pipen-cli-gbatch 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

pipen_cli_gbatch/__init__.py

@@ -79,7 +79,7 @@ from pipen.cli import CLIPlugin
 from pipen.scheduler import GbatchScheduler
 from pipen_poplog import LogsPopulator
 
-__version__ = "0.0.3"
+__version__ = "0.0.5"
 __all__ = ("CliGbatchPlugin", "CliGbatchDaemon")
 
 
@@ -317,7 +317,7 @@ class CliGbatchDaemon:
 
     def _show_scheduler_opts(self):
         """Log the scheduler options for debugging purposes."""
-        logger.debug("Scheduler Options:")
+        logger.info("Scheduler Options:")
         for key, val in self.config.items():
             if key in (
                 "workdir",
@@ -337,7 +337,7 @@ class CliGbatchDaemon:
             ):
                 continue
 
-            logger.debug(f"- {key}: {val}")
+            logger.info(f"- {key}: {val}")
 
     async def _run_wait(self):  # pragma: no cover
         """Run the pipeline and wait for completion.
@@ -498,7 +498,7 @@ class CliGbatchDaemon:
                 )
                 sys.exit(1)
 
-            if "name" not in self.config:
+            if "name" not in self.config or not self.config.name:
                 self.config["name"] = "PipenCliGbatchDaemon"
 
     async def run(self):  # pragma: no cover
@@ -551,10 +551,10 @@ class XquteCliGbatchPlugin:  # pragma: no cover
 
     def _clear_residues(self):
         """Clear any remaining log residues and display them."""
-        if self.stdout_populator.residue:
+        if self.stdout_populator and self.stdout_populator.residue:
             logger.info(f"/STDOUT {self.stdout_populator.residue}")
             self.stdout_populator.residue = ""
-        if self.stderr_populator.residue:
+        if self.stderr_populator and self.stderr_populator.residue:
             logger.error(f"/STDERR {self.stderr_populator.residue}")
             self.stderr_populator.residue = ""
 
@@ -595,15 +595,17 @@ class XquteCliGbatchPlugin:  # pragma: no cover
             # Make it less frequent
             return
 
-        stdout_lines = self.stdout_populator.populate()
-        self.stdout_populator.increment_counter(len(stdout_lines))
-        for line in stdout_lines:
-            logger.info(f"/STDOUT {line}")
+        if self.stderr_populator:
+            stdout_lines = self.stdout_populator.populate()
+            self.stdout_populator.increment_counter(len(stdout_lines))
+            for line in stdout_lines:
+                logger.info(f"/STDOUT {line}")
 
-        stderr_lines = self.stderr_populator.populate()
-        self.stderr_populator.increment_counter(len(stderr_lines))
-        for line in stderr_lines:
-            logger.error(f"/STDERR {line}")
+        if self.stderr_populator:
+            stderr_lines = self.stderr_populator.populate()
+            self.stderr_populator.increment_counter(len(stderr_lines))
+            for line in stderr_lines:
+                logger.error(f"/STDERR {line}")
 
     @plugin.impl
     async def on_job_killed(self, scheduler, job):
@@ -767,17 +769,57 @@ class CliGbatchPlugin(CLIPlugin):  # pragma: no cover
             CONFIG_FILES,
             known_parsed.profile,
         )
+
+        def is_valid(val: Any) -> bool:
+            """Check if a value is valid (not None, not empty string, not empty list).
+            """
+            if val is None:
+                return False
+            if isinstance(val, bool):
+                return True
+            return bool(val)
+
         # update parsed with the defaults
         for key, val in defaults.items():
+            if (
+                key == "mount"
+                and val
+                and getattr(known_parsed, key, None)
+            ):
+                if not isinstance(val, (tuple, list)):
+                    val = [val]
+                val = list(val)
+
+                kp_mount = getattr(known_parsed, key)
+                val.extend(kp_mount)
+                setattr(known_parsed, key, val)
+                continue
+
             if (
                 key == "command"
                 or val is None
-                or getattr(known_parsed, key, None) is not None
+                or is_valid(getattr(known_parsed, key, None))
             ):
                 continue
 
             setattr(known_parsed, key, val)
 
