Core / Utility Split

[marehr]

We split the core module into core module and utility module: (Card)

• core is everything strongly coupled with our library, required by > 1 module, and is not stand-alone.
• utility contains features not related to biological use cases and could potentially live as stand-alone libraries outside of SeqAn.
• Here is a gist with an overview of the current state of core and the possible split.

https://gist.github.com/rrahn/f6b09ad67bebd14bd9c58f77c53e0450

for extracting core into utility; e.g. tuple etc, type_traits into utility.

@marehr

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09.12.2019

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We will split all files into either utility or core. see the protocol for further details

https://github.com/seqan/seqan3/wiki/Core-Meeting-notes#2019-12-09-rrahn

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Acceptance criteria

• Including the old header should not break the current code.
• Including the old header should raise a deprecation warning and output the new header that needs to be included.

Tasks per header

• copy the header to the correct place
• shortly check if all header includes are correct: remove unused, order alphabetically, put seqan3/std/* headers to the top
• possibly rename the header
• deprecate old header with header deprecation macro:

  SEQAN3_DEPRECATED_HEADER(
     "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/alphabet/aminoacid/translation_new.hpp> instead.")

• deprecate old header doxygen file section: add [DEPRECATED] at begin of brief and add \deprecated This header is deprecated and will be removed in SeqAn-3.1.0; Please \#include <new header> instead. tag.
• move all related tests, snippets etc to match new folder structure
• run all tests to see if nothing depends on old header anymore
• live happily ever after

submodule/header assignment (please see gist https://gist.github.com/rrahn/f6b09ad67bebd14bd9c58f77c53e0450)

• algorithm [@Irallia]
  Open Questions:
  • algorithm/pipeable_config_element.hpp -> Needs discussion/resolution
• char_operations [@smehringer]
• concept [@simonsasse]
  • Move core/concept/core_language.hpp -> utility/detail/exposition_only_concept.hpp [@SGSSGene] ([PATCH] deprecate core_language.hpp seqan3#2351)
• detail (except debug_stream?) [@eseiler]
• parallel [@MitraDarja]
• simd [@marehr]
  Open Questions:
  • utility/simd/simd_algorithm.hpp -> utility/simd/algorithm.hpp? ([MISC] move {core => utility}/simd seqan3#2260 (comment))
• type_list submodule [@rrahn]
• type_traits [@joergi-w]
• top-level header [@Irallia]
  • bit_manipulation.hpp [@marehr & @Irallia] (Introduce <bit> shim-header seqan3#2292 & Infra/core/move header bit manipulation to utility detail seqan3#2294)
  • common_tuple [@eaasna]
  • math.hpp [@marehr]
  • pod_tuple [@eaasna, @smehringer]
  • tuple_utility.hpp [@SGSSGene]
    Open Questions:
  • add_enum_bitwise_operators.hpp
  • all.hpp
  • debug_stream.hpp

[rrahn]

Core meeting 2020-11-10

How to split the modules on a technical level.

Requirements:

• Including the old header should not break the current code.
• Including the old header should raise a deprecation warning and output the new header that needs to be included.

Open questions:

• What happens with the header-tests?
  • We will use some deprecation macro that allows us to deprecate an unused header.
  • This macro will be disabled when running the header tests.
• Should we, and if so how, also deprecate the header documentation?
  • In the file description add doxygen comment (See above Core / Utility Split #160 (comment))
  • add [DEPRECATED] at the beginning of the brief section of the file block.

[rrahn]

Resolution - Core meeting 2020-11-23

• We will remove detail/all.hpp headers and public all.hpp should not include detail headers.

• We remove them without any deprecation notice.

• If an existing all header includes partially from deprecated headers we add a

  #if SEQAN3_VERSION_MAJOR == 3 && SEQAN3_VERSION_MAJOR >= 1
       #pragma warning "DEV NOTICE: Remove the deprecated header #include <deprecated_header>."
  #endif

[smehringer]

Resolution 14-12-2020

• pipeable_config_element should be moved into detail (@rrahn will tackle this)

  • Move file to core/configuration/detail
  • Move to seqan3::detail namespace
  • Rename to configuration_element_base
  • Make sure that the documentation of the configuration class does not refer any detail stuff (regarding the detail::pipeable_config_element).
  • Follow up: Check if interface documentation of "pipeability" could be put into pipeable_config_element and every config element can pull in this documentation.
  • See follow-up ticket pipeable_config_element should be moved into detail #288

• Move core/concept/core_language.hpp -> utility/detail/exposition_only_concept.hpp
  (Later we might discuss if we should remove some of the concept completely)

  • Done by [PATCH] deprecate core_language.hpp seqan3#2351

• Move core/simd/simd_algorithm -> utility/simd/algorithm.hpp (@marehr )

  • Done by [MISC] move {core => utility}/simd seqan3#2260

[marehr]

I close this now, because it is mainly done. We have one follow-up ticket #288