Update genesis

lczech · Feb 13, 2024 · 6bfffc2 · 6bfffc2
1 parent e84f122
commit 6bfffc2
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Showing 15 changed files with 48 additions and 47 deletions.
diff --git 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
diff --git 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
@@ -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 <fstream>
 #include <stdexcept>

diff --git 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 <http://www.gnu.org/licenses/>.
 
     Contact:
-    Lucas Czech <lucas.czech@h-its.org>
-    Exelixis Lab, Heidelberg Institute for Theoretical Studies
-    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
+    Lucas Czech <lczech@carnegiescience.edu>
+    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 <algorithm>
 #include <cassert>

diff --git 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
@@ -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 <stdexcept>
 

diff --git 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 <limits>
 #include <memory>

diff --git 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 <limits>
 #include <memory>

diff --git 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 <stdexcept>
 

diff --git 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 <string>
 #include <vector>

diff --git 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
@@ -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 <cassert>

diff --git 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 <string>
 #include <vector>

diff --git 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";
 }