Merge pull request #4 from AgPipeline/develop

Merging develop to main branch - no review

.github/workflows/action_pylint.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+cp ./.github/workflows/*.py ./
+

.github/workflows/algorithm_rgb.py

@@ -0,0 +1,62 @@
+"""My nifty plot-level RGB algorithm
+"""
+
+# Importing modules. Please add any additional import statements below
+import numpy as np
+
+# Definitions
+# Please replace these definitions' values with the correct ones
+VERSION = '1.0'
+
+# Information on the creator of this algorithm
+ALGORITHM_AUTHOR = 'Unknown'
+ALGORITHM_AUTHOR_EMAIL = ''
+ALGORITHM_CONTRIBUTORS = [""]
+
+ALGORITHM_NAME = 'my nifty one'
+ALGORITHM_DESCRIPTION = 'This algorithm calculates the niftyness of RGB plot-level images'
+
+# Citation information for publication (more information in HOW_TO.md)
+CITATION_AUTHOR = 'unknown'
+CITATION_TITLE = ''
+CITATION_YEAR = ''
+
+# The name of one or more variables returned by the algorithm, separated by commas (more information in HOW_TO.md)
+# If only one name is specified, no comma's are used.
+# Note that variable names cannot have comma's in them: use a different separator instead. Also,
+# all white space is kept intact; don't add any extra whitespace since it may cause name comparisons
+# to fail.
+# !! Replace the content of this string with your variable names
+VARIABLE_NAMES = 'size of image channels'
+
+# Variable units matching the order of VARIABLE_NAMES, also comma-separated.
+# For each variable name in VARIABLE_NAMES add the unit of measurement the value represents.
+# !! Replace the content of this string with your variables' unit
+VARIABLE_UNITS = 'pixels'
+
+# Variable labels matching the order of VARIABLE_NAMES, also comma-separated.
+# This is an optional definition and can be left empty.
+VARIABLE_LABELS = ''
+
+# Optional override for the generation of a BETYdb compatible csv file
+# Set to False to suppress the creation of a compatible file
+WRITE_BETYDB_CSV = True
+
+# Optional override for the generation of a TERRA REF Geostreams compatible csv file
+# Set to False to suppress the creation of a compatible file
+WRITE_GEOSTREAMS_CSV = True
+
+
+# Entry point for plot-level RBG algorithm
+def calculate(pxarray: np.ndarray):
+    """Calculates one or more values from plot-level RGB data
+    Arguments:
+        pxarray: Array of RGB data for a single plot
+    Return:
+        Returns one or more calculated values
+    """
+    # ALGORITHM: replace the following lines with your algorithm
+    channel_size = pxarray[:, :, 1].size
+
+    # RETURN: replace the following return with your calculated values. Be sure to order them as defined in VARIABLE_NAMES above
+    return channel_size

.github/workflows/pylint_check.yaml

@@ -0,0 +1,82 @@
+name: Enforcing pylint checks
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+    tags:
+      - v*
+
+jobs:
+  update_python:
+    runs-on: ubuntu-latest
+    name: Running pylint checks
+    steps:
+      - name: Current python version
+        run: python3 --version || echo python3 not installed
+      - name: Install Python 3.7
+        run: sudo apt-get install -y --no-install-recommends python3.7 python3-pip && sudo ln -sfn /usr/bin/python3.7 /usr/bin/python3
+        id: install_python_3_7
+      - name: Updated python version
+        run: python3 --version
+      - name: PYTHONPATH environment variable
+        run: echo ${PYTHONPATH}
+      - name: Update pip
+        run: python3 -m pip install --upgrade --no-cache-dir pip
+        id: pip-install
+      - name: Fetch/update setuptools
+        run: python3 -m pip install --upgrade --no-cache-dir setuptools
+        id: setuptools-install
+      - 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
+        run: sudo apt-get update
+      - name: Fetch/update pylint
+        run: python3 -m pip install --upgrade --no-cache-dir pylint
+        id: pylint-install
+      - name: Fetch source code
+        uses: actions/checkout@v2
+        id: fetch-source
+      - name: Finding files
+        run: find . -type f -name "*.py" > action_pylint_files.txt
+        id: find-python-files
+      - name: Install system requirements
+        shell: bash
+        run: 'sudo apt-get install -y python3-gdal gdal-bin libgdal-dev gcc g++ python3.7-dev'
+        id: install-gdal-other-reqs
+      - name: Install Python numpy
+        shell: bash
+        run: 'python3 -m pip install --upgrade --no-cache-dir numpy wheel terrautils'
+        id: install-python-numpy
+      - name: Install Python pygdal
+        shell: bash
+        run: 'sudo python3 -m pip install --no-cache-dir pygdal==2.2.3.5'
+        id: install-python-pygdal
+      - name: Install system requirements from source
+        shell: bash
+        run: '[ -s "packages.txt" ] && (cat packages.txt | xargs apt-get install -y --no-install-recommends) || (echo "No addtional packages to install")'
+        id: install-system-reqs
+      - name: Install Python requirements from source
+        shell: bash
+        run: '[ -s "requirements.txt" ] && (python3 -m pip install --no-cache-dir -r requirements.txt) || (echo "No Python packages to install")'
+        id: install-python-reqs
+      - name: Run action pylint script
+        shell: bash
+        run: '[ -s ".github/workflows/action_pylint.sh" ] && (chmod +x ".github/workflows/action_pylint.sh" && ./.github/workflows/action_pylint.sh) || (echo "Error running shell script")'
+        id: run-special-action-script
+      - name: Fetching pylint.rc file
+        run: wget https://raw.githubusercontent.com/AgPipeline/Organization-info/master/pylint.rc
+        id: fetch_pylint_resource
+      - name: Listing
+        run: ls -la
+      - name: Files to be linted
+        run: cat action_pylint_files.txt
+      - name: Running pylint
+        run: cat action_pylint_files.txt | xargs python3 -m pylint --rcfile ./pylint.rc
+

