feat: add mccc by smlloyd · Pull Request #217 · pysmo/aimbat

smlloyd · 2026-02-21T13:17:04Z

📚 Documentation preview 📚: https://aimbat--217.org.readthedocs.build/en/217/

codecov · 2026-02-21T13:20:19Z

Codecov Report

❌ Patch coverage is 57.56824% with 171 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.04%. Comparing base (e119129) to head (e9013c8).
⚠️ Report is 2 commits behind head on master.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/aimbat/utils/_json.py	12.19%	36 Missing ⚠️
src/aimbat/cli/_pick.py	35.13%	24 Missing ⚠️
src/aimbat/cli/_plot.py	55.00%	18 Missing ⚠️
src/aimbat/core/_event.py	41.37%	17 Missing ⚠️
src/aimbat/cli/_align.py	41.66%	14 Missing ⚠️
src/aimbat/core/_seismogram.py	42.85%	12 Missing ⚠️
src/aimbat/cli/_event.py	74.41%	11 Missing ⚠️
src/aimbat/core/_iccs.py	38.46%	8 Missing ⚠️
src/aimbat/core/_snapshot.py	27.27%	8 Missing ⚠️
src/aimbat/utils/_uuid.py	71.42%	8 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #217      +/-   ##
==========================================
- Coverage   94.37%   88.04%   -6.34%     
==========================================
  Files          45       46       +1     
  Lines        1707     1890     +183     
==========================================
+ Hits         1611     1664      +53     
- Misses         96      226     +130

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Copilot

Pull request overview

This PR introduces MCCC alignment support and reshapes the CLI/data-dumping pathways to return/print structured JSON and render parameter tables via Rich, alongside some dependency updates.

Changes:

Add an MCCC runner (run_mccc) and a new align CLI command to run ICCS or MCCC alignment.
Refactor multiple dump_* helpers to return JSON strings (using Pydantic TypeAdapter) and update CLIs/tests accordingly.
Reorganise CLI commands (e.g. event parameter …, seismogram parameter …, new plot … / pick …) and remove the old iccs CLI module.

Reviewed changes

Copilot reviewed 33 out of 36 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
uv.lock	Updates Python dependency lock entries (e.g. greenlet, mkdocstrings-python, sqlmodel, pysmo).
flake.lock	Updates pinned Nixpkgs revision/hash.
tests/test_station.py	Updates station dump test to validate returned JSON via `TypeAdapter`.
tests/test_seismogram.py	Updates CLI subcommand paths and validates dump JSON via `TypeAdapter`; updates plot CLI invocation.
tests/test_event.py	Updates event CLI paths (`parameter` subcommand), and validates dump JSON via `TypeAdapter`.
tests/test_data.py	Updates data dump test to validate returned JSON via `TypeAdapter`.
src/aimbat/utils/_uuid.py	Improves UUID prefix matching via SQL and extends `uuid_shortener` to accept a model class + UUID string.
src/aimbat/utils/_style.py	Minor table styling cleanup.
src/aimbat/utils/_json.py	Replaces JSON dumping with `json_to_table` for rendering dict/list-of-dicts as Rich tables.
src/aimbat/utils/_active_event.py	Updates import path for CLI hints.
src/aimbat/utils/init.py	Reorders star-imports for utils modules.
src/aimbat/models/_models.py	Converts `AimbatSeismogram.end_time` to a Pydantic `computed_field` for serialisation.
src/aimbat/core/_station.py	Changes station dump to return JSON string (`dump_station_table_to_json`).
src/aimbat/core/_snapshot.py	Adds snapshot dump-to-JSON helper (string or python JSON).
src/aimbat/core/_seismogram.py	Adds seismogram dump-to-JSON and parameter dump/list helpers; uses `json_to_table`.
src/aimbat/core/_iccs.py	Adds `run_mccc`; renames ICCS plot function to `plot_iccs_seismograms`.
src/aimbat/core/_event.py	Adds event dump-to-JSON and parameter dump/list helpers; uses `json_to_table`.
src/aimbat/core/_data.py	Changes data dump to return JSON string (`dump_data_table_to_json`).
src/aimbat/cli/iccs.py	Removes legacy `iccs` CLI module (replaced by `align`/`plot`/`pick`).
src/aimbat/cli/_utils/sampledata.py	Updates imports to new CLI common module path.
src/aimbat/cli/_utils/app.py	Fixes relative imports for utils CLI app wiring.
src/aimbat/cli/_utils/init.py	Adds package init and exports `app`.
src/aimbat/cli/_station.py	Updates station dump to print returned JSON via `rich.print_json`.
src/aimbat/cli/_snapshot.py	Adds snapshot `dump` command and updates imports.
src/aimbat/cli/_seismogram.py	Adds seismogram `dump`, introduces `parameter` subcommands, and adds parameter dump/list commands.
src/aimbat/cli/_project.py	Updates imports to new CLI common module path.
src/aimbat/cli/_plot.py	Introduces new `plot` CLI (data/stack/image).
src/aimbat/cli/_pick.py	Introduces new `pick` CLI for interactive ICCS parameter updates.
src/aimbat/cli/_event.py	Introduces `parameter` subcommands, adds event `dump`, and reorders/updates commands.
src/aimbat/cli/_data.py	Updates data dump to print returned JSON via `rich.print_json`.
src/aimbat/cli/_common.py	Introduces `PlotParameters` / `IccsPlotParameters` dataclasses and adjusts global params.
src/aimbat/cli/_align.py	Adds `align iccs` and `align mccc` CLI commands.
src/aimbat/app.py	Rewires top-level CLI to new module names (`_align`, `_plot`, `_pick`, etc.).
src/aimbat/aimbat_types/_pydantic.py	Inlines timedelta validators and adds `PlainSerializer` for timedelta JSON output.
src/aimbat/_lib/validators.py	Removes now-redundant pandas timedelta validator helpers.
src/aimbat/_config.py	Expands settings help text (with minor spelling issues).