+        mount_as_cwd = getattr(known_parsed, "mount_as_cwd", None)
+        cwd = getattr(known_parsed, "cwd", None)
+        delattr(known_parsed, "mount_as_cwd")
+        if mount_as_cwd and cwd:
+            print(
+                "\033[1;4mError\033[0m: --mount-as-cwd and --cwd "
+                "cannot be used together.\n"
+            )
+            sys.exit(1)
+
+        mount = getattr(known_parsed, "mount", None) or []
+        if mount_as_cwd:
+            mount.append(f"{mount_as_cwd}:/mnt/disks/.cwd")
+            setattr(known_parsed, "mount", mount)
+            setattr(known_parsed, "cwd", "/mnt/disks/.cwd")
+
         return known_parsed
 
     def exec_command(self, args: Namespace) -> None:

pipen_cli_gbatch/daemon_args.toml

@@ -120,7 +120,7 @@ help = "The location to run the job."
 flags = ["--mount"]
 # type = "list"
 default = []
-action = "clear_append"
+action = "append"
 help = """The list of mounts to mount to the VM, each in the format of SOURCE:TARGET, where SOURCE must be either a Google Storage Bucket path (gs://...).
 You can also use named mounts like `INDIR=gs://my-bucket/inputs` and the directory will be mounted to `/mnt/disks/INDIR` in the VM;
 then you can use environment variable `$INDIR` in the command/script to refer to the mounted path.
@@ -128,6 +128,14 @@ You can also mount a file like `INFILE=gs://my-bucket/inputs/file.txt`. The pare
 and the file will be available at `/mnt/disks/INFILE/inputs/file.txt` in the VM. `$INFILE` can also be used in the command/script to refer to the mounted path.
 """
 
+[[groups.arguments]]
+flags = ["--mount-as-cwd"]
+type = "str"
+help = """The directory to mount as the current working directory of the command.
+This is a shortcut for `--mount <cloudpath>:/mnt/disks/.cwd --cwd /mnt/disks/.cwd`.
+The <cloudpath> must be a Google Storage Bucket path (gs://...).
+"""
+
 [[groups.arguments]]
 flags = ["--service-account"]
 type = "str"

{pipen_cli_gbatch-0.0.3.dist-info → pipen_cli_gbatch-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pipen-cli-gbatch
-Version: 0.0.3
+Version: 0.0.5
 Summary: A pipen cli plugin to run command via Google Cloud Batch
 License: MIT
 Author: pwwang
@@ -13,6 +13,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: google-cloud-storage (>=3.0.0,<4.0.0)
 Requires-Dist: pipen (>=0.17.19,<0.18.0)
 Requires-Dist: pipen-poplog (>=0.3.6,<0.4.0)

pipen_cli_gbatch-0.0.5.dist-info/RECORD

@@ -0,0 +1,6 @@
+pipen_cli_gbatch/__init__.py,sha256=2LBMKrJyLLGIjYbquvMyerJYXoD9WJzYgrLEM9yNwEE,30280
+pipen_cli_gbatch/daemon_args.toml,sha256=Yqty1vsNTUQKf411tFTExE1dGM5OHGYcI7ANQm0N-CQ,7170
+pipen_cli_gbatch-0.0.5.dist-info/METADATA,sha256=tD81_KwxU8f-H-AFV7hAAPDj_H8ay7zdG-u93Ezgfmc,11301
+pipen_cli_gbatch-0.0.5.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pipen_cli_gbatch-0.0.5.dist-info/entry_points.txt,sha256=Z9NLeCpRo-rb8wss5mB5TBcG-_RbdlPA49b8Ma5pvQA,57
+pipen_cli_gbatch-0.0.5.dist-info/RECORD,,

{pipen_cli_gbatch-0.0.3.dist-info → pipen_cli_gbatch-0.0.5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any

pipen_cli_gbatch-0.0.3.dist-info/RECORD

@@ -1,6 +0,0 @@
-pipen_cli_gbatch/__init__.py,sha256=rpkQ3NA8g4zNnzKaBz3jNZVKNDIIEPRewHK1OCvR9EA,28766
-pipen_cli_gbatch/daemon_args.toml,sha256=PZJ7DHIvGsfVxPwDT0rhdHQb6WxnA10ebXnQOfv4faM,6879
-pipen_cli_gbatch-0.0.3.dist-info/METADATA,sha256=jzaT7B6fAHU8xkUfINHPBOFezxnXUPm0GhiYLEft4Dg,11250
-pipen_cli_gbatch-0.0.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pipen_cli_gbatch-0.0.3.dist-info/entry_points.txt,sha256=Z9NLeCpRo-rb8wss5mB5TBcG-_RbdlPA49b8Ma5pvQA,57
-pipen_cli_gbatch-0.0.3.dist-info/RECORD,,