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Add a scan example script
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‎README.md‎

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@@ -13,73 +13,57 @@ For demonstration purposes, this repository contains three Python packages, but
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## Example usage
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There is an example script, [`demo.py`](demo.py), that demonstrates how to use the `fix` function to fix a dataset. The script can be run with the following command:
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There is an example script, [`demo_fix.py`](demo_fix.py), that demonstrates how to use the `fix` function to fix a dataset. The script can be run with the following command:
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```bash
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uv run --extra dev demo.py
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uv run --extra dev demo_fix.py
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```
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Below is an example using Ipython:
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Additionally, there is a script, [`demo_scan.py`](demo_scan.py), that demonstrates how to scan a dataset for problems and generate a fixer configuration. The script can be run with the following command:
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```bash
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uv run --extra dev demo_scan.py
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```
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Below is an example of using the `fix` function in Ipython:
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```python
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In [1]: import xarray as xr
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In [1]: from fixer import fix
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In [2]: from fixer import fix
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In [2]: from fixer_cmip7.tests.test_fixes import create_test_dataset
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In [3]: ds = xr.open_dataset(
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...: "~/climate_data/CMIP6/CMIP/BCC/BCC-ESM1/historical/r1i1p1f1/Amon/tas/gn/v20181214/tas_Amon_BCC-ESM1_historical_r1i1p1f1_gn_185001-201412.nc",
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...: chunks={"time": 100},
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...: )
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...:
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In [3]: ds = create_test_dataset()
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In [4]: ds
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Out[4]:
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<xarray.Dataset> Size: 65MB
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Dimensions: (time: 1980, bnds: 2, lat: 64, lon: 128)
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<xarray.Dataset> Size: 200B
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Dimensions: (time: 1, y: 2, x: 3, bounds: 2)
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Coordinates:
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* time (time) object 16kB 1850-01-16 12:00:00 ... 2014-12-16 12:00:00
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* lat (lat) float64 512B -87.86 -85.1 -82.31 ... 82.31 85.1 87.86
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* lon (lon) float64 1kB 0.0 2.812 5.625 8.438 ... 351.6 354.4 357.2
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height float64 8B ...
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Dimensions without coordinates: bnds
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* time (time) object 8B 1850-01-16 12:00:00
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lat (y) float64 16B -85.1 -87.86
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lon (x) float64 24B 0.0 2.812 5.625
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height2m float64 8B 2.0
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Dimensions without coordinates: y, x, bounds
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Data variables:
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time_bnds (time, bnds) object 32kB dask.array<chunksize=(100, 2), meta=np.ndarray>
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lat_bnds (lat, bnds) float64 1kB dask.array<chunksize=(64, 2), meta=np.ndarray>
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lon_bnds (lon, bnds) float64 2kB dask.array<chunksize=(128, 2), meta=np.ndarray>
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tas (time, lat, lon) float32 65MB dask.array<chunksize=(100, 64, 128), meta=np.ndarray>
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Attributes: (12/49)
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Conventions: CF-1.7 CMIP-6.2
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activity_id: CMIP
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branch_method: Standard
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branch_time_in_child: 0.0
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branch_time_in_parent: 2110.0
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comment: The model integration starts from the piControl e...
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... ...
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title: BCC-ESM1 output prepared for CMIP6
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tracking_id: hdl:21.14100/e6e5eb74-9e45-44db-9dbe-d6236596b068
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variable_id: tas
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variant_label: r1i1p1f1
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license: CMIP6 model data produced by BCC is licensed unde...
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cmor_version: 3.3.2
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In [5]: result = fix(
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...: ds,
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...: name="MIP-DRS7.CMIP7.CMIP.CCCma.CanESM6-MR.historical.r2i1p1f1.glb.mon.tas.tavg-h2m-hxy-u.g13s.v20250622",
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...: )
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...:
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time_bounds (time, bounds) object 16B 1850-01-01 00:00:00 1850-02-01 00:...
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lat_bounds (y, bounds) float64 32B -83.7 -86.48 -86.48 -90.0
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lon_bounds (x, bounds) float64 48B -1.406 1.406 1.406 4.219 4.219 7.031
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temp (time, y, x) float64 48B 24.47 24.25 24.01 24.82 24.21 24.61
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In [6]: result
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Out[6]:
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<xarray.Dataset> Size: 65MB
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Dimensions: (time: 1980, lat: 64, lon: 128, bnds: 2)
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In [5]: fix(ds, name="MIP-DRS7.CMIP7.CMIP.CCCma.CanESM6-MR.historical.r2i1p1f1.glb.mon.tas.tavg-h2m-hxy-u.g13s.v20250622")
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Out[5]:
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<xarray.Dataset> Size: 176B
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Dimensions: (time: 1, lat: 2, lon: 3, bnds: 2)
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Coordinates:
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* time (time) object 16kB 1850-01-16 12:00:00 ... 2014-12-16 12:00:00
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* lat (lat) float64 512B -87.86 -85.1 -82.31 ... 82.31 85.1 87.86
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* lon (lon) float64 1kB 0.0 2.812 5.625 8.438 ... 351.6 354.4 357.2
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* time (time) object 8B 1850-01-16 12:00:00
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* lat (lat) float64 16B -85.1 -87.86
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* lon (lon) float64 24B 0.0 2.812 5.625
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height float64 8B 2.0
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Dimensions without coordinates: bnds
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Data variables:
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tas (time, lat, lon) float32 65MB dask.array<chunksize=(100, 64, 128), meta=np.ndarray>
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time_bnds (time, bnds) object 32kB dask.array<chunksize=(100, 2), meta=np.ndarray>
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lat_bnds (lat, bnds) float64 1kB dask.array<chunksize=(64, 2), meta=np.ndarray>
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lon_bnds (lon, bnds) float64 2kB dask.array<chunksize=(128, 2), meta=np.ndarray>
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tas (time, lat, lon) float32 24B 297.6 297.4 297.2 298.0 297.4 297.8
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time_bnds (time, bnds) object 16B 1850-01-01 00:00:00 1850-02-01 00:00:00
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lat_bnds (lat, bnds) float64 32B -83.7 -86.48 -86.48 -90.0
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lon_bnds (lon, bnds) float64 48B -1.406 1.406 1.406 4.219 4.219 7.031
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```

