seaflowpy 0.14.0

A Python library for SeaFlow data.

Seaflowpy

A Python package for SeaFlow flow cytometer data.

Install

This package is compatible with Python 3.7.

Command-line tool as single-file download

Single file executables of the seaflowpy command-line tool for MacOS and Linux can be downloaded from the project's github release page.

Docker

Docker image are available from Docker Hub at ctberthiaume/seaflowpy.

docker run -it ctberthiaume/seaflowpy seaflowpy version

The Docker build file is in this repo at /Dockerfile.

PyPI

pip3 install seaflowpy

Source

This will clone the repo and create a new virtual environment seaflowpy. venv can be replaced with virtualenv, conda, etc.

git clone https://github.com/armbrustlab/seaflowpy
cd seaflowpy
python3 -m venv seaflowpy
source seaflowpy/bin/activate
pip3 install -r requirements.txt
pip3 install .
# Confirm the seaflowpy command-line tool is accessible
seaflowpy version
deactivate

Integration with R

To call seaflowpy from R, update the PATH environment variable in ~/.Renviron. For example:

PATH=${PATH}:${HOME}/venvs/seaflowpy/bin

Testing

Seaflowpy uses pytest for testing. Tests can be run from this directory as pytest to test the installed version of the package, or run tox to install the source into a temporary virtual environment for testing.

Command-line interface

All seaflowpy CLI tools are accessible from the seaflowpy executable. Run seaflowpy --help to begin exploring the CLI usage documentation.

SFL validation workflow

SFL validation sub-commands are available under the seaflowpy sfl command. The usage details for each command can be accessed as seaflowpy sfl <cmd> -h.

seaflowpy sfl convert-gga

Converts GGA coordinate values to decimal degree. Otherwise the file is unchanged.

seaflowpy sfl dedup

Remove lines in an SFL file with duplicate "FILE" values. Because it's impossible to know which of the duplicated SFL entries corresponds to which EVT file, all duplicate rows are removed. A unique list of removed files is printed to STDERR.

seaflowpy sfl manifest

Compare EVT files listed in an SFL file with EVT files on-disk or in cloud object storage. This can serve as a quick sanity check for the internal consistency of a SeaFlow cruise data folder. NB, it's normal for one file to be missing from the SFL file or EVT day of year folder around midnight.

seaflowpy sfl print

Print a standard version of an SFL file with only the necessary columns. The correct day of year folder will be added to "FILE" column values if not present. "DATE" column will be created if not present from "FILE" column values (only applies to new-style datestamped file names). Any other required columns which are missing will be created with "NA" values.

seaflowpy sfl validate

Validate key values in an SFL file. The following checks are performed:

• all required columns are present
• "FILE" column values have day of year folders, are in the proper format, in chronological order, and are unique
• "DATE" column values are in the proper format, represent valid date and times, and are UTC
• "LAT" and "LON" coordinate column values are valid decimal degree values

Because some of these errors can affect every row of the file (e.g. out of order files), only the first error of each type is printed. To get a full printout of all errors run the command with --verbose.

Development

Build

To build source tarball, wheel, PyInstaller files, and Docker image, run ./build.sh. This will

• create dist with source tarball and wheel file

• executable files in ./pyinstaller/macos/dist/seaflowpy and ./pyinstaller/linux64/dist/seaflowpy

• Docker image named seaflowpy:<version>

To remove all build files, run git clean -fd.

PyInstaller files and Docker image create depend on the wheel file located in dist.

Updating requirements files

Create a new virtual environment

python3 -m venv newenv
source newenv/bin/actviate

And install seaflowpy

pip3 install .

Then freeze the requirements

pip3 freeze | grep -v seaflowpy >requirements.txt

Then install dev dependencies and freeze

pip3 install pylint pytest tox twine
pip3 freeze | grep -v seaflowpy >requirements-dev.txt

Do some testing, then leave this temporary virtual environment

deactivate