labtasker 0.2.5__tar.gz → 0.2.7__tar.gz

{labtasker-0.2.5 → labtasker-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: labtasker
-Version: 0.2.5
+Version: 0.2.7
 Summary: A task queue system for lab experiments
 Author-email: Your Name <your.email@example.com>
 License: Apache License 2.0
@@ -11,31 +11,27 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: <4.0,>=3.8.1
+Requires-Python: <4.0,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: python-dotenv<2.0.0,>=1.0.1
 Requires-Dist: pymongo<5.0.0,>=4.0.0
-Requires-Dist: fastapi<0.116.0,>=0.115.0
-Requires-Dist: uvicorn[standard]<0.35.0,>=0.15.0
-Requires-Dist: click<9.0.0,>=8.1.0
+Requires-Dist: fastapi<0.117.0,>=0.115.0
+Requires-Dist: uvicorn[standard]<0.36.0,>=0.15.0
+Requires-Dist: click<9.0.0,>=8.2.0
 Requires-Dist: passlib<2.0.0,>=1.7.0
-Requires-Dist: antlr4-python3-runtime<5.0.0,>=4.13.0
 Requires-Dist: pydantic-settings<3.0.0,>=2.8.0
 Requires-Dist: httpx[socks]<0.29.0,>=0.28.0
-Requires-Dist: typer<0.16.0,>=0.15.0
+Requires-Dist: typer<0.17.0,>=0.16.0
 Requires-Dist: loguru<0.8.0,>=0.7.0
 Requires-Dist: ruamel-yaml<0.19.0,>=0.18.10
 Requires-Dist: pyyaml<7.0.0,>=6.0.0
 Requires-Dist: tomlkit<0.14.0,>=0.13.2
 Requires-Dist: importlib-metadata<9.0.0,>=8.5.0
-Requires-Dist: packaging<25.0,>=24.2
+Requires-Dist: packaging<26.0,>=24.2
 Requires-Dist: sse-starlette<3.0.0,>=2.1.3
 Requires-Dist: httpx-sse<0.5.0,>=0.4.0
 Requires-Dist: stamina<26.0.0,>=25.1.0
@@ -43,6 +39,7 @@ Requires-Dist: noneprompt<0.2.0,>=0.1.9
 Requires-Dist: mongomock<4.4.0,>=4.3.0
 Requires-Dist: jsonpickle<5.0.0,>=4.0.2
 Requires-Dist: mslex<2.0.0,>=1.3.0
+Requires-Dist: pexpect<5.0.0,>=4.9.0
 Provides-Extra: dev
 Requires-Dist: pytest<9.0.0,>=8.0.0; extra == "dev"
 Requires-Dist: pytest-cov<7.0.0,>=5.0.0; extra == "dev"
@@ -53,9 +50,9 @@ Requires-Dist: flake8<8.0.0,>=7.0.0; extra == "dev"
 Requires-Dist: pre-commit<5.0.0,>=3.0.0; extra == "dev"
 Requires-Dist: freezegun<2.0.0,>=1.5.0; extra == "dev"
 Requires-Dist: pytest-docker<4.0.0,>=3.0.0; extra == "dev"
-Requires-Dist: pytest-asyncio<0.27.0,>=0.24.0; extra == "dev"
+Requires-Dist: pytest-asyncio<1.1.0,>=0.24.0; extra == "dev"
 Requires-Dist: asgi-lifespan<3.0.0,>=2.1.0; extra == "dev"
-Requires-Dist: tox<4.26.0,>=4.24.0; extra == "dev"
+Requires-Dist: tox<4.28.0,>=4.24.0; extra == "dev"
 Requires-Dist: pytest-dependency<0.7.0,>=0.6.0; extra == "dev"
 Requires-Dist: pytest-sugar<2.0.0,>=1.0.0; extra == "dev"
 Provides-Extra: doc

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.2.5"
+__version__ = "0.2.7"
 
 from labtasker.client.client_api import *
 from labtasker.client.core.config import get_client_config

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/cli/config.py

@@ -48,9 +48,10 @@ def config(
         # 1.1 Copy existing configuration to the temporary file (if it exists)
         config_path = get_labtasker_client_config_path()
         if config_path.exists():
-            with open(config_path, "rb") as existing_config, open(
-                temp_file_path, "wb"
-            ) as temp_file:
+            with (
+                open(config_path, "rb") as existing_config,
+                open(temp_file_path, "wb") as temp_file,
+            ):
                 temp_file.write(existing_config.read())
 
