loop-step 2024.11.18

A SEAMM plug-in which provides loops in flowcharts.

SEAMM Loop Plug-in

A SEAMM plug-in which provides loops in flowcharts.

This plug-in provides looping control structures for flowcharts, like a for loop in a programming language.

• Free software: BSD license

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

• Code: https://github.com/molssi-seamm/loop_step

Features

• Simple for i = # to # by # loops

• Foreach loop over elements in a list

• For row loop over rows in a table (see the table plug-in)

Acknowledgements

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

2024.11.18: Removed automatic output of structures.

• While often convenient, writing out the structure at the end of the loop was not a reasonable default. If you want the structure, add a write_structure step in the loop.

2024.11.14: Enhancement: loop control

• Added methods in the loop_step module to break from a loop, break_loop(), continue a loop, continue_loop(), and totally skip an iteration, removing any files associated with it, skip_iteration.

2024.10.15: Bugfix: incorrectly wrapping text description of substeps

• When printing the description of the substeps in the loop, the code incorrectly wrapped the text, which caused issues with e.g. tables.

2024.8.23 – Enhancement to ‘For’ loops

• For integer loops, ensure that the loop variable is an integer and make the directory name be value of the loop variable to make it easier to find the iteration of interest.

2024.8.21 – Bugfix: Error selecting systems by name

• There was a bug selecting system by name in the For Systems in Database branch.

2024.8.16 – Improved handling for For Systems in Database

• Added ability to get all configurations for each system, as well as using matching or regexps for the names of configurations to select.

2024.7.30 – Further improving naming of loop subdirectories

• For loops now use the value of loop index as the subdirectory

• Improved handling of lists for ForEach loops so blank-delimited lists work properly. Quotes can be used for values with embedded blanks, much like the Linux commandline.

2024.7.28 – Improved naming of loop subdirectories

• The subdirectories now start at 1, not 0, to make counting more normal

• When looping over systems, now have the option to name the directories after the system or configuration name, not the iteration number.

2023.11.9 – Bugfix: “For” loops could crash

• For loops could crash writing to write final_structure.mmcif before the directory had been made.

2023.10.30 – Improved consistency of printing loop information

2023.4.24 – Better support for rerunning/restarting jobs

• Remove ‘iteration.out’ if it already exists.

2023.2.15 – Starting to add loops over structures in the database

• Reorganized the documentation and changed to the standard MolSSI theme.

2022.1.16 – Improved error handling

• Wrote the traceback for any errors caught to item_nnn/stderr.out to aid debugging.

2021.12.21 – Cleaned up the printing

2021.12.12 – Error handling and querying for loops over tables

• Errors in the body of the loop are caught and can be ignored or handled in different ways at the direction of the user.

• When looping over rows in a table, a query can be used to select the rows to operate on.

2021.10.13 – updated to Python 3.8 and 3.9

2021.6.3 – updated for internal changes in argument parsing

2021.2.11 (11 February 2021)

• Updated the README file to give a better description.

• Updated the short description in setup.py to work with the new installer.

• Added keywords for better searchability.

2021.2.4 (4 February 2021)

• Updated for compatibility with the new system classes in MolSystem 2021.2.2 release.

2020.12.4 (4 December 2020)

• Internal: switching CI from TravisCI to GitHub Actions, and in the process moving documentation from ReadTheDocs to GitHub Pages where it is consolidated with the main SEAMM documentation.

2020.11.2 (2 November 2020)

• Updated to be compatible with the new command-line argument handling.

2020.10.1 (1 October 2020)

• Bugfix: fixed a blocking bug in handling of periodic system.

2020.9.25.1 (25 September 2020)

• Internal: added a missed installation requirement.

2020.9.25 (25 September 2020)

• Updated to be compatible with the new system classes in MolSystem.

2020.8.3 (3 August 2020)

• Bugfix: corrected problem that caused nested loops to fail sometimes.

2020.7.0 (23 July 2020)

• Write the structure out at the end of each iteration so that it can be viewed in the dashboard.

0.9 (15 April 2020)

• Support for plots in the dashboard.

0.7.0 (17 December 2019)

• General clean-up of code and output.

0.6 (8 September 2019)

• Cleaned up description.

• Internal: preparing for using PyUp to check dependencies.

0.2.0 (2019-07-29)

• First release on PyPI.

0.1.0 (2019-01-13)

• First version created in GitHub.