Merge branch 'dev' into beta

RedLeader962 · RedLeader962 · commit ea95b8374a11 · 2025-07-03T08:07:13.000-04:00
diff --git a/README.md b/README.md
@@ -226,8 +226,8 @@ your-project-repository/
   └── README.md                       <- Created if it did not already exist
 ```
 Note: 
-- Any directory or file that already exist will be updated, not overriden.
-- Content of the artifact direcotry is persistent. It will remain available even if the container is stoped or removed. 
+- Existing file and directories with the same name will be safeguarded with the suffix `.old`, not overriden.
+- Content of the artifact directory is persistent. It will remain available even if the container is stopped or removed. 
 
 ### Create, run and stop DN container
 
diff --git a/documentation/command/init.md b/documentation/command/init.md
@@ -69,7 +69,7 @@ If you run `dna init` on an already initialized project, you'll be prompted:
 ```bash
 $ dna init
 [WARNING] This project is already DNA initialized since .dockerized_norlab directory already exists.
-If you continue, missing files will be created and existing ones will be updated.
+If you continue, existing file and directories with the same name will be safeguarded with the suffix '.old', not overriden."
 Do you want to continue [y/N]
 ```
 
diff --git a/documentation/install.md b/documentation/install.md
@@ -43,11 +43,11 @@ DNA can be installed using different methods depending on your system configurat
 
 ### Platform Support
 
-| Platform       | Architecture | Status |
-|----------------|------------|---------|
-| NVIDIA Jetson (L4T) | arm64 | ✅ Fully supported |
-| macOS          | arm64 (Apple Silicon) | ✅ Fully supported |
-| Linux          | x86_64 | ✅ Fully supported |
+| Platform       | Architecture | Status                                         |
+|----------------|------------|------------------------------------------------|
+| NVIDIA Jetson (L4T) | arm64 | ✅ Fully supported                              |
+| macOS          | arm64 (Apple Silicon) | ✅ Fully supported                              |
+| Linux          | x86_64 | ✅ Fully supported                              |
 | Linux          | arm64 | ⚠️ Not supported (for now, will be implemented if requested) |
 
 
diff --git a/documentation/offline_installation.md b/documentation/offline_installation.md
@@ -23,6 +23,7 @@ Before attempting offline installation, ensure these tools are available:
 | Docker Buildx  | Multi-architecture build | Included with Docker Desktop or separate install |
 | Git            | Version control | System package manager |
 | Tree           | Directory visualization | System package manager |
+| rsync          | Fast incremental file transfer | System package manager |
 
 ### Platform-Specific Prerequisites
 
diff --git a/src/lib/commands/init.bash b/src/lib/commands/init.bash
@@ -56,13 +56,68 @@ function dna::get_super_project_acronym() {
     return 0
 }
 
+function dna::portable_copy() {
+    # Copy function using rsync with backup functionality
+    # Arguments: source destination
+    local source="$1"
+    local destination="$2"
+    local super_project_root="${3:-$(pwd)}"
+
+    # Use rsync with backup functionality (no --update flag to preserve existing files)
+    if [[ -d "$source" ]]; then
+        # For directories, ensure trailing slash for proper rsync behavior
+        rsync --backup --suffix='.old' --recursive "${source%/}/" "$destination" || return 1
+    else
+        # For files
+        rsync --backup --suffix='.old' "$source" "$destination" || return 1
+    fi
+
+    # Validate file ownership and permissions match the super project
+    dna::validate_file_ownership_and_permissions "$destination" "$super_project_root" || return 1
+
+    return 0
+}
+
+function dna::validate_file_ownership_and_permissions() {
+    # Validate that copied files/directories have ownership and permissions matching the super project
+    # Arguments: target_path super_project_root
+    local target_path="$1"
+    local super_project_root="$2"
+
+    # Get super project ownership and permissions
+    local super_project_owner
+    local super_project_group
+    #local super_project_perms
+
+    super_project_owner=$(stat -c '%U' "$super_project_root" 2>/dev/null || stat -f '%Su' "$super_project_root" 2>/dev/null)
+    super_project_group=$(stat -c '%G' "$super_project_root" 2>/dev/null || stat -f '%Sg' "$super_project_root" 2>/dev/null)
+    #super_project_perms=$(stat -c '%a' "$super_project_root" 2>/dev/null || stat -f '%A' "$super_project_root" 2>/dev/null)
+
+    # Recursively fix ownership and permissions for the target path
+    if [[ -d "$target_path" ]]; then
+        # For directories, apply to all contents
+        find "$target_path" -type f -exec chown "${super_project_owner}:${super_project_group}" {} \; 2>/dev/null || true
+        find "$target_path" -type d -exec chown "${super_project_owner}:${super_project_group}" {} \; 2>/dev/null || true
+        find "$target_path" -type f -exec chmod 644 {} \; 2>/dev/null || true
+        find "$target_path" -type d -exec chmod 755 {} \; 2>/dev/null || true
+    else
+        # For files
+        chown "${super_project_owner}:${super_project_group}" "$target_path" 2>/dev/null || true
+        chmod 644 "$target_path" 2>/dev/null || true
+    fi
+
+    return 0
+}
+
 
 function dna::init_command() {
     local super_project_root
     super_project_root=$(pwd)
     local line_format="${MSG_LINE_CHAR_BUILDER_LVL2}"
     local line_style="${MSG_LINE_STYLE_LVL2}"
 
