Installation fails due to unmaintained datrie dependency in Snakemake on modern Linux

[daxrpm]

Installation fails due to unmaintained datrie dependency in Snakemake on modern Linux

Summary

When installing reana-client (or any package depending on reana-commons[snakemake]) on modern Linux systems with GCC >=14, the installation fails due to compilation errors in the datrie dependency. This issue originates from the fact that datrie is unmaintained and incompatible with recent compilers.

Details

• datrie is a dependency of older Snakemake versions (<8.29.1).
• Snakemake is used in reana-commons for workflow support, and reana-commons is a dependency of reana-client.
• The datrie repository has not been maintained for over 5 years. There is a pull request that addresses the compilation issue, but it has not been merged.
• Related issue in datrie: pytries/datrie#101

Example error log

      src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap_copy’:
      src/datrie.c:26374:61: error: passing argument 1 of ‘alpha_map_clone’ from incompatible pointer type [-Wincompatible-pointer-types]
      26374 |   __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:26374:31: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
      26374 |   __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:27044:50: error: passing argument 1 of ‘alpha_map_add_range’ from incompatible pointer type [-Wincompatible-pointer-types]
      27044 |   __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/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for datrie

Upstream Fix in Snakemake

• The Snakemake team removed the datrie dependency in PR #3176, addressing #3105 and #2970.
• This fix is available starting from v8.29.1.

Current State in reana-commons

• reana-commons currently uses snakemake==8.27.1 and snakemake-storage-plugin-xrootd which depends on snakemake ^8.18.0.
• As a result, installation fails on modern systems due to the unmaintained datrie dependency.

Proposed Solution

• Update snakemake-storage-plugin-xrootd to latest version.
• Update the Snakemake dependency in reana-commons to >=8.29.1 (which is used in snakemake-storage-plugin-xrootd:latest or the latest compatible version).
• Ensure all tests pass and there are no regressions.

References

• pytries/datrie#101
• pytries/datrie#99
• snakemake/snakemake#3176
• snakemake/snakemake#3105
• snakemake/snakemake#2970
• snakemake v8.29.1 release notes

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Impact:

This issue blocks the installation of any component depending on reana-commons[snakemake] on modern Linux distributions and affects reproducibility and maintainability for new users and contributors.

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Notes

I've tested the installation process on Fedora 41, Fedora 42, Arch Linux, and Ubuntu 24.04 LTS (Desktop), using Python 3.13, 3.12, and 3.11, with gcc 14 and 15 (All failed) .
If there's any consideration I might have missed, please let me know.