more

.devel/roxygen2-patch.R

@@ -1,26 +1,15 @@
-# Copyleft (C) 2020-2022, Marek Gagolewski <https://www.gagolewski.com>
-# Adding author and other metadata to every Rd file
+# Copyleft (C) 2021-2024, Marek Gagolewski <https://www.gagolewski.com>
+# Adding author and other metadata to every Rd file;
+# There is one and only one official manual. Ad- and tracker-free.
+# Enjoy the free internet.
 
 library("roxygen2")
 
 postprocess_contents <- function(contents)
 {
     stopifnot(is.character(contents), length(contents)==1, !is.na(contents))
 
-    if (!stringi::stri_detect_regex(
-        contents, "% Please edit documentation in R/.*\\\\name", dotall=TRUE)
-    ) return(contents)
-
-    if (!stringi::stri_detect_fixed(contents, "\\author")) {
-        contents <- stringi::stri_paste(contents,
-            "\\author{\n",
-            "\\href{https://www.gagolewski.com/}{Marek Gagolewski} ",
-            "and other contributors\n",
-            "}\n")
-    }
-
-    # There is one and only one official manual. Ad- and tracker-free.
-    # Enjoy the free internet.
+    author <- "\\href{https://www.gagolewski.com/}{Marek Gagolewski} and other contributors\n"
 
     seealso <- stringi::stri_paste(
         "The official online manual of \\pkg{genieclust} at ",
@@ -33,6 +22,17 @@ postprocess_contents <- function(contents)
         "\n"
     )
 
+    if (!stringi::stri_detect_regex(
+        contents, "% Please edit documentation in R/.*\\\\name", dotall=TRUE)  # fixed comment generated by roxugen2
+    ) return(contents)
+
+    if (!stringi::stri_detect_fixed(contents, "\\author")) {
+        contents <- stringi::stri_paste(contents,
+            "\\author{\n",
+            author,
+            "}\n")
+    }
+
     if (!stringi::stri_detect_fixed(contents, "\\seealso{\n")) {
         contents <- stringi::stri_paste(
             contents,
@@ -52,15 +52,15 @@ postprocess_contents <- function(contents)
 
 # ########################################################################### #
 
-# taken from roxygen2 7.2.1 by Hadley Wickham et al.
-write_if_different <- function (path, contents, href = NULL, check = TRUE)
+# taken from roxygen2 7.3.2 by Hadley Wickham et al.
+write_if_different <- function (path, contents, command=NULL, check=TRUE)
 {
     if (!file.exists(dirname(path))) {
         dir.create(dirname(path), showWarnings = FALSE)
     }
     name <- basename(path)
     if (check && !made_by_roxygen(path)) {
-        cli::cli_warn(c("Skipping {.path {name}}", x = "It already exists and was not generated by roxygen2."))
+        cli::cli_inform(c(x = "Skipping {.path {name}}", i = "It already exists and was not generated by roxygen2."))
         return(FALSE)
     }
     line_ending <- detect_line_ending(path)
@@ -75,12 +75,14 @@ write_if_different <- function (path, contents, href = NULL, check = TRUE)
 
 
     if (!str_detect(name, "^[a-zA-Z][a-zA-Z0-9_.-]*$")) {
-        cli::cli_warn(c("Skipping {.path {name}}", x = "Invalid file name"))
+        cli::cli_inform(c(x = "Skipping {.path {name}}", i = "Invalid file name"))
         FALSE
     }
     else {
-        if (!is.null(href)) {
-            name <- cli::style_hyperlink(name, href)
+        if (!is.null(command)) {
+            scheme <- "x-r-run"
+            url <- paste0(scheme, ":", command)
+            name <- cli::style_hyperlink(name, url)
         }
         cli::cli_inform("Writing {.path {name}}")
         writeBin(charToRaw(contents), path)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: genieclust
 Type: Package
 Title: Fast and Robust Hierarchical Clustering with Noise Points Detection
-Version: 1.1.5-9001
-Date: 2024-06-17
+Version: 1.1.5-9002
+Date: 2024-07-22
 Authors@R: c(
     person("Marek", "Gagolewski",
         role = c("aut", "cre", "cph"),
@@ -49,4 +49,4 @@ Suggests:
 LinkingTo: Rcpp
 Encoding: UTF-8
 SystemRequirements: OpenMP
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

genieclust/__init__.py

@@ -21,7 +21,7 @@
 # ############################################################################ #
 
 # version string, e.g., "1.0.0.9001" or "1.1.1"
-__version__ = "1.1.5.9001"
+__version__ = "1.1.5.9002"
 
 
 from . import plots

genieclust/cluster_validity.pyx

@@ -42,8 +42,9 @@ For even more details, see the
 # ############################################################################ #
 
 
-cimport numpy as np
 import numpy as np
+cimport numpy as np
+np.import_array()
 from . cimport c_compare_partitions
 from . cimport c_cvi
 

genieclust/compare_partitions.pyx

@@ -36,8 +36,9 @@ For more details, see the
 # ############################################################################ #
 
 
-cimport numpy as np
 import numpy as np
+cimport numpy as np
+np.import_array()
 from . cimport c_compare_partitions
 
 

genieclust/inequality.pyx

@@ -28,9 +28,9 @@ Inequality measures
 # ############################################################################ #
 
 
-cimport cython
-cimport numpy as np
 import numpy as np
+cimport numpy as np
+np.import_array()
 from . cimport c_inequality
 
 ctypedef fused T:

genieclust/internal.pyx

@@ -36,11 +36,9 @@ Internal functions and classes
 # ############################################################################ #
 
 
-
-
-cimport cython
-cimport numpy as np
 import numpy as np
+cimport numpy as np
+np.import_array()
 import os
 
 cimport libc.math

genieclust/tools.pyx

@@ -33,13 +33,9 @@ Functions one might find useful, but not necessarily
 # ############################################################################ #
 
 
-
-
-
-
-cimport cython
-cimport numpy as np
 import numpy as np
+cimport numpy as np
+np.import_array()
 
 
 cimport libc.math