demo.py renamed to demo_fix.py

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"""Test some stuff."""
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"""Demonstrate how to apply fixes to a dataset."""
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# ruff: noqa: T201
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import xarray as xr
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from __future__ import annotations
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from fixer import fix
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from fixer_cmip7.tests.test_fixes import create_test_dataset
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def main() -> None:
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"""CMORize a file as an example."""
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ds = xr.open_dataset(
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"~/climate_data/CMIP6/CMIP/BCC/BCC-ESM1/historical/r1i1p1f1/Amon/tas/gn/v20181214/tas_Amon_BCC-ESM1_historical_r1i1p1f1_gn_185001-201412.nc",
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chunks={"time": 100},
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)
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"""CMORize a dataset as an example."""
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ds = create_test_dataset()
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print("Original:\n", ds)
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print("Converting..")
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print()
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print("Fixing..")
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result = fix(
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ds,
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name="MIP-DRS7.CMIP7.CMIP.CCCma.CanESM6-MR.historical.r2i1p1f1.glb.mon.tas.tavg-h2m-hxy-u.g13s.v20250622",
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)
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print("Result:\n", result)
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print("Fixed dataset:\n", result)
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print("Saving to NetCDF..")
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result.to_netcdf("tas_fixed.nc")
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import iris.loading # noqa: PLC0415
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except ImportError:
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return
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print("Loading with Iris..")
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cube = iris.load_cube("tas_fixed.nc")
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print(cube.summary())
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if iris.loading.LOAD_PROBLEMS.problems:

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