write rawfiles (single file) and read rawfiles in order (#66)

* read subfiles with unordered and missing frames

* save work debugging

* Revert "save work debugging"

This reverts commit e791992a05.

* Revert "read subfiles with unordered and missing frames"

This reverts commit 1177fd129d.

* throw when two frames have different frame numbers

* write single part RawFile (working beta)

* correct total number of frames in master file

* add new mythen file with syncd frames

* read frames with same frame number

* clang-tidy fixes, formatting, add tests

* improve readability in loop

* fix failing tests

---------

Co-authored-by: Bechir <bechir.brahem420@gmail.com>

include/aare/aare.hpp

@@ -1 +1,7 @@
-// This is the top level header to include and what most users will use
+// This is the top level header to include and what most users will use
+
+// include all header files
+#include "aare/core.hpp"
+#include "aare/file_io.hpp"
+#include "aare/network_io.hpp"
+#include "aare/utils.hpp"

include/aare/core.hpp

@@ -0,0 +1,8 @@
+#include "aare/core/CircularFifo.hpp"
+#include "aare/core/DType.hpp"
+#include "aare/core/Frame.hpp"
+#include "aare/core/NDArray.hpp"
+#include "aare/core/NDView.hpp"
+#include "aare/core/defs.hpp"
+// #include "aare/core/VariableSizeClusterFinder.hpp"
+#include "aare/core/ProducerConsumerQueue.hpp"

include/aare/file_io.hpp

@@ -0,0 +1,8 @@
+// ClusterFile.hpp  File.hpp  FileInterface.hpp  NumpyFile.hpp  NumpyHelpers.hpp  RawFile.hpp  SubFile.hpp
+#include "aare/file_io/ClusterFile.hpp"
+#include "aare/file_io/File.hpp"
+#include "aare/file_io/FileInterface.hpp"
+#include "aare/file_io/NumpyFile.hpp"
+#include "aare/file_io/NumpyHelpers.hpp"
+#include "aare/file_io/RawFile.hpp"
+#include "aare/file_io/SubFile.hpp"

include/aare/network_io.hpp

@@ -0,0 +1,5 @@
+#include "aare/network_io/ZmqHeader.hpp"
+#include "aare/network_io/ZmqSocket.hpp"
+#include "aare/network_io/ZmqSocketReceiver.hpp"
+#include "aare/network_io/ZmqSocketSender.hpp"
+#include "aare/network_io/defs.hpp"

include/aare/utils.hpp

@@ -0,0 +1,3 @@
+#include "aare/utils/compare_files.hpp"
+#include "aare/utils/json.hpp"
+#include "aare/utils/logger.hpp"