         # 1.2 Open the temporary file in the editor and validate changes

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/cli/loop.py

@@ -1,11 +1,14 @@
 """Implements `labtasker loop xxx`"""
 
 import json
+import os
 import subprocess
 import sys
 from collections import defaultdict
+from pathlib import Path
 from typing import List, Optional
 
+import pexpect
 import typer
 from typing_extensions import Annotated
 
@@ -24,7 +27,6 @@ from labtasker.client.core.logging import (
     logger,
     set_verbose,
     stderr_console,
-    stdout_console,
     verbose_print,
 )
 
@@ -42,6 +44,76 @@ class InfiniteDefaultDict(defaultdict):
         return super().get(key, default)
 
 
+def _check_pty_available(opt: bool) -> bool:
+    if opt and os.name == "nt":
+        stderr_console.print(
+            "[bold orange1]Warning:[/bold orange1] PTY is not available on Windows. "
+            "Disabling PTY support."
+        )
+        return False
+    return opt
+
+
+def _stream_child_output(child) -> None:
+    """Stream the output of a pexpect child in real-time, supporting progress bars."""
+    try:
+        while True:
+            try:
+                output = child.read_nonblocking(size=1024, timeout=0.1)
+                if output:
+                    # keep \r
+                    sys.stdout.write(output)
+                    sys.stdout.flush()
+            except pexpect.TIMEOUT:
+                continue
+            except pexpect.EOF:
+                break
+    finally:
+        child.close()
+
+
+def _run_with_pty(cmd, shell_exec=None, use_shell=False):
+    """Run a command with PTY support for interactive programs."""
+    if use_shell:
+        shell_exec = shell_exec or "/bin/sh"
+        child = pexpect.spawn(shell_exec, ["-c", cmd], encoding="utf-8")
+    else:
+        child = pexpect.spawn(cmd[0], cmd[1:], encoding="utf-8")
+
+    _stream_child_output(child)
+
+    return child.exitstatus
+
+
+def _run_with_subprocess(cmd, shell_exec=None, use_shell=False):
+    """Run a command using standard subprocess approach."""
+    with subprocess.Popen(
+        args=cmd,
+        stdin=subprocess.PIPE,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        text=True,
+        executable=shell_exec,
+        shell=use_shell,
+    ) as process:
+        while True:
+            output = process.stdout.readline()
+            error = process.stderr.readline()
+
+            if output:
+                sys.stdout.write(output.strip())
+                sys.stdout.flush()
+            if error:
+                sys.stderr.write(error.strip())
+                sys.stderr.flush()
+
+            # Break when process completes and streams are empty
+            if process.poll() is not None and not output and not error:
+                break
+
+        return process.returncode
+
+
 @app.command()
 @cli_utils_decorator
 def loop(
@@ -55,10 +127,16 @@ def loop(
     option_cmd: str = typer.Option(
         None,
         "--command",
-        "--command",
+        "--cmd",
         "-c",
         help="Specify the command to run with shell=True. Supports the same argument interpolation the same way as the positional argument. Except you need to quote the entire command.",
     ),
+    script_path: Optional[Path] = typer.Option(
+        None,
+        exists=True,
+        readable=True,
+        help="Path to a script file that contains the command to execute. The script will run with '%(...)' placeholders replaced by the retrieved task arguments.",
+    ),
     executable: Optional[str] = typer.Option(
         None,
         "--executable",
@@ -83,6 +161,11 @@ def loop(
         None,
         help="Time in seconds before a task is considered stalled if no heartbeat is received.",
     ),
+    use_pty: bool = typer.Option(
+        os.name == "posix",  # enabled by default on POSIX systems
+        callback=_check_pty_available,
+        help="Use pseudo terminal on POSIX systems for better interactive program support.",
+    ),
     verbose: bool = typer.Option(  # noqa
         False,
         "--verbose",
@@ -101,19 +184,30 @@ def loop(
     This will fetch tasks with 'input_file' and 'output_dir' arguments and run the command
     with those values substituted. Tasks are processed until the queue is empty.
     """
-    if cmd and option_cmd:
+    # Ensure only one of [CMD], [--command], or [--script-path] is specified
+    cmd_sources = [cmd, option_cmd, script_path]
+    cmd_sources = list(filter(None, cmd_sources))  # Remove None values dynamically
+    if len(cmd_sources) > 1:
         raise typer.BadParameter(
-            "Only one of [CMD] and [--command] can be specified. Please use one of them."
+            "Only one of [CMD], [--command], or [--script-path] can be specified. Choose one."
         )
 
