Merge pull request #2752 from SGSSGene/fix/bgzf_thread_count_variable

[FIX] make a bgzf_thread_count a single variable

CHANGELOG.md

@@ -51,6 +51,10 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 #### I/O
  * Changed default of `output_options::fasta_blank_before_id` to `false`
    ([\#2769](https://github.com/seqan/seqan3/pull/2769)).
+ * Changed default of `bgzf_thread_count` to `4` instead of determining the numbers of cores of the
+   machine it is running on ([\#2911](https://github.com/seqan/seqan3/pull/2911)).
+ * `bgzf_thread_count` is now a single global variable instead of having an instance per translation unit
+   ([\#2752](https://github.com/seqan/seqan3/pull/2752)).
 
 # 3.1.0
 

doc/cookbook/compression_threads.cpp

@@ -2,12 +2,17 @@
 //![example]
 #include <seqan3/io/all.hpp>
 
+
+// The `bgzf_thread_count` is a variable that can only be changed during run time of the program.
 // This does not work, the value must be overwritten within a function.
-// seqan3::contrib::bgzf_thread_count = 1u;
+// seqan3::contrib::bgzf_thread_count = 1u; // Doesn't work
 
 int main()
 {
-    // Use one thread for (de-)compression.
+    // Here we change the number of threads to `1`. This is a global
+    // change and will effect the every future bgzf decompression call
+    // which doesn't specify an explicit thread count parameter.
+    // Already running decompression calls are unaffected by this
     seqan3::contrib::bgzf_thread_count = 1u;
 
     // Read/Write compressed files.

include/seqan3/contrib/stream/bgzf_stream_util.hpp

@@ -37,7 +37,7 @@ namespace seqan3::contrib
 
 /*!\brief A static variable indicating the number of threads to use for the bgzf-streams. Defaults to 4.
  */
-[[maybe_unused]] inline static uint64_t bgzf_thread_count = 4;
+[[maybe_unused]] inline uint64_t bgzf_thread_count = 4;
 
 // ============================================================================
 // Forwards