control-parameters-step 2023.11.15

A SEAMM plug-in for defining command-line parameters for a flowchart.

Control Parameters Step

Description

A SEAMM plug-in for defining command-line parameters for a flowchart. This plug-in provides a step in a SEAMM flowchart where a user can define required and optional arguments for the flowchart as a whole. When the flowchart is run, the command-line is parsed and the arguments placed in variables that can then be used by other steps.

This can be used to pass file names or SMILES strings for the molecules to run; or give the temperature and pressure; or any appropriate parameters that the flowchart author feels are relevant.

When run from the command-line, giving the option –help provides help on these control parameters as well as other options for the run:

bash-3.2$ ../flowcharts/psi4.flow --help
usage: ../flowcharts/psi4.flow [options] plug-in [options] plug-in [options] ...

positional arguments:
  SMILES                The SMILES string for the input molecule

optional arguments:
  -h, --help            show this help message and exit
  --method {b3lyp-d3mbj,mp2,ccsd}
                        The type of calculation
...

• Free software: BSD-3-Clause

• Documentation: https://molssi-seamm.github.io/control_parameters_step/index.html

Features

• Graphical user interface (GUI) to define the parameters.

• Mandatory and optional arguments, as well as flags for boolean options.

• Default values for optional arguments.

• Follows standard, familiar Unix conventions for command-line arguments.

• Help provided by -h or –help options.

Credits

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award OAC-1547580 and CHE-2136142.

History

2023.11.15: Improved handling of boolean options

• Properly support using boolean options on the commandline as just a flag to indicate True.

2023.11.6: Bugfix for choices in control parameters

• Ensuring compatibility of older flowcharts with improved handling of choices in the control parameters, necessitated by the Web GUI.

2023.10.21: Improved handling of choices

• When editing the choices for a parameter, the entryfield now accepts the choices separated by spaces. If a choice has spaces or other special characters they can be protected with quotes or backslash in the normal fashion for shell arguments.

2023.7.10: Bugfix handling parameters with 0+ values

• The default was not correctly handled for control parameters with 0+ arguments, where they need to be a list.

2023.1.23: Fixed issue with parameters with ‘_’

• Fixed issue with ‘-’ and ‘_’ in parameter/variable names

• Revamped documentation to the new MolSSI style and diátaxis layout.

• (internal) Moved from LGTM to GitHub CodeQL for code quality analysis

2022-6-6: Fixed bugs when editing parameters

• Also added button to remove a parameter.

2022.2.9: Added ‘files’ to parameter types

• Added ‘files’ to parameter types. Needed for job submission

2021.10.13: Cleaned up the GUI

• Made the dialog larger

• Show all parameters

• Made appropriate comboboxes read only

2021.6.3: Update for internal change in argument parsing

• Updated for the SEAMM argument parser moving to seamm_util

2021.2.9: Improved description for the installer

• Added to the README text, and made it conform to the standard style

2020.12.4: First working release

Adds functionality to SEAMM for specifying key control parameters, items such as the structure, temperature, and pressure, and use them as command-line parameters. In the future, we will also provide the ability to set them when submitting a flowchart from the Python or web interfaces.

0.1 (2020-10-06)

• First release on PyPI.