-    cmd = cmd if cmd else option_cmd
-    if not cmd and not sys.stdin.isatty():
-        # try reading multi-line cmd from stdin if shell mode
-        cmd = sys.stdin.read()
+    # 1. Assign from cmd or option_cmd
+    input_cmd = cmd or option_cmd
+
+    # 2. Assign from script_path if provided
+    if script_path and input_cmd is None:
+        with open(script_path, "r") as f:
+            input_cmd = f.read().strip()
 
-    if not cmd:
+    # 3. Try reading from stdin if shell mode is enabled
+    if not input_cmd and not sys.stdin.isatty():
+        input_cmd = sys.stdin.read().strip()
+
+    # Final validation: ensure a command is present
+    if not input_cmd:
         raise typer.BadParameter(
-            "Command cannot be empty. Either specify via positional argument [CMD] or `--command`."
+            "Command cannot be empty. Specify via positional argument [CMD] or `--command` or `--script-path`."
         )
 
     parsed_filter = parse_filter(extra_filter)
@@ -125,13 +219,13 @@ def loop(
     # Generate required fields dict
     dummy_variable_table = InfiniteDefaultDict()
     try:
-        _, queried_keys = cmd_interpolate(cmd, dummy_variable_table)
+        _, queried_keys = cmd_interpolate(input_cmd, dummy_variable_table)
     except (CmdParserError, KeyError, TypeError) as e:
         raise typer.BadParameter(f"Command error with exception {e}")
 
     required_fields = list(queried_keys)
 
-    logger.info(f"Got command: {cmd}")
+    logger.info(f"Got command: {input_cmd}")
 
     @loop_run(
         required_fields=required_fields,
@@ -142,48 +236,29 @@ def loop(
         pass_args_dict=True,
     )
     def run_cmd(args):
-        # Interpolate command
-
-        (
-            interpolated_cmd,
-            _,
-        ) = cmd_interpolate(
-            cmd,
-            args,
-        )
+        interpolated_cmd, _ = cmd_interpolate(input_cmd, args)
         logger.info(f"Prepared to run interpolated command: {interpolated_cmd}")
 
-        use_shell = False
-        if isinstance(interpolated_cmd, str):
-            use_shell = True
-
-        with subprocess.Popen(
-            args=interpolated_cmd,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
-            text=True,
-            executable=executable,
-            shell=use_shell,
-        ) as process:
-            while True:
-                output = process.stdout.readline()
-                error = process.stderr.readline()
-
-                if output:
-                    stdout_console.print(output.strip())
-                if error:
-                    stderr_console.print(error.strip())
+        use_shell = isinstance(interpolated_cmd, str)
 
-                # Break loop when process completes and streams are empty
-                if process.poll() is not None and not output and not error:
-                    break
+        try:
+            if use_pty:
+                # Use pexpect with PTY on POSIX systems
+                exit_code = _run_with_pty(interpolated_cmd, executable, use_shell)
+            else:
+                # Standard subprocess approach for non-PTY execution
+                exit_code = _run_with_subprocess(
+                    interpolated_cmd, executable, use_shell
+                )
 
-            process.wait()
-            if process.returncode != 0:
+            if exit_code != 0:
                 raise _LabtaskerJobFailed(
-                    "Job process finished with non-zero exit code."
+                    f"Job process finished with non-zero exit code: {exit_code}"
                 )
 
+        except Exception as e:
+            raise _LabtaskerJobFailed(f"Error running command: {str(e)}")
+
         logger.info(f"Task {task_info().task_id} ended.")
 
     run_cmd()

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/cli_utils.py

@@ -635,7 +635,11 @@ def make_a_choice(
         default=default,
         keyboard_interrupt_default=keyboard_interrupt_default,
     )
-    return asyncio.run(prompt.prompt_async())
+
+    try:
+        return asyncio.run(prompt.prompt_async())
+    except Exception:  # EOFError:  # e.g. closed connection under special circumstances
+        return default
 
 
 ls_format_iter = {

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/cmd_parser/generated/LabCmd.py

@@ -1,9 +1,8 @@
 # Generated from labtasker/client/core/cmd_parser/generated/LabCmd.g4 by ANTLR 4.13.2
 # encoding: utf-8
-import sys
+from labtasker.vendor.antlr4 import *
 from io import StringIO
-
-from antlr4 import *
+import sys
 
 if sys.version_info[1] > 5:
     from typing import TextIO

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/cmd_parser/generated/LabCmdLexer.py

