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[MISC] Use new layout #197

Merged
merged 11 commits into from
Aug 28, 2023
Merged

[MISC] Use new layout #197

merged 11 commits into from
Aug 28, 2023

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eseiler
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@eseiler eseiler commented Aug 25, 2023

TODO:

  • Update prefixes
  • display_layout
  • serialisation?
  • cleanup parsing for config/userbins
  • tests for parsing/userbins
auto read_layout_file(std::istream & stream)
{
    chopper::configuration cfg{};
    // read chopper user bins (?)
    // read chopper config
    // read hibf config
    // read hibf layout
    return all; // tuple
}
chopper::configuration::write_to
{
    // Call cereal on members
}

write_to/read_from same as in hibf lib

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codecov bot commented Aug 25, 2023

Codecov Report

Patch coverage: 97.22% and project coverage change: -0.09% ⚠️

Comparison is base (d614ec3) 95.66% compared to head (dca13a2) 95.58%.

❗ Current head dca13a2 differs from pull request most recent head aa8008e. Consider uploading reports for the commit aa8008e to get more accurate results

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #197      +/-   ##
==========================================
- Coverage   95.66%   95.58%   -0.09%     
==========================================
  Files          13       13              
  Lines         646      634      -12     
==========================================
- Hits          618      606      -12     
  Misses         28       28              
Files Changed Coverage Δ
include/chopper/sketch/read_hll_files_into.hpp 100.00% <ø> (ø)
include/chopper/layout/hibf_statistics.hpp 98.39% <87.50%> (+<0.01%) ⬆️
include/chopper/configuration.hpp 100.00% <100.00%> (ø)
include/chopper/input_functor.hpp 56.25% <100.00%> (ø)
include/chopper/layout/output.hpp 100.00% <100.00%> (ø)
include/chopper/sketch/output.hpp 100.00% <100.00%> (ø)
src/chopper_layout.cpp 92.30% <100.00%> (ø)

☔ View full report in Codecov by Sentry.
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@@ -86,7 +86,7 @@ struct configuration
archive(CEREAL_NVP(determine_best_tmax));
archive(CEREAL_NVP(force_all_binnings));

archive(CEREAL_NVP(hibf_config));
// archive(CEREAL_NVP(hibf_config));
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Suggested change
// archive(CEREAL_NVP(hibf_config));

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can be done in a follow up pr

@smehringer
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smehringer commented Aug 26, 2023

I'm not sure what exactly you mean by all the open todo points. Maybe we should discuss them before merging this PR.

@@ -17,6 +17,7 @@
#include <seqan3/utility/range/to.hpp>
#include <seqan3/utility/views/join_with.hpp>

#include "../api/api_test.hpp"
#include "cli_test.hpp"

// check if each chopper submodule can work with the output of the other
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@eseiler eseiler Aug 28, 2023

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chopper_layout_with_tax // tax is ignored
With TAX, otherwise same as chopper_layout2


return filenames;
}

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Add read_layout_file

namespace chopper::layout
{

inline void read_config_from(configuration & config, std::istream & stream)
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@seqan-actions seqan-actions added lint and removed lint labels Aug 28, 2023
@eseiler eseiler merged commit d780239 into seqan:main Aug 28, 2023
17 checks passed
@eseiler eseiler deleted the misc/layout branch August 28, 2023 14:19
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3 participants