Merge pull request #108 from rseng/update/analysis-2024-02-14

Update from update/analysis-2024-02-14
rseng · Feb 14, 2024 · dc6ff3a · dc6ff3a
2 parents 9dc6e5d + 5edfe92
commit dc6ff3a
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diff --git a/_data/repos_counts_languages.json b/_data/repos_counts_languages.json
@@ -1,5 +1,5 @@
 {
-    "Python": 5857,
+    "Python": 5858,
     "R": 2227,
     "Cpp": 441,
     "Js": 1690,

diff --git a/_data/stats.json b/_data/stats.json
@@ -1,9 +1,9 @@
 {
-    "python_deps": 4840,
+    "python_deps": 4841,
     "cpp_deps": 441,
     "r_deps": 2227,
     "js_deps": 1690,
     "go_deps": 246,
     "total_repos": 5312,
-    "total_parsed": 2718
+    "total_parsed": 2719
 }
diff --git a/_repos/github/adrientaudiere/MiscMetabar/DESCRIPTION b/_repos/github/adrientaudiere/MiscMetabar/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.1
+Version: 0.7.8
 Authors@R: person("Adrien", "Taudière", email = "adrien.taudiere@zaclys.net",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
-Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatic pipeline in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerfull by integrating a large number of analysis, some of them from other R packages.  
+Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatics pipelines in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerful by integrating a large number of analysis, some of them from other R packages.  
 License: AGPL-3
 Encoding: UTF-8
 LazyData: true
@@ -74,19 +74,7 @@ Suggests:
     venneuler,
     vctrs,
     viridis,
-    withr,
-    datawizard,
-    formattable,
-    ggforce,
-    ggtree,
-    gtExtras,
-    MicrobiotaProcess,
-    pillar,
-    pointblank,
-    summarytools,   
-    svglite,
-    tidytree,
-    treeio
+    withr
 RoxygenNote: 7.3.1
 URL: https://github.com/adrientaudiere/MiscMetabar,
     https://adrientaudiere.github.io/MiscMetabar/

diff --git a/_repos/github/biocore/sortmerna/CMakeLists.txt b/_repos/github/biocore/sortmerna/CMakeLists.txt
@@ -7,11 +7,9 @@
 
 cmake_minimum_required(VERSION 3.21)
 project(sortmerna CXX C)
-
 set(CMAKE_CXX_STANDARD 17)
 
 find_package(Git)
-
 string(TIMESTAMP GIT_DATE_TIME "%Y/%m/%d %H:%M:%S" UTC)
 
 #
@@ -30,7 +28,9 @@ endif()
 string(REGEX REPLACE "[^0-9a-f]+" "" GIT_SHA "${GIT_SHA}")
 
 # Read sortmerna version from version.h file.
-file(READ include/version.h version_header_file)
+set(VERSION_FILE include/version.h)
+message("parsing version file: ${VERSION_FILE}")
+file(READ ${VERSION_FILE} version_header_file)
 string(REGEX MATCH "#define SORTMERNA_MAJOR ([0-9]+)" _ ${version_header_file})
 set(SORTMERNA_VERSION_MAJOR ${CMAKE_MATCH_1})
 string(REGEX MATCH "#define SORTMERNA_MINOR ([0-9]+)" _ ${version_header_file})
@@ -39,41 +39,21 @@ string(REGEX MATCH "#define SORTMERNA_PATCH ([0-9]+)" _ ${version_header_file})
 set(SORTMERNA_VERSION_PATCH ${CMAKE_MATCH_1})
 set(SORTMERNA_VERSION ${SORTMERNA_VERSION_MAJOR}.${SORTMERNA_VERSION_MINOR}.${SORTMERNA_VERSION_PATCH})
 
