Merge pull request #19 from A2-ai/windows

Windows Support + Bug Fixes

Author: mduncans

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

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main, windows]
   pull_request:
     branches: main
 
@@ -20,6 +20,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: '4.5'}
+          - {os: windows-latest, r: '4.5'}
           - {os: ubuntu-latest,  r: '4.5'}
           - {os: ubuntu-latest,  r: '4.4'}
           - {os: ubuntu-latest,  r: '4.3'}
@@ -44,11 +46,27 @@ jobs:
         run: |
           perl -i -pe 's|^r_version = "4\.[0-9\.]+"$|r_version = "${{ matrix.config.r }}"|' rproject.toml
           cat rproject.toml
+        if: runner.os != 'Windows'
+
+      - name: replace-rversion (Windows)
+        run: |
+          $rVersion = "${{ matrix.config.r }}"
+          (Get-Content rproject.toml) -replace '^r_version = "4\.[0-9\.]+"$', "r_version = `"$rVersion`"" | Set-Content rproject.toml
+          Get-Content rproject.toml
+        shell: pwsh
+        if: runner.os == 'Windows'
 
       - name: rv-plan
         run: rv plan
+        if: runner.os != 'Windows'
+
+      - name: rv-plan (Windows)
+        run: rv.exe plan
+        shell: cmd
+        if: runner.os == 'Windows'
 
       - name: rv-sysdeps-install (Linux)
+        if: runner.os == 'Linux'
         run: |
           MISSING_DEPS=$(rv plan --json | jq -r '.installed[].sys_deps[]? | select(.status == "absent") | .name')
           if [ -n "$MISSING_DEPS" ]; then
@@ -59,12 +77,19 @@ jobs:
           else
             echo "All system dependencies are present"
           fi
+
       - name: rv-sync
         run: rv sync
+        if: runner.os != 'Windows'
 
       - run: git config --global user.email "[email protected]"
       - run: git config --global user.name "r-cmd-check"
 
+      - name: rv-sync (Windows)
+        run: rv.exe sync
+        shell: cmd
+        if: runner.os == 'Windows'
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: reportifyr
 Title: Reproducible Reporting Made Simple with R
-Version: 0.3.1
+Version: 0.3.2
 Authors@R: c(
     person("Jacob", "Dumbleton", , "[email protected]", role = c("aut", "cre")),
     person("Matthew", "Smith", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,3 +1,18 @@
+# reportifyr 0.3.2
+## Improvements
+
+* Added Windows support for `uv` installation, ensuring the setup script now works on both Unix-like (Unix/Mac) and Windows platforms.
+
+## Minor Improvements
+
+* Added a `uv` version check such that the installed version is compared against requested version before installing requested version.
+* Removed comments from JSON outputs.
+
+## Bug Fixes
+
+* Fixed changes to `.python_dependency_version.json` in `.venv` not being propagated to the `.python_dependency_version.json` in `report_dir_name`.
+* Fixed an issue where user supplied `python.version` via `options('python.version')` was creating a new line in both `.python_dependency_version.json` files.
+
 # reportifyr 0.3.1
 ## Minor Improvements
 

R/initialize_python.R

@@ -17,6 +17,11 @@ initialize_python <- function(continue = NULL) {
     continue <- continue()
   }
 
+  # Handle logical TRUE/FALSE as well as character Y/n
+  if (is.logical(continue)) {
+    continue <- if (continue) "Y" else "n"
+  }
+
   if (tolower(continue) != "y") {
     if (continue == "n") {
       log4r::info(.le$logger, "User declined installation. No changes made.")
@@ -34,7 +39,14 @@ initialize_python <- function(continue = NULL) {
 
   log4r::info(.le$logger, "Installation confirmed.")
 
