[TEST] implement sequence generator #1985

Irallia · 2020-07-15T13:08:15Z

resolves part of seqan/product_backlog#12

The first commit will be done by another PR: #1995 ([TEST] Repair seqan2 tests)

codecov · 2020-07-15T13:47:26Z

Codecov Report

Merging #1985 into master will increase coverage by 0.00%.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1985   +/-   ##
=======================================
  Coverage   97.97%   97.98%           
=======================================
  Files         262      262           
  Lines       10045    10054    +9     
=======================================
+ Hits         9842     9851    +9     
  Misses        203      203

Impacted Files	Coverage Δ
include/seqan3/range/views/move.hpp
include/seqan3/alphabet/nucleotide/dna4.hpp
include/seqan3/alphabet/nucleotide/dna3bs.hpp
include/seqan3/core/detail/debug_stream_range.hpp
include/seqan3/io/detail/record.hpp
include/seqan3/alphabet/hash.hpp
...ignment/pairwise/policy/affine_gap_init_policy.hpp
...qan3/alignment/pairwise/edit_distance_unbanded.hpp
include/seqan3/alphabet/quality/phred63.hpp
.../matrix/detail/combined_score_and_trace_matrix.hpp
... and 513 more

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test/include/seqan3/test/performance/sequence_generator.hpp

marehr

First round :)

test/unit/test/sequence_generator_test.cpp

test/include/seqan3/test/performance/sequence_generator.hpp

test/unit/test/sequence_generator_test.cpp

marehr

2nd Round :)

test/unit/test/sequence_generator_test.cpp

test/include/seqan3/test/performance/sequence_generator.hpp

Irallia · 2020-08-26T11:55:37Z

I get an error message in the seqan2 part of the sequence_generator_test. Should I just remove this part as it will be covered later?

In file included from .../seqan3/test/unit/test/sequence_generator_test.cpp:12:
.../seqan3/test/include/seqan3/test/performance/sequence_generator.hpp: In instantiation of 'sequence_t seqan3::test::random_sequence_generator<sequence_t>::operator()(generator_t&&) const [with generator_t = std::mersenne_twister_engine<long long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>&; sequence_t = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >]':
..../seqan3/test/unit/test/sequence_generator_test.cpp:101:68:   required from here
.../seqan3/test/include/seqan3/test/performance/sequence_generator.hpp:81:33: error: use of invalid variable template 'alphabet_size<alphabet_t>'
   81 |             max_alphabet_rank = alphabet_size<alphabet_t> - 1ull;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~

eseiler · 2020-08-26T13:21:23Z

Seems like you are using the operator() in the seqan2 part, which then calls seqan3 stuff on seqan2 alphabets.
Wouldn't you need to call generate_sequence_seqan2 for the seqan2 part?

marehr

next round :)

test/unit/test/sequence_generator_test.cpp

Irallia · 2020-08-28T09:18:17Z

If you approve I will rebase and clear up the history.

marehr

Thank you, we are nearly done :)

test/include/seqan3/test/performance/sequence_generator.hpp

test/unit/test/sequence_generator_test.cpp

marehr

Thank you, we are very close to finish :)

test/include/seqan3/test/performance/sequence_generator.hpp

marehr

Thank you :) Second Reviewer do your work!

rrahn

This is already a big start towards a better design :).
I found some issues that should be addressed. Otherwise it looks fine to me.
Thank you!

rrahn · 2020-09-09T13:52:15Z

test/include/seqan3/test/performance/sequence_generator.hpp

-    std::uniform_int_distribution<size_t> dis_alpha(0ull, max_val);
-    std::uniform_int_distribution<size_t> dis_length(len - variance, len + variance);
+public:
+


Suggested change

rrahn · 2020-09-09T13:52:41Z

test/include/seqan3/test/performance/sequence_generator.hpp

+    ~random_sequence_generator() = default; //!< Defaulted
+
+    /*!\brief Initialises a random sequence generator which generates sequences with a given mean size.
+     * \param[in] size          The size of the random sequence.