@@ -1,8 +1,7 @@
 # Generated from labtasker/client/core/cmd_parser/generated/LabCmdLexer.g4 by ANTLR 4.13.2
-import sys
+from labtasker.vendor.antlr4 import *
 from io import StringIO
-
-from antlr4 import *
+import sys
 
 if sys.version_info[1] > 5:
     from typing import TextIO

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/cmd_parser/generated/LabCmdListener.py

@@ -1,5 +1,5 @@
 # Generated from labtasker/client/core/cmd_parser/generated/LabCmd.g4 by ANTLR 4.13.2
-from antlr4 import *
+from labtasker.vendor.antlr4 import *
 
 if "." in __name__:
     from .LabCmd import LabCmd

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/cmd_parser/parser.py

@@ -1,8 +1,6 @@
 import os
 from typing import Any, Dict, List, Set, Tuple, Union
 
-from antlr4 import CommonTokenStream, InputStream, ParserRuleContext, ParseTreeWalker
-from antlr4.error.ErrorListener import ErrorListener
 from rich import print
 from rich.console import Console
 from rich.text import Text
@@ -17,6 +15,13 @@ from labtasker.client.core.exceptions import (
     CmdTypeError,
 )
 from labtasker.client.core.logging import stderr_console
+from labtasker.vendor.antlr4 import (
+    CommonTokenStream,
+    InputStream,
+    ParserRuleContext,
+    ParseTreeWalker,
+)
+from labtasker.vendor.antlr4.error.ErrorListener import ErrorListener
 
 # Posix quote and windows quote
 if os.name == "nt":
@@ -158,10 +163,10 @@ def format_print_error(
 
 
 class CmdListener(LabCmdListener):
-    def __init__(self, variable_table, quote_dict: bool):
+    def __init__(self, variable_table, use_quote: bool):
         super().__init__()
         self.variable_table = variable_table
-        self.quote_dict = quote_dict
+        self.use_quote = use_quote
 
         self.result_str = ""
         self.args = set()
@@ -191,12 +196,15 @@ class CmdListener(LabCmdListener):
 
         if isinstance(self.variable, dict):
             # convert dict into bash string
-            if self.quote_dict:
+            # reverse quotes simplifies the conventional Python string representation
+            if self.use_quote:
                 self.result_str += quote(reverse_quotes(str(self.variable)))
             else:
                 self.result_str += reverse_quotes(str(self.variable))
         else:
-            self.result_str += str(self.variable)
+            self.result_str += (
+                quote(str(self.variable)) if self.use_quote else str(self.variable)
+            )
 
         self.variable = None
 
@@ -290,9 +298,7 @@ def cmd_interpolate(
         interpolated_cmd = []
         involved_keys = set()
         for c in cmd:
-            interpolated_str, keys = interpolate_str(
-                c, variable_table, quote_dict=False
-            )
+            interpolated_str, keys = interpolate_str(c, variable_table, use_quote=False)
             interpolated_cmd.append(interpolated_str)
             involved_keys.update(keys)
 
@@ -300,14 +306,14 @@ def cmd_interpolate(
 
 
 def interpolate_str(
-    input_str: str, variable_table: Dict[str, Any], quote_dict: bool = True
+    input_str: str, variable_table: Dict[str, Any], use_quote: bool = True
 ) -> Tuple[str, Set[str]]:
     """
 
     Args:
         input_str:
         variable_table:
-        quote_dict: quote dict string using shlex.quote
+        use_quote: quote dict or strings using shlex.quote
 
     Returns:
         interpolated str, involved keys
@@ -325,7 +331,7 @@ def interpolate_str(
     try:
         tree = parser.command()
         # Walk the parse tree with the custom listener
-        listener = CmdListener(variable_table=variable_table, quote_dict=quote_dict)
+        listener = CmdListener(variable_table=variable_table, use_quote=use_quote)
         walker = ParseTreeWalker()
         walker.walk(listener, tree)
     except CmdParserError as e:

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/config.py

@@ -99,7 +99,7 @@ def requires_client_config(
             if not _config and not get_labtasker_client_config_path().exists():
                 stderr_console.print(
                     "[bold red]Error:[/bold red] Configuration not initialized. "
-                    "Run [orange1]`labtasker config`[/orange1] to initialize configuration."
+                    "Run [orange1]`labtasker init`[/orange1] to initialize configuration."
                 )
                 raise typer.Exit(-1)
 

