Merge pull request #3020 from eseiler/doc/changelog

[DOC] Update changelog

CHANGELOG.md

@@ -28,30 +28,67 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 
 ## New features
 
-#### Build system
+#### Alphabet
+  * `seqan3::cigar` can now be assigned from `std::string_view` ([\#2966](https://github.com/seqan/seqan3/pull/2966)).
+  * Added `seqan3::views::char_strictly_to`. Behaves like `seqan3::views::char_to`, but throws on invalid
+    input ([\#2898](https://github.com/seqan/seqan3/pull/2898)).
+
+#### I/O
+ * Added `seqan3::sequence_file_option::fasta_ignore_blanks_before_id` to ignore blanks before IDs when reading FASTA
+   files. E.g., `>       some_id` will only store `"some_id"` as ID
+   ([\#2770](https://github.com/seqan/seqan3/pull/2770)).
+
+#### Search
+  * Improved performance of `seqan3::counting_vector::operator+=` ([\#2930](https://github.com/seqan/seqan3/pull/2930)).
 
-* We now use Doxygen version 1.9.3 to build our documentation ([\#2923](https://github.com/seqan/seqan3/pull/2923)).
+#### Utility
+  * Added `seqan3::list_traits::repeat` ([\#2899](https://github.com/seqan/seqan3/pull/2899)).
 
 ## Notable Bug-fixes
 
+#### Core
+  * Added missing implementations for AVX512 ([\#2920](https://github.com/seqan/seqan3/pull/2920) and
+    [\#2926](https://github.com/seqan/seqan3/pull/2926)).
+
 #### IO
+  * FASTA files containing IDs starting with `>`, e.g., `> >MyID`, are now parsed correctly
+    ([\#2869](https://github.com/seqan/seqan3/pull/2869)).
 
-* Fixed an issue parsing FASTA files containing sequence IDs that start with `>`
- ([\#2869](https://github.com/seqan/seqan3/pull/2869)).
+#### Search
+  * Relaxed `kmer_hash_view::iterator` difference requirement ([\#2931](https://github.com/seqan/seqan3/pull/2931)).
+  * Relaxed `seqan3::views::minimiser` requirements to be C++20-compatible
+    ([\#2845](https://github.com/seqan/seqan3/pull/2845)).
+  * Relaxed `seqan3::views::kmer_hash` requirements to be C++20-compatible
+    ([\#2843](https://github.com/seqan/seqan3/pull/2843)).
 
 #### Utility
 
-* `seqan3::views::single_pass_input` cannot propagate the `std::ranges::output_range` property, because it cannot
-  satisfy the following requirement ([\#2775](https://github.com/seqan/seqan3/pull/2775)):
-  ```cpp
-  *it++ = value;
-  // must be the same as
-  *it = value; ++it;
-  // but it actually would be the same as
-  ++it; *it = value;
-  ```
+  * `seqan3::views::single_pass_input` cannot propagate the `std::ranges::output_range` property because it cannot
+    satisfy the following requirement ([\#2775](https://github.com/seqan/seqan3/pull/2775)):
+    ```cpp
+    *it++ = value;
+    // must be the same as
+    *it = value; ++it;
+    // but it actually would be the same as
+    ++it; *it = value;
+    ```
+  * Fixed signature of `seqan3::detail::store_sse4`. This might have affected some public API
+    ([\#2893](https://github.com/seqan/seqan3/pull/2893)).
+  * Relaxed `seqan3::views::to_simd` requirements to be C++20-compatible
+    ([\#2849](https://github.com/seqan/seqan3/pull/2849)).
 
 ## API changes
+GCC 7, 8, and 9 have been removed. All headers in `seqan3/std/` except `charconv` and `new` have been deprecated, please
+use the equivalent `std` includes.
+The namespace `std::cpp20` has been deprecated, please use `std::`.
+
+`seqan3::views::to` has been changed to `seqan3::ranges::to`. Since it is not a view anymore, it cannot be properly
+deprecated. Please keep this in mind if you encounter errors with `seqan3::views::to`.
+
+#### Compiler
+  * Dropped support for GCC 7 and 8 ([\#2891](https://github.com/seqan/seqan3/pull/2891)).
+  * Dropped support for GCC 9 ([\#2952](https://github.com/seqan/seqan3/pull/2952)).
+  * Removed C++17 support ([\#2915](https://github.com/seqan/seqan3/pull/2915)).
 
 #### I/O
  * Changed the default of `output_options::fasta_blank_before_id` to `false`
@@ -66,6 +103,24 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
   * Replaced `seqan3::views::to` (implemented via range-v3) with `seqan3::ranges::to` (implemented in SeqAn3).
     `seqan3::ranges::to` provides a subset of C++23's `std::ranges::to` and will be replaced with the STL-equivalent
     in a future version ([\#2969](https://github.com/seqan/seqan3/pull/2969)).
+  * Replaced the implementation of `seqan3::views::chunk`. It is now implemented in SeqAn3 and does not use
+    the range-v3 implementation anymore. `seqan3::views::chunk` is similar to C++23's `std::views::chunk`
+    and will be replaced with the STL-equivalent in a future version
+    ([\#2975](https://github.com/seqan/seqan3/pull/2975)).
+  * Replaced the implementation of `seqan3::views::join_with`. It is now implemented in SeqAn3 and does not use
+    the range-v3 implementation anymore. `seqan3::views::join_with` is equivalent to C++23's `std::views::join_with`
+    and will be replaced with the STL-equivalent in a future version
+    ([\#2973](https://github.com/seqan/seqan3/pull/2973)).
+  * Replaced the implementation of `seqan3::views::zip`. It is now implemented in SeqAn3 and does not use
+    the range-v3 implementation anymore. `seqan3::views::zip` is equivalent to C++23's `std::views::zip`
+    and will be replaced with the STL-equivalent in a future version
+    ([\#2971](https://github.com/seqan/seqan3/pull/2971)).
+
+#### Dependencies
+  * We now use Doxygen version 1.9.4 to build our documentation ([\#2979](https://github.com/seqan/seqan3/pull/2979)).
+  * Removed range-v3 ([\#2998](https://github.com/seqan/seqan3/pull/2998)).
+  * Updated cereal to 1.3.2 ([\#3012](https://github.com/seqan/seqan3/pull/3012)).
+  * Updated sdsl-lite to 3.0.1 ([\#3012](https://github.com/seqan/seqan3/pull/3012)).
 
 # 3.1.0
 
@@ -843,7 +898,7 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 
 #### Argument parser
 
-* The `seqan3::value_list_validator` is not constructible from a std::initialiser_list any more
+* The `seqan3::value_list_validator` is not constructible from a std::initialiser_list anymore
   (e.g. `seqan3::value_list_validator{{1,2,3}}` does not work, use `seqan3::value_list_validator{1,2,3}` instead)
   ([\#1298](https://github.com/seqan/seqan3/pull/1298)).
 * Changed class signature of input/output file validators:

include/seqan3/utility/views/chunk.hpp

@@ -830,7 +830,7 @@ namespace seqan3::views
  *
  * \hideinitializer
  *
- * \experimentalapi
+ * \noapi{This is a implementation of the C++23 chunk_view. It will be replaced with std::views::chunk.}
  */
 inline constexpr auto chunk = detail::chunk_fn{};