[PATCH] deprecate core_language.hpp by SGSSGene · Pull Request #2351 · seqan/seqan3

SGSSGene · 2021-01-25T13:33:43Z

Move content of core/concept/core_language.hpp to utility/detail/exposition_only_concept.hpp
Added deprecation to core_language.hpp and a forward include to exposition_only_concept.hpp
Changed all header files to new include path
Changed all unittest to new include path

Resolves part of seqan/product_backlog#160

SGSSGene · 2021-01-25T13:34:06Z

This is solving partly seqan/product_backlog#160

codecov · 2021-01-25T14:03:28Z

Codecov Report

Merging #2351 (7b01ba2) into master (94a4e22) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2351   +/-   ##
=======================================
  Coverage   98.21%   98.21%           
=======================================
  Files         265      265           
  Lines       10806    10806           
=======================================
  Hits        10613    10613           
  Misses        193      193

Impacted Files	Coverage Δ
...lude/seqan3/alignment/matrix/alignment_optimum.hpp	`100.00% <ø> (ø)`
...qan3/alignment/matrix/detail/affine_cell_proxy.hpp	`100.00% <ø> (ø)`
...atrix/detail/alignment_score_matrix_one_column.hpp	`100.00% <ø> (ø)`
.../detail/alignment_score_matrix_one_column_base.hpp	`100.00% <ø> (ø)`
.../matrix/detail/combined_score_and_trace_matrix.hpp	`100.00% <ø> (ø)`
...qan3/alignment/matrix/detail/matrix_coordinate.hpp	`100.00% <ø> (ø)`
...nment/matrix/detail/score_matrix_single_column.hpp	`100.00% <ø> (ø)`
...qan3/alignment/matrix/detail/trace_matrix_full.hpp	`100.00% <ø> (ø)`
...ment/pairwise/detail/alignment_algorithm_state.hpp	`100.00% <ø> (ø)`
...n3/alignment/pairwise/policy/affine_gap_policy.hpp	`100.00% <ø> (ø)`
... and 17 more

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Irallia

Thank you!
Could you please move the belonging tests aswell?

Irallia · 2021-01-26T12:05:50Z

 #include <random>

-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>
 #include <seqan3/std/iterator>

 #include "auxiliary.hpp"


Could you also move and rename this test?
test/unit/std/concept/core_language_test.cpp -> test/unit/utility/detail/exposition_only_concept_test.cpp
And double check if there are snipptes or performance tests to move?

marehr · 2021-02-01T10:37:48Z

2021-02-01 Core Meeting

We talked about documentation inconsistencies.

We found that the documentation of seqan3::detail::template_specialisation_of is wrong

Remove addtogroup
Fix namespace of seqan3::template_specialisation_of -> seqan3::detail::template_specialisation_of, see here

Move concept group from core to utility. Keep seqan3::implicitly_convertible_to and so on public, but explicitly mark them as \noapi.

SGSSGene · 2021-02-05T13:21:40Z

Some question came up:

where to put the \defgroup utility_concept Concept. Everywhere else it is inside an all.hpp, but I don't really have one. I have put it for now into utility/all.hpp
core/all.hpp had an unuseful concept description. I for now removed it.

Irallia

Thanks, looks good now!
I think you can remove the include from the all.hpp, but you can do this together with the second review.

Irallia · 2021-02-08T10:59:45Z


 #include <seqan3/core/concept/cereal.hpp>
-#include <seqan3/core/concept/core_language.hpp>
+#include <seqan3/utility/detail/exposition_only_concept.hpp>


So far I know, we don't put detail things into all.hpp files.
@seqan/core is that correct?

Some question came up:

1. where to put the `\defgroup utility_concept Concept`. Everywhere else it is inside an all.hpp, but I don't really have one. I have put it for now into `utility/all.hpp` 2. core/all.hpp had an unuseful `concept` description. I for now removed it.

For detail folder there is no all.hpp.
We actually want to establish to never just include 'all.hpp' but only what you need. The 'all.hpp' are for the user, who is not so familiar with the different modules etc.
Things in detail are functionalities that are there for us and not for the user, so there is no 'all.hpp'.

So far I know, we don't put detail things into all.hpp files.
@seqan/core is that correct?

In general, you are right, but I think it is okay in this case. In the long-run we will remove that header.

marehr

Looks very good; just some (repetetive) remarks :)

- Move content of core/concept/core_language.hpp to utility/detail/exposition_only_concept.hpp - Added deprecation to core_language.hpp and a forward include to exposition_only_concept.hpp - Changed all header files to new include path - Changed all unittest to new include path

• remove from `concept` group • add missing `detail::` namespace scope

Co-authored-by: Marcel <marehr@users.noreply.github.com>

marehr

Thank you so much, it seems we are done. :)

SGSSGene mentioned this pull request Jan 25, 2021

Core / Utility Split seqan/product_backlog#160

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23 tasks

SGSSGene requested review from a team and Irallia and removed request for a team January 25, 2021 13:35

Irallia requested changes Jan 26, 2021

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SGSSGene force-pushed the patch/deprecate-core_language branch from 950d403 to e1bdf68 Compare February 5, 2021 13:16

SGSSGene force-pushed the patch/deprecate-core_language branch from e1bdf68 to fccb332 Compare February 5, 2021 13:24

marehr requested a review from Irallia February 8, 2021 09:09

Irallia approved these changes Feb 8, 2021

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Irallia requested a review from marehr February 8, 2021 11:03

marehr reviewed Feb 12, 2021

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SGSSGene force-pushed the patch/deprecate-core_language branch from e2fac71 to 08d176b Compare February 14, 2021 16:55

SGSSGene and others added 6 commits February 14, 2021 18:36

[FIX] rename unittest to utility/detail/exposition_only_concept_test.cpp

5dbb7c7

[FIX] doxygen - adjusting template_specicialisation_of

a93d692

• remove from `concept` group • add missing `detail::` namespace scope

[FIX] introducing to doxygen

c6bc2ea

[FIX] reorder of includes

23a21b9

Co-authored-by: Marcel <marehr@users.noreply.github.com>

[FIX] more reordering of includes

7b01ba2

SGSSGene force-pushed the patch/deprecate-core_language branch from 08d176b to 7b01ba2 Compare February 14, 2021 18:04

SGSSGene mentioned this pull request Feb 14, 2021

[INFRA] adds a helper script to check for missing includes #2376

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marehr self-requested a review February 15, 2021 09:11

marehr approved these changes Feb 15, 2021

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marehr merged commit a1d5d4d into seqan:master Feb 15, 2021

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SGSSGene commented Jan 25, 2021 •

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