-  cmd <- system.file("scripts/uv_setup.sh", package = "reportifyr")
+  # Detect platform and choose appropriate script
+  if (.Platform$OS.type == "windows") {
+    cmd <- system.file("scripts/uv_setup.ps1", package = "reportifyr")
+    log4r::info(.le$logger, "Windows platform detected, using PowerShell script")
+  } else {
+    cmd <- system.file("scripts/uv_setup.sh", package = "reportifyr")
+    log4r::info(.le$logger, "Unix-like platform detected, using bash script")
+  }
   log4r::info(
     .le$logger,
     paste0("Command for setting up virtual environment: ", cmd)
@@ -58,19 +70,37 @@ initialize_python <- function(continue = NULL) {
   is_new_env <- !dir.exists(venv_dir)
 
   # Run the setup script for both new and existing environments
-  result <- processx::run(
-    command = cmd,
-    args = args
-  )
+  if (.Platform$OS.type == "windows") {
+    # Run PowerShell script on Windows
+    result <- processx::run(
+      command = "powershell.exe",
+      args = c("-ExecutionPolicy", "Bypass", "-File", cmd, args)
+    )
+  } else {
+    # Run bash script on Unix-like systems
+    result <- processx::run(
+      command = cmd,
+      args = args
+    )
+  }
   # Get Python version AFTER environment exists
   pyvers <- get_py_version(getOption("venv_dir"))
   if (!is.null(pyvers)) {
-    log4r::info(.le$logger, paste0("Python version detected: ", pyvers))
-    # Add Python version to args for metadata
-    args <- c(args, pyvers)
+    # Find the index for "python.version" in args_name
+    idx <- match("python.version", args_name)
+    if (!is.na(idx) && length(args) >= idx) {
+      args[idx] <- pyvers  # replace existing value
+    } else {
+      args <- c(args, pyvers)  # append if not already present
+    }
   } else {
     log4r::warn(.le$logger, "Python version could not be detected")
-    args <- c(args, "")
+    idx <- match("python.version", args_name)
+    if (!is.na(idx) && length(args) >= idx) {
+      args[idx] <- ""
+    } else {
+      args <- c(args, "")
+    }
   }
 
   if (is_new_env) {
@@ -89,14 +119,18 @@ initialize_python <- function(continue = NULL) {
   }
 
   message(result$stdout)
+
+  # Refresh uv_path after installation in case it was just installed
+  uv_path <- get_uv_path(quiet = TRUE)
+
   # Log appropriate message based on whether we created or used existing environment
   if (is_new_env) {
     log4r::info(
       .le$logger,
       paste("Virtual environment created at: ", venv_dir)
     )
     log4r::debug(.le$logger, ".venv created")
-  } else if (file.exists(uv_path)) {
+  } else if (!is.null(uv_path) && file.exists(uv_path)) {
     log4r::info(
       .le$logger,
       paste("Virtual environment already present at: ", venv_dir)

R/initialize_report_project.R

@@ -62,6 +62,18 @@ initialize_report_project <- function(
     message(
       "reportifyr has already been initialized. Syncing with config file now."
     )
+
+    # Check if .venv directory still exists, recreate if missing
+    uv_path <- get_uv_path(quiet = TRUE)
+    args <- get_args(uv_path)
+    venv_dir <- file.path(args[[1]], ".venv")
+
+    if (!dir.exists(venv_dir)) {
+      log4r::warn(.le$logger, ".venv directory missing, reinitializing Python environment")
+      message("Python virtual environment missing. Reinitializing...")
+      metadata_path <- initialize_python()
+    }
+
     sync_report_project(project_dir, report_dir_name)
   }
 
@@ -262,17 +274,11 @@ create_init_file <- function(project_dir, report_dir, outputs_dir) {
   json_data <- jsonlite::toJSON(data, pretty = TRUE, auto_unbox = TRUE)
   log4r::debug(.le$logger, "Data converted to json string")
 
