[INFRA] Move core/algorithm into core/configuration #2255

Irallia · 2020-11-11T15:03:03Z

Resolves partly seqan/product_backlog#160

algorithm/concept.hpp -> core/configuration/detail/.
algorithm/configuration.hpp -> core/configuration/.
algorithm/configuration_element_debug_mode.hpp -> core/configuration/detail/.
algorithm/configuration_element_parallel_mode.hpp -> core/configuration/detail/.
algorithm/configuration_utility.hpp -> core/configuration/detail/.

Skipped: algorithm/pipeable_config_element.hpp (needs a decision)

Keep untouched:
algorithm/detail/... -> core/algorithm/detail/...
algorithm/algorithm_result_generator_range -> core/algorithm/algorithm_result_generator_range

Added new all.hpp's and adjusted the other ones.

Details for this: https://gist.github.com/rrahn/f6b09ad67bebd14bd9c58f77c53e0450

codecov · 2020-11-11T15:24:03Z

Codecov Report

Merging #2255 (1ae6a3f) into master (d37ba83) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master    #2255   +/-   ##
=======================================
  Coverage   98.15%   98.15%           
=======================================
  Files         262      262           
  Lines       10815    10815           
=======================================
  Hits        10616    10616           
  Misses        199      199

Impacted Files	Coverage Δ
...ude/seqan3/alignment/pairwise/alignment_result.hpp	`100.00% <ø> (ø)`
...gnment/pairwise/detail/policy_alignment_matrix.hpp	`100.00% <ø> (ø)`
...airwise/detail/policy_alignment_result_builder.hpp	`100.00% <ø> (ø)`
...ignment/pairwise/detail/policy_optimum_tracker.hpp	`97.82% <ø> (ø)`
...e/seqan3/alignment/pairwise/detail/type_traits.hpp	`100.00% <ø> (ø)`
...qan3/alignment/pairwise/edit_distance_unbanded.hpp	`99.31% <ø> (ø)`
...ignment/pairwise/policy/simd_affine_gap_policy.hpp	`100.00% <ø> (ø)`
...an3/search/configuration/default_configuration.hpp	`100.00% <ø> (ø)`
include/seqan3/search/search.hpp	`100.00% <ø> (ø)`
include/seqan3/search/search_result.hpp	`100.00% <ø> (ø)`
... and 4 more

Continue to review full report at Codecov.

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include/seqan3/core/algorithm/all.hpp

include/seqan3/core/configuration/detail/all.hpp

include/seqan3/core/algorithm/concept.hpp

include/seqan3/core/configuration/configuration.hpp

include/seqan3/core/algorithm/all.hpp

include/seqan3/core/algorithm/detail/all.hpp

include/seqan3/core/configuration/all.hpp

include/seqan3/core/configuration/detail/concept.hpp

include/seqan3/core/configuration/detail/configuration_utility.hpp

joergi-w

Thank you!

rrahn

Please do not remove the old seqan3/alignment/band in this PR. This has nothing to do with the change of the configuration header. Second the static band should be deprecated before it is removed in 3.1. Can you first revert these changes and then I look into the rest. Thank you

rrahn · 2020-11-23T08:38:47Z

include/seqan3/core/algorithm/all.hpp

-#include <seqan3/core/algorithm/configuration_utility.hpp>
-#include <seqan3/core/algorithm/configuration.hpp>
-#include <seqan3/core/detail/pack_algorithm.hpp>
+#include <seqan3/core/algorithm/detail/all.hpp>


please remove

rrahn · 2020-11-23T08:42:00Z

include/seqan3/core/algorithm/all.hpp

 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
+#include <seqan3/core/configuration/all.hpp> // ToDo: remove this with the release SeqAn-3.1.0.


Not sure how to handle this. This is likely to be forgotten.
I am thinking of this:

#if SEQAN3_VERSION_MAJOR == 3 && SEQAN3_VERSION_MINOR == 1 #pragma warning "Remove #include <seqan3/core/configuration/all.hpp> from this header." #endif

@marehr what do you think?

This was exactly the problem I tried to explain on Gitter on friday..

rrahn · 2020-11-23T08:42:31Z

include/seqan3/core/algorithm/concept.hpp

 * \author Rene Rahn <rene.rahn AT fu-berlin.de>
+ * \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/concept.hpp instead.


Suggested change

* \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/concept.hpp instead.

* \deprecated This header will be removed in 3.1.0; Please \#include <seqan3/core/configuration/detail/concept.hpp> instead.

I followed Marcel's example, which he created for us. (math) Now I had to make a lot of changes that did not match his example. Maybe next time you can look over the example as the core team before we take over all the mistakes there.

rrahn · 2020-11-23T08:43:48Z

include/seqan3/core/algorithm/configuration_element_debug_mode.hpp

+ * \deprecated This header will be removed in 3.1. Please use
+ *             seqan3/core/configuration/detail/configuration_element_debug_mode.hpp instead.


Suggested change

* \deprecated This header will be removed in 3.1. Please use

* seqan3/core/configuration/detail/configuration_element_debug_mode.hpp instead.

* \deprecated This header will be removed in 3.1.0; Please \#include <seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.

rrahn · 2020-11-23T08:44:32Z

include/seqan3/core/algorithm/configuration_element_debug_mode.hpp

+   "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "
+   "<seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.")


Suggested change

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "

"<seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.")

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.")

