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new_linter() now uses a config name arg instead of a bool arg; Split example notebook into two
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‎.gitignore‎

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# xrlint
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/xrlint_config.*
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/notebooks/xrlint_config.*
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# Logs
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*.log

‎CHANGES.md‎

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- XRLint CLI now outputs single results immediately to console,
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instead only after all results have been collected.
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- Refactored and renamed `CliEngine` into `XRLint`. Documented the class.
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- `new_linter()` now uses a config name arg instead of a bool arg.
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- Split example notebook into two
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## Early development snapshots
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‎docs/start.md‎

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@@ -105,6 +105,6 @@ import xrlint.all as xrl
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test_ds = xr.Dataset(attrs={"title": "Test Dataset"})
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linter = xrl.new_linter(recommended=True)
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linter = xrl.new_linter("recommended")
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linter.verify_dataset(test_ds)
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```

‎notebooks/mkdataset.py‎

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import numpy as np
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import xarray as xr
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nx = 2
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ny = 3
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nt = 4
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def make_dataset() -> xr.Dataset:
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"""Create a dataset that passes xrlint core rules."""
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return xr.Dataset(
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attrs=dict(title="SST-Climatology Subset"),
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coords={
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"x": xr.DataArray(
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np.linspace(-180, 180, nx),
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dims="x",
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attrs={"units": "degrees"}
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),
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"y": xr.DataArray(
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np.linspace(-90, 90, ny),
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dims="y",
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attrs={"units": "degrees"}
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),
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"time": xr.DataArray(
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[2010 + y for y in range(nt)],
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dims="time",
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attrs={"units": "years"}
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),
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"spatial_ref": xr.DataArray(
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0,
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attrs={
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"grid_mapping_name": "latitude_longitude",
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"semi_major_axis": 6371000.0,
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"inverse_flattening": 0,
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},
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),
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},
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data_vars={
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"sst": xr.DataArray(
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np.random.random((nt, ny, nx)),
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dims=["time", "y", "x"],
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attrs={"units": "kelvin", "grid_mapping": "spatial_ref"}
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),
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"sst_anomaly": xr.DataArray(
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np.random.random((nt, ny, nx)),
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dims=["time", "y", "x"],
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attrs={"units": "kelvin", "grid_mapping": "spatial_ref"}
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)
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},
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)
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def make_dataset_with_issues() -> xr.Dataset:
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"""Create a dataset that produces issues with xrlint core rules."""
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invalid_ds = make_dataset()
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invalid_ds.attrs = {}
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invalid_ds.sst.attrs["units"] = 1
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invalid_ds["sst_avg"] = xr.DataArray(
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np.random.random((nx, ny)),
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dims=["x", "y"],
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attrs={"units": "kelvin"}
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)
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return invalid_ds

