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Build System Rework#781

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dudoslav wants to merge 192 commits intoTileDB-Inc:mainTileDB-Inc/TileDB-VCF:mainfrom dudoslav:db/vcpkgdudoslav/TileDB-VCF:db/vcpkgCopy head branch name to clipboard

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Commits

Commits on Aug 28, 2024

• Add initial build wheels CI/CD pipeline

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• Fix working directory for cibuildwheels

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• Fix incorrect package-dir option

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• Disable all platforms except Ubuntu

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• Install zlib1g-dev

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• Fix install deps command

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• Install xz as well

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• Use BEFORE_ALL instead of BEFORE_BUILD

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• Update cibuildwheels version

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• Enable macos and windows wheels

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• Install autoreconf for macos

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• Add additional dependencies for macos build

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• Disable macos

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Commits on Aug 30, 2024

• Change mingw htslib hash

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Commits on Sep 3, 2024

• Quick rework CMake files

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Commits on Sep 9, 2024

• Fix widnows build

  

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• Fix install group

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• Make tests optional

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• Install tiledb.so

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• Also install tiledbvcf

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Commits on Sep 12, 2024

• Test wheels

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Commits on Sep 13, 2024

• Build with executables

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• Fix macos workflow

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• Modify macos workflow

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• Change linking check paths

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• Enable Macos wheel builds

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• Fix macos dependency install

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• Install autoconf instead of autoreconf

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Commits on Sep 17, 2024

• Change macosx deployment version

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• Enable sdist and testing

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• Fix sdist

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• Add pytest requires

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• Add test extra dependency group

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• Install sdist test group

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• Add python code as well

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• Install bcftools for tests

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• Fix install bcftools

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• Install build dependencies for sdist tests

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• Return MACOSX_DEPLOYMENT_TARGET to 11

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• MACOSX_DEPLOYMENT_TARGET to 13

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Commits on Sep 18, 2024

• Temporarily comment out failing test

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• Add install build dependencies to ci/cd

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• Fix missing dlls

  

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Commits on Oct 15, 2024

• Merge remote-tracking branch 'origin/main' into db/sc-52969/wheels

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Commits on Oct 17, 2024

• Initial vcpkg rework

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• Add vcpkg deps

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• Temporarily disable windows builds

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• Remove bcftools

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• Brew install

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• Do not run brew at all

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• Brew install automake

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Commits on Oct 18, 2024

• Effort to fix Windows builds

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• Set PATHS for find_* commands

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• Windows fixes

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• Copy upstream htslib vcpkg port.

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• Patch htslib port to fix failures when statically linking.

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• Ignore CMakeUserPresets.json.

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Commits on Oct 21, 2024

• Fix packaging for wheels

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Commits on Oct 22, 2024

• Fixing auditwheel issues

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• Fix issue with auditwheel

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Commits on Oct 23, 2024

• Install hts-3.dll on windows

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• Macos install bcftools

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• Fix DLL loading on windows

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Commits on Oct 30, 2024

• Fix UB array access

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• Merge remote-tracking branch 'origin/main' into db/vcpkg

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• Do not build for py38

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• Add autoconf to macos dependencies

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• Ignore macosx14 (arm) for now

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• Return UB into the code

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• Change element access

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Commits on Nov 4, 2024

• Remove redundant paranthesis

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Commits on Nov 5, 2024

• Remove group.dump() from LOG_DEBUG

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Commits on Nov 6, 2024

• Add missing include.

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• Bump minimum required CMake version to 3.21.

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• Simplify installing imported runtime artifacts.

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• Ignore dist directory everywhere.

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Commits on Nov 7, 2024

• Ignore env directory.

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• Merge branch 'main' into db/vcpkg

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• Enable build-wheels workflow.

