Merge pull request #41 from AgPipeline/develop

Merging develop to master - no review

.github/workflows/testing_checks.yaml

@@ -41,8 +41,6 @@ jobs:
         run: python3 -m pip install --upgrade --no-cache-dir pip
       - name: Fetch/update setuptools
         run: python3 -m pip install --upgrade --no-cache-dir setuptools
-      - name: Install python-apt
-        run: sudo apt-get install -y python-apt
       - name: HACK to fix apt-get update problem w/ different python versions
         run: 'cd /usr/lib/python3/dist-packages && sudo cp apt_pkg.cpython-36m-x86_64-linux-gnu.so apt_pkg.so'
       - name: Update apt-get

README.md

@@ -1,3 +1,8 @@
+[![license](https://img.shields.io/badge/license-BSD%203-green?logo=Open-Source-Initiative)](https://github.com/AgPipeline/transformer-canopycover/blob/master/LICENSE)
+
+[![Enforcing testing](https://github.com/AgPipeline/transformer-canopycover/workflows/Enforcing%20tests/badge.svg)](https://github.com/AgPipeline/transformer-canopycover/actions?query=workflow%3A%22Enforcing+tests%22)
+[![testing](https://github.com/AgPipeline/transformer-canopycover/workflows/Testing%20Docker%20image/badge.svg)](https://github.com/AgPipeline/transformer-canopycover/actions?query=workflow%3A%22Testing+Docker+image%22)
+
 # Transformer Canopy Cover
 
 Calculates canopy cover (the percentage pixels identified as a plant) on a plot level for one or more images that have been processed by the [soilmask transformer](https://github.com/AgPipeline/transformer-soilmask) to mask the soil.

canopycover.py

@@ -4,13 +4,13 @@
 
 import argparse
 import copy
+import datetime
 import logging
 import os
 import subprocess
 import tempfile
 from typing import Union
 import numpy as np
-import dateutil.parser
 from agpypeline import entrypoint, algorithm, geoimage
 from agpypeline.environment import Environment
 from osgeo import gdal, ogr
@@ -249,6 +249,24 @@ def get_plot_species(plot_name: str, full_md: list, args: argparse.Namespace) ->
     return args.species if args.species is not None else optional if optional is not None else "Unknown"
 
 
+def get_time_stamps(iso_timestamp: str, args: argparse.Namespace) -> list:
+    """Returns the date and the local time (offset is stripped) derived from the passed in timestamp
+    Args:
+        iso_timestamp: the timestamp string
+        args: the command line parameters
+    Return:
+        A list consisting of the date (YYYY-MM-DD) and a local timestamp (YYYY-MM-DDTHH:MM:SS)
+    """
+    if 'timestamp' in args and args.timestamp:
+        timestamp = datetime.datetime.fromisoformat(args.timestamp)
+    elif iso_timestamp:
+        timestamp = datetime.datetime.fromisoformat(iso_timestamp)
+    else:
+        return ['', '']
+
+    return [timestamp.strftime('%Y-%m-%d'), timestamp.strftime('%Y-%m-%dT%H:%M:%S')]
+
+
 class CanopyCover(algorithm.Algorithm):
     """Calculates canopy cover percentage on soil-masked image"""
 
@@ -265,6 +283,7 @@ def add_parameters(self, parser: argparse.ArgumentParser) -> None:
         # pylint: disable=no-self-use
         parser.add_argument('--species', dest="species", type=str, nargs='?',
                             help="name of the species associated with the canopy cover")
+        parser.add_argument('--timestamp', help='the timestamp to use in ISO 8601 format (eg:YYYY-MM-DDTHH:MM:SS')
 
     def check_continue(self, environment: Environment, check_md: dict, transformer_md: list, full_md: list) -> tuple:
         """Checks if conditions are right for continuing processing
@@ -309,11 +328,7 @@ def perform_process(self, environment: Environment, check_md: dict, transformer_
         # Disable pylint checks that would reduce readability
         # pylint: disable=unused-argument,too-many-locals,too-many-branches,too-many-statements
         # Setup local variables
-        localtime = ""
-        if check_md['timestamp']:
-            timestamp = dateutil.parser.parse(check_md['timestamp'])
-            if timestamp:
-                localtime = timestamp.strftime("%Y-%m-%dT%H:%M:%S")
+        (_, localtime) = get_time_stamps(check_md['timestamp'], environment.args)
 
         save_csv_filename = os.path.join(check_md['working_folder'], "canopycover.csv")
         save_file = open(save_csv_filename, 'w')