scientiflow-cli 0.4.3__tar.gz → 0.4.5__tar.gz

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scientiflow-cli
-Version: 0.4.3
+Version: 0.4.5
 Summary: CLI tool for scientiflow. This application runs on the client side, decodes pipelines, and executes them in the configured order!
 License: Proprietary
 Author: ScientiFlow

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "scientiflow-cli"
-version = "0.4.3"
+version = "0.4.5"
 description = "CLI tool for scientiflow. This application runs on the client side, decodes pipelines, and executes them in the configured order!"
 authors = ["ScientiFlow <scientiflow@gmail.com>"]
 license = "Proprietary"

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/scientiflow_cli/config.py

@@ -6,4 +6,4 @@ class Config:
         APP_BASE_URL = os.getenv("APP_BASE_URL", "https://www.backend.scientiflow.com/api")
     elif mode=="dev":
         APP_BASE_URL = "http://127.0.0.1:8000/api"
-        # APP_BASE_URL = os.getenv("APP_BASE_URL", "https://www.scientiflow-backend-dev.scientiflow.com/api")        
+        # APP_BASE_URL = os.getenv("APP_BASE_URL", "https://www.scientiflow-backend-dev.scientiflow.com/api")

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/scientiflow_cli/main.py

@@ -1,5 +1,9 @@
 import argparse
 import sys
+import pathlib
+import re
+from importlib import metadata as importlib_metadata
+from importlib.metadata import PackageNotFoundError
 from scientiflow_cli.cli.login import login_user
 from scientiflow_cli.cli.logout import logout_user
 from scientiflow_cli.pipeline.get_jobs import get_jobs
@@ -37,6 +41,30 @@ def display_help(parser):
 
     printer.print_table("Scientiflow Agent CLI", columns, rows)
 
+
+def get_package_version() -> str:
+    """Return the package version.
+
+    Try to get the installed package version via importlib.metadata. If the
+    package isn't installed (PackageNotFoundError), fall back to reading the
+    `pyproject.toml` file in the project root.
+    """
+    try:
+        return importlib_metadata.version("scientiflow-cli")
+    except PackageNotFoundError:
+        try:
+            # Project root is two levels up from this file: .../scientiflow_cli/main.py
+            project_root = pathlib.Path(__file__).resolve().parents[1]
+            pyproject = project_root / "pyproject.toml"
+            if pyproject.exists():
+                text = pyproject.read_text(encoding="utf-8")
+                m = re.search(r"^version\s*=\s*[\"']([^\"']+)[\"']", text, re.MULTILINE)
+                if m:
+                    return m.group(1)
+        except Exception:
+            pass
+    return "unknown"
+
 def main():
     parser = RichArgumentParser(description="Scientiflow Agent CLI", add_help=False)
     parser.formatter_class = lambda prog: argparse.HelpFormatter(prog, max_help_position=50)
@@ -44,6 +72,7 @@ def main():
     parser.add_argument('-h', '--help', action='store_true', help="Show this help message and exit")
     parser.add_argument('--login', action='store_true', help="Login using your scientiflow credentials")
     parser.add_argument('--logout', action='store_true', help="Logout from scientiflow")
+    parser.add_argument('-v', '--version', action='store_true', help="Show package version and exit")
     parser.add_argument('--list-jobs', action='store_true', help="Get all the pending jobs to execute")
     parser.add_argument('--set-base-directory', action='store_true', help="Set the base directory to the current working directory \nOptionally, use --hostname to specify the hostname for this server")
     parser.add_argument('-p', '--parallel', action='store_true', help=argparse.SUPPRESS)  # Hide -p or --parallel from --help
@@ -74,6 +103,11 @@ def main():
         display_help(parser)
         sys.exit()
 
+    if args.version:
+        version = get_package_version()
+        printer.print_message(f"Version: {version}", style="bold green")
+        sys.exit()
+
     try:
         if args.login:
             login_user(token=args.token)

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/scientiflow_cli/pipeline/decode_and_execute.py

@@ -1,7 +1,7 @@
 import subprocess
 import tempfile
 import os
-import re, shlex
+import re
 import multiprocessing
 import threading
 from concurrent.futures import ProcessPoolExecutor, as_completed
@@ -55,6 +55,10 @@ class PipelineExecutor:
         self.background_jobs_count = 0  # Track number of active background jobs
         self.background_jobs_completed = 0  # Track completed background jobs
         self.background_jobs_lock = threading.Lock()  # Thread-safe counter updates
+        
+        # For resuming: flag to track if we've reached the resume point
+        self.resume_mode = (job_status == "running" and current_node_from_config is not None)
+        self.reached_resume_point = False
 
         # Set up job-specific log file
         self.log_file_path = os.path.join(self.base_dir, self.project_title, self.job_dir_name, "logs", "output.log")
@@ -109,27 +113,9 @@ class PipelineExecutor:
         except Exception as e:
             print(f"[ERROR] Failed to update terminal output: {e}")
 
