Testing C++11 compilation #309

quantumjot · 2023-04-27T07:27:11Z

This is a test of compilation of the latest version of btrack using an older compiler for compatibility.

@markdane @ania-m-b @nthndy - could you try this fix out, since I know you were all having issues on your respective machines?

git clone -b fix-makefile https://github.com/quantumjot/btrack.git
cd btrack
./build.sh
pip install -e .

deprecated-napari-hub-preview-bot · 2023-04-27T07:34:11Z

Preview page for your plugin is ready here:
https://preview.napari-hub.org/quantumjot/btrack/309
Updated: 2023-04-27T07:46:01.160069

codecov-commenter · 2023-04-27T07:36:25Z

Codecov Report

Patch and project coverage have no change.

Comparison is base (6cbd357) 84.87% compared to head (5606ac8) 84.87%.

❗ Current head 5606ac8 differs from pull request most recent head c969653. Consider uploading reports for the commit c969653 to get more accurate results

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Additional details and impacted files

@@           Coverage Diff           @@
##             main     #309   +/-   ##
=======================================
  Coverage   84.87%   84.87%           
=======================================
  Files          30       30           
  Lines        1957     1957           
  Branches      296      296           
=======================================
  Hits         1661     1661           
  Misses        212      212           
  Partials       84       84

☔ View full report in Codecov by Sentry.
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paddyroddy · 2023-04-27T09:16:53Z

To support older versions of C++ we could look into https://docs.github.com/en/actions/hosting-your-own-runners/managing-self-hosted-runners/about-self-hosted-runners

paddyroddy · 2023-04-27T12:31:46Z

Had a look. The old link https://github.com/eigenteam/eigen-git-mirror says it is deprecated and may be removed at any time. Hence why we removed it.

nthndy · 2023-04-27T12:39:50Z

(will give this a go tomorrow as I don't have my macbook on me today)

nthndy · 2023-04-28T07:37:12Z

works for me!

ania-m-b · 2023-04-28T13:46:15Z

For macOS Mojave 10.14.6 users if you struggle to get btrack to work you may notice these errors:

When trying to run tracks in your notebook:

[ERROR][2023/04/28 01:22:50 PM] Exception caught:
 - btrack_version: 0.6.1.dev31
 - system_platform: macOS-10.14.6-x86_64-i386-64bit
 - system_python: 3.10.11
 - function: <function load_library at 0x12ec90f70>
 - exception: dlopen(/Users/username/Documents/btrack_0.6.0/btrack/btrack/libs/libtracker.dylib, 6): image not found
 - arguments: (PosixPath('/Users/username/Documents/btrack_0.6.0/btrack/btrack/libs/libtracker'),)
 - keywords: {}

While building:

mkdir: ./btrack/libs: File exists
mkdir: ./btrack/obj: File exists
Compiling btrack from source...
rm -f ./btrack/obj/bayes.o ./btrack/obj/hyperbin.o ./btrack/obj/hypothesis.o ./btrack/obj/inference.o ./btrack/obj/interface.o ./btrack/obj/manager.o ./btrack/obj/motion.o ./btrack/obj/pdf.o ./btrack/obj/tracker.o ./btrack/obj/tracklet.o ./btrack/obj/wrapper.o
clang++ -arch x86_64 -arch arm64 -c -std=c++11 -m64 -fPIC -I"./btrack/include" -DDEBUG=false -DBUILD_SHARED_LIB -O3  -c btrack/src/bayes.cc -o btrack/obj/bayes.o
In file included from btrack/src/bayes.cc:17:
In file included from ./btrack/include/bayes.h:20:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/algorithm:642:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/cstring:61:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/string.h:61:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/string.h:61:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/_types.h:27:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/_types.h:32:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/cdefs.h:784:2: error:
      Unsupported architecture
#error Unsupported architecture
 ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [btrack/obj/bayes.o] Error 1

To overcome this issue in your btrack folder go to Makefile(txt file) and remove this bit :
-arch arm64
from the line where it appears. Save the new Makefile and repeat ./build.sh

This will result in successful outcome. Then install the whole package!