Suggested change

* \param[in] size The size of the random sequence.

* \param[in] size The size of the random sequence.

rrahn · 2020-09-09T13:53:07Z

test/include/seqan3/test/performance/sequence_generator.hpp

+
+    /*!\brief Initialises a random sequence generator which generates sequences with a given mean size.
+     * \param[in] size          The size of the random sequence.
+     * \param[in] size_variance The variance of the random sequence size.


Suggested change

* \param[in] size_variance The variance of the random sequence size.

* \param[in] size_variance The variance of the random sequence size (defaults to `0`).

rrahn · 2020-09-09T13:54:05Z

test/include/seqan3/test/performance/sequence_generator.hpp

+     */
+
+    /*!\brief Returns a random sequence for a set size (and variance).
+     * \param[in,out] random_generator e.g. std::mt19937 with a seed of 42


Suggested change

* \param[in,out] random_generator e.g. std::mt19937 with a seed of 42

* \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42

rrahn · 2020-09-09T13:54:32Z

test/include/seqan3/test/performance/sequence_generator.hpp

+
+    /*!\brief Returns a random sequence for a set size (and variance).
+     * \param[in,out] random_generator e.g. std::mt19937 with a seed of 42
+     * \returns a random generated sequence.


Suggested change

* \returns a random generated sequence.

* \returns a generated random sequence.

rrahn · 2020-09-09T13:56:39Z

test/include/seqan3/test/performance/sequence_generator.hpp

+        std::uniform_int_distribution<size_t> alphabet_rank_distribution(0ull, max_alphabet_rank);
+        std::uniform_int_distribution<size_t> sequence_size_distribution(size - size_variance, size + size_variance);
+
+        size_t sequence_size = sequence_size_distribution(random_generator);


Suggested change

size_t sequence_size = sequence_size_distribution(random_generator);

size_t const sequence_size = sequence_size_distribution(random_generator);

rrahn · 2020-09-09T13:56:52Z

test/include/seqan3/test/performance/sequence_generator.hpp

+
+        size_t sequence_size = sequence_size_distribution(random_generator);
+        sequence_t random_sequence(sequence_size);
+        std::ranges::generate(random_sequence, [&]() -> alphabet_t


Suggested change

std::ranges::generate(random_sequence, [&]() -> alphabet_t

std::ranges::generate(random_sequence, [&] () -> alphabet_t

rrahn · 2020-09-09T14:03:40Z

test/include/seqan3/test/performance/sequence_generator.hpp

+        std::uniform_int_distribution<size_t> sequence_size_distribution(size - size_variance, size + size_variance);
+
+        size_t sequence_size = sequence_size_distribution(random_generator);
+        sequence_t random_sequence(sequence_size);


Pheww, can we actually assume that this does in fact always does what we expect? I think this is not handled properly by the concepts yet. The biggest problem that I see is handling the SeqAn2 sequence types which do not have push_back or resize member functions. So I guess later on we need to use a helper function to differentiate between sequences that have a resize member function. For now I propose to add this inline requires clause in the head of the class template:

requires requires (sequence_t & s) { {s.resize()}; }

And then use here the resize member function instead of the constructor.

rrahn · 2020-09-17T11:45:39Z

test/include/seqan3/test/performance/sequence_generator.hpp

+template <typename sequence_t>
+//!\cond
+    requires (std::ranges::output_range<sequence_t, std::ranges::range_value_t<sequence_t>> &&
+              requires (sequence_t & s) { {s.resize(1)}; } )


Suggested change

requires (sequence_t & s) { {s.resize(1)}; } )

requires (sequence_t & s) { {s.resize(1)}; })

rrahn · 2020-09-17T11:47:45Z

test/include/seqan3/test/performance/sequence_generator.hpp

        else
-            sequence.push_back(assign_rank_to(dis_alpha(gen), alphabet_t{}));
+            max_alphabet_rank = alphabet_size<alphabet_t> - 1ull;


