add execute_command in SSH context #475

thangckt · 2024-07-27T19:08:49Z

solve issue #474

Summary by CodeRabbit

New Features
- Introduced an optional parameter execute_command for executing a command immediately after establishing an SSH connection.
Documentation
- Updated the documentation for the arginfo function to include details about the new execute_command parameter and its usage.

- add option: "strategy": {"customized_script_header_template_file": ""}, - add option: `sge_pe_name`

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Update pbs.py

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feat: `dpdisp run` (deepmodeling#456)

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put `sge_pe_name` in `kwargs`

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coderabbitai · 2024-07-27T19:08:58Z

Walkthrough

The recent changes introduce an optional execute_command parameter to the SSHContext class, allowing users to specify a command for execution immediately after establishing an SSH connection. This enhancement improves the usability and functionality of the class, making it easier for users to automate tasks during the connection process. Additionally, the documentation for the arginfo function has been updated to reflect this new parameter, ensuring clarity in its usage.

Changes

Files	Change Summary
`dpdispatcher/contexts/ssh_context.py`	Added `execute_command` parameter to `__init__` method of `SSHContext` class and updated `_setup_ssh` method to execute it post-connection. Updated `arginfo` documentation for clarity.

Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 723f0b9 and a9fbadf.

Files selected for processing (1)

dpdispatcher/contexts/ssh_context.py (5 hunks)

Additional context used

GitHub Check: codecov/patch

dpdispatcher/contexts/ssh_context.py

[warning] 242-243: dpdispatcher/contexts/ssh_context.py#L242-L243
Added lines #L242 - L243 were not covered by tests

Additional comments not posted (3)

dpdispatcher/contexts/ssh_context.py (3)

47-47: LGTM! Ensure documentation is updated.

The new parameter execute_command has been correctly added to the method signature and stored as an instance variable.

Line range hint 345-393:
LGTM!

The new argument descriptor for execute_command is correctly added to the arginfo method.

47-47: LGTM!

The execute_command parameter is correctly included in the remote_profile argument.

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codecov · 2024-07-27T19:10:41Z

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 56.12%. Comparing base (723f0b9) to head (a9fbadf).
Report is 18 commits behind head on master.

Files with missing lines	Patch %	Lines
dpdispatcher/contexts/ssh_context.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #475      +/-   ##
==========================================
- Coverage   59.92%   56.12%   -3.80%     
==========================================
  Files          39       40       +1     
  Lines        3845     3859      +14     
==========================================
- Hits         2304     2166     -138     
- Misses       1541     1693     +152

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

coderabbitai

Actionable comments posted: 1

coderabbitai · 2024-07-27T19:12:36Z

dpdispatcher/contexts/ssh_context.py

+        if self.execute_command is not None:
+            self.exec_command(self.execute_command)


LGTM! Add tests for the new functionality.

The new logic to execute the command if execute_command is not None is correctly implemented.

Do you want me to generate the unit testing code or open a GitHub issue to track this task?

Tools

GitHub Check: codecov/patch

[warning] 242-243: dpdispatcher/contexts/ssh_context.py#L242-L243
Added lines #L242 - L243 were not covered by tests

thangckt and others added 30 commits March 26, 2024 16:25

revise SGE

11fe336

- add option: "strategy": {"customized_script_header_template_file": ""}, - add option: `sge_pe_name`

Update pbs.py

8140a43

Update pbs.py

b893544

Update pbs.py

82b7262

add sge_qe_name

01ffd14

Update pbs.py

56e3afe

y

703aa49

Update submission.py

2c3b38a

u

f73e0f9

[pre-commit.ci] auto fixes from pre-commit.com hooks

957cf4a

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Update pbs.py

034c9d7

Update pbs.py

3f07742

Merge branch 'PR' into master

499c691

Merge pull request #1 from thangckt/master

76150bf

u

[pre-commit.ci] auto fixes from pre-commit.com hooks

ef28a1b

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u

65dca91

Merge pull request #2 from thangckt/master

ffe52e1

u

[pre-commit.ci] auto fixes from pre-commit.com hooks

8d7b566

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u

8c50c4f

Merge branch 'PR' into master

89d2a41

Merge pull request #3 from thangckt/master

2093336

u

[pre-commit.ci] auto fixes from pre-commit.com hooks

920984d

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y

c8f5657

Merge branch 'master' of https://github.com/thangckt/dpdispatcher

ef6ebeb

Merge branch 'PR' into master

f56fa50

Merge pull request #4 from thangckt/master

e06c648

u

[pre-commit.ci] auto fixes from pre-commit.com hooks

6d6c973

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Update pbs.py

dae7909

Merge pull request #5 from thangckt/master

4ca179c

Update pbs.py

[pre-commit.ci] auto fixes from pre-commit.com hooks

83644c3

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thangckt and others added 22 commits May 7, 2024 19:19

Merge pull request #8 from deepmodeling/master

d02adf6

feat: `dpdisp run` (deepmodeling#456)

Merge pull request #9 from deepmodeling/master

3aca952

[pre-commit.ci] pre-commit autoupdate (deepmodeling#457)

Merge branch 'master' into PR

9fc0f84

Merge pull request #10 from deepmodeling/master

95b8aa5

fetch master

Merge pull request #11 from thangckt/master

cc7efcd

fetch master

u

99589d3

[pre-commit.ci] auto fixes from pre-commit.com hooks

711da1d

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Update test_lsf_script_generation.py

1e0c21e

Merge branch 'PR' of https://github.com/thangckt/dpdispatcher into PR

10cf5d3

Merge pull request #12 from thangckt/PR

416a767

put `sge_pe_name` in `kwargs`

Update test_lsf_script_generation.py

e530cf6

Merge pull request #13 from deepmodeling/master

5adce1b

fetch

Update pbs.py

4084a31

[pre-commit.ci] auto fixes from pre-commit.com hooks

9b1c566

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change sge_pe_name to pe_name

fc690ae

Update ssh_context.py

cfbc5dd

Merge branch 'master' into master

81f52a3

[pre-commit.ci] auto fixes from pre-commit.com hooks

7bbc485

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37da47c

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Merge pull request #14 from deepmodeling/master

02f1449

fetch

Update SSHcontext: add execute command

c13be3b

[pre-commit.ci] auto fixes from pre-commit.com hooks

a9fbadf

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coderabbitai bot reviewed Jul 27, 2024

View reviewed changes

njzjz approved these changes Jul 27, 2024

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njzjz merged commit 1f1bacf into deepmodeling:master Jul 27, 2024
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njzjz linked an issue Jul 27, 2024 that may be closed by this pull request

How to execute ssh command in machine.json #474

Closed

njzjz mentioned this pull request Jul 27, 2024

Implementation for jump connection #426

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add execute_command in SSH context #475

add execute_command in SSH context #475

thangckt commented Jul 27, 2024 •

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		if self.execute_command is not None:
		self.exec_command(self.execute_command)

add execute_command in SSH context #475

add execute_command in SSH context #475

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thangckt commented Jul 27, 2024 • edited by coderabbitai bot Loading

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thangckt commented Jul 27, 2024 •

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