dpdispatcher 0.6.6__py3-none-any.whl → 1.0.0__py3-none-any.whl

dpdispatcher/utils/utils.py

@@ -2,6 +2,7 @@ import base64
 import hashlib
 import hmac
 import os
+import shlex
 import struct
 import subprocess
 import time
@@ -89,6 +90,7 @@ def rsync(
     port: int = 22,
     key_filename: Optional[str] = None,
     timeout: Union[int, float] = 10,
+    proxy_command: Optional[str] = None,
 ):
     """Call rsync to transfer files.
 
@@ -104,6 +106,8 @@ def rsync(
         identity file name
     timeout : int, default=10
         timeout for ssh
+    proxy_command : str, optional
+        ProxyCommand to use for SSH connection
 
     Raises
     ------
@@ -124,20 +128,30 @@ def rsync(
     ]
     if key_filename is not None:
         ssh_cmd.extend(["-i", key_filename])
+
+    # Use proxy_command if provided
+    if proxy_command is not None:
+        ssh_cmd.extend(["-o", f"ProxyCommand={proxy_command}"])
+
+    # Properly escape the SSH command for rsync's -e option
+    ssh_cmd_str = " ".join(shlex.quote(part) for part in ssh_cmd)
+
     cmd = [
         "rsync",
-        # -a: archieve
-        # -z: compress
-        "-az",
+        # -r: recursive, -l: links, -p: perms, -t: times, -D: devices/specials
+        # -z: compress (exclude -o: owner, -g: group to avoid permission issues)
+        "-rlptDz",
         "-e",
-        " ".join(ssh_cmd),
+        ssh_cmd_str,
         "-q",
         from_file,
         to_file,
     ]
-    ret, out, err = run_cmd_with_all_output(cmd, shell=False)
+    # Convert to string for shell=True
+    cmd_str = " ".join(shlex.quote(arg) for arg in cmd)
+    ret, out, err = run_cmd_with_all_output(cmd_str, shell=True)
     if ret != 0:
-        raise RuntimeError(f"Failed to run {cmd}: {err}")
+        raise RuntimeError(f"Failed to run {cmd_str}: {err}")
 
 
 class RetrySignal(Exception):
@@ -191,7 +205,7 @@ def retry(
             else:
                 # raise all exceptions
                 raise RuntimeError(
-                    "Failed to run %s for %d times" % (func.__name__, current_retry)
+                    f"Failed to run {func.__name__} for {current_retry} times"
                 ) from errors[-1]
 
         return wrapper

{dpdispatcher-0.6.6.dist-info → dpdispatcher-1.0.0.dist-info}/METADATA

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: dpdispatcher
-Version: 0.6.6
+Version: 1.0.0
 Summary: Generate HPC scheduler systems jobs input scripts, submit these scripts to HPC systems, and poke until they finish
 Author: DeepModeling
-License: GNU LESSER GENERAL PUBLIC LICENSE
+License:                    GNU LESSER GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
          Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
@@ -186,32 +186,33 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: paramiko
-Requires-Dist: dargs >=0.4.1
+Requires-Dist: dargs>=0.4.1
 Requires-Dist: requests
-Requires-Dist: tqdm >=4.9.0
+Requires-Dist: tqdm>=4.9.0
+Requires-Dist: typing_extensions; python_version < "3.7"
 Requires-Dist: pyyaml
-Requires-Dist: tomli >=1.1.0 ; python_version < "3.11"
-Requires-Dist: typing-extensions ; python_version < "3.7"
-Provides-Extra: bohrium
-Requires-Dist: oss2 ; extra == 'bohrium'
-Requires-Dist: tqdm ; extra == 'bohrium'
-Requires-Dist: bohrium-sdk ; extra == 'bohrium'
-Provides-Extra: cloudserver
-Requires-Dist: oss2 ; extra == 'cloudserver'
-Requires-Dist: tqdm ; extra == 'cloudserver'
-Requires-Dist: bohrium-sdk ; extra == 'cloudserver'
+Requires-Dist: tomli>=1.1.0; python_version < "3.11"
 Provides-Extra: docs
-Requires-Dist: sphinx ; extra == 'docs'
-Requires-Dist: myst-parser ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme >=1.0.0rc1 ; extra == 'docs'
-Requires-Dist: numpydoc ; extra == 'docs'
-Requires-Dist: deepmodeling-sphinx >=0.1.1 ; extra == 'docs'
-Requires-Dist: dargs >=0.3.1 ; extra == 'docs'
-Requires-Dist: sphinx-argparse <0.5.0 ; extra == 'docs'
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: deepmodeling-sphinx>=0.3.0; extra == "docs"
+Requires-Dist: dargs>=0.3.1; extra == "docs"
+Requires-Dist: sphinx-argparse<0.5.0; extra == "docs"
+Provides-Extra: cloudserver
+Requires-Dist: oss2; extra == "cloudserver"
+Requires-Dist: tqdm; extra == "cloudserver"
+Requires-Dist: bohrium-sdk; extra == "cloudserver"
+Provides-Extra: bohrium
+Requires-Dist: oss2; extra == "bohrium"
+Requires-Dist: tqdm; extra == "bohrium"
+Requires-Dist: bohrium-sdk; extra == "bohrium"
 Provides-Extra: gui
-Requires-Dist: dpgui ; extra == 'gui'
+Requires-Dist: dpgui; extra == "gui"
 Provides-Extra: test
-Requires-Dist: dpgui ; extra == 'test'
+Requires-Dist: dpgui; extra == "test"
+Dynamic: license-file
 
 # DPDispatcher
 
@@ -221,11 +222,19 @@ Requires-Dist: dpgui ; extra == 'test'
 [![Documentation Status](https://readthedocs.org/projects/dpdispatcher/badge/)](https://dpdispatcher.readthedocs.io/)
 
 DPDispatcher is a Python package used to generate HPC (High-Performance Computing) scheduler systems (Slurm/PBS/LSF/Bohrium) jobs input scripts, submit them to HPC systems, and poke until they finish.
-​
+
 DPDispatcher will monitor (poke) until these jobs finish and download the results files (if these jobs are running on remote systems connected by SSH).
 
 For more information, check the [documentation](https://dpdispatcher.readthedocs.io/).
 
+## Credits
+
+Please cite the following paper if you use this project in your work:
+
+- Fengbo Yuan, Zhaohan Ding, Yun-Pei Liu, Kai Cao, Jiahao Fan, Cao Thang Nguyen, Yuzhi Zhang, Haidi Wang, Yixiao Chen, Jiameng Huang, Tongqi Wen, Mingkang Liu, Yifan Li, Yong-Bin Zhuang, Hao Yu, Ping Tuo, Yaotang Zhang, Yibo Wang, Linfeng Zhang, Han Wang, Jinzhe Zeng, DPDispatcher: Scalable HPC Task Scheduling for AI-Driven Science, _J. Chem. Inf. Model._, 2025, DOI: [10.1021/acs.jcim.5c02081](https://doi.org/10.1021/acs.jcim.5c02081). [![Citations](https://citations.njzjz.win/10.1021/acs.jcim.5c02081)](https://badge.dimensions.ai/details/doi/10.1021/acs.jcim.5c02081)
+
+This project was separated out from the [DP-GEN](https://github.com/deepmodeling/dpgen) project (Section 3.3 in [its paper](https://doi.org/10.1016/j.cpc.2020.107206)) to be used by more workflow software.
+
 ## Installation
 
 DPDispatcher can be installed by `pip`:
@@ -248,7 +257,3 @@ See [Getting Started](https://dpdispatcher.readthedocs.io/en/latest/getting-star
 
 DPDispatcher is maintained by Deep Modeling's developers and welcomes other people.
 See [Contributing Guide](CONTRIBUTING.md) to become a contributor! 🤓
-
-## References
-
-DPDispatcher is derived from the [DP-GEN](https://github.com/deepmodeling/dpgen) package. To mention DPDispatcher in a scholarly publication, please read Section 3.3 in the [DP-GEN paper](https://doi.org/10.1016/j.cpc.2020.107206).

dpdispatcher-1.0.0.dist-info/RECORD

@@ -0,0 +1,49 @@
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{dpdispatcher-0.6.6.dist-info → dpdispatcher-1.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

dpdispatcher-0.6.6.dist-info/RECORD

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