Using the Tools

Installation

Scintillometry supports installation with conda, mamba, and pip.

Install with Conda/Mamba

Create or activate your preferred conda environment then run:

git clone https://github.com/gampnico/scintillometry.git
make install

Install the package with optional dependencies:

make install-tests   # install with dependencies for tests
make install-docs    # install and build local documentation
make install-all     # install with tests and build local documentation
make install-dev     # install with dependencies for development

Installation uses conda if mamba is unavailable. Micromamba may also work, but is not currently supported. Whilst dependencies are installed with conda/mamba, the Scintillometry package is installed as an editable with pip.

Install with Pip

If conda/mamba are not your package managers, then run:

git clone https://github.com/gampnico/scintillometry.git
pip install -e .

Install the package with optional dependencies:

pip install -e .[tests]       # install with dependencies for tests
pip install -e .[docs]        # install with dependencies for documentation
pip install -e .[tests,docs]  # no whitespace after comma
pip install -e .[dev]         # install with dependencies for development

Run from Terminal

View all command-line arguments:

python3 ./src/scintillometry/main.py -h
make commands  # if you prefer less typing

Usage:

src/scintillometry/main.py [-h] [-i <input_data>] [-p <path_data>] [-d] [...] [-v]

Required arguments:

-i, --input <path>: Path to raw BLS data.
-t, --transect <path>: Path to topographical path transect.

Optional switches:

-h, --help: Show this help message and exit.
-z, --dry-run: Dry run of model.
-v, --verbose: Verbose mode.

Optional arguments:

-e, --eddy <str>: Path to eddy covariance data (innFLUX).
-p, --profile <str>: Path to temperature and humidity profiles (HATPRO).
-t, --timezone <str>: Convert to local timezone. Default “CET”.
-c, --calibrate <float float>: Recalibrate path lengths.
-s, --stability <str>: Set default stability condition.
-s, --switch-time <str>: Override local time of switch between stability regimes.
-k, --station-id <str>: ZAMG station ID (Klima-ID). Default 11803.
--location <str>: Location of experiment. Overrides any other location metadata.
--beam-wavelength <int>: Transmitter beam wavelength, nm. Default 850 nm.
--beam-error <int>: Transmitter beam wavelength error, nm. Default 20 nm.

Import as Package

Scintillometry and its submodules can be imported as a Python module:

import scintillometry
from scintillometry.wrangler.data_parser import parse_scintillometer

MOST functions are stored in their respective class:

from scintillometry.backend.iterations import IterationMost

workflow = IterationMost()
workflow.most_method(dataframe, eff_h, stability, coeff_id="an1988")

These classes inherit from the AtmosConstants class:

from scintillometry.backend.constants import AtmosConstants

constants = AtmosConstants()
kelvin = constants.kelvin  # 273.15

Make Things Simple

The provided Makefile adds shortcuts for more complex commands. View all the available shortcuts:

make help

Available shortcuts:

help:: Display this help screen.
install:: Install with conda.
install-tests:: Install with dependencies for tests.
install-docs:: Install with local documentation.
install-all:: Install package with tests & documentation.
install-dev:: Install in development mode.
commands:: Display help for scintillometry package.
test:: Format code and run tests.
doc:: Build documentation.
format:: Format all python files.
coverage:: Run pytest with coverage.
flake8:: Lint with flake8.
pylint:: Lint with Pylint.
scalene:: Profile with scalene (Python 3.9+).
black:: Format all python files with black.
isort:: Optimise python imports.
run:: Alias for make commands.
pkg:: Run test, build documentation, build package.
commit:: Format, test, then commit.

Some of these shortcuts will only work if the optional dependencies were installed.

Run Tests

Install dependencies for tests:

make install-tests

Run tests with coverage from the package root:

make tests

Logs are placed in the ./logs/ folder.

Build Local Documentation

Install dependencies for documentation:

make install-docs

Build the documentation:

make docs

Formatting breaks if sphinx_rtd_theme version is less than 1.1.