Restructuring #2

AdityaPandeyCN · 2025-07-23T15:12:25Z

This PR restructures the project directory following our ROOT project. The benchmark folder and other files will be updated continuously to make it a proper package.

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> restructured the directory Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> changed folder names Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> restructuring the project Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

vgvassilev · 2025-07-28T06:59:38Z

tools/checkindex.cxx

-#include "utils.h"
-
-#include "ramrecord.C"
+#include "../inc/ttree/Utils.h"


If the tools folder is where the executables are we need to find a better solution to this. The CMakeLists in tools should start depending on ttree and then it will need to automatically adjust the include paths so that you do not need to type ../inc.

vgvassilev · 2025-07-28T07:00:37Z

tools/samtoramntuple.cxx

@@ -1,8 +1,9 @@
 // samtoramntuple.C
 // SAM to RAM converteR

-#include "RAMntuplerecord.C"
-#include "RAMNTupleRecord.h"
+#include "../src/rntuple/RAMNTupleRecord.cxx"


Why we have to include the cxx file here?

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

vgvassilev · 2025-07-28T17:09:38Z

CMakeLists.txt


-add_library(ramtools_tree STATIC
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/inc/ttree)


We should probably use target_include_directories. include_directories is not recommended unless there is a good reason for it.

vgvassilev · 2025-07-28T17:10:52Z

CMakeLists.txt

+ROOT_GENERATE_DICTIONARY(G__ramtools_tree
+    RAMRecord.h
+    Utils.h
+    CigarOps.h
+    LINKDEF ${CMAKE_CURRENT_SOURCE_DIR}/inc/ttree/LinkDef.h
+    MODULE ramtools_tree
+)
+
+add_library(ramtools_tree SHARED


Why not combining these two by using ROOT_STANDARD_LIBRARY_PACKAGE?

Getting errors after implementing this
CMake Error at /home/aditya/root-6.35-ntuple/share/root/cmake/RootMacros.cmake:1237 (install): install DIRECTORY given no DESTINATION! Call Stack (most recent call first): /home/aditya/root-6.35-ntuple/share/root/cmake/RootMacros.cmake:1428 (ROOT_INSTALL_HEADERS) CMakeLists.txt:22 (ROOT_STANDARD_LIBRARY_PACKAGE)

The message says it all, right? We need to pass some install directory of the component..

vgvassilev · 2025-07-28T17:11:49Z

tools/ramview.cxx

@@ -15,8 +15,8 @@
 #include <TTreeIndex.h>
 #include <TTreePerfStats.h>

-#include "../inc/ttree/Utils.h"
-#include "../inc/ttree/RAMRecord.h"
+#include "Utils.h"


Ideally these should be ttree/Utils.h to be able to know what's where...

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

CMakeLists.txt

vgvassilev · 2025-07-29T18:58:52Z

inc/rntuple/RAMNTupleRecord.h

+};
+
+// CIGAR operation codes (from BAM format)
+#include "../ttree/CigarOps.h"


Suggested change

#include "../ttree/CigarOps.h"

#include "ttree/CigarOps.h"

vgvassilev · 2025-07-29T19:00:02Z

inc/ttree/RAMRecord.h

-const UChar_t RAM_CIGAR_P     = 6;
-const UChar_t RAM_CIGAR_EQUAL = 7;
-const UChar_t RAM_CIGAR_X     = 8;
+#include "CigarOps.h"


Suggested change

#include "CigarOps.h"

#include "ttree/CigarOps.h"

vgvassilev · 2025-07-29T19:00:50Z

src/rntuple/RAMNTupleRecord.cxx

@@ -0,0 +1,749 @@
+//
+// RAMNTupleRecord.cpp


Suggested change

// RAMNTupleRecord.cpp

// RAMNTupleRecord.cxx

vgvassilev · 2025-07-29T19:02:07Z

src/rntuple/RAMNTupleRecord.cxx

+         const auto &entries = index_view(0);
+         fgIndex->SetEntries(entries);
+      } catch (...) {
+         // Field doesn't exist


That's something we should rework maybe not part of this PR. We should not rely on exceptions to check if a field exists or not...

vgvassilev · 2025-07-29T19:03:52Z

test/CMakeLists.txt

@@ -0,0 +1,37 @@
+include(FetchContent)


This is how we are doing this reliably: https://github.com/vgvassilev/clad/blob/master/cmake/modules/CladGoogleTest.cmake

vgvassilev · 2025-07-29T19:07:01Z

tools/CMakeLists.txt

+    if(${tool_name} MATCHES "ntuple")
+        target_link_libraries(${tool_name} PRIVATE
+            ramtools_ntuple
+            ROOT::Core
+            ROOT::RIO
+            ROOT::ROOTNTuple
+            ROOT::ROOTNTupleUtil
+        )
+    else()
+        target_link_libraries(${tool_name} PRIVATE
+            ramtools_tree
+            ROOT::Core
+            ROOT::RIO
+            ROOT::Tree
+        )


The dependencies should come from the outside as LIBRARY or something like that. We can use ROOT_EXECUTABLE.

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

AdityaPandeyCN · 2025-07-30T05:32:13Z

I have tried to address the suggestions also apologies for the foolish errors I have made.

vgvassilev

Can we add some basic linux CI?

.clang-format

vgvassilev · 2025-07-30T06:59:25Z

CMakeLists.txt

@@ -1,44 +1,75 @@
 cmake_minimum_required(VERSION 3.16)
+project(ramtools VERSION 1.0.0 LANGUAGES C CXX)  


Why C here?

Actually build was failing with empty CMAKE_C_COMPILER variable error so added C to check, now have removed passing it explicitly.

