feat(snakemake): upgrade to Snakemake 8.27.1

[Alputer]

Remove unnecessary snakemake dependencies. They are already included in the snakemake package.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 1 line in your changes missing coverage. Please review.

Project coverage is 41.55%. Comparing base (8f0bde7) to head (4d01234).
Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
reana_commons/version.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #476   +/-   ##
=======================================
  Coverage   41.55%   41.55%           
=======================================
  Files          28       28           
  Lines        2024     2024           
=======================================
  Hits          841      841           
  Misses       1183     1183           

Files with missing lines	Coverage Δ
reana_commons/version.py	0.00% <0.00%> (ø)

[tiborsimko]

todo: ‏Please explain in the commit message body why this is OK, for example that the upstream Snakemake 8 version already provides these packages as default. (After you check with py311 and above.)

[tiborsimko]

todo: ‏For the release commit, please use capital S in Snakemake.

[tiborsimko]

todo: ‏Please rebase against latest master.

[tiborsimko]

question: ‏BTW if you are in the middle of retesting various Snakemake examples and Python versions, perhaps you could have a look whether we cannot upgrade from 8.24.1 to a higher officially released Snakemake version? (Currently 8.27.1.) This is fully optional, as we can also do it later.

[tiborsimko]

After you check with py311 and above.

BTW I checked locally with tox and everything is OK except for Python 3.13:

$ tox
  py38: OK (41.41=setup[26.56]+cmd[14.85] seconds)
  py39: OK (48.24=setup[33.53]+cmd[14.71] seconds)
  py310: OK (46.67=setup[31.93]+cmd[14.74] seconds)
  py311: OK (16.04=setup[1.22]+cmd[14.82] seconds)
  py312: OK (43.06=setup[25.77]+cmd[17.29] seconds)
  py313: FAIL code 1 (247.95 seconds)

The problem with Python 3.13 are related to building the datrie extension:

...
      building 'datrie' extension
      creating build/temp.linux-x86_64-cpython-313/src
      gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O3 -fPIC -Ilibdatrie -I/home/tibor/private/project/reana/src/reana-commons/.tox/py313/include -I/usr/include/python3.13 -c src/datrie.c -o build/temp.linux-x86_64-cpython-313/src/datrie.o
      src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie___init__’:
      src/datrie.c:5669:53: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
       5669 |   __pyx_v_self->_c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
            |                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                     |
            |                                                     struct AlphaMap *
      In file included from src/datrie.c:1248:

This is most likely due to datrie troubles with gcc 14.2.1 which is the version that I'm using.

A workaround is to set flags:

$ export CFLAGS="-Wno-error=incompatible-pointer-types" ; export CXXFLAGS="-Wno-error=incompatible-pointer-types"; tox -e py313
  py313: OK (47.39=setup[31.21]+cmd[16.18] seconds)
  congratulations :) (47.62 seconds)

See also pytries/datrie#101