[MISC] Deprecate views::take_until #2604

SGSSGene · 2021-05-05T08:50:30Z

seqan3::views::take_until is moved to seqan3/io/detail for
internal use only. As an alternative please use
std::views::take_while in combination with std::not_fn.
or if using the seqan3::views::take_until_and_consume_* version add an extra std::views::drop_while to reproduce the same results.
moved snippets and test accordingly.
add CHANGLELOG entry

vercel · 2021-05-05T08:50:35Z

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SGSSGene · 2021-05-05T08:51:40Z

What is currently missing is a more elaborated deprecation warning on how to replace take_until_*_constume with std::views::take_while

codecov · 2021-05-05T09:42:35Z

Codecov Report

Merging #2604 (038edae) into master (adc0324) will not change coverage.
The diff coverage is 98.93%.

@@           Coverage Diff           @@
##           master    #2604   +/-   ##
=======================================
  Coverage   98.27%   98.27%           
=======================================
  Files         273      273           
  Lines       10795    10795           
=======================================
  Hits        10609    10609           
  Misses        186      186

Impacted Files	Coverage Δ
include/seqan3/io/detail/take_view.hpp	`98.33% <ø> (ø)`
...lude/seqan3/io/sam_file/detail/format_sam_base.hpp	`97.82% <ø> (ø)`
include/seqan3/io/detail/take_until_view.hpp	`98.18% <98.18%> (ø)`
include/seqan3/alphabet/views/trim_quality.hpp	`100.00% <100.00%> (ø)`
include/seqan3/io/sam_file/detail/cigar.hpp	`97.75% <100.00%> (ø)`
include/seqan3/io/sam_file/format_bam.hpp	`96.29% <100.00%> (ø)`
include/seqan3/io/sam_file/format_sam.hpp	`97.44% <100.00%> (ø)`
include/seqan3/io/sequence_file/format_embl.hpp	`100.00% <100.00%> (ø)`
include/seqan3/io/sequence_file/format_fasta.hpp	`98.68% <100.00%> (ø)`
include/seqan3/io/sequence_file/format_fastq.hpp	`100.00% <100.00%> (ø)`
... and 4 more

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Irallia

It is possible that one of the includes is not needed, since I could not find a take_until in the file.

include/seqan3/io/sam_file/format_bam.hpp

SGSSGene · 2021-05-05T10:23:06Z

@Irallia I have update the deprecation message in take_until_view.hpp for the 4 instances take_until, take_until_and_consume and the *_throw_* stuff. Can you take a very close look that it is understandable? thank you :-)

Irallia

Thanks for the tip, I took a look at it.
I'm really not good at formulating nice English sentences, but I may have a few small improvements.

include/seqan3/io/detail/take_until_view.hpp

marehr · 2021-05-07T22:30:22Z

include/seqan3/io/detail/take_until_view.hpp

+ * as their non-consuming counter-parts if the underlying range models at least `std::forward_range`.
+ * If, however, the underlying range is a pure `std::input_range`, the view will keep moving the underlying


Suggested change

* as their non-consuming counter-parts if the underlying range models at least `std::forward_range`.

* If, however, the underlying range is a pure `std::input_range`, the view will keep moving the underlying

* as their non-consuming counter-parts if the underlying range models at least `std::ranges::forward_range`.

* If, however, the underlying range is a pure `std::ranges::input_range`, the view will keep moving the underlying

Irallia

One review you did not answer and one more I found. Also, the comment from marcel is still open (you changed it to std::range:: but it should be std::ranges::).

include/seqan3/io/detail/take_until_view.hpp

Irallia

Perfect, thank you!

eseiler · 2021-05-10T14:34:28Z

CHANGELOG.md

+* We deprecated `seqan3::views::take_until` and it will be removed in 3.1.0. Use `std::views::take_while` in
+  combination with `std::not_fn` ([\#2604](https://github.com/seqan/seqan3/pull/2604)).


I would have just said "with an inverted predicated/condition"

Or just "Use std::views::take_while(std::not(predicate)) instead" (I'd prefer this).

