Getting started¶
This guide installs trasgu from a fresh checkout, copies a packaged minimal example, inspects the run configuration, and runs it.
trasgu is designed to fit many Chimera matrices efficiently. A run starts with a trasgu.yaml file, and the first practical question is how to split the matrix collection into chunks so the work can be fitted independently and, when needed, in parallel.
If you only want to try trasgu, GitHub Codespaces provides a ready-to-use environment. See GitHub Codespaces.
Install¶
git clone https://github.com/SantanderMetGroup/trasgu.git
cd trasgu
uv sync --frozen --no-dev
On Windows PowerShell, activate the environment with:
.\.venv\Scripts\Activate.ps1
On macOS or Linux:
source .venv/bin/activate
Inspect the run configuration¶
The minimal example is a run directory: it contains the trasgu.yaml file used by the CLI commands and the input file it references.
trasgu_examples minimal ./minimal
cd minimal
cat trasgu.yaml
The file points to the input data and sets the number of Chimera matrices fitted per chunk:
data_file: input6_500_gumbel_high.txt
chunk_size: 1000
chunk_size controls the job size. Smaller chunks are easier to rerun and monitor; larger chunks reduce scheduling overhead but take longer per job.
Run the minimal example¶
trasgu_count_chunks
trasgu_time_fit
trasgu_run --dry-run
trasgu_run
trasgu_monitor
trasgu_combine
trasgu_count_chunks prints how many chunks this trasgu.yaml will create. trasgu_time_fit estimates the time for one configured chunk from a small sample before the full run starts.
The workflow writes chunk files to .trasgu_minimal/ and combines them into fit_minimal.csv next to trasgu.yaml.
After this works, see Examples to choose a run directory for CSV input, selected columns, local Chimera data, custom controls, local parallelism, or cluster execution.
Check the result¶
head fit_minimal.csv
Expected columns:
vine_id,n_parameters,aic
Run without activating the environment¶
From the run directory, use uv run and point it to the project root:
uv run --project .. --frozen trasgu_run --dry-run