1. 13 Jun, 2022 1 commit
    • TURPIN Laurent's avatar
      [Modularize] Stop recording stats in rep-reports · 798dd9f8
      TURPIN Laurent authored
      In ReplicationReport, remove attributes that correspond to statistics of
      individual that can be recomputed by reading the genome. A major problem
      was also when recording Trees, if statistics was not computed, the
      values are completely wrong. Finally, checking if execution is
      repeatable, the contant of tree files might change according to a spooky
      and hardly predictable state (AEVOL_NO_STATS)
      798dd9f8
  2. 10 Jun, 2022 1 commit
  3. 22 Mar, 2021 1 commit
  4. 08 Mar, 2021 1 commit
  5. 13 Oct, 2020 3 commits
  6. 08 Sep, 2020 1 commit
  7. 07 Sep, 2020 1 commit
  8. 30 Jul, 2020 1 commit
  9. 12 Feb, 2020 1 commit
  10. 30 Aug, 2018 1 commit
  11. 24 Aug, 2018 1 commit
  12. 23 Aug, 2018 1 commit
  13. 16 Aug, 2018 1 commit
  14. 24 May, 2016 1 commit
  15. 30 Oct, 2015 1 commit
  16. 29 Oct, 2015 2 commits
  17. 28 Oct, 2015 1 commit
    • Vincent Liard's avatar
      shorten safe getter names · e10a4e7a
      Vincent Liard authored
      Looking forward to honour Google Style guide, the purpose is to rename getters
      from get_var() to var(). Many of such renames cause conflicts, though. In this
      commit, only the safe names were changed.
      
      grep -rEo '\bget_\w+\(' --include '*.h' --no-filename --exclude-dir tests \
       | sed -e 's/get_//' -e 's/($//' \
       | sort -u \
       | xargs -n 1 -I% sh -c "grep -roq '\b%\b' --include '*.cpp' --include '*.h' --exclude-dir tests || echo %" \
       | xargs -n1 -I% sh -c "find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 \
       | xargs -0 sed -i -r 's/\bget_%\(/%\(/g'"
      
      Yes. I know...
      
      http://google-styleguide.googlecode.com/svn/trunk/cppguide.html#Function_Names
      e10a4e7a
  18. 27 Oct, 2015 3 commits
    • Vincent Liard's avatar
      remove (void)s · 90e4e148
      Vincent Liard authored
      Functions with empty argument list should be declared f() rather than f(void).
      90e4e148
    • Vincent Liard's avatar
      uniformize headers · c4cac25a
      Vincent Liard authored
      Took aevol_run.cpp's header as reference header and set it for all Aevol source files.
      c4cac25a
    • Vincent Liard's avatar
      fix _member_variables to member_variables_ [epic] · 286881e3
      Vincent Liard authored
      * Find member variables that could clash
      
      : grep -rEo --no-filename '\w+' --include '*.cpp' --include '*.h' | sort -u | grep '^_' > _litigious_tokens.txt
      : grep -rEo --no-filename '\w+' --include '*.cpp' --include '*.h' | sort -u | grep '_$' > litigious_tokens_.txt
      : grep -Fx -f <(sed -e 's/_$//' litigious_tokens_.txt) <(sed -e 's/^_//' _litigious_tokens.txt)
      : cat clashes.txt
      : | xargs -n 1 -I% sh -c "echo --- % --- ; grep -rlE --include '*.cpp' --include '*.h' '\W_%'
      : | xargs grep -l '%_\W'"
      
      From the resulting list,
      files of interest, trimmed:
      ExpManager.h | t_end
      GeneticUnit.cpp | dna rna_list
      
      False positives removed (needed no action)
      Dna.cpp | indiv
      ExpManager_X11.cpp | win
      GeneticUnit.cpp | non_coding_computed
      GeneticUnit.cpp | transcribed
      Individual.cpp | modularity
      OutputManager.cpp | tree
      PhenotypicTargetHandler.cpp | var_sigma var_tau
      Protein.cpp | gen_unit height mean width
      ReplicationReport.cpp | indiv
      Rna.cpp | gen_unit
      StatRecord.cpp
      Stats.cpp | exp_m
      
      * Manual fixes
      [x] ExpManager.h | t_end
      [x] GeneticUnit.cpp | dna rna_list (almost false positive, would have caused no harm)
      
      * Automatic fix all other symbols
      : find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0
      : | xargs -0 sed -i -r -e 's/([^a-zA-Z0-9_])_([a-zA-Z0-9][a-zA-Z0-9_]+)/\1\2_/g'
      
      * Minor afterhand fixes
      fix OPENMP_ and changed_ with similar `find | xargs sed`s
      
      * Check there are no more _members
      : grep -rEo --no-filename '[^a-zA-Z0-9_]_[a-zA-Z0-9][a-zA-Z0-9_]+' --include '*.cpp' --include '*.h' --exclude-dir tests
      : | sed -e 's/^.//' | sort -u
      286881e3
  19. 12 Aug, 2015 1 commit
  20. 06 Jul, 2015 1 commit
    • David Parsons's avatar
      aevol-2 Create mutation class hierarchy · 6615dbb4
      David Parsons authored
      Instead of a single class with switches everywhere, mutations are now
      handled through a proper polymorphism.
      
      Here is the class hierarchy:
      Mutation
        <-- LocalMutation
              <-- PointMutation
              <-- SmallInsertion
              <-- SmallDeletion
        <-- Rearrangement
              <-- Duplication
              <-- Deletion
              <-- Translocation
              <-- Inversion
        <-- HT
              <-- InsertionHT
              <-- ReplacementHT
      6615dbb4
  21. 30 Jun, 2015 1 commit
  22. 29 Jun, 2015 3 commits
  23. 19 Jun, 2015 1 commit
    • David Parsons's avatar
      Refactor tree management · b85cae02
      David Parsons authored
      The responsability of the creation of the tree was shared between
      different entities (the tree of course, but also the individuals
      and their dna).
      This made it really difficult to deal with.
      
      The solution presented here isn't optimal (yet ?). In particular,
      trees had to be temporarily disabled for experiments with plasmids.
      The tree now handles itself more independently. It is filled with
      naive ReplicationReports which will have to be :
        - initialized at the beginning of a replication
        - filled in at the end of a replication
        - finalized at the end of a generation
      
      In the future, it would be nice to implement that as an Observer
      pattern to decouple the involved classes
      b85cae02
  24. 17 Jun, 2015 4 commits
  25. 12 Mar, 2015 1 commit
  26. 26 Feb, 2015 1 commit
  27. 20 Feb, 2015 2 commits
    • Vincent Liard's avatar
      remove ae_ from filenames ae_dna_replic_report.* · 93a3b7d6
      Vincent Liard authored
      And fix #includes and libaevol/Makefile.am.
      93a3b7d6
    • Vincent Liard's avatar
      rename ae_dna_replic_report · 274fdca0
      Vincent Liard authored
      Renamed ae_dna_replic_report to DnaReplicReport.
      Renamed member variables with no prefix _ and with a trailing _.
      
      Variable names should not start with and underscore as these names are
      reserved to the compiler implementation. (C++03 standard:
      §17.4.3.1.2/1). But class member variables can END with a trailing
      underscore.
      274fdca0
  28. 19 Feb, 2015 2 commits