Site generation #67

claudio525 · 2025-10-22T02:00:51Z

Adds support for generating custom site grids. See the Wiki page for details.

…pport for generating NZ wide custom grid.

gemini-code-assist · 2025-10-22T02:01:11Z

Summary of Changes

Hello @claudio525, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the workflow by introducing a robust framework for generating custom virtual simulation site grids. This new capability allows users to define specific criteria for site selection, ensuring consistency across different simulation sets while maintaining the flexibility for tailored analyses. The change also involves the removal of an outdated 'merge timeslices' utility, simplifying the overall system architecture.

Highlights

New Site Generation System: Introduced a comprehensive system for generating custom virtual site grids, allowing for flexible sub-sampling of a high-density general grid based on various filters like region, uniform spacing, land-only, and basin-specific spacing.
Removal of Merge Timeslices Functionality: The merge-ts utility, its associated Python script, Cython loop, and related configurations have been completely removed from the workflow, streamlining the codebase.
Enhanced Documentation: New detailed documentation has been added to the wiki, outlining the background, custom grid generation process, and plot generation capabilities of the new site generation feature.
New Command-Line Interface: A new command-line script, site_gen_cmds.py, has been added to facilitate the generation of custom site grids and their visual representation.

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Copilot

Pull Request Overview

This PR adds comprehensive support for generating custom virtual site grids for earthquake simulations. The main purpose is to enable creation of domain-specific site grids by sub-sampling a high-density "general" grid, ensuring consistency across simulation sets while allowing customization. Additionally, this PR removes the deprecated merge timeslices functionality.

Key changes:

New site_gen.py module implementing custom grid generation with configurable filters (land-only, regional bounds, uniform spacing, basin-specific spacing)
CLI commands in site_gen_cmds.py for grid generation and visualization
Removal of merge timeslices stage and related code

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
workflow/site_gen.py	Core implementation of general and custom grid classes with filtering capabilities
workflow/scripts/site_gen_cmds.py	Command-line interface for grid generation and plotting
workflow/scripts/plan_workflow.py	Removed deprecated MergeTimeslices stage identifier
workflow/scripts/merge_ts_loop.pyx	Deleted Cython implementation for timeslice merging
workflow/scripts/merge_ts.py	Deleted merge timeslices script
workflow/init.py	Removed merge timeslices documentation reference
wiki/Stages.md	Removed merge timeslices stage documentation
wiki/Site-Generation.md	Added comprehensive documentation for site generation feature
setup.py	Deleted setup file for Cython extensions
pyproject.toml	Removed merge-ts console script entry point

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workflow/site_gen.py

wiki/Site-Generation.md

gemini-code-assist

Code Review

This pull request introduces a significant new feature for generating custom site grids, while also cleaning up by removing the old merge-ts functionality. The new site generation code is well-structured, but I've found several critical issues related to coordinate transformations that will cause incorrect geographical plotting of domains and sources. There are also some high-severity correctness issues in the grid-masking logic and inconsistencies between the implementation and the new documentation. Addressing these points will be crucial for the feature to work as intended and be understood by users. I've also included some medium-severity suggestions to improve code quality and usability.

workflow/scripts/site_gen_cmds.py

workflow/site_gen.py

wiki/Site-Generation.md

workflow/scripts/site_gen_cmds.py

workflow/site_gen.py

wiki/Site-Generation.md

workflow/site_gen.py

lispandfound · 2025-10-22T20:04:00Z

These LLM comments look mostly reasonable. I'll take a pass at it once they are resolved.

lispandfound · 2025-10-22T20:04:31Z

See also: the pytest coverage checks are failing. You need some tests for your code.

Copilot

Pull Request Overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 8 comments.

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workflow/site_gen.py

workflow/scripts/site_gen_cmds.py

wiki/Site-Generation.md

Copilot

Pull Request Overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

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Copilot · 2025-11-04T00:33:28Z

workflow/site_gen.py

+            - basin: The basin the site is in (if any).
+            - Z1.0: The Z1.0 value for the site (if vel_model_version is provided).
+            - Z2.5: The Z2.5 value for the site (if vel_model_version is provided).
+            - site_code: The site code.


The docstring is missing documentation for the 'Vs30' column. According to line 701, 'Vs30' is loaded from the NZGMDB data for real sites, and this column is referenced in the plotting code (site_gen_cmds.py lines 169, 177, 199, 207). The documentation should include: - Vs30: Time-averaged shear-wave velocity in the top 30 meters (m/s) (for real sites only).

Suggested change

- site_code: The site code.

- site_code: The site code.

- Vs30: Time-averaged shear-wave velocity in the top 30 meters (m/s) (for real sites only).

Copilot · 2025-11-04T00:33:29Z

tests/test_site_gen.py

+
+
+
+
+


Remove unnecessary blank lines (lines 415-418). These are leftover whitespace that should be cleaned up.

Suggested change

tests/test_site_gen.py

claudio525 added 7 commits October 2, 2025 10:19

Remove merge_ts

0bc078f

Remove merge_ts

b2ac444

Initial version of virtual sites grid code.

eb60f74

Improvements

1d228f4

Renaming.

c496e3a

Documentation update

f3e0e95

Fixed site name generation, bug fixes, plotting improvments, added su…

e3e4a40

…pport for generating NZ wide custom grid.

claudio525 requested review from AndrewRidden-Harper, Copilot, joelridden, lispandfound and sungeunbae October 22, 2025 02:00

Copilot AI reviewed Oct 22, 2025

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gemini-code-assist bot reviewed Oct 22, 2025

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claudio525 added 2 commits October 23, 2025 12:39

Switched to config based approach.

f37632e

Saving

87b1417

claudio525 marked this pull request as draft October 23, 2025 20:35

Testing, bug fixes, minor improvements

24a4456

claudio525 requested a review from Copilot October 28, 2025 01:46

Copilot AI reviewed Oct 28, 2025

View reviewed changes

claudio525 added 4 commits October 29, 2025 10:23

LLM PR comments

95c2c02

Bug fix, more tests

1d1279e

Merge branch 'pegasus' into virt_sites_grid

26bb7eb

Address PR checks

fb336fc

claudio525 requested a review from Copilot November 4, 2025 00:31

Copilot AI reviewed Nov 4, 2025

View reviewed changes

PR test fixes.

9d6e346

	- site_code: The site code.
	- site_code: The site code.
	- Vs30: Time-averaged shear-wave velocity in the top 30 meters (m/s) (for real sites only).

Site generation #67

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Site generation #67

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claudio525 commented Oct 22, 2025

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gemini-code-assist bot commented Oct 22, 2025

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lispandfound commented Oct 22, 2025

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