dev-python/snakemake: version bump 8.16.0

[mschubert]

incl. deps and pinned versions as in upstream

[Nowa-Ammerlaan]

There's a compile failure in dev-python/datrie that is blocking this:

>>> Emerging (1 of 1) dev-python/datrie-0.8.2-r1::science
* datrie-0.8.2.tar.gz BLAKE2B SHA512 size ;-) ...                                                                                                                                                                                                                    [ ok ]
>>> Unpacking source...
>>> Unpacking datrie-0.8.2.tar.gz to /tmp/portage/dev-python/datrie-0.8.2-r1/work
>>> Source unpacked in /tmp/portage/dev-python/datrie-0.8.2-r1/work
>>> Preparing source in /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2 ...
* Build system packages:
*   dev-python/setuptools         : 70.2.0
>>> Source prepared.
>>> Configuring source in /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2 ...
>>> Source configured.
>>> Compiling source in /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2 ...
* python3_12: running distutils-r1_run_phase distutils-r1_python_compile
python3.12 setup.py build -j 8
warning: src/cdatrie.pxd:34:4: 'TrieData' redeclared
Compiling src/datrie.pyx because it changed.
[1/1] Cythonizing src/datrie.pyx
running build
running build_clib
building 'datrie' library
creating /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312
creating /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie
creating /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/alpha-map.o
libdatrie/datrie/alpha-map.c: In function ‘alpha_map_char_to_trie’:
libdatrie/datrie/alpha-map.c:500:21: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘AlphaChar’ {aka ‘unsigned int’} [-Wsign-compare]
500 |     if (alpha_begin <= ac && ac <= alpha_map->alpha_end)
|                     ^~
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/darray.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/darray.o
libdatrie/datrie/darray.c: In function ‘da_fread’:
libdatrie/datrie/darray.c:239:22: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare]
239 |     if (d->num_cells > SIZE_MAX / sizeof (DACell))
|                      ^
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/dstring.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/dstring.o
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/fileutils.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/fileutils.o
libdatrie/datrie/fileutils.c: In function ‘file_read_chars’:
libdatrie/datrie/fileutils.c:103:52: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
103 |     return (fread (buff, sizeof (char), len, file) == len);
|                                                    ^~
libdatrie/datrie/fileutils.c: In function ‘file_write_chars’:
libdatrie/datrie/fileutils.c:109:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
109 |     return (fwrite (buff, sizeof (char), len, file) == len);
|                                                     ^~
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/tail.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/tail.o
libdatrie/datrie/tail.c: In function ‘tail_fread’:
libdatrie/datrie/tail.c:144:22: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare]
144 |     if (t->num_tails > SIZE_MAX / sizeof (TailBlock))
|                      ^
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/trie-string.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie-string.o
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -c libdatrie/datrie/trie.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie.o
x86_64-pc-linux-gnu-ar rcs /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie.a /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/alpha-map.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/darray.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/dstring.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/fileutils.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/tail.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie-string.o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie.o
running build_ext
building 'datrie' extension
creating /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/src
x86_64-pc-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -O3 -pipe -march=skylake -mtune=skylake -fPIC -Ilibdatrie -I/usr/include/python3.12 -c src/datrie.c -o /tmp/portage/dev-python/datrie-0.8.2-r1/work/datrie-0.8.2-python3_12/temp.linux-x86_64-cpython-312/src/datrie.o
src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie___init__’:
src/datrie.c:5673:53: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
5673 |   __pyx_v_self->_c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
|                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
|                                                     |
|                                                     struct AlphaMap *
In file included from src/datrie.c:1248:
src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
120 | Trie *  trie_new (const AlphaMap *alpha_map);
|                   ~~~~~~~~~~~~~~~~^~~~~~~~~
src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie_6clear’:
src/datrie.c:6351:47: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
6351 |   __pyx_v__c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
|                              ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
|                                               |
|                                               struct AlphaMap *
src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
120 | Trie *  trie_new (const AlphaMap *alpha_map);
|                   ~~~~~~~~~~~~~~~~^~~~~~~~~
src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap___cinit__’:
src/datrie.c:27404:30: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
27404 |   __pyx_v_self->_c_alpha_map = alpha_map_new();
|                              ^
src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap_2__dealloc__’:
src/datrie.c:27460:32: error: passing argument 1 of ‘alpha_map_free’ from incompatible pointer type [-Wincompatible-pointer-types]
27460 |     alpha_map_free(__pyx_v_self->_c_alpha_map);
|                    ~~~~~~~~~~~~^~~~~~~~~~~~~~
|                                |
|                                struct AlphaMap *
In file included from src/datrie.c:1247:
src/../libdatrie/datrie/alpha-map.h:72:39: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
72 | void        alpha_map_free (AlphaMap *alpha_map);
|                             ~~~~~~~~~~^~~~~~~~~
src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap_copy’:
src/datrie.c:27875:61: error: passing argument 1 of ‘alpha_map_clone’ from incompatible pointer type [-Wincompatible-pointer-types]
27875 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
|                                                 ~~~~~~~~~~~~^~~~~~~~~~~~~~
|                                                             |
|                                                             struct AlphaMap *
src/../libdatrie/datrie/alpha-map.h:70:46: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
70 | AlphaMap *  alpha_map_clone (const AlphaMap *a_map);
|                              ~~~~~~~~~~~~~~~~^~~~~
src/datrie.c:27875:31: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
27875 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
|                               ^
src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap__add_range’:
src/datrie.c:28566:50: error: passing argument 1 of ‘alpha_map_add_range’ from incompatible pointer type [-Wincompatible-pointer-types]
28566 |   __pyx_v_code = alpha_map_add_range(__pyx_v_self->_c_alpha_map, __pyx_v_begin, __pyx_v_end);
|                                      ~~~~~~~~~~~~^~~~~~~~~~~~~~
|                                                  |
|                                                  struct AlphaMap *
src/../libdatrie/datrie/alpha-map.h:74:45: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
74 | int         alpha_map_add_range (AlphaMap  *alpha_map,
|                                  ~~~~~~~~~~~^~~~~~~~~
error: command '/usr/bin/x86_64-pc-linux-gnu-gcc' failed with exit code 1

[mschubert]

I've added the gcc14 compilation workaround as described here: pytries/datrie#99

(no relbump because this only fixes new installations)

[Nowa-Ammerlaan]

Thanks 👍