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  1. May 27, 2016
  2. Oct 30, 2015
  3. Oct 29, 2015
    • Vincent Liard's avatar
      rename remaining get_xxx() to xxx() · 3244d2e1
      Vincent Liard authored
      Magic command for reference:
      find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 | xargs -0 sed -i -r 's/\bget_(\w+)\b/\1/g'
      3244d2e1
  4. Oct 28, 2015
    • 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
  5. Oct 27, 2015
    • 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
  6. Oct 16, 2015
  7. Oct 12, 2015
  8. Aug 12, 2015
  9. Jul 10, 2015
  10. Jun 17, 2015
  11. May 28, 2015
  12. May 27, 2015
  13. Apr 23, 2015
    • Vincent Liard's avatar
      rename class ae_genetic_unit to GeneticUnit · 4716966b
      Vincent Liard authored and David Parsons's avatar David Parsons committed
      Conflicts:
      	src/libaevol/ae_dna.cpp
      	src/libaevol/ae_dna.h
      	src/libaevol/ae_individual.cpp
      	src/libaevol/ae_individual.h
      	src/libaevol/ae_individual_X11.cpp
      	src/libaevol/genetic_unit.cpp
      	src/libaevol/genetic_unit.h
      	src/libaevol/param_loader.cpp
      4716966b
  14. Apr 22, 2015
  15. Apr 17, 2015
  16. Mar 13, 2015
  17. Mar 12, 2015
  18. Mar 09, 2015
  19. Mar 06, 2015
  20. Feb 26, 2015
  21. Feb 24, 2015
  22. Feb 17, 2015
  23. Feb 12, 2015
  24. Dec 08, 2014
    • Vincent Liard's avatar
      wrap ae_* in namespace aevol · c7e0790b
      Vincent Liard authored
      The name convention ae_* for aevol-related classes and functions comes
      from C language lacking namespaces. It was meant to prevent name
      clashes. Since C++ provides namespaces, this commit wraps everything
      inside an "aevol" namespace.
      
      This means that there is no need anylonger to name classes according to
      ae_*. But any new class needs to be within the aevol namespace if it is
      part of aevol or to start with a "using" clause if it relies on aevol.
      c7e0790b
  25. Nov 19, 2014
    • Vincent Liard's avatar
      remove variables defined but never used · 95447357
      Vincent Liard authored
      Several variables were declared, defined but never used in the end. This
      commit comments them out. The question should be considered more deeply
      to remove them cleanly.
      95447357
  26. Oct 24, 2014
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