[MISC] Rename {core->utlity}/char_operations/predicate.hpp. #2254

smehringer · 2020-11-11T13:22:37Z

Header File: {core->utlity}/char_operations/predicate.hpp.

Note this is only one header file, since it already touches a lot of code, I kept them separate.

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
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 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

codecov · 2020-11-11T14:06:37Z

Codecov Report

Merging #2254 (18e9deb) into master (8a7e498) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2254   +/-   ##
=======================================
  Coverage   98.15%   98.15%           
=======================================
  Files         262      262           
  Lines       10815    10815           
=======================================
  Hits        10616    10616           
  Misses        199      199

Impacted Files	Coverage Δ
include/seqan3/alphabet/mask/masked.hpp	`100.00% <ø> (ø)`
include/seqan3/argument_parser/argument_parser.hpp	`98.78% <ø> (ø)`
...ude/seqan3/argument_parser/detail/format_parse.hpp	`96.80% <ø> (ø)`
include/seqan3/io/alignment_file/format_bam.hpp	`95.58% <ø> (ø)`
include/seqan3/io/alignment_file/format_sam.hpp	`98.13% <ø> (ø)`
...clude/seqan3/io/alignment_file/format_sam_base.hpp	`98.74% <ø> (ø)`
...de/seqan3/io/alignment_file/sam_tag_dictionary.hpp	`100.00% <ø> (ø)`
include/seqan3/io/sequence_file/format_embl.hpp	`100.00% <ø> (ø)`
include/seqan3/io/sequence_file/format_fasta.hpp	`98.78% <ø> (ø)`
include/seqan3/io/sequence_file/format_fastq.hpp	`100.00% <ø> (ø)`
... and 2 more

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include/seqan3/utility/char_operations/all.hpp

smehringer · 2020-11-17T11:07:52Z

@rrahn polite ping :)

rrahn · 2020-11-17T19:12:07Z

include/seqan3/argument_parser/argument_parser.hpp

+#include <seqan3/utility/char_operations/predicate.hpp>
 #include <seqan3/core/detail/test_accessor.hpp>
 #include <seqan3/io/stream/concept.hpp>


include order

rrahn · 2020-11-17T19:12:30Z

include/seqan3/io/alignment_file/format_bam.hpp

@@ -21,7 +21,7 @@
 #include <seqan3/alphabet/detail/convert.hpp>
 #include <seqan3/alphabet/nucleotide/sam_dna16.hpp>
 #include <seqan3/core/bit_manipulation.hpp>
-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:12:40Z

include/seqan3/io/alignment_file/format_sam.hpp

@@ -19,7 +19,7 @@
 #include <string>
 #include <vector>

-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:12:51Z

include/seqan3/io/alignment_file/format_sam_base.hpp

@@ -20,7 +20,7 @@
 #include <string>
 #include <vector>

-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:12:59Z

include/seqan3/io/alignment_file/sam_tag_dictionary.hpp

@@ -15,7 +15,7 @@
 #include <map>
 #include <variant>

-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:15:12Z

test/unit/alphabet/nucleotide/rna5_test.cpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------

 #include <seqan3/alphabet/nucleotide/rna5.hpp>
-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:15:19Z

test/unit/alphabet/nucleotide/sam_dna16_test.cpp

@@ -6,7 +6,7 @@
 // -----------------------------------------------------------------------------------------------------

 #include <seqan3/alphabet/nucleotide/sam_dna16.hpp>
-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:15:26Z

test/unit/range/views/istreambuf_test.cpp

@@ -12,7 +12,7 @@
 #include <seqan3/std/ranges>

 #include <seqan3/alphabet/nucleotide/dna5.hpp>
-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:15:31Z

test/unit/range/views/persist_test.cpp

@@ -12,7 +12,7 @@
 #include <range/v3/algorithm/copy.hpp>
 #include <range/v3/view/unique.hpp>

-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-17T19:15:36Z

test/unit/utility/char_operations/char_predicate_test.cpp

@@ -14,7 +14,7 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/alphabet/nucleotide/dna5.hpp>
 #include <seqan3/alphabet/nucleotide/rna5.hpp>
-#include <seqan3/core/char_operations/predicate.hpp>
+#include <seqan3/utility/char_operations/predicate.hpp>


include order

rrahn · 2020-11-23T08:35:57Z

test/snippet/range/views/take_until.cpp

-#include <seqan3/core/char_operations/predicate.hpp> // for is_char
 #include <seqan3/core/debug_stream.hpp>              // for debug_stream
 #include <seqan3/range/views/single_pass_input.hpp>  // for views::single_pass_input
 #include <seqan3/range/views/take_until.hpp>         // for views::take_until*
-#include <seqan3/std/ranges>                         // for std::views::reverse
+#include <seqan3/utility/char_operations/predicate.hpp> // for is_char


Please, either align them or remove the alignment.

smehringer force-pushed the utility_renaming branch from 1004412 to 39d1b4a Compare November 11, 2020 13:50

smehringer force-pushed the utility_renaming branch from 39d1b4a to 1bc32ef Compare November 11, 2020 14:17

smehringer requested review from a team, simonsasse and MitraDarja and removed request for a team and simonsasse November 11, 2020 14:17

MitraDarja approved these changes Nov 12, 2020

View reviewed changes

MitraDarja requested review from a team and rrahn and removed request for a team November 12, 2020 12:22

smehringer force-pushed the utility_renaming branch from 1bc32ef to 024679a Compare November 16, 2020 09:10

simonsasse reviewed Nov 16, 2020

View reviewed changes

include/seqan3/utility/char_operations/all.hpp Outdated Show resolved Hide resolved

smehringer force-pushed the utility_renaming branch 2 times, most recently from 77abf68 to d07d9ec Compare November 17, 2020 09:01

rrahn requested changes Nov 17, 2020

View reviewed changes

smehringer requested a review from rrahn November 18, 2020 08:39

rrahn requested changes Nov 23, 2020

View reviewed changes

rrahn self-requested a review November 23, 2020 11:05

rrahn approved these changes Nov 23, 2020

View reviewed changes

[MISC] Rename {core->utlity}/char_operations/predicate.hpp.

18e9deb

smehringer force-pushed the utility_renaming branch from 68f8db7 to 18e9deb Compare November 23, 2020 11:32

smehringer merged commit b6e8e19 into seqan:master Nov 23, 2020

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[MISC] Rename {core->utlity}/char_operations/predicate.hpp. #2254

[MISC] Rename {core->utlity}/char_operations/predicate.hpp. #2254

smehringer commented Nov 11, 2020 •

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smehringer commented Nov 17, 2020

rrahn Nov 17, 2020

rrahn Nov 17, 2020

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rrahn Nov 23, 2020

[MISC] Rename {core->utlity}/char_operations/predicate.hpp. #2254

[MISC] Rename {core->utlity}/char_operations/predicate.hpp. #2254

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smehringer commented Nov 11, 2020 •

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