README.md

Python Analysis

Open Python in the directory where you want to run the analysis. The downloaded scripts use that current working directory as the analysis workspace. By default, the scripts read:

<current-directory>/data/NESLTER_transect

write results under:

<current-directory>/results

By default, logs are written under:

<current-directory>/logs

Run the scripts from the intended workspace, or pass explicit --data-dir, --results-dir, and --log-dir paths. Relative paths are resolved from the current directory.

Install the Python metric and IFCB processing dependencies separately in the active project environment.

Download the Python analysis scripts into the current working directory:

import urllib.request

exec(
    urllib.request.urlopen(
        "https://raw.githubusercontent.com/anhph95/ifcbtools/main/analysis/community-variability/python/install_analysis_scripts.py"
    )
    .read()
    .decode("utf-8")
)

To replace existing copies, run:

import urllib.request

IFCB_ANALYSIS_OVERWRITE = True
exec(
    urllib.request.urlopen(
        "https://raw.githubusercontent.com/anhph95/ifcbtools/main/analysis/community-variability/python/install_analysis_scripts.py"
    )
    .read()
    .decode("utf-8")
)

Open the copied scripts and build on them. Keep ifcb_common.py in the same directory as the analysis scripts because each script imports it with from ifcb_common import ....

Each script also writes timestamped .out.log and .err.log files under <current-directory>/logs. Use --log-level DEBUG for more detail or --log-dir PATH to choose another log directory; terminal logging remains enabled. Each log begins with the command-line arguments and resolved workflow paths; secret-like parameter names are automatically redacted.