C++ code formatting

Author: gregorgorjanc

tskitr/.Rbuildignore

@@ -6,10 +6,11 @@
 ^test\.trees$
 ^.*\.o$
 ^.*\.so$
+^\.clang-format$
 ^\.covrignore$
 ^\.github$
-^pkg_dev_notes\.md
-^codecov\.yaml
-^notes_pkg_dev\.Rmd
-^inst/examples/create_test\.trees\.R
-^inst/examples/create_test\.trees\.py
+^pkg_dev_notes\.md$
+^codecov\.yaml$
+^notes_pkg_dev\.Rmd$
+^inst/examples/create_test\.trees\.R$
+^inst/examples/create_test\.trees\.py$

tskitr/.clang-format

@@ -0,0 +1,3 @@
+BasedOnStyle: LLVM
+IndentWidth: 2
+ColumnLimit: 80

tskitr/R/RcppExports.R

@@ -1,19 +1,11 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-#' @name ts_metadata_length
-#' @title Get the length of metadata in a tree sequence and its tables
-#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t} object.
-#' @details This function returns the length of metadata stored on the tree
-#'   sequence and in each table by calling
-#'   \code{tsk_treeseq_get_metadata_length()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_metadata_length} on tree sequence and
-NULL
-
 #' Report the version of installed kastore C API
 #'
 #' @details The version is stored in the installed header \code{kastore.h}.
 #' @return A named vector with three elements \code{major}, \code{minor}, and
-#'     \code{patch}.
+#'   \code{patch}.
 #' @examples
 #' kastore_version()
 #' @export
@@ -25,7 +17,7 @@ kastore_version <- function() {
 #'
 #' @details The version is defined in the installed header \code{tskit/core.h}.
 #' @return A named vector with three elements \code{major}, \code{minor}, and
-#'     \code{patch}.
+#'   \code{patch}.
 #' @examples
 #' tskit_version()
 #' @export
@@ -38,9 +30,10 @@ tskit_version <- function() {
 #' @param file a string specifying the full path of the tree sequence file.
 #' @param options integer bitwise options (see details).
 #' @details This function calls \code{tsk_treeseq_load()} from the tskit C API.
-#'   See \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_load}
-#'   for more details.
-#' @return Tree sequence as an external pointer to a \code{tsk_treeseq_t} object.
+#'   \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_load}
+#'   provides more details.
+#' @return Tree sequence as an external pointer to a \code{tsk_treeseq_t}
+#'   object.
 #' @examples
 #' ts_file <- system.file("examples/test.trees", package = "tskitr")
 #' ts <- tskitr::ts_load(ts_file) # slendr also has ts_load()!
@@ -54,12 +47,13 @@ ts_load <- function(file, options = 0L) {
 
 #' Write a tree sequence to file.
 #'
-#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t} object.
-#' @param file a string specifying the full path of the tree sequence file.
+#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t}
+#'   object.
+#' @param file a string specifying the full path of the tree sequence file
 #' @param options integer bitwise options (see details).
 #' @details This function calls \code{tsk_treeseq_dump()} from the tskit C API
-#'   See \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_dump}
-#'   for more details.
+#'   \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_dump}
+#'   provides more details.
 #' @return No return value, called for side effects.
 #' @examples
 #' ts_file <- system.file("examples/test.trees", package = "tskitr")
@@ -73,26 +67,41 @@ ts_dump <- function(ts, file, options = 0L) {
 }
 