+    # rsync is now a required dependency and should be available
+
     # ....cli......................................................................................
     while [[ $# -gt 0 ]]; do
         case "$1" in
@@ -87,7 +142,7 @@ function dna::init_command() {
 
     # Check if .dockerized_norlab already exists
     if [[ -d ".dockerized_norlab" ]]; then
-        n2st::print_msg_warning "This project is already DNA initialized since ${MSG_DIMMED_FORMAT}.dockerized_norlab${MSG_END_FORMAT} directory already exists.\nIf you continue, missing file will be created and existing one will be updated."
+        n2st::print_msg_warning "This project is already DNA initialized since ${MSG_DIMMED_FORMAT}.dockerized_norlab${MSG_END_FORMAT} directory already exists.\nIf you continue, existing file and directories with the same name will be safeguarded with the suffix '.old', not overriden."
         read -r -n 1 -p "Do you want to continue [y/N]" option_update
         if [[ "${option_update}" == "y" || "${option_update}" == "Y" ]]; then
           :
@@ -113,12 +168,12 @@ function dna::init_command() {
     n2st::print_msg "Initializing DNA project: ${super_project_name} in ${super_project_root}"
 
     # Copy template files
-    sudo cp --update -r "${DNA_LIB_PATH}/template/.dockerized_norlab/" . || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/.dockerized_norlab/" . "$super_project_root" || return 1
 
     cd "${super_project_root}/.dockerized_norlab/" || return 1
 
     # Rename the super project DNA meta .env file
-    sudo mv --force "${super_project_root}/.dockerized_norlab/.env.PLACEHOLDER_SUPER_PROJECT_NAME" "${super_project_root}/.dockerized_norlab/.env.${super_project_name}" || return 1
+    mv -f "${super_project_root}/.dockerized_norlab/.env.PLACEHOLDER_SUPER_PROJECT_NAME" "${super_project_root}/.dockerized_norlab/.env.${super_project_name}" || return 1
 
     # Replace placeholders in the .env.dna file
     cd "${super_project_root}/.dockerized_norlab/configuration/" || return 1
@@ -149,28 +204,28 @@ function dna::init_command() {
     cd "${super_project_root}" || return 1
 
     {
-      sudo mkdir -p artifact/optuna_storage &&
-      sudo mkdir -p external_data &&
-      sudo mkdir -p src/launcher/configs &&
-      sudo mkdir -p src/dna_example &&
-      sudo mkdir -p tests/test_dna_example
+      mkdir -p artifact/optuna_storage &&
+      mkdir -p external_data &&
+      mkdir -p src/launcher/configs &&
+      mkdir -p src/dna_example &&
+      mkdir -p tests/test_dna_example
     } || return 1
 
-    sudo cp --update -r "${DNA_LIB_PATH}/template/artifact/README.md" artifact/ || return 1
-    sudo cp --update -r "${DNA_LIB_PATH}/template/artifact/optuna_storage/README.md" artifact/optuna_storage/ || return 1
-    sudo cp --update -r "${DNA_LIB_PATH}/template/external_data/README.md" external_data/ || return 1
-    sudo cp --update -r "${DNA_LIB_PATH}/template/src/launcher" src/ || return 1
-    sudo cp --update -r "${DNA_LIB_PATH}/template/src/dna_example" src/ || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/artifact/README.md" artifact/ "$super_project_root" || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/artifact/optuna_storage/README.md" artifact/optuna_storage/ "$super_project_root" || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/external_data/README.md" external_data/ "$super_project_root" || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/src/launcher" src/ "$super_project_root" || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/src/dna_example" src/ "$super_project_root" || return 1
     if [[ ! -f "src/README.md" ]]; then
-      sudo cp --update -r "${DNA_LIB_PATH}/template/src/README.md" src/ || return 1
+      dna::portable_copy "${DNA_LIB_PATH}/template/src/README.md" src/ "$super_project_root" || return 1
     fi
-    sudo cp --update -r "${DNA_LIB_PATH}/template/tests" . || return 1
+    dna::portable_copy "${DNA_LIB_PATH}/template/tests" . "$super_project_root" || return 1
 
