Refactor 24 trend#198

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gonzalezma wants to merge 481 commits into

refactor_24from

refactor_24_trend

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Commits on Mar 10, 2026

Typehint on load_data

rprospero
authored and
DrPaulSharp
committed
Fix up Source parser

rprospero
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DrPaulSharp
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Add raw data to xml metadata

rprospero
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DrPaulSharp
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Add raw handling to reader

rprospero
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DrPaulSharp
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Enable raw data filter

rprospero
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DrPaulSharp
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Start testing data filter

rprospero
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DrPaulSharp
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Run through code formatter

rprospero
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DrPaulSharp
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Simplify metadata filtering

rprospero
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DrPaulSharp
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Raise KeyError instead of ValueError

rprospero
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DrPaulSharp
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Fix up ascii reader tests

rprospero
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DrPaulSharp
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Update creation of SasData in trend

rprospero
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DrPaulSharp
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Properly compare named units with unnamed units

rprospero
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DrPaulSharp
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Enforce loading test reference files in UTF-8

rprospero
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Skeleton framework for SESANS data

rprospero
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Start parsing sesans header

rprospero
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Start parsing SESANS sample metadata

rprospero
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Include SESANS angle metadata

rprospero
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Multiple SESANS files in reader test

rprospero
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Parse actual data from SES files

rprospero
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Add Raw SESANS Node Data

rprospero
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Update XML test references to include apertures

rprospero
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SESANS metadata as a process, not an aperture

rprospero
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DrPaulSharp
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Fixup lint

rprospero
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DrPaulSharp
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Make changes suggested in PR review

rprospero
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DrPaulSharp
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Fix simple typos from rebase

rprospero
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DrPaulSharp
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Add equality testing for quantities

rprospero
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DrPaulSharp
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More tests for quantities

rprospero
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DrPaulSharp
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Fix meshmerge calculation

rprospero
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Ruff format.

jamescrake-merani
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This comment was repetitive.

jamescrake-merani
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DrPaulSharp
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Ruff format.

jamescrake-merani
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DrPaulSharp
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Function to guess the dataset type.

jamescrake-merani
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Function for loading a file with default params.

jamescrake-merani
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Ruff format.

jamescrake-merani
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Remove imports ruff is complaining aren't used.

jamescrake-merani
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Added a test to make sure 2d data gets read right.

jamescrake-merani
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DrPaulSharp
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Makes sure the dataset type gets guessed.

jamescrake-merani
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DrPaulSharp
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Use basename for sasdata ascii name.

jamescrake-merani
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DrPaulSharp
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Be consistent with how basename is called.

jamescrake-merani
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DrPaulSharp
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Move comment to avoid odd Ruff format.

jamescrake-merani
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DrPaulSharp
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Move comment again.

jamescrake-merani
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DrPaulSharp
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Fixed test.

jamescrake-merani
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DrPaulSharp
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Created an import metadata function.

jamescrake-merani
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DrPaulSharp
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Remove the old function.

jamescrake-merani
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DrPaulSharp
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Use the new import function.

jamescrake-merani
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DrPaulSharp
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Remove these imports.

jamescrake-merani
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DrPaulSharp
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Need to use keywords for this dataclass.

jamescrake-merani
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DrPaulSharp
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Import the mumag data for testing.

jamescrake-merani
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DrPaulSharp
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Added a case for mumag data.

jamescrake-merani
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DrPaulSharp
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Added test for loading ascii data with metadata.

jamescrake-merani
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DrPaulSharp
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Use params filenames not just filenames.

jamescrake-merani
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DrPaulSharp
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Fixed column parameters.

jamescrake-merani
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DrPaulSharp
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Doh. Missing commas on filename list.

jamescrake-merani
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DrPaulSharp
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Roll the raw metadata into the metadata object.

jamescrake-merani
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DrPaulSharp
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Need to fill in all the parameters.