Many thanks to @quantumjot for solving this issue!!!

markdane · 2023-05-17T20:03:42Z

This works for me too. Thank you. Sorry about the delay but I've been running btrack on a virtual machine to get around this. Glad to move it all back on our cluster computer. BTW, the optimization is much faster now.

paddyroddy

Some comments

paddyroddy · 2023-05-26T09:23:25Z

build.sh

@@ -7,7 +7,7 @@ mkdir ./btrack/obj
 # clone Eigen
 if [ ! -e ./btrack/include/eigen/signature_of_eigen3_matrix_library ]
 then
-  git clone https://gitlab.com/libeigen/eigen.git ./btrack/include/eigen
+  git clone --depth 1 --branch 3.3.9 https://gitlab.com/libeigen/eigen.git ./btrack/include/eigen


This seems like a good compromise rather than using the old repository. I've just realised that --branch here also accepts tags https://stackoverflow.com/a/39067940/7359333. My concern at first was that they may delete the branch.

paddyroddy · 2023-05-26T09:26:55Z

Makefile

-	XLD_FLAGS = -arch x86_64 -arch arm64
+	XLDFLAGS =


Curious to know whether any of the XLDFLAGS are actually required?

For some of the compilers they are required (I think!)

paddyroddy · 2023-05-26T09:34:16Z

btrack/include/tracker.h

@@ -20,7 +20,7 @@
 #include <algorithm>
 #include <cmath>
 #include <ctime>
-#include <filesystem>
+// #include <experimental/filesystem>


Here and elsewhere should we just remove rather than comment out?

I think I'd like to leave this in if possible, since we might want to reinstate it once we can move back to C++17 (or greater). Probably fine to delete though, it's not an essential function - mostly used for debugging.

paddyroddy · 2023-07-27T14:55:32Z

FYI, I can no longer compile on my machine. Do we want to support old machines or new ones? I'm on an M1 macOS

quantumjot · 2023-07-27T15:17:57Z

Weird - I just tried compiling on my M1 Mac and it was fine

paddyroddy · 2023-08-08T16:14:43Z

I'm still having issues on my standard M1. On my M1 Max I haven't had such issues. Not sure why (unless it's from a previous build on the M1 Max).