Copilot · 2026-02-21T13:23:04Z

+def print_seismogram_parameter_table(session: Session, short: bool) -> None:
+    """Print a pretty table with AIMBAT seismogram parameter values for the active event.
+
+    Args:


Docstring Args section omits the session parameter even though it’s required by the function signature. Please document session for consistency with other public core helpers in this module.

Suggested change

Args:

Args:

session: Database session used to query seismogram parameters for the

active event.

Copilot · 2026-02-21T13:23:05Z

    These defaults control the default behavior of AIMBAT within a project.
-    They can be changed using environment variables of the same name, or by
-    adding a `.env` file to the current working directory.
+    Overriding these defaults can be done on a per-project basis in the


Use British English spelling in docstrings: behavior → behaviour.

Copilot · 2026-02-21T13:23:05Z

+    if isinstance(data, dict):
+        key_kw = {**common_column_kwargs, **column_kwargs.get("Key", {})}
+        val_kw = {**common_column_kwargs, **column_kwargs.get("Value", {})}
+        table.add_column(key_kw.pop("header", "Key"), **key_kw)
+        table.add_column(val_kw.pop("header", "Value"), **val_kw)


common_column_kwargs is forwarded into Table.add_column(...) (via key_kw/val_kw/col_kw). Callers in this PR pass {"highlight": True}, but highlight is a Table(...) constructor argument (not an add_column kwarg) in Rich; this will raise TypeError: add_column() got an unexpected keyword argument 'highlight' at runtime. Consider either removing highlight support from common_column_kwargs/validating allowed keys, or adding a highlight: bool parameter to make_table(...)/json_to_table(...) and applying it when the Table is constructed instead of when columns are added.

Copilot · 2026-02-21T13:23:05Z

+            data=active_event.parameters.model_dump(mode="json"),
+            title=f"Event parameters for event: {uuid_shortener(session, active_event) if short else str(active_event.id)}",
+            skip_keys=["id", "event_id"],
+            common_column_kwargs={"highlight": True},
+            column_kwargs={


Same issue as above: common_column_kwargs={"highlight": True} will be forwarded into Table.add_column(...) by json_to_table(...), which is not a valid column kwarg in Rich and will raise at runtime. Remove it here or apply highlight at table construction time instead.

Copilot · 2026-02-21T13:23:06Z

-    They can be changed using environment variables of the same name, or by
-    adding a `.env` file to the current working directory.
+    Overriding these defaults can be done on a per-project basis in the
+    fllowing ways (in order of precedence):


Typo in docstring: fllowing → following.