.github/workflows/transformer_class.py

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+"""Class instance for Transformer
+"""
+
+import argparse
+
+# pylint: disable=unused-argument
+class Transformer():
+    """Generic class for supporting transformers
+    """
+    def __init__(self, **kwargs):
+        """Performs initialization of class instance
+        Arguments:
+            kwargs: additional parameters passed into Transformer instance
+        """
+        self.args = None
+
+    def add_parameters(self, parser: argparse.ArgumentParser) -> None:
+        """Adds processing parameters to existing parameters
+        Arguments:
+            parser: instance of argparse
+        """
+
+    # pylint: disable=no-self-use
+    def get_transformer_params(self, args: argparse.Namespace, metadata: list) -> dict:
+        """Returns a parameter list for processing data
+        Arguments:
+            args: result of calling argparse.parse_args
+            metadata: the list of loaded metadata
+        Return:
+            A dictionary of parameter names and value to pass to transformer
+        """
+        self.args = args
+
+        params = {}
+        return params
+
+    # pylint: disable=no-self-use
+    def retrieve_files(self, transformer_params: dict, metadata: list) -> tuple:
+        """Retrieves files as needed to make them available for processing
+        Arguments:
+            transformer_params: the values returned from get_transformer_params() call
+            metadata: the loaded metadata
+        Return:
+            A tuple consisting of the return code and an optional error message.
+        Notes:
+            A negative return code is considered an error and an associated message, if specified,
+            will be  treated as such.
+        """
+        return 0, "everything's in order"

Dockerfile

@@ -1,4 +1,4 @@
-FROM agdrone/drone-base-image:1.2
+FROM agdrone/agpypeline:1.0
 LABEL maintainer="Chris Schnaufer <[email protected]>"
 
 COPY requirements.txt packages.txt /home/extractor/
@@ -25,6 +25,9 @@ RUN [ -s /home/extractor/requirements.txt ] && \
     (echo "No python modules to install" && \
     rm /home/extractor/requirements.txt)
 
-USER extractor
 
 COPY *.py /home/extractor/
+RUN chmod a+x /home/extractor/transformer.py
+
+USER extractor
+ENTRYPOINT  ["/home/extractor/transformer.py"]

configuration.py

@@ -1,29 +1,35 @@
 """Contains transformer configuration information
 """
+from agpypeline.configuration import Configuration
 
-# The version number of the transformer
-TRANSFORMER_VERSION = '1.0'
 
-# The transformer description
-TRANSFORMER_DESCRIPTION = 'Base for plot-level RGB-based algorithm transformers'
+class ConfigurationRgbBase(Configuration):
+    """Configuration for RGB Plot base transformer template"""
+    # Silence this error until we have public methods
+    # pylint: disable=too-few-public-methods
+    # The version number of the transformer
+    transformer_version = '1.0'
 
-# Short name of the transformer
-TRANSFORMER_NAME = 'rgb-plot-level-base'
+    # The transformer description
+    transformer_description = 'Base for plot-level RGB-based algorithm transformers'
 
-# The sensor associated with the transformer
-TRANSFORMER_SENSOR = 'stereoTop'
+    # Short name of the transformer
+    transformer_name = 'rgb-plot-level-base'
 
-# The transformer type (eg: 'rgbmask', 'plotclipper')
-TRANSFORMER_TYPE = 'rgb.algorithm.base'
+    # The sensor associated with the transformer
+    transformer_sensor = 'stereoTop'
 
-# The name of the author of the extractor
-AUTHOR_NAME = 'Chris Schnaufer'
+    # The transformer type (eg: 'rgbmask', 'plotclipper')
+    transformer_type = 'rgb.algorithm.base'
 
-# The email of the author of the extractor
-AUTHOR_EMAIL = '[email protected]'
+    # The name of the author of the extractor
+    author_name = 'Chris Schnaufer'
 
-# Contributors to this transformer
-CONTRUBUTORS = []
+    # The email of the author of the extractor
+    author_email = '[email protected]'
 
-# Repository URI of where the source code lives
-REPOSITORY = 'https://github.com/AgPipeline/drone-pipeline-transformer'
+    # Contributors to this transformer
+    contributors = []
+
+    # Repository URI of where the source code lives
+    repository = 'https://github.com/AgPipeline/plot-base-rgb'

packages.txt

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+liblas-bin

requirements.txt

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+liblas
+agpypeline==0.0.20