jamescrake-merani
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DrPaulSharp
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Forgot process :P

jamescrake-merani
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Consider both of these.

jamescrake-merani
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Combine both metadata so we go through all of them

jamescrake-merani
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DrPaulSharp
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Raw metadata is in lists.

jamescrake-merani
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DrPaulSharp
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I don't know what these decimals were.

jamescrake-merani
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DrPaulSharp
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Start implementing ModellingRequirements

rprospero
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DrPaulSharp
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Start testing modelling requirements

rprospero
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DrPaulSharp
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Start adding better tests for ModellingRequirements

rprospero
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DrPaulSharp
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Flip order of parameters on compose

rprospero
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DrPaulSharp
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Don't assume that Sesans includes smear

rprospero
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DrPaulSharp
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Enable left composition by null model

rprospero
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DrPaulSharp
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support right addition of NullModel

rprospero
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DrPaulSharp
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Allow preprocess and postprocess steps

rprospero
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DrPaulSharp
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Start performing Hankel transform for SESANS

rprospero
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DrPaulSharp
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Ignore slit smearing before SESANS

rprospero
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DrPaulSharp
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Pull sesans metadata from file

rprospero
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DrPaulSharp
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Add unit test for Hankel transform

rprospero
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DrPaulSharp
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Fix units with error calculation

rprospero
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DrPaulSharp
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χ² squared based test

rprospero
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DrPaulSharp
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Code Review Suggestions

rprospero
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DrPaulSharp
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Fix up rename in compose

rprospero
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DrPaulSharp
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Fix uncertainty in SESANS parser

rprospero
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DrPaulSharp
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Update SESANS units in unit_kinds

rprospero
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DrPaulSharp
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Applies auto fixes for ruff rule F401
DrPaulSharp
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Applies auto fixes for ruff rule E714
DrPaulSharp
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Applies auto fixes for ruff rule F541
DrPaulSharp
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Test should fail when there's no data.

James Crake-Merani
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DrPaulSharp
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Added a get default unit function.

James Crake-Merani
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DrPaulSharp
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Use the new get default unit function.

James Crake-Merani
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DrPaulSharp
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Pass in the unit group as well.

James Crake-Merani
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DrPaulSharp
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Return value if it isn't None.

James Crake-Merani
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DrPaulSharp
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Set the dataset type properly.

James Crake-Merani
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DrPaulSharp
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Expect 2D test to fail.

James Crake-Merani
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Use Quantity in models

rprospero
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DrPaulSharp
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Don't use a quantity for model post processing

rprospero
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DrPaulSharp
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Basic Pinhole model

rprospero
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DrPaulSharp
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Refactor pinhole tests

rprospero
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DrPaulSharp
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Fix radius bug in smearing

rprospero
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DrPaulSharp
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More realisting δq

rprospero
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DrPaulSharp
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Combine Smearing and Sesans tests

rprospero
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Define model metadata in constructor

rprospero
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DrPaulSharp
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Better testing range for pinhole

rprospero
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Add slit smearing

rprospero
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DrPaulSharp
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Remove old commented code

rprospero
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DrPaulSharp
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Vectorise slit calculation

rprospero
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Check combination of slit models

rprospero
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Decrease logical depth of linear_extrapolation

rprospero
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DrPaulSharp
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Decrease logical depth of slit_resolution

rprospero
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Decrease logical depth of geometric_extrapolation

rprospero
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Apply PR changes

rprospero
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DrPaulSharp
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Fixes ruff linting errors (#140)
DrPaulSharp
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Adds Pyupgrade (UP) ruleset and rules SIM118 & SIM300 to ruff linter (#144)
DrPaulSharp
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Applies fixes for isort (I) ruff ruleset (#146)
DrPaulSharp
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Fixes whitespace errors
DrPaulSharp
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Fix hours, days, and years

rprospero
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DrPaulSharp
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Add command for explicitly formatting quantity units

rprospero
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DrPaulSharp
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Add test harness for serialisation

