New reticulate

.github/workflows/R-CMD-check.yaml

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/setup-python@v4
         if: matrix.config.python != 'debug'
         with:
-          python-version: 3.9
+          python-version: 3.11
 
-      - name: setup forest
-        run: |
-          pip install git+https://github.com/onnela-lab/forest@develop
+      # - name: setup forest
+      #   run: |
+      #     pip install git+https://github.com/onnela-lab/forest@45fb41038bd46c25d9e6a4442aa74fa03b501317
 
       - uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: walking
 Title: Segments Accelerometry Data into Walking using the Python `forest` Module
-Version: 0.3.2
+Version: 0.4.0
 Authors@R: 
     person(given = "John",
            family = "Muschelli",
@@ -13,14 +13,14 @@ Description: Interfaces the `forest` Python
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     assertthat,
     dplyr,
     lubridate,
     magrittr,
     matrixStats,
-    reticulate,
+    reticulate (>= 1.4.1),
     signal,
     tidyr
 Suggests: 

NAMESPACE

@@ -5,11 +5,6 @@ export(estimate_steps_forest)
 export(estimate_steps_sdt)
 export(estimate_steps_verisense)
 export(find_walking)
-export(forest_requirement)
-export(forest_version)
-export(forest_version_pip)
-export(have_forest)
-export(install_forest)
 export(preprocess_bout)
 export(preprocess_bout_r)
 export(resample_accel_data)

NEWS.md

@@ -0,0 +1,5 @@
+# walking 0.4.0
+
+* New `reticulate` initialization.
+* Removing `install_forest` and the like.
+* Initial CRAN submission.

R/api.R

@@ -10,7 +10,7 @@
 #' @rdname estimate_steps
 #' @examples
 #' csv_file = system.file("test_data_bout.csv", package = "walking")
-#' if (requireNamespace("readr", quietly = TRUE) && walking::have_forest()) {
+#' if (requireNamespace("readr", quietly = TRUE)) {
 #'   x = readr::read_csv(csv_file)
 #'   colnames(x)[colnames(x) == "UTC time"] = "time"
 #'   out = estimate_steps_forest(x, sample_rate_analysis = 10L)

R/find_walking.R

@@ -27,7 +27,7 @@
 #'
 #' @examples
 #' csv_file = system.file("test_data_bout.csv", package = "walking")
-#' if (requireNamespace("readr", quietly = TRUE) && walking::have_forest()) {
+#' if (requireNamespace("readr", quietly = TRUE)) {
 #'   x = readr::read_csv(csv_file)
 #'   colnames(x)[colnames(x) == "UTC time"] = "time"
 #'   res = find_walking(data = x)

R/sdt.R

@@ -34,7 +34,8 @@ sdt_count_steps <- function(
   rm(list = c("vm", "X", "Y", "Z", "demean_vm", "filt_vm", "peak",
               "HEADER_TIMESTAMP"))
   location = match.arg(location, choices = c("wrist", "waist"))
-  threshold = ifelse(location == "wrist", 0.0267, 0.0359)
+  # fixed thresholds for wrist and waist May23, 2025
+  threshold = ifelse(location == "wrist", 0.0359, 0.0267)
 
   data = standardize_data(data, subset = TRUE)
   assertthat::assert_that(

R/verisense_count_steps.R

@@ -183,7 +183,7 @@ create_peak_info = function(segments) {
 #'
 #' @examples
 #' csv_file = system.file("test_data_bout.csv", package = "walking")
-#' if (requireNamespace("readr", quietly = TRUE) && walking::have_forest()) {
+#' if (requireNamespace("readr", quietly = TRUE)) {
 #'   x = readr::read_csv(csv_file)
 #'   colnames(x)[colnames(x) == "UTC time"] = "time"
 #'   out = verisense_count_steps(x, sample_rate = 10L)

R/zzz.R

@@ -0,0 +1,9 @@
+.onLoad <- function(...) {
+  # ref = "v0.2"
+  ref = "45fb41038bd46c25d9e6a4442aa74fa03b501317"
+  url = "https://github.com/onnela-lab/forest"
+  url = paste0("git+", url)
+  ref = sub("^@", "", ref)
+  url = paste0(url, "@", ref)
+  reticulate::py_require(url, python_version = "3.11")
+}

tests/testthat.R

@@ -9,4 +9,9 @@
 library(testthat)
 library(walking)
 
+# if (walking::have_walking_condaenv()) {
+#   walking::unset_reticulate_python()
+#   walking::use_walking_condaenv()
+# }
+
 test_check("walking")

walking.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 61f5e877-0e4c-49c6-8d46-f348ca15f168
 
 RestoreWorkspace: No
 SaveWorkspace: No