-
-#include(ExternalProject)
+message("PROJECT_BINARY_DIR = ${PROJECT_BINARY_DIR}")
 message("CMAKE_CXX_COMPILER_ID = ${CMAKE_CXX_COMPILER_ID}") # 'GNU' on Ubuntu
 message("CMAKE_CONFIGURATION_TYPES = ${CMAKE_CONFIGURATION_TYPES}")
 message("CMAKE_HOST_SYSTEM_NAME = ${CMAKE_HOST_SYSTEM_NAME}")
 message("CMAKE_HOST_SYSTEM_VERSION = ${CMAKE_HOST_SYSTEM_VERSION}")
 message("CMAKE_HOST_SYSTEM = ${CMAKE_HOST_SYSTEM}")
-message("PROJECT_BINARY_DIR = ${PROJECT_BINARY_DIR}")
 message("CMAKE_BINARY_DIR = ${CMAKE_BINARY_DIR}")
 message("CMAKE_CURRENT_BINARY_DIR = ${CMAKE_CURRENT_BINARY_DIR}")
 message("RUNTIME_OUTPUT_DIRECTORY_RELEASE = ${RUNTIME_OUTPUT_DIRECTORY_RELEASE}")
-
-# append sortmerna custom modules to cmake modules
-message("CMAKE_CURRENT_LIST_DIR: ${CMAKE_CURRENT_LIST_DIR}")
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake/modules/")
+message("CMAKE_CXX_FLAGS_DEBUG: ${CMAKE_CXX_FLAGS_DEBUG}")
+message("CMAKE_C_FLAGS_DEBUG: ${CMAKE_C_FLAGS_DEBUG}")
 
 set(EXTERNAL_DEPS ${CMAKE_SOURCE_DIR}/3rdparty CACHE PATH "Installation directory for 3rd party dependencies")
-set(ZLIB_URL https://github.com/madler/zlib.git CACHE STRING "ZLib GitHub URL")
-#set(ZLIB_ROOT ${EXTERNAL_DEPS}/zlib CACHE PATH "ZLIB installation directory")
-set(ROCKSDB_URL https://github.com/facebook/rocksdb.git CACHE STRING "RocksDB GitHub URL")
-set(ROCKSDB_SRC ${EXTERNAL_DEPS}/rocksdb CACHE PATH "RocksDB source root directory")
-set(ROCKSDB_DIST ${EXTERNAL_DEPS}/rocksdb/dist CACHE PATH "RocksDB installation directory")
-#set(RAPIDJSON_URL https://github.com/Tencent/rapidjson CACHE STRING "RapidJSON GitHub URL")
-#set(RAPIDJSON_HOME ${EXTERNAL_DEPS}/rocksdb CACHE PATH "RapidJSON installation directory")
 set(DIRENTWIN_URL https://github.com/tronkko/dirent CACHE STRING "Dirent-Windows interface GitHub URL")
 set(DIRENTWIN_HOME ${EXTERNAL_DEPS}/dirent CACHE PATH "Dirent-Windows interface installation directory")
-set(CONCURRENTQUEUE_URL https://github.com/cameron314/concurrentqueue CACHE STRING "Concurrent queue library GitHub URL")
-set(CONCURRENTQUEUE_HOME ${EXTERNAL_DEPS}/concurrentqueue CACHE PATH "Concurrent queue library installation directory")
-#set(gflags_DIR  ${EXTERNAL_DEPS}/gflags/dist/lib/cmake/gflags CACHE PATH "GFlags library configuration")
-
-option(ROCKSDB_USE_STATIC_LIBS "Use static RocksDB library" ON)
-option(ZLIB_STATIC "Use static ZLib library" ON)
-
-message("CMAKE_CXX_FLAGS_DEBUG: ${CMAKE_CXX_FLAGS_DEBUG}")
-message("CMAKE_C_FLAGS_DEBUG: ${CMAKE_C_FLAGS_DEBUG}")
 
 option(WITH_TESTS "Select whether to build tests" OFF)
 
@@ -87,51 +67,13 @@ endif()
 message("CMAKE_CXX_FLAGS_RELEASE: ${CMAKE_CXX_FLAGS_RELEASE}")
 message("EXTRA_CXX_FLAGS_RELEASE: ${EXTRA_CXX_FLAGS_RELEASE}")
 
