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test #46

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wants to merge 87 commits into from
Closed

test #46

wants to merge 87 commits into from

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@absternator absternator mentioned this pull request Feb 13, 2025
Merged
5 tasks
@absternator
Add gcc-multilib to environment.yml dependencies
7a7ade0
@absternator
Replace gcc-multilib with cuda-toolkit in environment.yml dependencies
8b0722e
@absternator
Fix spelling of 'cudatoolkit' in environment.yml dependencies
1f40427
@absternator
Add nvcc, libgfortran, and cuda to environment.yml dependencies
2832c6d
@absternator
Remove 'cuda' from environment.yml dependencies
e3d19ed
@absternator
Remove cudatoolkit, nvcc, and libgfortran-ng from environment.yml dep…
6a6daf7 
…endencies
@absternator
Update CMakeLists.txt to find Python components and require pybind11 …
16f55c9 
…configuration
@absternator
Refactor CMakeLists.txt to improve CUDA module configuration and linking
7dab093
@absternator
Set C++ standard for pybind11 to C++14 in CMakeLists.txt
61ba689
@absternator
Add pybind11 header inclusion in python_bindings.cpp
78814dc
@absternator
Update GitHub Actions workflow to use Ubuntu 22.04 and fix hash_base …
b8cab06 
…struct definition in Boost
@absternator
Update GitHub Actions workflow to use latest Ubuntu version and simpl…
e9fe625 
…ify hash_base struct definition in Boost
@absternator
Remove deprecated CMake policy setting for CUDA_ARCHITECTURES in CMak…
c88915f 
…eLists.txt
@absternator
Update CMakeLists.txt to set C++ standard to 11 and enforce required …
3c60087 
…Python components in find_package; update pybind11 version in environment.yml
@absternator
Update CMakeLists.txt to set C++ standard to 14
05dcbbb
@absternator
Add support for CPU-only compilation and include directories in CMake…
f00eac4 
…Lists.txt
@absternator
Update GitHub Actions workflow to use Ubuntu 22.04 and Python 3.13
a5920f6
@absternator
Update GitHub Actions workflow to use Ubuntu latest and Python 3.10; …
85dedb8 
…remove unused C++ standard setting in CMakeLists.txt
@absternator
Add <locale> header to wtsne.hpp for locale support
d8795cc
@absternator
Add includes for <cstdint> and <algorithm> in python_bindings.cpp
30d4823
@absternator
Add include directories for target and remove unused includes in pyth…
ecd8ffb 
…on_bindings.cpp
@absternator
Update CMakeLists.txt to set C++ standard to 17 and improve include d…
e40625d 
…irectory handling
@absternator
Revert "Update CMakeLists.txt to set C++ standard to 17 and improve i…
fb0fba8 
…nclude directory handling"

This reverts commit e40625d.
@absternator
Update CMakeLists.txt to set C++ standard to 17 and adjust CUDA policy
6a876b4
@absternator
Update CMakeLists.txt to set C++ standard to 20 and enable new CUDA p…
7020330 
…olicy
@absternator
Downgrade C++ standard to 14 and add GCC 13 specific compile definitions
9791753
@absternator
Update CMakeLists.txt to set C++ standard to 17 and remove GCC 13 spe…
1fcae94 
…cific compile definitions
@absternator
Update Python version in GitHub Actions workflow from 3.10 to 3.13
4d92cbb
@absternator
Fix type casting in kseq.h to ensure proper size calculation
12936d2
@absternator
Comment out _FORTIFY_SOURCE definition in CMakeLists.txt for CPU libr…
e2e201a 
…ary build
@absternator
Add wchar.h include to pairsnp.hpp and wtsne.hpp for wide character s…
0cd54ab 
…upport
@absternator
Add wchar.h include to python_bindings.cpp for wide character support
58d485f 
Remove wchar.h include from wtsne.hpp to clean up unused dependencies
@absternator
Fix formatting of include directive in vendor/features.h
c47a509
@absternator
Update CMakeLists.txt for required packages and optimize compiler fla…
2037dc7 
…gs; add debug output in normalise_vector function
@absternator
Optimize compiler flags in CMakeLists.txt for improved performance
9da067b
@absternator
Remove redundant wchar.h include from pairsnp.hpp and adjust CMake CX…
7ebbe27 
…X_FLAGS for optimization
@absternator
Remove debug output from normalise_vector function for cleaner perfor…
6d4d04b 
…mance
@absternator
Increase _FORTIFY_SOURCE level in CMakeLists.txt for enhanced security
5d9c270
@absternator
Decrease _FORTIFY_SOURCE level in CMakeLists.txt for compatibility
2604c7d
@absternator
Set _FORTIFY_SOURCE level to 0 in CMakeLists.txt and setup.py for com…
a5dab16 
…patibility
@absternator
Remove _FORTIFY_SOURCE setting from setup.py and replace wchar.h with…
ec98319 
… cwchar in python_bindings.cpp for improved compatibility and standard compliance
@absternator
Add <cwchar> and <wchar.h> includes for improved compatibility in pyt…
d41e865 
…hon_bindings.cpp and wtsne.hpp
@absternator
Remove unused Boost headers and update CMakeLists.txt to include Boos…
351f29a 
…t directories for improved compatibility
@absternator
Remove Boost Dockerfile and extraction script; update environment.yml…
4ce3e62 
… to include boost-cpp dependency
@absternator
Remove _FORTIFY_SOURCE definition from CMakeLists.txt for improved co…
d1fd90f 
…mpatibility
@absternator
Remove unused includes from python_bindings.cpp and wtsne.hpp for imp…
772ca20 
…roved code clarity
@absternator
Refactor conditional_probabilities function to use max limits for bet…
6bbe18f 
…a values and optimize loop indexing; add debug output for P values
@absternator
Refactor conditional_probabilities function to simplify loop indexing…
1eaa0de 
… and remove debug output for P values
@absternator
Update Python version matrix in GitHub Actions workflow to include Py…
8a54a65 
…thon 3.9
@absternator
Update GitHub Actions workflow to support multiple OS versions in the…
8da8c4d 
… Python build matrix
@absternator
Merge branch 'master' of https://github.com/bacpop/mandrake into test…
bc215c2 
…-pipelines
@absternator
Update CMake configuration for CUDA support and simplify pybind11 int…
6b70726 
…egration
@absternator
Refactor pairsnp function to improve performance by replacing atomic …
0243945 
…variables with simpler types and optimizing OpenMP scheduling
@absternator
Clean up Python bindings and improve code formatting in wtsne.hpp
fce872b
@absternator
Bump version to 1.2.4
08f3954
@absternator absternator deleted the test-pipelines branch February 26, 2025 08:32
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@absternator