
+#include "client/jobobject.h"
+#include "avogadromolequeueexport.h"
+
 namespace Avogadro {
 namespace Core {
 class Molecule;

avogadro/molequeue/client/client.cpp

@@ -5,11 +5,13 @@
 
 #include "client.h"
 
+#include <qglobal.h>
+#include <qnamespace.h>
+#include <qregexp.h>
+
 #include "jsonrpcclient.h"
 #include "jobobject.h"
 
-#include <QtCore/QJsonDocument>
-
 namespace Avogadro::MoleQueue {
 
 Client::Client(QObject *parent_) : QObject(parent_), m_jsonRpcClient(nullptr)

avogadro/molequeue/client/client.h

@@ -6,14 +6,24 @@
 #ifndef AVOGADRO_MOLEQUEUE_CLIENT_H
 #define AVOGADRO_MOLEQUEUE_CLIENT_H
 
-#include "avogadromolequeueexport.h"
-
+#include <qhash.h>
+#include <qjsonarray.h>
+#include <qjsonobject.h>
+#include <qjsonvalue.h>
+#include <qlist.h>
+#include <qobject.h>
+#include <qobjectdefs.h>
+#include <qstring.h>
 #include <QtCore/QJsonArray>
 #include <QtCore/QJsonObject>
 #include <QtCore/QObject>
 #include <QRegExp>
 #include <QtCore/QHash>
 
+#include "avogadromolequeueexport.h"
+
+class QRegExp;
+
 namespace Avogadro {
 namespace MoleQueue {
 

avogadro/molequeue/client/jobobject.cpp

@@ -5,7 +5,7 @@
 
 #include "jobobject.h"
 
-#include <QtCore/QJsonArray>
+#include <qjsonvalue.h>
 
 namespace Avogadro::MoleQueue {
 

avogadro/molequeue/client/jobobject.h

@@ -6,13 +6,16 @@
 #ifndef AVOGADRO_MOLEQUEUE_JOBOBJECT_H
 #define AVOGADRO_MOLEQUEUE_JOBOBJECT_H
 
-#include "avogadromolequeueexport.h"
-
+#include <qjsonarray.h>
+#include <qjsonobject.h>
+#include <qstring.h>
+#include <qvariant.h>
 #include <QtCore/QJsonObject>
-
 #include <QtCore/QString>
 #include <QtCore/QVariant>
 
+#include "avogadromolequeueexport.h"
+
 namespace Avogadro {
 namespace MoleQueue {
 

avogadro/molequeue/client/jsonrpcclient.cpp

@@ -5,10 +5,12 @@
 
 #include "jsonrpcclient.h"
 
-#include <QtCore/QJsonDocument>
-#include <QtCore/QDataStream>
-#include <QtCore/QTimer>
-#include <QtNetwork/QLocalSocket>
+#include <qdatastream.h>
+#include <qjsondocument.h>
+#include <qjsonvalue.h>
+#include <qlocalsocket.h>
+#include <qnamespace.h>
+#include <qtimer.h>
 
 namespace Avogadro::MoleQueue {
 

avogadro/molequeue/client/jsonrpcclient.h

@@ -6,11 +6,16 @@
 #ifndef AVOGADRO_MOLEQUEUE_JSONRPCCLIENT_H
 #define AVOGADRO_MOLEQUEUE_JSONRPCCLIENT_H
 
-#include "avogadromolequeueexport.h"
-
+#include <qbytearray.h>
+#include <qjsonobject.h>
+#include <qobject.h>
+#include <qobjectdefs.h>
+#include <qstring.h>
 #include <QtCore/QJsonObject>
 #include <QtCore/QObject>
 
+#include "avogadromolequeueexport.h"
+
 class QLocalSocket;
 
 namespace Avogadro {

avogadro/molequeue/inputgeneratordialog.cpp

@@ -4,9 +4,12 @@
 ******************************************************************************/
 
 #include "inputgeneratordialog.h"
-#include "ui_inputgeneratordialog.h"
 
+#include "ui_inputgeneratordialog.h"
 #include "inputgeneratorwidget.h"
+#include "avogadro/molequeue/inputgenerator.h"
+
+class QWidget;
 
 namespace Avogadro::MoleQueue {