Suggested change

fllowing ways (in order of precedence):

following ways (in order of precedence):

Copilot · 2026-02-21T13:23:06Z

+                "event_id": lambda x: (
+                    uuid_shortener(session, AimbatEvent, str_uuid=x) if short else x
+                ),
+            },
+            common_column_kwargs={"highlight": True},
+            column_kwargs={


common_column_kwargs={"highlight": True} is passed into json_to_table(...), but json_to_table currently forwards common_column_kwargs into Table.add_column(...). In Rich, highlight is a table-level option (constructor kwarg), so this will raise at runtime when listing parameters. Either drop this kwarg here, or adjust json_to_table/make_table to apply highlight when creating the table.

Copilot · 2026-02-21T13:23:06Z

+        title=title,
+        skip_keys=["id"],
+        column_order=["seismogram_id", "select"],
+        common_column_kwargs={"highlight": True},


common_column_kwargs={"highlight": True} is passed to json_to_table(...), but json_to_table forwards these kwargs into Table.add_column(...). highlight is a table-level option in Rich (constructor kwarg), so this will raise at runtime when running seismogram parameter list. Remove this kwarg here or update json_to_table/make_table to handle it at table creation.

Suggested change

common_column_kwargs={"highlight": True},

Copilot · 2026-02-21T13:23:06Z

+def uuid_shortener[T: AimbatTypes](
    session: Session,
-    aimbat_obj: AimbatTypes,
-    min_length: int = settings.min_id_length,
+    aimbat_obj: T | type[T],
+    min_length: int = 2,
+    str_uuid: str | None = None,


uuid_shortener no longer uses settings.min_id_length as its default and instead hard-codes min_length=2. This means user/project configuration of min_id_length in settings will be ignored unless every call site passes min_length explicitly. Consider restoring min_length: int = settings.min_id_length (and keeping the ability to override it per-call).

Copilot · 2026-02-21T13:23:06Z

+) -> str | list[dict[str, Any]]:
+    """Dump the `AimbatSnapshot` table data to json."""
+
+    logger.info("Dumping AimbatSeismogramtable to json.")


The log message refers to AimbatSeismogramtable, which looks like a copy/paste mistake and makes logs confusing when dumping snapshots. Update it to mention the snapshot table (and add a missing space if needed).

Suggested change

logger.info("Dumping AimbatSeismogramtable to json.")

logger.info("Dumping AimbatSnapshot table to json.")

Copilot · 2026-02-21T13:23:07Z

+def run_mccc(session: Session, iccs: ICCS, all_events: bool = False) -> None:
+    """Run MCCC algorithm.
+
+    Args:
+        session: Database session.
+        iccs: ICCS instance.
+        all_events: Whether to run MCCC for all events.
+    """
+
+    logger.info(f"Running MCCC with {all_events=}.")
+
+    cc_seismograms = (
+        iccs.cc_seismograms
+        if all_events
+        else [s for s in iccs.cc_seismograms if s.parent_seismogram.select]
+    )


Parameter name and docstring are misleading: all_events is used to decide whether to include all seismograms vs only parent_seismogram.select, not whether to run across multiple events. Renaming to something like include_deselected/include_all_seismograms (and updating the log line) would make the API self-describing and avoid confusion with the CLI flag.

Copilot AI review requested due to automatic review settings February 21, 2026 13:17

Copilot started reviewing on behalf of smlloyd February 21, 2026 13:17 View session

Copilot AI reviewed Feb 21, 2026

View reviewed changes

feat: add mccc

e9013c8

smlloyd force-pushed the mccc branch from 7cfe6c4 to e9013c8 Compare February 21, 2026 13:35

smlloyd merged commit 3a889ed into master Feb 21, 2026
21 checks passed

smlloyd deleted the mccc branch February 21, 2026 13:39

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

feat: add mccc#217

feat: add mccc#217
smlloyd merged 1 commit intomasterfrom
mccc

smlloyd commented Feb 21, 2026 •

edited by github-actions Bot

Loading

Uh oh!

codecov Bot commented Feb 21, 2026 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Copilot AI Feb 21, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

	fllowing ways (in order of precedence):
	following ways (in order of precedence):

	logger.info("Dumping AimbatSeismogramtable to json.")
	logger.info("Dumping AimbatSnapshot table to json.")

Conversation

smlloyd commented Feb 21, 2026 • edited by github-actions Bot Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov Bot commented Feb 21, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Feb 21, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

smlloyd commented Feb 21, 2026 •

edited by github-actions Bot

Loading

codecov Bot commented Feb 21, 2026 •

edited

Loading