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NASA Harmony service that concatenates netCDF4 data files along an existing dimension

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[//]: # (Using deprecated `align="center"` for the logo image and badges above, because of https://stackoverflow.com/a/62383408)

# Overview
_____

_STITCHEE_ (STITCH by Extending a dimEnsion) is used for concatenating netCDF data *along an existing dimension*,
and it is designed as both a standalone utility and for use as a service in [Harmony](https://harmony.earthdata.nasa.gov/).

## Getting started, with uv

1. Follow the instructions for installing `uv` [here](https://docs.astral.sh/uv/).
2. Install `stitchee`, with its dependencies, by running the following from the repository directory:

```shell
uv sync
```

To install with optional dependencies:

```shell
uv sync --extra dev --extra harmony
```

## How to test `stitchee` locally

```shell
uv run pytest tests/
```

## Contributing

We welcome contributions! This project uses:
- **Git Flow** branching strategy with automated semantic versioning
- **CI/CD** for testing, security scanning, and deployment
- **Protected branches** (main, develop, release/*, hotfix/*)

**Quick workflow:**
1. Create feature branch from `develop`: `git checkout -b feature/your-feature`
2. Write code, tests, and update `CHANGELOG.md`
3. Open PR to `develop` - CI runs tests and security scans
4. After approval and merge, CI handles versioning automatically

**For developers:** See **[.github/CI-CD-README.md](.github/CI-CD-README.md)** for complete CI/CD workflows and branching strategy.

## Usage

For example:

```shell
uv run stitchee /path/to/files/directory -o output.nc --concat_method xarray-combine
```

Command line options:
```shell
$ uv run stitchee --help
usage: stitchee [-h] -o PATH [--concat_method {xarray-concat,xarray-combine}] [--concat_dim DIM] [--sorting_variable VAR] [--xarray_arg_compat COMPAT]
                [--xarray_arg_combine_attrs ATTRS] [--xarray_arg_join JOIN] [-O] [-v]
                INPUT [INPUT ...]

Concatenate netCDF files along existing dimensions.

options:
  -h, --help            show this help message and exit
  -O, --overwrite       Overwrite output file if it exists
  -v, --verbose         Enable verbose output to stdout; useful for debugging

Required Arguments:
  INPUT                 Input specification: multiple file paths, directory path, text file with file list, or single file to copy
  -o PATH, --output_path PATH
                        Output file path for concatenated result

Concatenation Options:
  --concat_method {xarray-concat,xarray-combine}
                        Concatenation method (default: xarray-concat)
  --concat_dim DIM      Dimension to concatenate along (required for xarray-concat)
  --sorting_variable VAR
                        Name of a variable to use for sorting datasets before concatenation (e.g., 'time')

xarray Arguments:
  --xarray_arg_compat COMPAT
                        'compat' argument passed to xarray concatenation function
  --xarray_arg_combine_attrs ATTRS
                        'combine_attrs' argument passed to xarray concatenation function
  --xarray_arg_join JOIN
                        'join' argument passed to xarray concatenation function

Examples:
  stitchee file1.nc file2.nc -o output.nc --concat_dim time
  stitchee /path/to/files/directory -o output.nc --concat_method xarray-combine
  stitchee filelist.txt -o output.nc --concat_dim time --sorting_variable time
```

---
This package is NASA Software Release Authorization (SRA) # LAR-20433-1

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