-
-    # def replace_variables(self, command: str) -> str:
-    #     """Replace placeholders like ${VAR} with environment values."""
-    #     print(self.environment_variables)
-    #     return re.sub(r'\$\{(\w+)\}', lambda m: self.environment_variables.get(m.group(1), m.group(0)), command)
-
     def replace_variables(self, command: str) -> str:
-        """Replace placeholders like ${VAR} with environment values.
-        - If value is a list: safely join into space-separated arguments (quoted).
-        - Otherwise: use the old behavior (direct substitution).
-        """
-        def replacer(match):
-            key = match.group(1)
-            value = self.environment_variables.get(key, match.group(0))
-            # ✅ Special handling for lists
-            if isinstance(value, list):
-                return " ".join(shlex.quote(str(v)) for v in value)
-            # ✅ Default: keep original behavior for strings, numbers, None
-            return self.environment_variables.get(key, match.group(0))
-        return re.sub(r'\$\{(\w+)\}', replacer, command)
-        
+        """Replace placeholders like ${VAR} with environment values."""
+        return re.sub(r'\$\{(\w+)\}', lambda m: self.environment_variables.get(m.group(1), m.group(0)), command)
 
     def execute_command(self, command: str):
         """Run the command in the terminal, display output in real-time, and log the captured output."""
@@ -214,7 +200,35 @@ class PipelineExecutor:
 
         self.current_node = node
         current_node = self.nodes_map[node]
-
+        
+        # Check if we've reached the resume point
+        if self.resume_mode and not self.reached_resume_point:
+            if node == self.current_node_from_config:
+                self.reached_resume_point = True
+                node_label = current_node['data'].get('label', node)
+                printer.print_message(f"[INFO] Reached resume point: {node_label} - continuing execution", style="bold green")
+            else:
+                # Skip execution for this node, just traverse
+                if current_node['type'] == "splitterParent":
+                    collector = None
+                    for child in self.adj_list[node]:
+                        if self.nodes_map[child]['data']['active']:
+                            collector = self.dfs(child)
+                    if collector and self.adj_list[collector]:
+                        return self.dfs(self.adj_list[collector][0])
+                    return
+                elif current_node['type'] == "splitter-child":
+                    if current_node['data']['active'] and self.adj_list[node]:
+                        return self.dfs(self.adj_list[node][0])
+                    return
+                elif current_node['type'] == "terminal":
+                    if self.adj_list[node]:
+                        return self.dfs(self.adj_list[node][0])
+                    return
+                elif current_node['type'] == "collector":
+                    return node if self.adj_list[node] else None
+
+        # Normal execution (either not in resume mode or already reached resume point)
         if current_node['type'] == "splitterParent":
             collector = None
             for child in self.adj_list[node]:
@@ -297,13 +311,14 @@ class PipelineExecutor:
         current_status = self.job_status
         
         if current_status == "running":
-            # Job is already running, resume from current node
+            # Job is already running, resume from start but skip until current node
             current_node_id = self.current_node_from_config
             if current_node_id and current_node_id in self.nodes_map:
                 # Get the label from the current node
                 current_node_label = self.nodes_map[current_node_id]['data'].get('label', current_node_id)
-                printer.print_message(f"[INFO] Resuming execution from current node: {current_node_label}", style="bold blue")
-                starting_node = current_node_id
+                printer.print_message(f"[INFO] Resuming job - will skip to node: {current_node_label}", style="bold blue")
+                # Start from the beginning (start_node or root)
+                starting_node = self.start_node or next(iter(self.root_nodes), None)
             else:
                 printer.print_message("[WARNING] Current node not found, starting from beginning", style="bold yellow")
                 starting_node = self.start_node or next(iter(self.root_nodes), None)

{scientiflow_cli-0.4.3 → scientiflow_cli-0.4.5}/scientiflow_cli/utils/singularity.py

@@ -39,18 +39,23 @@ def install_singularity():
 
     printer.print_message("[bold yellow][+] Installing Singularity[/bold yellow]")
     os_release_path = Path("/etc/os-release")
-    ubuntu_codename = None
+    os_codename = None
+
     if os_release_path.exists():
         for line in os_release_path.read_text().splitlines():
-            if line.startswith("UBUNTU_CODENAME="):
-                ubuntu_codename = line.split("=")[1]
+            if line.startswith("VERSION_CODENAME="):
+                os_codename = line.split("=")[1]
                 break
 
-    if not ubuntu_codename:
-        raise ValueError("[bold red]Could not determine Ubuntu codename from /etc/os-release.[/bold red]")
+    if not os_codename:
+        raise ValueError("[bold red]Could not determine Ubuntu / Debian codename from /etc/os-release.[/bold red]")
+    
+    if os_codename == "bookworm":
+        printer.print_message("[bold yellow][+] WARNING: Debian distros are not officially supported. Compatibility issues may arise[/bold yellow]")
+        os_codename = "jammy"
 
-    singularity_url = f"https://github.com/sylabs/singularity/releases/download/v{SINGULARITY_VERSION}/singularity-ce_{SINGULARITY_VERSION}-{ubuntu_codename}_amd64.deb"
-    temp_file = Path(f"/tmp/singularity-ce_{SINGULARITY_VERSION}-{ubuntu_codename}_amd64.deb")
+    singularity_url = f"https://github.com/sylabs/singularity/releases/download/v{SINGULARITY_VERSION}/singularity-ce_{SINGULARITY_VERSION}-{os_codename}_amd64.deb"
+    temp_file = Path(f"/tmp/singularity-ce_{SINGULARITY_VERSION}-{os_codename}_amd64.deb")
 
     printer.print_message("[bold cyan]Downloading Singularity package...[/bold cyan]")
     progress, task = printer.create_progress_bar("[cyan]Downloading...", total=100)