Suggested change

max_alphabet_rank = alphabet_size<alphabet_t> - 1ull;

max_alphabet_rank = seqan3::alphabet_size<alphabet_t> - 1ull;

rrahn · 2020-09-17T11:50:35Z

test/include/seqan3/test/performance/sequence_generator.hpp

+            if constexpr (std::is_same_v<alphabet_t, uint64_t>)
+                return alphabet_rank_distribution(random_generator);
+            else
+                return assign_rank_to(alphabet_rank_distribution(random_generator), alphabet_t{});


Suggested change

return assign_rank_to(alphabet_rank_distribution(random_generator), alphabet_t{});

return seqan3::assign_rank_to(alphabet_rank_distribution(random_generator), alphabet_t{});

rrahn

Minor stuff only. Please rebase right away. I approve already.

rrahn · 2020-10-08T10:37:30Z

test/include/seqan3/test/performance/sequence_generator.hpp

+     */
+
+    /*!\brief Returns a random sequence for a set size (and variance).
+     * \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42


Suggested change

* \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42

* \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42.

rrahn · 2020-10-08T10:37:41Z

test/include/seqan3/test/performance/sequence_generator.hpp

+
+    /*!\brief Returns a random sequence for a set size (and variance).
+     * \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42
+     * \returns a generated random sequence.


Suggested change

* \returns a generated random sequence.

* \returns A generated random sequence.

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia marked this pull request as draft July 16, 2020 11:15

marehr self-requested a review July 27, 2020 09:12

Irallia force-pushed the TEST/implement_sequence_generator branch 5 times, most recently from d61513a to 5cde5e6 Compare July 28, 2020 15:46

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[TEST] Implement random_sequence class with call operator() and tests

c7bb6d2

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

Irallia force-pushed the TEST/implement_sequence_generator branch from d6012fc to c7bb6d2 Compare October 8, 2020 11:00

rrahn merged commit a5700db into seqan:master Oct 8, 2020

eseiler mentioned this pull request Oct 16, 2020

format_sam_benchmark not terminating in Debug mode #2225

Closed

smehringer mentioned this pull request Jan 11, 2021

Implement a sequence generator for the tests and benchmarks of the library such that it is easier to handle the generation of sequences inbetween different calls. seqan/product_backlog#12

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[TEST] implement sequence generator #1985

[TEST] implement sequence generator #1985

Irallia commented Jul 15, 2020 •

edited by rrahn

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	* \param[in] size The size of the random sequence.
	* \param[in] size The size of the random sequence.

	* \param[in] size_variance The variance of the random sequence size.
	* \param[in] size_variance The variance of the random sequence size (defaults to `0`).

	* \param[in,out] random_generator e.g. std::mt19937 with a seed of 42
	* \param[in,out] random_generator, e.g. std::mt19937 with a seed of 42

	* \returns a random generated sequence.
	* \returns a generated random sequence.

	size_t sequence_size = sequence_size_distribution(random_generator);
	size_t const sequence_size = sequence_size_distribution(random_generator);

	std::ranges::generate(random_sequence, [&]() -> alphabet_t
	std::ranges::generate(random_sequence, [&] () -> alphabet_t

	requires (sequence_t & s) { {s.resize(1)}; } )
	requires (sequence_t & s) { {s.resize(1)}; })

	max_alphabet_rank = alphabet_size<alphabet_t> - 1ull;
	max_alphabet_rank = seqan3::alphabet_size<alphabet_t> - 1ull;

	return assign_rank_to(alphabet_rank_distribution(random_generator), alphabet_t{});
	return seqan3::assign_rank_to(alphabet_rank_distribution(random_generator), alphabet_t{});

[TEST] implement sequence generator #1985

[TEST] implement sequence generator #1985

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Irallia commented Jul 15, 2020 •

edited by rrahn

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codecov bot commented Jul 15, 2020 •

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