Python wrapper for CLI programs #200
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
eirrgang
force-pushed
the
gmxapi-198
branch
2 times, most recently
from
ce4cffe
to
d670a18
Compare
eirrgang
commented
Dec 14, 2018
src/gmx/__init__.py
Outdated
| @@ -103,6 +103,194 @@ def run(work=None): | |||
| return status | |||
|
|
|||
|
|
|||
| def commandline_operation(executable=None, shell=False, arguments=None, input=None, output=None): | |||
There was a problem hiding this comment.
arguments keyword needs to come second for the syntax we've been talking about. Move shell to the end.
Suggested change
| def commandline_operation(executable=None, shell=False, arguments=None, input=None, output=None): | |
| def commandline_operation(executable=None, arguments=None, input=None, output=None, shell=False): |
Trivial initial implementation creates a callable object for command lines: gmx.commandline_operation. Work in progress: * Manage input and output file descriptors and data. * Use in gmxapi workflow.
Trivial initial implementation creates a callable object for command lines. If command is not an absolute path, try to find the executable using shell PATH semantics. Work in progress: * Manage input and output file descriptors and data. * Use in gmxapi workflow.
Trivial initial implementation creates a callable object for command lines. If command is not an absolute path, try to find the executable using shell PATH semantics. Input and output filehandles are set to `/dev/null` (or the null device detected by Python 3). Work in progress: * Manage input and output file descriptors and data. * Use in gmxapi workflow.
* Remove keyword_arguments. * Add `input` and `output` arguments.
Removing the empty list for `__all__` allows pydoc and `help()` to generate help text for module functions that do not begin with an underscore (`_`).
We want `arguments` to be the first keyword argument after `executable`
to allow syntax like `gmx.commandline_operation('gmx', 'trjcat', ...)`.
Move `shell` kwarg to end of signature.
helper creates a work element. to do: * introduce gmx.Operation placeholder for WorkElement replacement * collect discrete parts - high-level interface helper - utility / implementation - graph handling - Director for session launcher with subscription, dependency, and topology * more examples
|
Moved to gmxapi 0.1 development at GROMACS master |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
work in progress
fixes #198
supports issue #190
Note that this change will not manage data dependencies (issue #203), but execution order can be managed through the normal WorkElement
dependsmechanism.To do: