diff --git a/CMakeLists.txt b/CMakeLists.txt index f7f7cf3..657aa36 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -138,7 +138,7 @@ include( "${CMAKE_CURRENT_LIST_DIR}/tools/cmake/DownloadDependency.cmake" ) # These are replaced by tools/cmake/update_dependencies.sh to the hashes that are currently checked out. # Thus, do not replace the hashes manually! SET( CLI11_COMMIT_HASH "13becaddb657eacd090537719a669d66d393b8b2" ) #CLI11_COMMIT_HASH# -SET( genesis_COMMIT_HASH "60a519711602f14d6c44765a477a104ac009e847" ) #genesis_COMMIT_HASH# +SET( genesis_COMMIT_HASH "6b08cb22be0af409c3de9daac1416a3f42359a3d" ) #genesis_COMMIT_HASH# SET( sparsepp_COMMIT_HASH "6bfe3b4bdb364993e612d6bb729d680cf4c77649" ) #sparsepp_COMMIT_HASH# # Call the github download function, which takes four arguments: diff --git a/libs/genesis b/libs/genesis index 60a5197..6b08cb2 160000 --- a/libs/genesis +++ b/libs/genesis @@ -1 +1 @@ -Subproject commit 60a519711602f14d6c44765a477a104ac009e847 +Subproject commit 6b08cb22be0af409c3de9daac1416a3f42359a3d diff --git a/src/commands/analyze/correlation.cpp b/src/commands/analyze/correlation.cpp index 8bc08f9..2480e62 100644 --- a/src/commands/analyze/correlation.cpp +++ b/src/commands/analyze/correlation.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -37,6 +37,7 @@ #include "genesis/utils/containers/matrix.hpp" #include "genesis/utils/core/algorithm.hpp" #include "genesis/utils/core/fs.hpp" +#include "genesis/utils/math/correlation.hpp" #include "genesis/utils/math/matrix.hpp" #include "genesis/utils/math/statistics.hpp" #include "genesis/utils/text/string.hpp" diff --git a/src/commands/analyze/placement_factorization.cpp b/src/commands/analyze/placement_factorization.cpp index f342d72..78c0a5e 100644 --- a/src/commands/analyze/placement_factorization.cpp +++ b/src/commands/analyze/placement_factorization.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -39,9 +39,9 @@ #include "genesis/utils/io/output_target.hpp" #include "genesis/utils/math/regression/dataframe.hpp" #include "genesis/utils/math/regression/glm.hpp" -#include "genesis/utils/tools/color.hpp" -#include "genesis/utils/tools/color.hpp" -#include "genesis/utils/tools/color/list_sequential.hpp" +#include "genesis/utils/color/color.hpp" +#include "genesis/utils/color/color.hpp" +#include "genesis/utils/color/list_sequential.hpp" #include #include diff --git a/src/commands/prepare/extract.cpp b/src/commands/prepare/extract.cpp index 9f59889..b6c8c33 100644 --- a/src/commands/prepare/extract.cpp +++ b/src/commands/prepare/extract.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2020 Lucas Czech and HITS gGmbH + Copyright (C) 2014-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -16,9 +16,9 @@ along with this program. If not, see . Contact: - Lucas Czech - Exelixis Lab, Heidelberg Institute for Theoretical Studies - Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany + Lucas Czech + Department of Plant Biology, Carnegie Institution For Science + 260 Panama Street, Stanford, CA 94305, USA */ #include "commands/prepare/extract.hpp" @@ -55,7 +55,7 @@ #include "genesis/utils/formats/csv/reader.hpp" #include "genesis/utils/io/input_source.hpp" #include "genesis/utils/text/string.hpp" -#include "genesis/utils/tools/color/list_qualitative.hpp" +#include "genesis/utils/color/list_qualitative.hpp" #include #include diff --git a/src/main.cpp b/src/main.cpp index d0687e1..42d5527 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -150,7 +150,7 @@ int main( int argc, char** argv ) LOG_BOLD << message; } - } catch( genesis::except::ExistingFileError const& error ) { + } catch( genesis::utils::ExistingFileError const& error ) { // Special case for existing files: This is very common, and we want a nice and useful // error messsage for this one! @@ -162,7 +162,7 @@ int main( int argc, char** argv ) ; LOG_BOLD << message; LOG_BOLD; - throw genesis::except::ExistingFileError( message, error.filename() ); + throw genesis::utils::ExistingFileError( message, error.filename() ); } catch( std::exception const& error ) { diff --git a/src/options/color_map.cpp b/src/options/color_map.cpp index 90bb334..822ad14 100644 --- a/src/options/color_map.cpp +++ b/src/options/color_map.