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  1. Feb 17, 2025
  2. Jun 12, 2024
    • Studer Gabriel's avatar
      enable pairwise sequence alignments with parasail · adb141f9
      Studer Gabriel authored
      Parasail: https://github.com/jeffdaily/parasail
      
      It's faster than the pairwise sequence algorithms we have in
      OpenStructure. However, the main reason to check out another solution
      is the fact that OpenStructure may return suboptimal alignment
      results. This is a result of how the dynamic programming table is built.
      If for a certain cell in the dynamic programming table a match state and
      insertion state score equally, match is preferred. There is a chance
      that we would get a better score later on if we would stick with the
      insertion state (gap open penalties vs. gap extension penalties).
      Not sure if this will be fixed in the near future.
      adb141f9
  3. Apr 05, 2024
    • Studer Gabriel's avatar
      disable numpy support in C++ layer · 728ad1c9
      Studer Gabriel authored
      Numpy support in C++ enabled features at two points:
      Efficient way of setting positions in entity handles or setting meshes
      in gfx.PrimList.
      
      Support for newer numpy versions would've required an effort to implement.
      As far as I know, no one uses these features (fingers crossed) so let's just
      dump numpy alltogether to simplify the build system.
      728ad1c9
  4. Nov 28, 2023
    • Xavier Robin's avatar
      Update module versions · dda2ac99
      Xavier Robin authored
      This updates the module versions to match the versions we currently use
      for the OST module on sciCORE.
      dda2ac99
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