Add XML by joelridden · Pull Request #88 · ucgmsim/nzgmdb

joelridden · 2026-01-06T02:07:27Z

Adds the XML station inventory files.
Reduces needed retrieval of inventory info from the FDSN by using local files.
Adds XML to the dropbox upload process.
Changed remove sensitivity to remove response.
Adjusted wiki and changelog.

gemini-code-assist · 2026-01-06T02:08:00Z

Summary of Changes

Hello @joelridden, 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 data processing pipeline by integrating local StationXML inventory files, which streamlines waveform processing by reducing external API calls. It also refines the instrument response removal mechanism from remove_sensitivity to remove_response for improved accuracy and flexibility. These changes are supported by updates across various modules, including data retrieval, calculation, and management, and are thoroughly documented in the changelog and wiki.

Highlights

StationXML Integration: Introduced the capability to fetch, save, and utilize local StationXML inventory files for waveform processing, reducing reliance on FDSN for inventory information.
Processing Logic Update: Switched from remove_sensitivity to remove_response in waveform processing across multiple modules, ensuring more accurate instrument response removal and handling different output types (ACC/VEL).
Dropbox Integration: Added support for zipping and uploading StationXML inventory files to Dropbox, and a corresponding option to ignore their download during archive retrieval.
Changelog and Wiki Updates: Updated the project's changelog to reflect new features and increased date range, and revised wiki documentation for SNR calculation, record processing, waveform extraction, and Dropbox upload to align with these changes.
Date Range Extension: Extended the data processing date range in the changelog to the end of 2025.

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gemini-code-assist

Code Review

This pull request introduces a significant improvement by caching station inventory XML files, which reduces reliance on FDSN services. The changes are extensive, touching data retrieval, processing, and documentation. The core logic of switching from remove_sensitivity to remove_response is correctly implemented.

However, I've identified a few issues:

A critical logic error in waveform_manipulation.py that inverts the inventory handling.
Code duplication and lack of error handling when reading XML files.
Inefficient and non-robust station data fetching in the new inventory_xml.py module.
A non-reproducible default date.

I've provided detailed comments and suggestions to address these points. Once these are resolved, the PR will be in great shape.

nzgmdb/data_processing/waveform_manipulation.py

nzgmdb/data_retrieval/inventory_xml.py

nzgmdb/calculation/snr.py

nzgmdb/data_retrieval/inventory_xml.py

# Conflicts: # nzgmdb/calculation/snr.py # nzgmdb/data_processing/process_observed.py # nzgmdb/data_processing/waveform_manipulation.py # nzgmdb/data_retrieval/sites.py # nzgmdb/mseed_management/reading.py

lispandfound

Just some minor type checking issues.

nzgmdb/calculation/snr.py

lispandfound · 2026-01-18T22:15:24Z

nzgmdb/phase_arrival/run_phasenet.py

+    bypass_row: pd.Series = None,
+    inventory: Inventory = None,


Suggested change

bypass_row: pd.Series = None,

inventory: Inventory = None,

bypass_row: pd.Series | None = None,

inventory: Inventory | None = None,

Can't use this sadly due to a forced python 3.8 or 3.9 for PhaseNet and GMC

lispandfound · 2026-01-18T22:15:40Z

nzgmdb/phase_arrival/run_phasenet.py

-def run_phasenet(
-    mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path | None = None
-):
+def run_phasenet(mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path = None):


Suggested change

def run_phasenet(mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path = None):

def run_phasenet(mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path | None = None):

Can't use this sadly due to a forced python 3.8 or 3.9 for PhaseNet and GMC

nzgmdb/data_processing/waveform_manipulation.py

nzgmdb/mseed_management/reading.py

wiki/Waveform-Extraction.md

joelridden added 3 commits January 5, 2026 15:25

download xmls

5e81ec9

remove response

4c7e980

wiki / log

8454d2c

gemini-code-assist bot reviewed Jan 6, 2026

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nzgmdb/data_processing/waveform_manipulation.py Outdated Show resolved Hide resolved

nzgmdb/data_retrieval/inventory_xml.py Outdated Show resolved Hide resolved

nzgmdb/calculation/snr.py Outdated Show resolved Hide resolved

nzgmdb/data_retrieval/inventory_xml.py Show resolved Hide resolved

import fix

2820303

joelridden marked this pull request as draft January 6, 2026 03:13

joelridden added 2 commits January 6, 2026 16:14

review

151c9b5

Merge remote-tracking branch 'origin/4p4' into xml

0a86865

# Conflicts: # nzgmdb/calculation/snr.py # nzgmdb/data_processing/process_observed.py # nzgmdb/data_processing/waveform_manipulation.py # nzgmdb/data_retrieval/sites.py # nzgmdb/mseed_management/reading.py

joelridden marked this pull request as ready for review January 15, 2026 23:01

joelridden requested review from AndrewRidden-Harper, claudio525, lispandfound and sungeunbae January 15, 2026 23:02

lispandfound requested changes Jan 18, 2026

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AndrewRidden-Harper previously approved these changes Jan 18, 2026

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nzgmdb/mseed_management/reading.py Outdated Show resolved Hide resolved

wiki/Waveform-Extraction.md Outdated Show resolved Hide resolved

pr comments

530c8ca

joelridden dismissed AndrewRidden-Harper’s stale review via 530c8ca January 19, 2026 00:22

unused imports

26aadd6

joelridden requested review from AndrewRidden-Harper and lispandfound January 19, 2026 01:15

sungeunbae approved these changes Jan 20, 2026

View reviewed changes

lispandfound approved these changes Jan 20, 2026

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joelridden merged commit 7af56eb into 4p4 Jan 20, 2026
5 checks passed

joelridden deleted the xml branch January 20, 2026 20:20

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Add XML#88

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joelridden merged 8 commits into4p4from
xml

joelridden commented Jan 6, 2026

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	def run_phasenet(mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path = None):
	def run_phasenet(mseed_files_ffp: Path, output_dir: Path, bypass_ffp: Path \| None = None):

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joelridden commented Jan 6, 2026

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