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -27,12 +27,12 @@ #include "genesis/utils/core/fs.hpp" #include "genesis/utils/text/string.hpp" -#include "genesis/utils/tools/color/functions.hpp" -#include "genesis/utils/tools/color/list_diverging.hpp" -#include "genesis/utils/tools/color/list_misc.hpp" -#include "genesis/utils/tools/color/list_qualitative.hpp" -#include "genesis/utils/tools/color/list_sequential.hpp" -#include "genesis/utils/tools/color/names.hpp" +#include "genesis/utils/color/functions.hpp" +#include "genesis/utils/color/list_diverging.hpp" +#include "genesis/utils/color/list_misc.hpp" +#include "genesis/utils/color/list_qualitative.hpp" +#include "genesis/utils/color/list_sequential.hpp" +#include "genesis/utils/color/names.hpp" #include diff --git a/src/options/color_map.hpp b/src/options/color_map.hpp index b971213..e32c602 100644 --- a/src/options/color_map.hpp +++ b/src/options/color_map.hpp @@ -3,7 +3,7 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,8 +28,8 @@ #include "tools/cli_option.hpp" -#include "genesis/utils/tools/color.hpp" -#include "genesis/utils/tools/color/map.hpp" +#include "genesis/utils/color/color.hpp" +#include "genesis/utils/color/map.hpp" #include #include diff --git a/src/options/color_norm.hpp b/src/options/color_norm.hpp index 2cb23c6..42d28db 100644 --- a/src/options/color_norm.hpp +++ b/src/options/color_norm.hpp @@ -3,7 +3,7 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,11 +28,11 @@ #include "tools/cli_option.hpp" -#include "genesis/utils/tools/color.hpp" -#include "genesis/utils/tools/color/normalization.hpp" -#include "genesis/utils/tools/color/norm_diverging.hpp" -#include "genesis/utils/tools/color/norm_linear.hpp" -#include "genesis/utils/tools/color/norm_logarithmic.hpp" +#include "genesis/utils/color/color.hpp" +#include "genesis/utils/color/normalization.hpp" +#include "genesis/utils/color/norm_diverging.hpp" +#include "genesis/utils/color/norm_linear.hpp" +#include "genesis/utils/color/norm_logarithmic.hpp" #include #include diff --git a/src/options/color_single.cpp b/src/options/color_single.cpp index 1b3c0b1..95e8eae 100644 --- a/src/options/color_single.cpp +++ b/src/options/color_single.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -25,9 +25,9 @@ #include "options/global.hpp" -#include "genesis/utils/tools/color/functions.hpp" +#include "genesis/utils/color/functions.hpp" +#include "genesis/utils/color/names.hpp" #include "genesis/utils/text/string.hpp" -#include "genesis/utils/tools/color/names.hpp" #include diff --git a/src/options/color_single.hpp b/src/options/color_single.hpp index f1f7d34..5c136a5 100644 --- a/src/options/color_single.hpp +++ b/src/options/color_single.hpp @@ -3,7 +3,7 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -28,7 +28,7 @@ #include "tools/cli_option.hpp" -#include "genesis/utils/tools/color.hpp" +#include "genesis/utils/color/color.hpp" #include #include diff --git a/src/options/file_output.cpp b/src/options/file_output.cpp index d8a625a..e392326 100644 --- a/src/options/file_output.cpp +++ b/src/options/file_output.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -245,7 +245,7 @@ void FileOutputOptions::check_output_files_nonexistence( warned_names.emplace( path ); } } else { - throw genesis::except::ExistingFileError( + throw genesis::utils::ExistingFileError( "Output file already exists: " + path + "\nUse " + allow_file_overwriting_flag + " to allow gappa to overwrite the file.", path diff --git a/src/options/tree_output.cpp b/src/options/tree_output.cpp index e54fec0..fd039f5 100644 --- a/src/options/tree_output.cpp +++ b/src/options/tree_output.cpp @@ -1,6 +1,6 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -26,8 +26,8 @@ #include "genesis/tree/drawing/functions.hpp" #include "genesis/utils/text/string.hpp" -#include "genesis/utils/tools/color/functions.hpp" -#include "genesis/utils/tools/color/helpers.hpp" +#include "genesis/utils/color/functions.hpp" +#include "genesis/utils/color/helpers.hpp" #include "genesis/utils/tools/tickmarks.hpp" #include diff --git a/src/options/tree_output.hpp b/src/options/tree_output.hpp index 5328b4b..ddf1c1a 100644 --- a/src/options/tree_output.hpp +++ b/src/options/tree_output.hpp @@ -3,7 +3,7 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2022 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -31,9 +31,9 @@ #include "options/file_output.hpp" #include "genesis/tree/common_tree/tree.hpp" -#include "genesis/utils/tools/color.hpp" -#include "genesis/utils/tools/color/map.hpp" -#include "genesis/utils/tools/color/normalization.hpp" +#include "genesis/utils/color/color.hpp" +#include "genesis/utils/color/map.hpp" +#include "genesis/utils/color/normalization.hpp" #include #include diff --git a/src/tools/version.hpp b/src/tools/version.hpp index 43077aa..b2823a6 100644 --- a/src/tools/version.hpp +++ b/src/tools/version.hpp @@ -3,7 +3,7 @@ /* gappa - Genesis Applications for Phylogenetic Placement Analysis - Copyright (C) 2017-2023 Lucas Czech + Copyright (C) 2017-2024 Lucas Czech This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -48,7 +48,7 @@ inline std::string gappa_header() |'' .|' || || | || | .|' || .|'|. || \n\ '.... '|..'|'. ||...' ||...' '|..'|. '||' ||:. \n\ '....' || || \n\ - '''' '''' " + gappa_version() + " (c) 2017-2023\n\ + '''' '''' " + gappa_version() + " (c) 2017-2024\n\ by Lucas Czech and Pierre Barbera\n"; }