‎notebooks/xrlint-api-demo.ipynb‎

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‎notebooks/xrlint-cli.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## XRLint CLI\n",
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"\n",
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"---"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Usage: xrlint [OPTIONS] [FILES]...\n",
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"\n",
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" Validate the given dataset FILES.\n",
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"\n",
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" Reads configuration from `./xrlint_config.*` if such file exists and unless\n",
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" `--no_config_lookup` is set or `--config` is provided. Then validates each\n",
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" dataset in FILES against the configuration. The default dataset patters are\n",
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" `**/*.zarr` and `**/.nc`. FILES may comprise also directories. If a\n",
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" directory is not matched by any file pattern, it will be traversed\n",
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" recursively. The validation result is dumped to standard output if not\n",
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" otherwise stated by `--output-file`. The output format is `simple` by\n",
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" default. Other inbuilt formats are `json` and `html` which you can specify\n",
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" using the `--format` option.\n",
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"\n",
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"Options:\n",
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" --no-config-lookup Disable use of default configuration from\n",
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" xrlint_config.*\n",
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" -c, --config FILE Use this configuration, overriding xrlint_config.*\n",
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" config options if present\n",
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" --print-config FILE Print the configuration for the given file\n",
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" --plugin MODULE Specify plugins. MODULE is the name of Python module\n",
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" that defines an 'export_plugin()' function.\n",
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" --rule SPEC Specify rules. SPEC must have format '<rule-name>:\n",
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" <rule-config>' (note the space character).\n",
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" -o, --output-file FILE Specify file to write report to\n",
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" -f, --format NAME Use a specific output format - default: simple\n",
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" --color / --no-color Force enabling/disabling of color\n",
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" --max-warnings COUNT Number of warnings to trigger nonzero exit code -\n",
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" default: 5\n",
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" --init Write initial configuration file and exit.\n",
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" --version Show the version and exit.\n",
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" --help Show this message and exit.\n"
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]
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}
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],
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"source": [
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"!xrlint --help"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'C:\\\\Users\\\\norma\\\\Projects\\\\xrlint\\\\notebooks'"
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]
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},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"import os\n",
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"os.getcwd()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Error: file xrlint_config.yaml already exists.\n"
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]
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}
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],
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"source": [
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"!xrlint --init"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"<xarray.backends.zarr.ZarrStore at 0x2b09f4c3010>"
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]
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},
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"execution_count": 7,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from mkdataset import make_dataset, make_dataset_with_issues\n",
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"\n",
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"make_dataset().to_zarr(\"valid.zarr\", mode=\"w\")\n",
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"make_dataset_with_issues().to_zarr(\"invalid.zarr\", mode=\"w\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"valid.zarr - ok\n",
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"\n",
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"invalid.zarr:\n",
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"dataset warn Missing 'title' attribute in dataset. dataset-title-attr\n",
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"dataset.attrs warn Missing metadata, attributes are empty. no-empty-attrs\n",
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"dataset.data_vars['sst'] warn Invalid 'units' attribute in variable 'sst'. var-units-attr\n",
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"\n",
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"3 warnings\n",
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"\n"
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]
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}
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],
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"source": [
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"!xrlint --no-color valid.zarr invalid.zarr"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 39,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"<div role=\"results\">\n",
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"<h3>Results</h3>\n",
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"<div role=\"result\">\n",
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"<p role=\"file\">valid.zarr - ok</p>\n",
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"</div>\n",
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"<hr/>\n",
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"<div role=\"result\">\n",
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"<p role=\"file\">invalid.zarr:</p>\n",
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"<table>\n",
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"<tbody>\n",
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"<tr><td>dataset </td><td>warn</td><td>Missing &#x27;title&#x27; attribute in dataset. </td><td>dataset-title-attr</td></tr>\n",
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"<tr><td>dataset.attrs </td><td>warn</td><td>Missing metadata, attributes are empty. </td><td>no-empty-attrs </td></tr>\n",
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"<tr><td>dataset.data_vars[&#x27;sst&#x27;]</td><td>warn</td><td>Invalid &#x27;units&#x27; attribute in variable &#x27;sst&#x27;.</td><td>var-units-attr </td></tr>\n",
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"</tbody>\n",
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"</table><p role=\"summary\">3 warnings</p>\n",
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"</div>\n",
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"</div>\n",
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"\n"
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]
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}
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],
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"source": [
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"!xrlint valid.zarr invalid.zarr -f html"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"{\n",
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" \"name\": \"<computed>\",\n",
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" \"plugins\": {\n",
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" \"__core__\": \"xrlint.plugins.core\"\n",
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" },\n",
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" \"rules\": {\n",
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" \"coords-for-dims\": 2,\n",
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" \"dataset-title-attr\": 1,\n",
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" \"grid-mappings\": 2,\n",
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" \"no-empty-attrs\": 1,\n",
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" \"var-units-attr\": 1\n",
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" }\n",
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"}\n"
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]
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}
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],
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"source": [
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"!xrlint --print-config valid.zarr"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.11"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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