 #' @name ts_summary
-#' @title Get the summary of properties and number of records in a tree sequence
-#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t} object.
-#' @details These functions return the summary of properties and number of records
-#'   in a tree sequence, by calling
-#'   \code{tsk_treeseq_get_num_provenances()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_provenances},
-#'   \code{tsk_treeseq_get_num_populations()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_populations},
-#'   \code{tsk_treeseq_get_num_migrations()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_migrations},
-#'   \code{tsk_treeseq_get_num_individuals()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_individuals},
-#'   \code{tsk_treeseq_get_num_samples()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_samples},
-#'   \code{tsk_treeseq_get_num_nodes()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_nodes},
-#'   \code{tsk_treeseq_get_num_edges()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_edges},
-#'   \code{tsk_treeseq_get_num_trees()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_trees},
-#'   \code{tsk_treeseq_get_num_sites()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_sites},
-#'   \code{tsk_treeseq_get_num_mutations()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_mutations},
-#'   \code{tsk_treeseq_get_sequence_length()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_sequence_length},
+#' @title Get the summary of properties and number of records in a tree
+#'   sequence
+#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t}
+#'   object.
+#' @details These functions return the summary of properties and number of
+#'   records in a tree sequence, by calling
+#'   \code{tsk_treeseq_get_num_provenances()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_provenances},
+#'   \code{tsk_treeseq_get_num_populations()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_populations},
+#'   \code{tsk_treeseq_get_num_migrations()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_migrations},
+#'   \code{tsk_treeseq_get_num_individuals()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_individuals},
+#'   \code{tsk_treeseq_get_num_samples()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_samples},
+#'   \code{tsk_treeseq_get_num_nodes()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_nodes},
+#'   \code{tsk_treeseq_get_num_edges()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_edges},
+#'   \code{tsk_treeseq_get_num_trees()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_trees},
+#'   \code{tsk_treeseq_get_num_sites()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_sites},
+#'   \code{tsk_treeseq_get_num_mutations()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_num_mutations},
+#'   \code{tsk_treeseq_get_sequence_length()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_sequence_length},
 #'   and
-#'   \code{tsk_treeseq_get_time_units()} \url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_time_units}.
+#'   \code{tsk_treeseq_get_time_units()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_time_units}.
 #'   from the tskit C API. See the linked documentation for more details.
-#' @return \code{ts_summary} returns a named list with the number/value for all items,
-#'     while other functions \code{ts_num_x} etc. return the number/value of each item.
+#' @return \code{ts_summary} returns a named list with the number/value for
+#'   all items, while other functions \code{ts_num_x} etc. return the
+#'   number/value of each item.
 #' @examples
 #' ts_file <- system.file("examples/test.trees", package = "tskitr")
 #' ts <- tskitr::ts_load(ts_file) # slendr also has ts_load()!
@@ -138,7 +147,8 @@ ts_num_individuals <- function(ts) {
     .Call(`_tskitr_ts_num_individuals`, ts)
 }
 
-#' @describeIn ts_summary Get the number of samples (of nodes) in a tree sequence
+#' @describeIn ts_summary Get the number of samples (of nodes) in a tree
+#'   sequence
 #' @export
 ts_num_samples <- function(ts) {
     .Call(`_tskitr_ts_num_samples`, ts)
@@ -186,6 +196,17 @@ ts_time_units <- function(ts) {
     .Call(`_tskitr_ts_time_units`, ts)
 }
 
+#' @name ts_metadata_length
+#' @title Get the length of metadata in a tree sequence and its tables
+#' @param ts tree sequence as an external pointer to a \code{tsk_treeseq_t}
+#'   object.
+#' @details This function returns the length of metadata stored on the tree
+#'   sequence and in each table by calling
+#'   \code{tsk_treeseq_get_metadata_length()}
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_treeseq_get_metadata_length}
+#'   on tree sequence and
+#'   \code{ts->tables->x->metadata_length} on each table \code{x}, e.g.,
+#'\url{https://tskit.dev/tskit/docs/stable/c-api.html#c.tsk_population_table_t.metadata_length},
 #'   from the tskit C API. See the linked documentation for more details.
 #' @return A named list with the length of metadata.
 #' @examples

tskitr/man/kastore_version.Rd

@@ -16,7 +16,7 @@ TSKIT_OBJECTS = $(TSKIT_SOURCES:.c=.o)
 # tskitr C++ sources & objects
 # TSKITR_SOURCES = $(wildcard *.cpp) # wildcard is a GNU extension and not desired on CRAN
 TSKITR_SOURCES = \
-	tskitr_minimal.cpp \
+	tskitr.cpp \
 	RcppExports.cpp
 # $(info TSKITR_SOURCES = $(TSKITR_SOURCES)) # for debugging, info is also a GNU extension
 TSKITR_OBJECTS = $(TSKITR_SOURCES:.cpp=.o)
@@ -33,7 +33,7 @@ PKG_CPPFLAGS = -I../inst/include -I../inst/include/tskit -I../inst/include/tskit
 # TODO: Remove asserts as per Writting R extensions manual #5
 #       https://github.com/HighlanderLab/tskitr/issues/5
 #       Note clang++ uses -DNDEBUG by default (see below output from devtools::install()) #5
-# clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/opt/homebrew/opt/gettext/include -I'/Users/ggorjanc/Library/R/arm64/4.5/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tskitr_minimal.cpp -o tskitr_minimal.o
+# clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I../inst/include/tskit -I../inst/include/tskit/tskit -I/opt/homebrew/opt/gettext/include -I'/Users/ggorjanc/Library/R/arm64/4.5/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tskitr.cpp -o tskitr.o
 # PKG_CFLAGS = -DNDEBUG
 # TODO: Should we port any flags from extern/tskit/c/meson.build to R build system? #6
 #       https://github.com/HighlanderLab/tskitr/issues/6