rprospero
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DrPaulSharp
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Add first real json property

rprospero
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Export data type

rprospero
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Add mask and model requirements

rprospero
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Start exporting metadata

rprospero
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Start adding sample details

rprospero
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Export process metadata

rprospero
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Export Instrument and Raw metadata

rprospero
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Support exporting Quantities

rprospero
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Remove unneeded default calls

rprospero
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Start writing decoder

rprospero
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Correctly export sample temperature

rprospero
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DrPaulSharp
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Fix notes nodes type

rprospero
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DrPaulSharp
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Decode metadata from json

rprospero
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DrPaulSharp
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Use proper bytes for numpy serialisation

rprospero
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DrPaulSharp
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Fix historical unit errors

rprospero
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Parse MetaNode

rprospero
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Use .json extension for JSON files

rprospero
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DrPaulSharp
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Establish settings for ruff and pycodestyle

rprospero
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DrPaulSharp
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Fix formatting

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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DrPaulSharp
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Adds main check to "transforms.py"
DrPaulSharp
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Start descending

rprospero
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Convert tail call recursion to loop

rprospero
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Enumerate keys for access

rprospero
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Descend into dicts

rprospero
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Fix access to dict items

rprospero
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Fix formatting and doctstrings

rprospero
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Enable tag collection

rprospero
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Fix PR Comments

rprospero
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DrPaulSharp
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Formatting fixes

rprospero
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DrPaulSharp
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Start encoding

rprospero
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DrPaulSharp
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Test saving with XML files

rprospero
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DrPaulSharp
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More tests for sample metadata

rprospero
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Switch to safe asserts

rprospero
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Start serialising process

rprospero
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Start serialising process

rprospero
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Write instrument tests

rprospero
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Start testing g5 round trip

rprospero
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Fix *most* of the round trip issues

rprospero
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Everything passes if we ignore raw

rprospero
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Start trying to serialise raw data

rprospero
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Simplify test setup

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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DrPaulSharp
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Attach metadata to every entry

rprospero
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DrPaulSharp
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Add comments to as_h5

rprospero
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DrPaulSharp
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Fix up file handling of test

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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DrPaulSharp
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Remove debugging print

rprospero
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Respond to PR suggestions

rprospero
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Adds local pre-commit hook for ruff linting auto fixes
DrPaulSharp
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Handle bytes type object in units parser

rprospero
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Fix underline length in metadata export

rprospero
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Fix import of actual sasdata

rprospero
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Tweak json handling

rprospero
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Fix most of HDF file loading

rprospero
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Properly save multidimensional data

rprospero
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Fix parsing of exception in test

rprospero
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Perform serialisation test on ALL example data

rprospero
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Export json

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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DrPaulSharp
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Fix json export of data objects

rprospero
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Fixes to json export

rprospero
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Respond to PR suggestions

rprospero
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Use file name as file id

rprospero
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157 refactor design documentation (#158)

lucas-wilkins
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Redesign tests (#155)

committed
Mark dataload test for faster turnaround

rprospero
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Ruff code formatting

rprospero
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Fix up HDF Test case

rprospero
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Start moving HDF tests into James test framework

rprospero
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Start moving XML into James test framework

rprospero
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Move round trip testing into main framework

rprospero
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Move json testing into test framework

rprospero
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Eliminate old testing detritus

rprospero
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Start on Sesans testing