Building btrack...
mkdir: cannot create directory ‘./btrack/libs’: File exists
mkdir: cannot create directory ‘./btrack/obj’: File exists
Compiling btrack from source...
rm -f ./btrack/obj/bayes.o ./btrack/obj/hyperbin.o ./btrack/obj/hypothesis.o ./btrack/obj/inference.o ./btrack/obj/interface.o ./btrack/obj/manager.o ./btrack/obj/motion.o ./btrack/obj/pdf.o ./btrack/obj/tracker.o ./btrack/obj/tracklet.o ./btrack/obj/wrapper.o
clang++ -arch x86_64 -arch arm64 -c -std=c++11 -m64 -fPIC -I"./btrack/include" -DDEBUG=false -DBUILD_SHARED_LIB -O3  -c btrack/src/bayes.cc -o btrack/obj/bayes.o
clang++ -arch x86_64 -arch arm64 -c -std=c++11 -m64 -fPIC -I"./btrack/include" -DDEBUG=false -DBUILD_SHARED_LIB -O3  -c btrack/src/hyperbin.cc -o btrack/obj/hyperbin.o
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:19:
./btrack/include/eigen/Eigen/src/Core/util/Macros.h:707:2: error: This compiler appears to be too old to be supported by Eigen
#error This compiler appears to be too old to be supported by Eigen
 ^
./btrack/include/eigen/Eigen/src/Core/util/Macros.h:950:79: error: constexpr function's return type 'void' is not a literal type
    template<typename T> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE constexpr void ignore_unused_variable(const T&) {}
                                                                              ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:157:37: error: no template named 'remove_const_t' in namespace 'std'; did you mean 'remove_const'?
struct is_void : is_same<void, std::remove_const_t<T>> {};
                               ~~~~~^~~~~~~~~~~~~~
                                    remove_const
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/remove_const.h:20:50: note: 'remove_const' declared here
template <class _Tp> struct _LIBCPP_TEMPLATE_VIS remove_const            {typedef _Tp type;};
                                                 ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:224:48: error: no member named 'enable_if_t' in namespace 'std'
template<typename T> struct array_size<T, std::enable_if_t<((T::SizeAtCompileTime&0)==0)>> {
                                          ~~~~~^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:224:90: error: expected unqualified-id
template<typename T> struct array_size<T, std::enable_if_t<((T::SizeAtCompileTime&0)==0)>> {
                                                                                         ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:255:17: error: 'auto' return without trailing return type; deduced return types are a C++14 extension
EIGEN_CONSTEXPR auto index_list_size(const T& x) {
                ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:256:18: error: no template named 'common_type_t' in namespace 'std'; did you mean 'common_type'?
  using R = std::common_type_t<std::ptrdiff_t, std::make_signed_t<decltype(x.size())>>;
            ~~~~~^~~~~~~~~~~~~
                 common_type
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/common_type.h:69:29: note: 'common_type' declared here
struct _LIBCPP_TEMPLATE_VIS common_type;
                            ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:256:53: error: no template named 'make_signed_t' in namespace 'std'; did you mean 'make_signed'?
  using R = std::common_type_t<std::ptrdiff_t, std::make_signed_t<decltype(x.size())>>;
                                               ~~~~~^~~~~~~~~~~~~
                                                    make_signed
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__type_traits/make_signed.h:65:29: note: 'make_signed' declared here
struct _LIBCPP_TEMPLATE_VIS make_signed
                            ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:309:38: error: no template named 'integer_sequence' in namespace 'std'; did you mean '__integer_sequence'?
using reduce_all = std::is_same<std::integer_sequence<bool, values..., true>,
                                ~~~~~^~~~~~~~~~~~~~~~
                                     __integer_sequence
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tuple:89:8: note: '__integer_sequence' declared here
struct __integer_sequence {
       ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:310:10: error: no template named 'integer_sequence' in namespace 'std'; did you mean '__integer_sequence'?
    std::integer_sequence<bool, true, values...> >;
    ~~~~~^~~~~~~~~~~~~~~~
         __integer_sequence
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tuple:89:8: note: '__integer_sequence' declared here
struct __integer_sequence {
       ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:315:24: error: no template named 'integer_sequence' in namespace 'std'; did you mean '__integer_sequence'?
    !std::is_same<std::integer_sequence<bool, values..., false>, std::integer_sequence<bool, false, values...> >::value>;
                  ~~~~~^~~~~~~~~~~~~~~~
                       __integer_sequence
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tuple:89:8: note: '__integer_sequence' declared here
struct __integer_sequence {
       ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:315:71: error: no template named 'integer_sequence' in namespace 'std'; did you mean '__integer_sequence'?
    !std::is_same<std::integer_sequence<bool, values..., false>, std::integer_sequence<bool, false, values...> >::value>;
                                                                 ~~~~~^~~~~~~~~~~~~~~~
                                                                      __integer_sequence
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__tuple:89:8: note: '__integer_sequence' declared here
struct __integer_sequence {
       ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:168:
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:335:68: error: no template named 'enable_if_t' in namespace 'std'
  template <typename C> static meta_yes testFunctor(C const *,std::enable_if_t<(sizeof(return_ptr<C>()->operator()())>0)> * = 0);
                                                              ~~~~~^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:344:68: error: no template named 'enable_if_t' in namespace 'std'
  template <typename C> static meta_yes testFunctor(C const *,std::enable_if_t<(sizeof(return_ptr<C>()->operator()(IndexType(0)))>0)> * = 0);
                                                              ~~~~~^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:353:68: error: no template named 'enable_if_t' in namespace 'std'
  template <typename C> static meta_yes testFunctor(C const *,std::enable_if_t<(sizeof(return_ptr<C>()->operator()(IndexType(0),IndexType(0)))>0)> * = 0);
                                                              ~~~~~^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:502:16: warning: variable templates are a C++14 extension [-Wc++14-extensions]
constexpr bool is_int_or_enum_v = std::is_enum<A>::value || std::is_integral<A>::value;
               ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:530:3: warning: use of this statement in a constexpr function is a C++14 extension [-Wc++14-extensions]
  if ((int) a == 0 || (int) b == 0) return 0;
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:533:3: warning: multiple return statements in constexpr function is a C++14 extension [-Wc++14-extensions]
  return plain_enum_min(a, b);
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:530:37: note: previous return statement is here
  if ((int) a == 0 || (int) b == 0) return 0;
                                    ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:531:37: note: previous return statement is here
  if ((int) a == 1 || (int) b == 1) return 1;
                                    ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:532:49: note: previous return statement is here
  if ((int) a == Dynamic || (int) b == Dynamic) return Dynamic;
                                                ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:546:3: warning: use of this statement in a constexpr function is a C++14 extension [-Wc++14-extensions]
  if ((int) a == 0 || (int) b == 0) return 0;
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:551:3: warning: multiple return statements in constexpr function is a C++14 extension [-Wc++14-extensions]
  return plain_enum_min(a, b);
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:546:37: note: previous return statement is here
  if ((int) a == 0 || (int) b == 0) return 0;
                                    ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:547:37: note: previous return statement is here
  if ((int) a == 1 || (int) b == 1) return 1;
                                    ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:548:49: note: previous return statement is here
  if ((int) a == Dynamic && (int) b == Dynamic) return Dynamic;
                                                ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:549:27: note: previous return statement is here
  if ((int) a == Dynamic) return (int) b;
                          ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:550:27: note: previous return statement is here
  if ((int) b == Dynamic) return (int) a;
                          ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:559:3: warning: use of this statement in a constexpr function is a C++14 extension [-Wc++14-extensions]
  if ((int) a == Dynamic || (int) b == Dynamic) return Dynamic;
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:560:3: warning: multiple return statements in constexpr function is a C++14 extension [-Wc++14-extensions]
  return plain_enum_max(a, b);
  ^
./btrack/include/eigen/Eigen/src/Core/util/Meta.h:559:49: note: previous return statement is here
  if ((int) a == Dynamic || (int) b == Dynamic) return Dynamic;
                                                ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:170:
./btrack/include/eigen/Eigen/src/Core/util/ForwardDeclarations.h:112:46: error: no type named 'conditional_t' in namespace 'std'
         typename StrideType = typename std::conditional_t<PlainObjectType::IsVectorAtCompileTime,InnerStride<1>,OuterStride<> > > class Ref;
                               ~~~~~~~~~~~~~~^~~~~~~~~~~~~
./btrack/include/eigen/Eigen/src/Core/util/ForwardDeclarations.h:112:59: error: expected ',' or '>' in template-parameter-list
         typename StrideType = typename std::conditional_t<PlainObjectType::IsVectorAtCompileTime,InnerStride<1>,OuterStride<> > > class Ref;
                                                          ^
./btrack/include/eigen/Eigen/src/Core/util/ForwardDeclarations.h:112:98: error: expected unqualified-id
         typename StrideType = typename std::conditional_t<PlainObjectType::IsVectorAtCompileTime,InnerStride<1>,OuterStride<> > > class Ref;
                                                                                                 ^
In file included from btrack/src/hyperbin.cc:17:
In file included from ./btrack/include/hyperbin.h:27:
In file included from ./btrack/include/tracklet.h:23:
In file included from ./btrack/include/eigen/Eigen/Dense:1:
In file included from ./btrack/include/eigen/Eigen/Core:172:
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:105:16: error: no template named 'conditional_t' in namespace 'std'
  typedef std::conditional_t<(sizeof(I1)<sizeof(I2)), I2, I1> type;
          ~~~~~^
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:195:3: warning: use of this statement in a constexpr function is a C++14 extension [-Wc++14-extensions]
  if((ArrayBytes % AlignmentBytes) == 0) {
  ^
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:200:5: warning: multiple return statements in constexpr function is a C++14 extension [-Wc++14-extensions]
    return 0;
    ^
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:196:5: note: previous return statement is here
    return AlignmentBytes;
    ^
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:198:5: note: previous return statement is here
    return compute_default_alignment_helper(ArrayBytes, AlignmentBytes/2);
    ^
./btrack/include/eigen/Eigen/src/Core/util/XprHelper.h:242:12: warning: variable declaration in a constexpr function is a C++14 extension [-Wc++14-extensions]
  unsigned row_major_bit = Options&RowMajor ? RowMajorBit : 0;
           ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
10 warnings and 20 errors generated.
make: *** [btrack/obj/hyperbin.o] Error 1

quantumjot added 7 commits March 23, 2023 12:03

test fix for makefile

caa9b7d

add filesystem lib

db1609b

use experimental

e20a80f

revert experimental

67f5e3e

experimental

25d52b3

Merge branch 'main' into fix-makefile

e965696

allow c++11 builds

5606ac8

remove redundant library

c969653

This was linked to issues Apr 27, 2023

Cannot load dylib on Intel macbooks #296

Closed

[BUG] glibc incompatibility #308

Closed

markdane mentioned this pull request May 22, 2023

[BUG] glibc incompatibility #308

Closed

paddyroddy assigned quantumjot May 26, 2023

paddyroddy added bug CI labels May 26, 2023

paddyroddy marked this pull request as ready for review May 26, 2023 09:16

paddyroddy self-requested a review May 26, 2023 09:16

paddyroddy approved these changes May 26, 2023

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quantumjot merged commit e750129 into main Jul 20, 2023

quantumjot deleted the fix-makefile branch July 20, 2023 13:20

quantumjot mentioned this pull request Jul 20, 2023

Few small issues with new packaging #291

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Testing C++11 compilation #309

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Testing C++11 compilation #309

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quantumjot commented Apr 27, 2023 •

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ania-m-b commented Apr 28, 2023 •

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