Add script split multifield ncs

.github/workflows/ci.yaml

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+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        script-dir: ["splitnc"]
+
+    steps:
+      - name: Install netcdf-bin
+        run: sudo apt-get install -y netcdf-bin
+
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: cd ${{ matrix.script-dir }}; pip install .[test]
+
+      - name: Run tests
+        run: cd ${{ matrix.script-dir }}; python -m pytest

splitnc/README.md

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+# splitnc
+This script splits multi-field netCDF files into single-field files.
+It is designed to work on ESM1.6's atmosphere and ice files.
+
+## Automatic Field Identification
+By default `splitnc` will attempt to identify the fields for a multi-field netCDF files by looking for variables that no other variables depend on.
+A variable that no others depend on is likely to be a field.
+E.g. many variables depend on `time`, but none depend on `sea_surface_temperature`.
+
+Alternatively the fields to separate to individual files can be specified as a comma separated list with the `--field-vars` command line option.
+`--field-vars` interprets each item as regex, e.g. one could use `--field-vars fld_.+` to match all variable names that start with the string `fld_`.
+
+## "Ancillary" Variables
+
+Some variables with no dependents should not be separated into individual files, these variables must be manually identified with the `--shared-vars` command line option.
+These variables will then be present in every output file.
+Regex is also supported for this option.
+
+If there are ancillary fields that should only be present in only some of the output field files then multiple invocations of `splitnc` using `--field-vars` and `--shared-vars` will be required.
+
+Example of these variables are the `latitude_longitude` found in atmosphere files or the `uarea`, `tmask`, `tarea`, `VGRDb`, `VGRDi`, `VGRDs` variables from ice files.
+
+## Config File
+
+The `-c`/`--command-line-file` option can be used to supply a filepath to a file that contains command line options.
+If this option is used, all other options supplied on the command line will be ignored.
+Newline characters in the file will be treated as whitespace, i.e. newlines can be used as well as spaces to separate command line arguments.
+
+For example to replicate this command line,
+```
+python splitnc.py --verbose --overwrite --output-dir /output/directory --shared-vars latitude_longitude --rename-regex "(?P<newname>.+)_\d+" /input/directory/*.nc
+```
+the following file could be used;
+```
+--verbose
+--overwrite
+--output-dir /output/directory
+--shared-vars latitude_longitude
+--rename-regex "(?P<newname>.+)_\d+"
+/input/directory/*.nc
+```
+
+## Command Line Options
+
+```quote
+usage: splitnc [-h] [--field-vars FIELD_VAR1,FIELD_VAR2,...] [--shared-vars SHARED_VAR1,SHARED_VAR2,...]
+               [--output-name-pattern OUTPUT_NAME_PATTERN] [--rename-regex REGEX] [--output-dir OUTPUT_DIR] [--overwrite] [-v]
+               [-c COMMAND_LINE_FILE]
+               [filepaths ...]
+
+Splits a multi-field netCDF file into separate one-field files
+
+positional arguments:
+  filepaths             One or more filepaths to process
+
+options:
+  -h, --help            show this help message and exit
+  --field-vars FIELD_VAR1,FIELD_VAR2,...
+                        Specify the names of the field variables to split into separate files - dimensions, bounds, and
+                        coordinates of these fields will be included in each file. Disables automatic field variable
+                        identification. Regex patterns can be used here.
+  --shared-vars SHARED_VAR1,SHARED_VAR2,...
+                        Specify the names of variables that should be shared across files that cannot be automatically
+                        identified, as a comma separated list. Regex patterns can be used here.
+  --excluded-vars EXCLUDED_VAR1,EXCLUDED_VAR2,...
+                        Specify the names of variables that should be excluded from files. This option can be used with
+                        automatic identification of field variables. Regex patterns can be used here.
+  --rename-regex REGEX  Look for duplicated coordinate names that match the given regex and rename them to the first
+                        "newname" capture group in the regex. E.g. "(?P<newname>.*)_\d+" will match "time_0" and rename
+                        it to "time".
+  --output-dir OUTPUT_DIR
+                        Output directory for the processed files. If not given output files will be placed in the same
+                        directory as the original file.
+  --overwrite           Overwrite existing files
+  --dont-update-history
+                        Disable automatic update of history attribute
+  -v, --verbose
+  -c COMMAND_LINE_FILE, --command-line-file COMMAND_LINE_FILE
+                        A file containing a list of command-line arguments. Newlines in this file will be ignored. If
+                        supplied all other command line arguments will be ignored.
+```
+
+## Example Usage
+
+`splitnc` just needs the `xarray` and `netCDF4` python modules.
+On Gadi use load any module with `xarray`, such as `conda/analysis3`.
+Alternatively create a new python environment and install `xarray` and `netCDF4`.
+
+### Atmosphere
+To use this script for split multi-field atmosphere files from ACCESS-ESM1.6:
+```bash
+python split-nc.py --shared-vars latitude_longitude  --rename-regex "(?P<newname>.+)_\\d+" $INPUT_DIR/*.nc
+```
+
+`splitnc` will automatically determine which variables are fields by looking at which variables depend on other variables.
+Variables with nothing depending on them are deemed to be fields.
+Alternatively one could use `--field-vars fld_.+` to match the variable names in these files.
+
+The `--rename-regex` option with the supplied regex will rename variables like
+`time_0` or `pseudo_level_0` are renamed to `time` or `pseudo_level`.
+
+The `--shared-vars` option will ensure that the variable `latitude_longitude` is
+included in all files even though none of the field variable depend on it.
+
+### Ice
+To use this script for split multi-field ice files from ACCESS-ESM1.6:
+```bash
+python split-nc.py --shared-vars uarea,tmask,tarea --excluded-vars VGRD. $INPUT_DIR/*.nc
+```
+
+In comparison to the atmosphere files, ice files have different shared-vars and there are no duplicated variables that require renaming.
+The variables `VGRDb`, `VGRDi`, and `VGRDs` are not required and can thus be excluded from the output.

splitnc/pyproject.toml

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+[project]
+name = "splitnc"
+version = "v0.1"
+authors = [
+    {name = "Joshua Torrance", email="joshua.torrance@anu.edu.au"},
+]
+maintainers = [
+    {name = "Joshua Torrance", email="joshua.torrance@anu.edu.au"},
+]
+description = "Split multi-field ESM1.6 files into single-field files"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "netcdf4",
+    "xarray",
+]
+
+[project.optional-dependencies]
+    test = [
+        "pytest",
+        "netCDF4",
+        "xarray>2025.1.2",
+    ]
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools",
+]
+
+[tool.pytest.ini_options]
+    testpaths = "test"
+    pythonpath = "."