CMakeLists.txt

vgvassilev · 2025-07-30T07:00:31Z

CMakeLists.txt

-  SOURCES  ramrecord.C
-  HEADERS  ramrecord.h
-  LIBRARIES ROOT::Core ROOT::RIO ROOT::Tree
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/inc)


Doesn't ROOT_STANDARD_LIBRARY_PACKAGE set this properly up?

vgvassilev · 2025-07-30T07:00:53Z

CMakeLists.txt

+    INSTALL_OPTIONS
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}
+)
+add_library(ramtools_ntuple SHARED


Why this is a separate library?

I thought it was better to separate them but now will make it one.

CMakeLists.txt

vgvassilev · 2025-07-30T07:02:59Z

cmake/ramtoolsConfig.cmake.in

+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/ramtoolsTargets.cmake") 
+


Why is this file needed?

vgvassilev · 2025-07-30T07:04:22Z

test/CMakeLists.txt

+add_executable(CountEntriesTest CountEntriesTest.cxx)
+target_link_libraries(CountEntriesTest PRIVATE
+    ramtools_tree
+    ramtools_ntuple
+    gtest
+    gtest_main
+)
+add_test(NAME CountEntriesTest COMMAND CountEntriesTest)
+set_tests_properties(CountEntriesTest PROPERTIES
+    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/tools
+    ENVIRONMENT "ROOT_INCLUDE_PATH=${CMAKE_SOURCE_DIR}/inc;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}"
+)
+
+add_executable(RamviewCountsTest RamviewCountsTest.cxx)
+target_link_libraries(RamviewCountsTest PRIVATE
+    ramtools_tree
+    ramtools_ntuple
+    gtest
+    gtest_main
+)


Can we move this into a cmake function? You can take a look at how it's done in clad...

.clang-format

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

vgvassilev · 2025-07-30T14:01:10Z

CMakeLists.txt

+set(CMAKE_INSTALL_LIBDIR lib)
+set(CMAKE_INSTALL_INCLUDEDIR include)
+
+set_property(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES ${CMAKE_CURRENT_SOURCE_DIR}/inc)


That's the same as include_directories. Why do we need this to be set globally?

I am still confused about this, not able to implement removing include directories.

I will need more information about that. Compiling which library fails if you remove that line?

Made some changes, what do you think about it now?

vgvassilev · 2025-07-30T14:02:58Z

test/CountEntriesTest.cxx

+#include <gtest/gtest.h>
+#include <TSystem.h>
+#include <TFile.h>
+#include <TTree.h>
+#include <ROOT/RNTupleReader.hxx>
+#include <iostream>
+#include <string>


The includes are not ordered by component and then alphabetically.

test/CountEntriesTest.cxx

vgvassilev · 2025-07-30T14:05:16Z

test/RamviewCountsTest.cxx

+    }
+};
+
+TEST_F(RamviewCountsTest, CompareViewCountsForRegion) {


Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

AdityaPandeyCN · 2025-08-12T11:04:35Z

Hello @vgvassilev Do you want me to address anything more for this PR?

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

CMakeLists.txt

tools/samtoram.cxx

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

Co-authored-by: Vassil Vassilev <v.g.vassilev@gmail.com>

inc/ramcore/SamParser.h

inc/ramcore/SamToNTuple.h

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> using ROOT_EXCEUTABLE Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

vgvassilev

Well done. LGTM.

AdityaPandeyCN marked this pull request as draft July 23, 2025 15:12

resolve merge conflicts

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AdityaPandeyCN marked this pull request as ready for review July 23, 2025 15:41

AdityaPandeyCN added 2 commits July 23, 2025 21:14

removed redundant files

f0e0ef4

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removed redundant files

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AdityaPandeyCN marked this pull request as draft July 23, 2025 16:16

conflict changes

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AdityaPandeyCN marked this pull request as ready for review July 24, 2025 03:56

vgvassilev reviewed Jul 28, 2025

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addressed wrong imports

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vgvassilev reviewed Jul 28, 2025

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AdityaPandeyCN added 3 commits July 29, 2025 11:48

making imports more clear and updating CMakeLists

2813225

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making imports better

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fixing imports

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vgvassilev reviewed Jul 29, 2025

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Fixed imports and addressed CMakeLists suggestions

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vgvassilev reviewed Jul 30, 2025

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merged ttree and rntuple libraries

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vgvassilev reviewed Jul 30, 2025

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Extract tool logic into a core library with tests

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changes to cmake

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vgvassilev reviewed Aug 13, 2025

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renamed ramcore library

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Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

Update ROOT version in CMakeLists.txt

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Co-authored-by: Vassil Vassilev <v.g.vassilev@gmail.com>

vgvassilev reviewed Aug 13, 2025

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AdityaPandeyCN added 2 commits August 13, 2025 21:22

added docs for main classes

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using ROOT_EXCEUTABLE

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Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> using ROOT_EXCEUTABLE Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

vgvassilev approved these changes Aug 14, 2025

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vgvassilev merged commit c8739a5 into compiler-research:develop Aug 14, 2025


		add_library(ramtools_tree STATIC
		include_directories(${CMAKE_CURRENT_SOURCE_DIR}/inc/ttree)

		@@ -1,44 +1,75 @@
		cmake_minimum_required(VERSION 3.16)
		project(ramtools VERSION 1.0.0 LANGUAGES C CXX)

		@PACKAGE_INIT@

		include("${CMAKE_CURRENT_LIST_DIR}/ramtoolsTargets.cmake")

Restructuring #2

Restructuring #2

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AdityaPandeyCN commented Jul 23, 2025

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AdityaPandeyCN commented Jul 30, 2025

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AdityaPandeyCN commented Aug 12, 2025

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