- May 27, 2016
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David Parsons authored
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- Oct 30, 2015
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Vincent Liard authored
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- Oct 29, 2015
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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'
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- Oct 28, 2015
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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
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- Oct 27, 2015
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Vincent Liard authored
Functions with empty argument list should be declared f() rather than f(void).
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Vincent Liard authored
Took aevol_run.cpp's header as reference header and set it for all Aevol source files.
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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
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- Oct 16, 2015
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David Parsons authored
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- Oct 12, 2015
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David Parsons authored
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- Aug 12, 2015
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ROUZAUD-CORNABAS Jonathan authored
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- Jul 10, 2015
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ROUZAUD-CORNABAS Jonathan authored
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- Jun 17, 2015
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David Parsons authored
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David Parsons authored
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David Parsons authored
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David Parsons authored
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David Parsons authored
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David Parsons authored
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David Parsons authored
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- May 28, 2015
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Vincent Liard authored
Genetic_Unit::_protein_list contained pointers to ae_protein's but it really owned them. Therefore it was changed so that objects are directly stored in the container. Which frees from maintaining memory.
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Vincent Liard authored
Genetic_Unit::_rna_list contained pointers to ae_rna's but it really owned them. Therefore it was changed so that objects are directly stored in the container. Which frees from maintaining memory.
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- May 27, 2015
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David Parsons authored
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- Apr 23, 2015
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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
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- Apr 22, 2015
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Vincent Liard authored
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- Apr 17, 2015
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David Parsons authored
Each Habitat has a PhenotyipcTarget handled through a PhenotypicTargetHandler. It can either be its own private instance or a shared instance among the whole World (for now, only shared mode is fully functional).
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- Mar 13, 2015
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David Parsons authored
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David Parsons authored
PRNGs are a typical example of entities whose ownership depends on the parameters provided to the system. There can either be a PRNG per individual (or grid-cell) or a single one may be used for the whole population. To avoid having to hand-manage these cases (and those I still haven't thought of), they are now handled through std::shared_ptr For consistency the other PRNGs are now handled through std::unique_ptr
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- Mar 12, 2015
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David Parsons authored
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- Mar 09, 2015
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David Parsons authored
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- Mar 06, 2015
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David Parsons authored
The gen_unit getters for rna and protein lists now take a parameter "strand" and returns the corresponding list
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David Parsons authored
This will be corrected in depth in a later commit
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- Feb 26, 2015
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Vincent Liard authored
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Vincent Liard authored
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Vincent Liard authored
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Vincent Liard authored
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- Feb 24, 2015
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Vincent Liard authored
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- Feb 17, 2015
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Vincent Liard authored
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- Feb 12, 2015
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Vincent Liard authored
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- Dec 08, 2014
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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.
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- Nov 19, 2014
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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.
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- Oct 24, 2014
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Vincent Liard authored
To conform to C++ 11 because it conflicts with user defined literals. (See http://en.cppreference.com/w/cpp/language/user_literal.) Avoids hundreds of warning messages when compiling -std=c++11: "invalid suffix on literal; C++11 requires a space between literal and string macro"
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