I think it's concise enough for a changelog, and it's more detailed in the documentation

Yes, much better, thx!

eseiler · 2021-05-10T14:44:23Z

include/seqan3/io/detail/take_until_view.hpp

+ * \deprecated A previous call `view | take_until_and_consume(is_space)` could be convert to
+ *             `view | std::take_while(std::not_fn(is_space)) | std::drop_while(is_space)`


Suggested change

* \deprecated A previous call `view | take_until_and_consume(is_space)` could be convert to

* `view | std::take_while(std::not_fn(is_space)) | std::drop_while(is_space)`

* \deprecated Use `std::take_while(std::not_fn(functor)) | std::drop_while(functor)` instead of

* `seqan3::views::take_until_and_consume(functor)`.

For me, this would be more helpful, because it reuses the functor which is mentioned in the brief, and technically you don't need the view |.

Could you adjust the other ones?
take_until should also get the "long" deprecation documentation

Is this correct though?

I thought this does the stuff in sequence. First take everything until the first space and after that skip all spaces.

Right now it would be for an element: first take (filter) everything until first space and from that resulting range drop until the first space. That means you should get an empty range.

Hah, right. Is there even an easy replacement?

No there isn't if it isn't an input iterator.
I would just write that we don't have a replacement for this.

Thanks for catching this! I remember Marcel and I already talked about this not being an appropriate replacement.
I now replaced the deprecation warning with "No alternative" as it was done in "as_const.hpp".

include/seqan3/range/views/all.hpp

- `seqan3::views::take_until` is moved to `seqan3/io/detail` for internal use only. As an alternative please use `std::views::take_while` in combination with `std::not_fn`. - moved snippets and test accordingly. - add CHANGLELOG entry

include/seqan3/io/detail/take_until_view.hpp

CHANGELOG.md

SGSSGene requested review from a team, marehr and Irallia and removed request for a team and marehr May 5, 2021 08:51

SGSSGene force-pushed the deprecate/take_until branch from 2c5a1a4 to abcd146 Compare May 5, 2021 08:53

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SGSSGene changed the title ~~[MISC] Dprecate views::take_until~~ [MISC] Deprecate views::take_until May 5, 2021

SGSSGene force-pushed the deprecate/take_until branch from 809a185 to 8ae9f58 Compare May 5, 2021 10:24

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SGSSGene force-pushed the deprecate/take_until branch 4 times, most recently from 4bb5226 to c9fee82 Compare May 10, 2021 08:41

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[MISC] Deprecate views::take_until

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- `seqan3::views::take_until` is moved to `seqan3/io/detail` for internal use only. As an alternative please use `std::views::take_while` in combination with `std::not_fn`. - moved snippets and test accordingly. - add CHANGLELOG entry

SGSSGene force-pushed the deprecate/take_until branch from b8baaae to 6eaee70 Compare May 11, 2021 07:27

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eseiler enabled auto-merge (squash) May 11, 2021 10:22

Merge branch 'master' into deprecate/take_until

038edae

eseiler merged commit 1b0a1fa into seqan:master May 11, 2021

marehr mentioned this pull request May 11, 2021

deprecate seqan3::views::take_until seqan/product_backlog#332

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[MISC] Deprecate views::take_until #2604

[MISC] Deprecate views::take_until #2604

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SGSSGene May 11, 2021

		* as their non-consuming counter-parts if the underlying range models at least `std::forward_range`.
		* If, however, the underlying range is a pure `std::input_range`, the view will keep moving the underlying

		* We deprecated `seqan3::views::take_until` and it will be removed in 3.1.0. Use `std::views::take_while` in
		combination with `std::not_fn` ([\#2604](https://github.com/seqan/seqan3/pull/2604)).

		* \deprecated A previous call `view \| take_until_and_consume(is_space)` could be convert to
		* `view \| std::take_while(std::not_fn(is_space)) \| std::drop_while(is_space)`

[MISC] Deprecate views::take_until #2604

[MISC] Deprecate views::take_until #2604

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