We said that it is ok to not wrap this around. I think it causes some displaying issues.

rrahn · 2020-11-23T08:44:51Z

include/seqan3/core/algorithm/configuration_element_parallel_mode.hpp

+ * \deprecated This header will be removed in 3.1. Please use
+ *             seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp instead.


Suggested change

* \deprecated This header will be removed in 3.1. Please use

* seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp instead.

* \deprecated This header will be removed in 3.1.0; Please \#include

* <seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp> instead.

rrahn · 2020-11-23T08:45:03Z

include/seqan3/core/algorithm/configuration_element_parallel_mode.hpp

+   "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "
+   "<seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp> instead.")


Suggested change

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "

"<seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp> instead.")

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/core/configuration/detail/configuration_element_parallel_mode.hpp> instead.")

Is your requested change here, that you want everything in one line, even if there are more than 120 characters?

rrahn · 2020-11-23T08:45:17Z

include/seqan3/core/algorithm/configuration_utility.hpp

+ * \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/configuration_utility.hpp
+ *             instead.


Suggested change

* \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/configuration_utility.hpp

* instead.

* \deprecated This header will be removed in 3.1.0; Please \#include <seqan3/core/configuration/detail/configuration_utility.hpp>

* instead.

rrahn · 2020-11-23T08:45:27Z

include/seqan3/core/algorithm/configuration_utility.hpp

+   "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "
+   "<seqan3/core/configuration/detail/configuration_utility.hpp> instead.")


Suggested change

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "

"<seqan3/core/configuration/detail/configuration_utility.hpp> instead.")

"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include <seqan3/core/configuration/detail/configuration_utility.hpp> instead.")

rrahn · 2020-11-23T08:46:36Z

include/seqan3/core/algorithm/detail/all.hpp

@@ -13,4 +13,5 @@
 #pragma once

 #include <seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp>
+#include <seqan3/core/algorithm/detail/execution_handler_parallel.hpp>


I think in general we don't want detail to be included inside of the all.hpp.
It basically is no functionality for the user and should be included through the public headers.

So we leave it for now but I would remove it later. Lets discuss this today in the group meeting

Irallia · 2020-11-23T15:29:05Z

You might want to check my changes before I rebase.

rrahn

OK one small thing. I couldn't find the header that should be removed later? The warning is only a message emitted by the compiler. The header include should still exist. Or did I miss it? You can rebase right away.

rrahn · 2020-11-25T10:11:27Z

include/seqan3/core/algorithm/all.hpp

 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
+#if SEQAN3_VERSION_MAJOR == 3 && SEQAN3_VERSION_MINOR == 1
+  #pragma warning "Remove #include <seqan3/core/configuration/all.hpp> from this header."


but where is the header?

working without the head... 😅

rrahn

some minor include order then it is good to go

rrahn · 2020-11-30T12:19:57Z

include/seqan3/core/configuration/detail/configuration_utility.hpp

+#include <seqan3/core/configuration/detail/concept.hpp>
+#include <seqan3/core/concept/tuple.hpp>


include order

algorithm/concept.hpp -> core/configuration/detail/. algorithm/configuration.hpp -> core/configuration/. algorithm/configuration_element_debug_mode.hpp -> core/configuration/detail/. algorithm/configuration_element_parallel_mode.hpp -> core/configuration/detail/. algorithm/configuration_utility.hpp -> core/configuration/detail/. Skipped: algorithm/pipeable_config_element.hpp (needs a decision) Keep untouched: algorithm/detail/... -> core/algorithm/detail/... algorithm/algorithm_result_generator_range -> core/algorithm/algorithm_result_generator_range Added new all.hpp's and adjusted the other ones. Signed-off-by: Lydia Buntrock <[email protected]>

rrahn

Thank you

PR seqan#2255 did the move from core/algorithm into core/configuration, but at the same time PR seqan#2247 changed one header. This seems like a misinterpreted merge conflict and this PR reintroduces the changes from seqan#2255. After checking the changes of seqan#2255, this seems to be the only missed change. This partially reverts commit 1ae6a3f.

Irallia self-assigned this Nov 11, 2020

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rrahn merged commit f66fe5b into seqan:master Dec 5, 2020

marehr mentioned this pull request Dec 22, 2020

[FIX] reintroduce changes lost due to merge conflicts #2315

Merged

Irallia deleted the INFRA/core/move_header_algorithm_to_configuration branch January 28, 2022 13:42

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[INFRA] Move core/algorithm into core/configuration #2255

[INFRA] Move core/algorithm into core/configuration #2255

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		#include <seqan3/core/algorithm/pipeable_config_element.hpp>
		#include <seqan3/core/configuration/all.hpp> // ToDo: remove this with the release SeqAn-3.1.0.

		* \author Rene Rahn <rene.rahn AT fu-berlin.de>
		* \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/concept.hpp instead.

		* \deprecated This header will be removed in 3.1. Please use
		* seqan3/core/configuration/detail/configuration_element_debug_mode.hpp instead.

		"This header is deprecated and will be removed in SeqAn-3.1.0; Please #include "
		"<seqan3/core/configuration/detail/configuration_element_debug_mode.hpp> instead.")

		* \deprecated This header will be removed in 3.1. Please use seqan3/core/configuration/detail/configuration_utility.hpp
		* instead.

		#include <seqan3/core/configuration/detail/concept.hpp>
		#include <seqan3/core/concept/tuple.hpp>

[INFRA] Move core/algorithm into core/configuration #2255

[INFRA] Move core/algorithm into core/configuration #2255

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