-  log4r::debug(.le$logger, "Adding warning message to json")
-  json_with_comment <- paste(
-    "// WARNING: This file is automatically generated on initialization. Do not edit by hand!",
-    json_data,
-    sep = "\n"
-  )
   path_name <- sub("/", "_", fs::path_rel(report_dir, project_dir))
   init_file <- file.path(project_dir, paste0(".", path_name, "_init.json"))
-  write(json_with_comment, file = init_file)
+  write(json_data, file = init_file)
 
   log4r::info(.le$logger, paste0("metadata written to file: ", init_file))
 
-  log4r::debug(.le$logger, "Exiting write_package_version_metadata function")
+  log4r::debug(.le$logger, "Exiting create_init_file function")
 }

R/sync_report_project.R

@@ -19,8 +19,10 @@ sync_report_project <- function(project_dir, report_dir_name = NULL) {
   # read in init.json files
   if (!is.null(report_dir_name)) {
     path_name <- sub("/", "_", report_dir_name)
+    report_dir <- file.path(project_dir, report_dir_name)
   } else {
     path_name <- "report"
+    report_dir <- file.path(project_dir, "report")
   }
   init_file <- file.path(project_dir, paste0(".", path_name, "_init.json"))
   log4r::debug(
@@ -45,11 +47,8 @@ sync_report_project <- function(project_dir, report_dir_name = NULL) {
     .le$logger,
     "Grabbing python deps info from options and filesystem"
   )
-  # Grab python dep info
   uv_path <- get_uv_path()
   args <- get_args(uv_path)
-  pyvers <- get_py_version(getOption("venv_dir"))
-  args <- c(args, pyvers)
   args_name <- c(
     "venv_dir",
     "python-docx.version",
@@ -58,6 +57,18 @@ sync_report_project <- function(project_dir, report_dir_name = NULL) {
     "uv.version",
     "python.version"
   )
+
+  pyvers <- get_py_version(getOption("venv_dir"))
+
+  # Ensure args has a slot for python.version
+  idx <- match("python.version", args_name)
+  if (length(args) < idx) {
+    args <- c(args, rep("", idx - length(args)))
+  }
+
+  # Replace (or set) python.version value
+  args[idx] <- pyvers
+
   py_version_data <- stats::setNames(as.list(args), args_name)
   formatted_deps <- paste0(
     names(py_version_data),
@@ -83,17 +94,23 @@ sync_report_project <- function(project_dir, report_dir_name = NULL) {
       )
     )
     log4r::debug(.le$logger, "Calling initialize_python now")
-    initialize_python(continue = "Y")
+    metadata_path <- initialize_python(continue = "Y")
     update_init_file <- TRUE
+
+    if (file.exists(metadata_path) && dir.exists(report_dir)) {
+      file.copy(
+        from = metadata_path,
+        to = file.path(report_dir, basename(metadata_path)),
+        overwrite = TRUE
+      )
+      log4r::debug(.le$logger, "Updating .python_dependency_versions.json in report_dir_name")
+    }
   }
   # Check config
   log4r::debug(.le$logger, "getting config path now")
-  if (!is.null(report_dir_name)) {
-    config_path <- file.path(project_dir, report_dir_name, "config.yaml")
-  } else {
-    config_path <- file.path(project_dir, "report", "config.yaml")
-  }
+  config_path <- file.path(report_dir, "config.yaml")
   log4r::debug(.le$logger, paste0("using config path: ", config_path))
+
   config <- yaml::read_yaml(
     config_path,
     handlers = list(logical = yaml::verbatim_logical)
@@ -149,12 +166,7 @@ sync_report_project <- function(project_dir, report_dir_name = NULL) {
     init$config <- config
 
     json_data <- jsonlite::toJSON(init, pretty = TRUE, auto_unbox = TRUE)
-    json_with_comment <- paste(
-      "// WARNING: This file is automatically generated on initialization. Do not edit by hand!",
-      json_data,
-      sep = "\n"
-    )
-    write(json_with_comment, file = init_file)
+    write(json_data, file = init_file)
   } else {
     message("Nothing to do")
   }