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Use CMakeLists.txt instead of Makefile #4

Merged
merged 41 commits into from
Jun 9, 2024
Merged

Use CMakeLists.txt instead of Makefile #4

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65e5b0b
Use CMakeLists.txt instead of Makefile
adamant-pwn Apr 24, 2024
106eb03
Update CMakeLists.txt
adamant-pwn May 13, 2024
660268d
Refactor CMakeLists.txt
adamant-pwn May 15, 2024
3fbcda9
Update
adamant-pwn May 15, 2024
0b10e4e
Use .a instead of .so, link pod5 with zstd
adamant-pwn May 15, 2024
d0863fc
Fix docker failure
adamant-pwn May 15, 2024
837cd9b
Update README.md
adamant-pwn May 15, 2024
6d530c7
Update README.md
adamant-pwn May 15, 2024
ae2e122
Add basic Dockerfile
adamant-pwn May 13, 2024
45d6504
Update Dockerfile
adamant-pwn May 15, 2024
1804191
Make test workflow
adamant-pwn May 15, 2024
20a273d
Checkout recursive
adamant-pwn May 15, 2024
a07df3e
Update branch name in workflow
adamant-pwn May 15, 2024
0882d3f
Redundant include <array>
adamant-pwn May 15, 2024
1617247
Use -h in GH workflow
adamant-pwn May 16, 2024
7b2c9d2
Run workflow for any PR
adamant-pwn May 16, 2024
f445400
Remove python bindings WIP, add proper handling of C/CXX
adamant-pwn May 16, 2024
35cacaf
Testing simplified RUCLIENT_ENABLED
adamant-pwn May 16, 2024
d894b6e
Use TARGET_NAME as an argument
adamant-pwn May 16, 2024
8d317cb
Try caching for workflows
adamant-pwn May 16, 2024
2a320c8
Try NOHDF5=ON by default
adamant-pwn May 16, 2024
33ce9dc
Try NOPOD5=ON
adamant-pwn May 16, 2024
722cf0f
Update
adamant-pwn May 17, 2024
ddcb274
Remove readuntil_fake
adamant-pwn May 17, 2024
721bee5
Remove log.txt
adamant-pwn May 17, 2024
001425e
Try build with POD5 and HDF5
adamant-pwn May 17, 2024
8f273f4
merged tflite branch and fixed cmake setup
maximilianmordig May 24, 2024
f8f053c
adding some fixes to the cmake file, and prototyping python integration
maximilianmordig May 24, 2024
dd0ac71
Fix slow5lib.so
adamant-pwn May 31, 2024
95fd6ae
wrote crude wrapper around rawhash for signal mapping
maximilianmordig Jun 3, 2024
1351418
added option to skip querying revcomp signal, small fixes
maximilianmordig Jun 4, 2024
e97d2fd
confirmed that alignment is the same for a single read
maximilianmordig Jun 4, 2024
4d6dbf5
cleaned up rawhash python wrapper
maximilianmordig Jun 4, 2024
a70f641
Try caching build directory
adamant-pwn Jun 5, 2024
1afd7a1
Lowercase repo owner
adamant-pwn Jun 5, 2024
feba398
Use CACHE STRING on ccache
adamant-pwn Jun 5, 2024
1f439d8
Remove build from .dockerignore for caching
adamant-pwn Jun 5, 2024
619ccce
Only run build-push-action once
adamant-pwn Jun 5, 2024
f4319f2
Try -j 2 with cached build directory
adamant-pwn Jun 5, 2024
63e1001
Use 3 cores and only cache build dir
adamant-pwn Jun 5, 2024
fcea20c
Try to use less space in workflows
adamant-pwn Jun 6, 2024
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3 changes: 2 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
bin/
build/
run_dir/

test/data/d1_*
Expand Down Expand Up @@ -84,4 +85,4 @@ extern/pod5*
test/evaluation/rawsamble/

extern/tensorflow/tflite_build/
test/evaluation/read_mapping/*.features
test/evaluation/read_mapping/*.features
6 changes: 6 additions & 0 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
cmake_minimum_required(VERSION 3.10)
project(RawHash2)

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
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add_subdirectory(src)
29 changes: 0 additions & 29 deletions Makefile
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