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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Modifies autogen code to match ruff rules
DrPaulSharp
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added rpms and ran to rebuild tables

paulneves77
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ran ruff fixes

paulneves77
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added 3D datatype and added Qz generalizations where obvious

paulneves77
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added first attempt at ND binner which can take in I(x,y,z,u,v,...) and rebin to an N dimensional regular grid

paulneves77
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added rebin and sketch of inplied qz for postprocessing

paulneves77
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updated rebin, added rpm to units, and working on testing readers

paulneves77
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the ND xubpixel binning appears to be working, and made some updates to the temporary hdf5 reader

paulneves77
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corrected errors in qz calculator, cleaned up test_hdf5_reader, improved NDrebin local testing

paulneves77
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corrected errors in qz calculator, cleaned up test_hdf5_reader, improved NDrebin local testing

paulneves77
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started cleaning up for pull request

paulneves77
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fixed temp_hdf5_reader to be slightly more compliant with NXcanSAS standards (now looks directly at canSAS_class instead of the group name. This is because the group name is allowed to be anything,…

paulneves77
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DrPaulSharp
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fixed apertures and run from none to empty list if missing, and fixed raw data loading if present

paulneves77
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DrPaulSharp
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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cleaned up code based on Jeff Kryzwon's suggestions and added test case for deduce_qz

paulneves77
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removed NDrebin from this branch.

paulneves77
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implemented minor cleanups to code

paulneves77
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fixed a few bugs and cleaned up more

paulneves77
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added raw back to metadata

paulneves77
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fixed some bugs with importing sasdata/test/sasdataloader/data/simpleexamplefile.h5. Also added support for when the NX_class attribute has a canSAS_class name. Also fixed bug when no instrument, s…

paulneves77
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fixed the collimation cansas_class attribute in the nxcansas_1Dand2D_multisasentry_multisasdata.h5, nxcansas_1Dand2D_multisasdata.h5, and nxcansas_1Dand2D_multisasentry.h5 test data files

paulneves77
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removed local path references, removed spurious units.py

paulneves77
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moved duplicate code in parse_quantity to a call of parse_float, changed name of parse_float_first to parse_float

paulneves77
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fixed minor error in reference output for nxcansas_1Dand2D_multisasdata and nxcansas_1Dand2D_multisasentry where the detector distance was read wrong because of the difference between node.astype(f…

paulneves77
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brought over NDrebin from refactor_24_3D branch

paulneves77
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updated NDrebin a bunch and also added NDrebin testing

paulneves77
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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added note on using NDrebin for M dimensional integration

paulneves77
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first pass at rebasing NDrebin to a class

paulneves77
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second pass at cleaning up NDrebin class

paulneves77
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NDrebin class ready for testing

paulneves77
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added unit testing for NDrebin

paulneves77
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removed temporary testing from NDrebin.py

paulneves77
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cleaned up NDrebin, removed old function, added documentation

paulneves77
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refactor NDRebin._build_limits to pass codescene review. vectorized and removed for loops and most conditional logic

paulneves77
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fixed bug in _build_limits

paulneves77
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indented code block, clarified non-vector comment, fixed typo, removed return in NDRebin __call__

paulneves77
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DrPaulSharp
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indented code block, clarified non-vector comment, fixed typo, removed return in NDRebin __call__

paulneves77
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Update date format in refactor roadmap
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Basic test harness for names

rprospero
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Base 62 encode the hash for shorter names

rprospero
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Name info in unique id for NamedQuantity

rprospero
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Ruff formatting

rprospero
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Properly attach run title and number to quantity information

rprospero
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Make the name a part of all quantities

rprospero
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Ensure that xml imports also include a proper name unique id

rprospero
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Ensure ASCII reader generates unique_id for data quantities

rprospero
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Refactor our id_header

rprospero
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[pre-commit.ci lite] apply automatic fixes for ruff linting errors

pre-commit-ci-lite[bot]
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DrPaulSharp
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Minor formatting fixes

rprospero
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Remove debugging print statements

rprospero
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Refactor operations (#184)

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Update refactor roadmap
DrPaulSharp
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Adds trig and exp operations (#186)
DrPaulSharp
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Commits on Mar 16, 2026

Commits on Mar 17, 2026

Fix method to_string() to handle correctly Quantity objects
gonzalezma
committed

Commits on Mar 20, 2026

Commits on Jun 3, 2026

Changes following review comments
gonzalezma
committed

Uh oh!

Commits

Commits on Mar 10, 2026