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Merged
tasansal merged 14 commits into from
Sep 7, 2025
Merged

Reorganize code and simplify schemas and logic everywhere #642

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e44e0ce
reorg and simplify
tasansal Sep 7, 2025
d208324
fix comparison of stats
tasansal Sep 7, 2025
197d620
fix regression in dataset attribute serialization
tasansal Sep 7, 2025
f7a3f91
ensure histogram alias is compared correctly
tasansal Sep 7, 2025
d463098
update docs references
tasansal Sep 7, 2025
1a8cc65
fix broken refs
tasansal Sep 7, 2025
fcd28f1
remove top level metadata ref
tasansal Sep 7, 2025
2c8bba9
remove blosc config refs (we now get from zarr)
tasansal Sep 7, 2025
08a140a
delete removed stats metadata wrapper
tasansal Sep 7, 2025
d11a987
update deps and remove safety
tasansal Sep 7, 2025
9b60d0c
fix numpy rng lint errors
tasansal Sep 7, 2025
328d5de
exclude lower level members
tasansal Sep 7, 2025
ebaca61
remove singleton from template registry title
tasansal Sep 7, 2025
b1f4633
make template registry api ref with autodoc
tasansal Sep 7, 2025
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1 change: 0 additions & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -13,7 +13,6 @@ jobs:
matrix:
include:
- { python: "3.13", os: "ubuntu-latest", session: "pre-commit" }
# - { python: "3.13", os: "ubuntu-latest", session: "safety" }
# - { python: "3.13", os: "ubuntu-latest", session: "mypy" }
# - { python: "3.12", os: "ubuntu-latest", session: "mypy" }
# - { python: "3.11", os: "ubuntu-latest", session: "mypy" }
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34 changes: 1 addition & 33 deletions docs/api_reference.md
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@@ -1,12 +1,5 @@
# API Reference

## Readers / Writers

```{eval-rst}
.. automodule:: mdio.api.accessor
:members:
```

## Data Converters

### Seismic Data
Expand All @@ -33,21 +26,10 @@ and
```{eval-rst}
.. automodule:: mdio.converters.segy
:members:
:exclude-members: grid_density_qc, parse_index_types, get_compressor
:exclude-members: grid_density_qc, parse_index_types, get_compressor, populate_dim_coordinates, populate_non_dim_coordinates

.. automodule:: mdio.converters.mdio
:members:

.. automodule:: mdio.converters.numpy
:members:
```

## Convenience Functions

```{eval-rst}
.. automodule:: mdio.api.convenience
:members:
:exclude-members: create_rechunk_plan, write_rechunked_values
```

## Core Functionality
Expand All @@ -58,17 +40,3 @@ and
.. automodule:: mdio.core.dimension
:members:
```

### Creation

```{eval-rst}
.. automodule:: mdio.core.factory
:members:
```

### Data I/O

```{eval-rst}
.. automodule:: mdio.core.serialization
:members:
```
2 changes: 1 addition & 1 deletion docs/data_models/chunk_grids.md
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Expand Up @@ -2,7 +2,7 @@
:tocdepth: 3
```

```{currentModule} mdio.schemas.chunk_grid
```{currentModule} mdio.builder.schemas.chunk_grid

```

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16 changes: 1 addition & 15 deletions docs/data_models/compressors.md
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Expand Up @@ -2,7 +2,7 @@
:tocdepth: 3
```

```{currentModule} mdio.schemas.compressors
```{currentModule} mdio.builder.schemas.compressors

```

Expand Down Expand Up @@ -65,20 +65,6 @@ For more details about compression modes, see [ZFP Documentation].

```{eval-rst}
.. autopydantic_model:: Blosc

----------

.. autoclass:: BloscAlgorithm()
:members:
:undoc-members:
:member-order: bysource

----------

.. autoclass:: BloscShuffle()
:members:
:undoc-members:
:member-order: bysource
```

:::
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2 changes: 1 addition & 1 deletion docs/data_models/data_types.md
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Expand Up @@ -2,7 +2,7 @@
:tocdepth: 3
```

```{currentModule} mdio.schemas.dtype
```{currentModule} mdio.builder.schemas.dtype

```

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2 changes: 1 addition & 1 deletion docs/data_models/dimensions.md
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Expand Up @@ -2,7 +2,7 @@
:tocdepth: 3
```

```{currentModule} mdio.schemas.dimension
```{currentModule} mdio.builder.schemas.dimension

```

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1 change: 0 additions & 1 deletion docs/data_models/index.md
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Expand Up @@ -5,6 +5,5 @@ This section contains the data models for the MDIO format.
```{toctree}
:maxdepth: 2

version_0
version_1
```
55 changes: 0 additions & 55 deletions docs/data_models/version_0.md
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41 changes: 16 additions & 25 deletions docs/data_models/version_1.md
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Expand Up @@ -2,7 +2,7 @@
:tocdepth: 3
```

```{currentModule} mdio.schemas.v1.dataset
```{currentModule} mdio.builder.schemas.v1.dataset

```

Expand Down Expand Up @@ -39,19 +39,16 @@
:::{dropdown} Variable

```{eval-rst}
.. autopydantic_model:: mdio.schemas.v1.variable.Variable
.. autopydantic_model:: mdio.builder.schemas.v1.variable.Variable
:inherited-members: BaseModel

.. autopydantic_model:: mdio.schemas.v1.variable.Coordinate
.. autopydantic_model:: mdio.builder.schemas.v1.variable.Coordinate
:inherited-members: BaseModel

.. autopydantic_model:: mdio.schemas.v1.variable.CoordinateMetadata
.. autopydantic_model:: mdio.builder.schemas.v1.variable.CoordinateMetadata
:inherited-members: BaseModel

.. automodule:: mdio.schemas.metadata
:members: UserAttributes

.. autopydantic_model:: mdio.schemas.v1.variable.VariableMetadata
.. autopydantic_model:: mdio.builder.schemas.v1.variable.VariableMetadata
:inherited-members: BaseModel
```

Expand All @@ -60,11 +57,7 @@
:::{dropdown} Units

```{eval-rst}
.. autopydantic_model:: mdio.schemas.v1.units.AllUnits
```

```{eval-rst}
.. automodule:: mdio.schemas.v1.units
.. automodule:: mdio.builder.schemas.v1.units
:members: LengthUnitModel,
TimeUnitModel,
AngleUnitModel,
Expand All @@ -79,14 +72,12 @@
:::{dropdown} Stats

```{eval-rst}
.. autopydantic_model:: mdio.schemas.v1.stats.StatisticsMetadata

.. autopydantic_model:: mdio.schemas.v1.stats.SummaryStatistics
.. autopydantic_model:: mdio.builder.schemas.v1.stats.SummaryStatistics

.. autopydantic_model:: mdio.schemas.v1.stats.EdgeDefinedHistogram
.. autopydantic_model:: mdio.builder.schemas.v1.stats.EdgeDefinedHistogram
:inherited-members: BaseModel

.. autopydantic_model:: mdio.schemas.v1.stats.CenteredBinHistogram
.. autopydantic_model:: mdio.builder.schemas.v1.stats.CenteredBinHistogram
:inherited-members: BaseModel
```

Expand All @@ -95,37 +86,37 @@
:::{dropdown} Enums

```{eval-rst}
.. autoclass:: mdio.schemas.v1.units.AngleUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.AngleUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.DensityUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.DensityUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.FrequencyUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.FrequencyUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.LengthUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.LengthUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.SpeedUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.SpeedUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.TimeUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.TimeUnitEnum()
:members:
:undoc-members:
:member-order: bysource

.. autoclass:: mdio.schemas.v1.units.VoltageUnitEnum()
.. autoclass:: mdio.builder.schemas.v1.units.VoltageUnitEnum()
:members:
:undoc-members:
:member-order: bysource
Expand Down
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