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/job_runner.py

@@ -233,12 +233,15 @@ def loop_run(
                             #    B. Ignore: Reset task to back to PENDING with retries count set to 0, as if this crashed run never happened
 
                             # 1. log exception
-                            logger.error(f"Task {current_task_id()} failed")
-                            if not isinstance(e, _LabtaskerJobFailed):
-                                stderr_console.print_exception(
-                                    # hide traceback from internals
-                                    suppress=[labtasker]
-                                )
+                            if isinstance(e, KeyboardInterrupt):
+                                logger.warning("KeyboardInterrupt detected")
+                            else:
+                                logger.error(f"Task {current_task_id()} failed")
+                                if not isinstance(e, _LabtaskerJobFailed):
+                                    stderr_console.print_exception(
+                                        # hide traceback from internals
+                                        suppress=[labtasker]
+                                    )
 
                             # 2. ask the user
                             _next_action = "report"  # one of ["report", "ignore"]
@@ -256,7 +259,7 @@ def loop_run(
                                     ),
                                 ]
                                 choice = make_a_choice(
-                                    question="Task failed with the above exception. You have 10 seconds to make a choice:",
+                                    question="Task interrupted or failed with the above info. You have 10 seconds to make a choice:",
                                     options=choices,
                                     # if timed out while waiting for user input, we assume the user is not present and report this crash by default
                                     default=choices[0],

{labtasker-0.2.5 → labtasker-0.2.7}/labtasker/client/core/query_transpiler.py

@@ -706,8 +706,8 @@ class QueryTranspiler(ast.NodeVisitor):
         # Python 3.8 and earlier uses an Index node
         if isinstance(node.slice, ast.Index):
             # Extract the value from the Index node
-            if isinstance(node.slice.value, ast.Constant):
-                index = node.slice.value.value
+            if isinstance(node.slice.value, ast.Constant):  # type: ignore[attr-defined]
+                index = node.slice.value.value  # type: ignore[attr-defined]
                 # Type check: only allow string and integer subscripts
                 if isinstance(index, (str, int)):
                     return f"{value}.{index}"
@@ -719,16 +719,16 @@ class QueryTranspiler(ast.NodeVisitor):
                         exception=QueryTranspilerValueError,
                     )
             # Handle negative indexing with unary operations
-            elif isinstance(node.slice.value, ast.UnaryOp) and isinstance(
-                node.slice.value.op, ast.USub
+            elif isinstance(node.slice.value, ast.UnaryOp) and isinstance(  # type: ignore[attr-defined]
+                node.slice.value.op, ast.USub  # type: ignore[attr-defined]
             ):
                 # Get the operand value if possible
                 operand_info = ""
                 try:
-                    if isinstance(node.slice.value.operand, ast.Constant):
-                        operand_info = f" (value: -{node.slice.value.operand.value})"
-                    elif isinstance(node.slice.value.operand, ast.Name):
-                        operand_info = f" (variable: -{node.slice.value.operand.id})"
+                    if isinstance(node.slice.value.operand, ast.Constant):  # type: ignore[attr-defined]
+                        operand_info = f" (value: -{node.slice.value.operand.value})"  # type: ignore[attr-defined]
+                    elif isinstance(node.slice.value.operand, ast.Name):  # type: ignore[attr-defined]
+                        operand_info = f" (variable: -{node.slice.value.operand.id})"  # type: ignore[attr-defined]
                 except AttributeError:
                     pass
 
@@ -742,7 +742,7 @@ class QueryTranspiler(ast.NodeVisitor):
                 self._report_error(
                     # More specific node location
                     node=node.slice.value,  # type: ignore
-                    msg=f"Unsupported index value type: {type(node.slice.value).__name__}",
+                    msg=f"Unsupported index value type: {type(node.slice.value).__name__}",  # type: ignore[attr-defined]
                     exception=QueryTranspilerValueError,
                 )
 

labtasker-0.2.7/labtasker/vendor/README.txt

@@ -0,0 +1,8 @@
+# Vendored dependencies
+
+This folder contains libraries that are vendored from third party packages.
+To add or modify a vendored library, just add or edit the corresponding dependency
+in `vendor.txt`, and then run the `scripts/get_vendored.py` script.
+
+**NOTE** all files in this folder apart from `__init__.py`, `vendor.txt`  and `README.txt` are
+dynamically generated; any manual modifications will be lost when running the `get_vendored` script