arbolab

Core utilities for ArboLab providing configuration, logging, database management, plotting helpers and a small metadata layer.

Installation

pip install -e .

Extras

Optional dependencies can be installed via extras:

pip install -e ".[plot]"       # seaborn, plotly
pip install -e ".[ml]"         # scipy, scikit-learn
pip install -e ".[latex]"      # jinja2, pylatexenc
pip install -e ".[linescale]"  # arbolab-linescale, pyserial
pip install -e ".[treeqinetic]" # arbolab-treeqinetic, pyserial
pip install -e ".[treecablecalc]" # arbolab-treecablecalc, pyserial
pip install -e ".[treemotion]" # arbolab-treemotion, pyserial
pip install -e ".[wind]"       # arbolab-wind, requests, beautifulsoup4, pandas, numpy
pip install -e ".[all]"        # install every optional dependency

The wind extras can also be installed from PyPI:

pip install arbolab[wind]

Usage

The package exposes a small user-facing API centered around the :class:Lab container. Import it from the top-level package and either create a new laboratory configuration with setup or load an existing one with load:

from arbolab import Lab

# create a new lab and persist its config/database
lab = Lab.setup(load_plugins=True)

# later, reload the same lab (defaults to a file named after the working directory)
lab = Lab.load("lab.duckdb")

# attached sensor adapters are available via lab.sensors
print(lab.sensors.keys())

Adapter plugins are discovered via the arbolab.adapters entry point group and loaded automatically when load_plugins is True.

Custom sensor packages

Third-party sensors integrate by implementing the :class:~arbolab.adapter.Adapter protocol and exposing an entry point:

[project.entry-points."arbolab.adapters"]
"mysensor" = "my_package:MyAdapter"

Installing such a package makes it discoverable by :meth:Lab.setup when load_plugins is True.

Domain entities such as :class:Project or :class:Series live in arbolab.classes and operate on the active Lab instance. Measurements captured from sensors are represented by :class:Measurement objects. Each measurement stores additional metadata fields like unit (physical unit of the recorded values), sample_rate (in Hz) and sensor_type. These fields provide defaults and are validated via Pydantic to ensure consistency. The database representation of a laboratory is called :class:LabEntry to avoid confusion with the user-facing container.

Entities deriving from :class:BaseEntity can store identifiers from external systems in a JSON mapping. Use :meth:set_external_id to register a value such as {"sensor_serial": "1234"} and :meth:get_external_id to retrieve it later.

Configuration

Configuration values can be supplied via environment variables or a YAML file. The Config class and its nested sections are implemented using Pydantic models which provide validation and type coercion. The configuration layout looks as follows:

# config.yaml
working_dir: /tmp/lab           # defaults to the current directory
db_url: duckdb:///lab.duckdb    # optional database URL (defaults to duckdb:///<working_dir_name>.duckdb)
logging:
  level: INFO                   # log level, use "NONE" to disable logging
  use_colors: true
  save_to_file: false
  tune_matplotlib: false

Load the configuration with:

from arbolab import Config

cfg = Config.from_file("config.yaml")

The same fields can be provided via environment variables named ARBOLAB_WORKING_DIR, ARBOLAB_DB_URL, ARBOLAB_LOGGING__LEVEL, ARBOLAB_LOGGING__USE_COLORS, ARBOLAB_LOGGING__SAVE_TO_FILE and ARBOLAB_LOGGING__TUNE_MATPLOTLIB.

Database table prefix

To avoid name clashes between sensor packages, database tables can be prefixed via the ARBOLAB_DB__TABLE_PREFIX environment variable. For example, setting ARBOLAB_DB__TABLE_PREFIX=ls_ will create tables like ls_measurements and ls_sensors. All foreign keys and sequences use the same prefix.

Updating configuration

Use Lab.update_config to adjust settings at runtime. It applies changes via Pydantic's model_copy and dispatches reconfiguration hooks based on the fields that changed so logging, database connections, plotting defaults and persistence refresh independently.

Path parameters

Functions that accept file system paths support both strings and pathlib.Path instances. This applies to helpers such as :meth:Config.from_file and :meth:Lab.load as well as to :class:Config itself:

from pathlib import Path
from arbolab import Config

Config(working_dir="/tmp/lab")
Config(working_dir=Path("/tmp/lab"))

Development

python -m venv .venv
source .venv/bin/activate   # Windows: .venv\Scripts\activate
pip install -e ".[dev]"
pytest