     # ....Create root README.md files if it does't exist...........................................
     cd "${super_project_root}" || return 1
 
     if [[ ! -f "README.md" ]]; then
-        sudo touch "README.md"  || return 1
+        touch "README.md"  || return 1
         cat > "README.md" << EOF
 # ${super_project_name}
 
@@ -185,7 +240,7 @@ EOF
 
     if [[ ! -f ".gitignore" ]]; then
         # Case: file does not exist => copy template
-        sudo cp "${DNA_LIB_PATH}/template/.gitignore" .gitignore || return 1
+        dna::portable_copy "${DNA_LIB_PATH}/template/.gitignore" .gitignore "$super_project_root" || return 1
     else
         # Case: file exist => append required .gitignore entries
         cat >> ".gitignore" << EOF
@@ -207,7 +262,7 @@ EOF
 
     if [[ ! -f ".dockerignore" ]]; then
         # Case: file does not exist => copy template
-        sudo cp "${DNA_LIB_PATH}/template/.dockerignore" .dockerignore  || return 1
+        dna::portable_copy "${DNA_LIB_PATH}/template/.dockerignore" .dockerignore "$super_project_root" || return 1
     else
         # Case: file exist => append required .gitignore entries
       cat >> ".dockerignore" << EOF
diff --git a/src/lib/core/utils/setup_host_dna_requirements.bash b/src/lib/core/utils/setup_host_dna_requirements.bash
@@ -139,20 +139,27 @@ function dna::install_dna_software_requirements() {
   if [[ $(uname) == "Darwin" ]]; then
     if command -v brew >/dev/null 2>&1; then
         n2st::print_msg "Using Homebrew for package management"
-        brew update && brew install git || return 1
-        brew update && brew install tree || return 1
+        brew update \
+          && brew install git \
+          && brew install tree \
+          && brew install rsync \
+          || return 1
     elif command -v port >/dev/null 2>&1; then
         n2st::print_msg "Using MacPorts for package management"
-        sudo port install git || exit 1
-        sudo port install tree || exit 1
+        sudo port install git \
+          && sudo port install tree \
+          && sudo port install rsync \
+          || exit 1
     else
         n2st::print_msg_error "Neither Homebrew nor MacPorts is installed" && return 1
     fi
   else
     sudo apt-get update &&
       sudo apt-get install --assume-yes \
         git \
-        tree
+        tree \
+        rsync \
+      || return 1
   fi
 
 
diff --git a/src/lib/template/.dockerized_norlab/configuration/Dockerfile b/src/lib/template/.dockerized_norlab/configuration/Dockerfile
@@ -77,7 +77,7 @@ EOF
 # USER NOTES: ADD YOUR CODE BEFORE THIS LINE
 
 # ====DN-project final=============================================================================
-FROM --platform=${TARGETPLATFORM} user-project-custom-steps AS final
+FROM user-project-custom-steps AS final
 # ⚠️ USER NOTES: Dont change code in this stage unless you know what your doing.
 ARG TARGETPLATFORM
 ARG BUILDPLATFORM
diff --git a/src/lib/template/.dockerized_norlab/configuration/project_requirements/shell.requirements.bash b/src/lib/template/.dockerized_norlab/configuration/project_requirements/shell.requirements.bash
@@ -2,7 +2,6 @@
 
 # ====Example======================================================================================
 apt-get update \
-  && apt-get upgrade -y \
   && apt-get install -y \
     vim \
   && apt-get autoremove -y \
diff --git a/tests/tests_bats/test_init.bats b/tests/tests_bats/test_init.bats