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• clang-format

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Commits on Nov 12, 2024

• Clean up code

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• Do not build windows wheels

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• REMOVE: Print failed vcpkg log

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• Install libtool on macosx

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• Add PIC to tiledbvcf when building python

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• Fix typo

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Commits on Nov 13, 2024

• Change order of installs

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• Install libtool on macos sdist-test

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• Use different install target

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• Change linking checks

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• Force shared libs for tests

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• Fix linking check path

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• Always build and install executable

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• Add builtin-baseline to vcpkg.json

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• Set proper RPATH to executable

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Commits on Nov 14, 2024

• Remove EXCLUDE_FROM_ALL from test target

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• Pin catch2 version

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• Use ctest

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• Change Windows CI commands

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• Fix tiledbvcf path in cli tests

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Commits on Nov 18, 2024

• Add option to FORCE_EXTERNAL_DEPENDENCIES

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Commits on Nov 19, 2024

• Do not install libtiledbvcf build deps

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Commits on Nov 26, 2024

• Install conda dependencies

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• Change build for only python bindings

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• No need to install conda deps

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• Empty commit

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• Find pre-built tiledbvcf

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• Add debug log

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• Fix shared build for Conda

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• Fix install paths

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• Find file instead of find library

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• DEBUG logs

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• Download artifact

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• Uncomment tests

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• Update CI to account for the superbuild's removal.

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• Enable tests by default.

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Commits on Nov 27, 2024

• Build all targets in CI.

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• Fix nightly CI

  

  Dušan Baran

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• Build shared libs in nightly

  

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• Pass TileDB_DIR into CMake

  

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• Also install py dependencies in nightly

  

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Commits on Dec 2, 2024

• Do not set RPath

  

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• Do not set RPATH

  

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• RPath test

  

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Commits on Dec 3, 2024

• Revert RPath changes and implement new CI

  

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• Install build dependencies

  

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• Comment out CLI tests and install ninja

  

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• Fix apt-get command

  

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• Install ninja-build

  

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• Change python -m to pip install

  

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• POSITION_INDEPENDENT_CODE

  

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• Also install pip in conda env

  

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• Install bcftools

  

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• Add debug logging

  

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• Add additional debug logs

  

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• Use micromamba env

  

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• Install dependencies in conda env

  

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• Use micromamba-shell

  

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• Set cmake prefix path

  

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• Install htslib from bioconda

  

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• Install catch2 from conda

  

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• Change catch2 includes

  

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• Use correct catch2 header

  

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• Revert "Use correct catch2 header"

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• Revert "Change catch2 includes"

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• Pin catch2 in Conda

  

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• Comment out catch2 tests

  

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• install pytest

  

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• Use correct shell

  

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• Install python bindings dependencies

  

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• Add debug log

  

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• Fix python module path

  

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• Add configurable RPath

  

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• Do not install libtiledb

  

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• Pin Tiledb version

  

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• c stdlib version

  

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• allow-shlib-undefined

  

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• Fix linker option

  

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• Print ldd of conda libtiledb.so

  

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• Add linking logs

  

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• Use LD_LIBRARY_PATH in tests

  

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• Print python module linking

  

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• Copy libtiledbvcf into library path

  

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• Install tiledb-py for tests

  

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• Install bcftools for tests

  

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Commits on Dec 4, 2024

• Run tests for libtiledbvcf

  

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• Install cli test dependencies

  

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• Install htslib from channel tiledb

  

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• Move binary to top level

  

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• Proper RPATH linking

  

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Commits on Dec 9, 2024

• Properly handle install prefix subpaths

  

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• Install module logic

  

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• For conda test, do not install do subfolder

  

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• Find in correct folder

  

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• Test correct paths

  

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• Always install python bindings under tiledbvcf

  

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Commits on Dec 10, 2024

• Set CMAKE_INSTALL_PREFIX before project

  

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• Always install python bindings into tiledbvcf

  

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• Fix install paths

  

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Commits on Dec 13, 2024

• Merge remote-tracking branch 'origin/main' into db/vcpkg

  

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• Macos CI/CD build options

  

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• Uncomment failing test

  

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• Uncomment java tests

  

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• Fix nightly build

  

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Commits on Dec 16, 2024

• Gradle use cmake

  

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• Install dependencies before building java bindings

  

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• Add debug logs

  

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Commits on Dec 17, 2024

• Change find path for native lib for java

  

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• Merge remote-tracking branch 'origin/main' into db/vcpkg

  

  Dušan Baran

  committed
  41d7f4a

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• Fix java bindings find_library

  

  Dušan Baran

  committed
  415fff8

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• Fix include paths for java

  

  Dušan Baran

  committed
  c69c63b

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• Fix find native lib

  

  Dušan Baran

  committed
  da25ebb

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