-## download zlib
-#if(SRC_ZLIB AND NOT EXISTS ${EXTERNAL_DEPS}/zlib)
-#	execute_process(COMMAND git clone --depth 1 https://github.com/madler/zlib
-#		WORKING_DIRECTORY ${EXTERNAL_DEPS}
-#	)
-#endif()
-
-## Download RocksDB
-#if(SRC_ROCKSDB AND NOT EXISTS ${EXTERNAL_DEPS}/rocksdb)
-#	execute_process(COMMAND git clone --depth 1 https://github.com/facebook/rocksdb
-#		WORKING_DIRECTORY ${EXTERNAL_DEPS}
-#	)
-#endif()
-
-#
-# modify RocksDB thirdparty.inc - no need, it is modified before building RocksDB
-#
-#option(ROCKSDB_3RDPARTY_INC "Modify rocksdb/thirdparty.inc" OFF)
-#if (ROCKSDB_3RDPARTY_INC)
-#	include(smr_utils)
-#	rocksdb_edit_3rdparty_inc()
-#endif(ROCKSDB_3RDPARTY_INC)
-
-
-## Download Rapidjson
-#(SRC_RAPIDJSON AND NOT EXISTS ${EXTERNAL_DEPS}/rapidjson)
-#	execute_process(COMMAND git clone --depth 1 https://github.com/Tencent/rapidjson
-#		WORKING_DIRECTORY ${EXTERNAL_DEPS}
-#	)
-#endif()
-
 # download dirent. Only dirent.h used from this project - no need to build
 if(WIN32 AND NOT EXISTS ${DIRENTWIN_HOME})
 	execute_process(COMMAND git clone --depth 1 ${DIRENTWIN_URL}
 		WORKING_DIRECTORY ${EXTERNAL_DEPS}
 )
 endif()
 
-## Download concurrentqueue
-#if(NOT EXISTS ${EXTERNAL_DEPS}/concurrentqueue)
-#	execute_process(COMMAND git clone --depth 1 https://github.com/cameron314/concurrentqueue
-#		WORKING_DIRECTORY ${EXTERNAL_DEPS}
-#	)
-#endif()
-
 # build build_version
 set(BUILD_VERSION_CPP ${CMAKE_BINARY_DIR}/build_version.cpp)
 configure_file(src/util/build_version.cpp.in ${BUILD_VERSION_CPP} @ONLY)
@@ -149,27 +91,20 @@ if(WIN32)
 	add_subdirectory(${CMAKE_SOURCE_DIR}/src/winapi)
 endif()
 
-## build indexdb
-#add_subdirectory(${CMAKE_SOURCE_DIR}/src/indexdb)
-
 ## build sortmerna
 add_subdirectory(${CMAKE_SOURCE_DIR}/src/sortmerna)
 
 if (WITH_TESTS)
   add_subdirectory (tests/sortmerna)
 endif ()
 
-# Installation and packaging
-#set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/dist CACHE PATH "Install path prefix, prepended onto install directories.")
-
-#include(GNUInstallDirs)
 include(CMakePackageConfigHelpers)
 
 set(package_config_destination ${CMAKE_INSTALL_PREFIX}/cmake/sortmerna)
 message("package_config_destination: ${package_config_destination}")
 
 configure_package_config_file(
-	${CMAKE_CURRENT_LIST_DIR}/cmake/sortmernaConfig.cmake.in sortmernaConfig.cmake
+	${CMAKE_SOURCE_DIR}/cmake/sortmernaConfig.cmake.in sortmernaConfig.cmake
 	INSTALL_DESTINATION ${package_config_destination}
 )
 

diff --git a/_repos/github/leapigufpb/FuzzyClass/DESCRIPTION b/_repos/github/leapigufpb/FuzzyClass/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: FuzzyClass
 Title: Fuzzy and Non-Fuzzy Classifiers
-Version: 0.1.5.900
+Version: 0.1.6
 Authors@R:
     c(person("Jodavid", "Ferreira", email = "jodavid@protonmail.com",role = c("aut","cre"), comment = c(ORCID = "0000-0002-2131-6464")),
       person("Ronei", "Moraes", email = "ronei@de.ufpb.br",role = c("ctb"), comment = c(ORCID = "0000-0001-8436-8950")),