Refactor parallel subpackage to use dataframes and grouping

[nfahlgren]

Describe your changes
This PR makes several major changes to the parallel subpackage.

.github/workflows/continuous-integration.yml:

• Use pip to install PlantCV instead of setup.py.

plantcv/parallel/__init__.py:

• Remove deprecated functions convert_datetime_to_unixtime and check_date_range.
• Import new workflow_inputs function and WorkflowInputs class. These are from new module for handling workflow inputs in Jupyter notebooks and scripts was added to make it easier to migrate from Jupyter to a parallel workflow script.
• WorkflowConfig default timestamp format was updated to an ISO 8601 UTC datetime.
• Remove WorkflowConfig coprocess attribute and replace with groupby and group_name attributes. The new attributes are used to group images in the new dataframe-based metadata parser framework and name the image inputs to parallel workflows.
• A new rotation metadata attribute was added to WorkflowConfig.
• The plantbarcode metadata attribute in WorkflowConfig was renamed to barcode to be more general.

plantcv/parallel/parsers.py:

• The parsers module was completely rewritten to reduce complexity and utilize dataframes for easier filtering and grouping.
• A new input data format (phenodata) was added to the parsers module.
• All data formats in the parsers module are read into a common data structure, which allows them to all be converted to a dataframe using a single method. New data formats can be added by adding a new private function and reading the data into the common data structure.
• Dataframes in the parser module can be grouped on one or more metadata terms, the grouped dataframe is passed to the job builder module.

plantcv/parallel/job_builder.py:

• The job builder module was updated to handle grouped dataframes and remove coprocessing logic.
• The job builder module was updated to pass arguments to the new workflow_inputs-based argparse framework.
• The job builder module can automatically name workflow input images if requested (e.g., image1, image2, etc.)
• Temp JSON files are now named with unique alphanumeric identifiers (UUID) since they can represent data for multiple images.

plantcv/parallel/workflow_inputs.py:

• New module for defining/handling standard workflow inputs in both Jupyter and parallel workflow script contexts.
• The WorkflowInputs class is used to set Jupyter notebook input variables in a framework that is compatible with the command-line arguments used in parallel workflow scripts.
• The workflow_inputs function creates a standardized argparse command-line argument parser for workflows.

plantcv/parallel/process_results.py:

• The JSON output file is now formatted with line returns and indentation for easier viewing.

plantcv/utils/converters.py:

• The json2csv util function was updated to handle grouped output data.
• json2csv now only outputs a single CSV file in long format.

Additionally, relevant tests were added/updated. Documentation was updated where necessary.

Type of update
Is this a: New feature or feature enhancement

Associated issues
Closes #474
Closes #423
Closes #538
Replaces #759

[codecov]

Codecov Report

Merging #887 (6c88106) into 4.x (19beef2) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##               4.x      #887   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files          159       160    +1     
  Lines         6738      6714   -24     
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- Hits          6738      6714   -24     

Flag	Coverage Δ
unittests	100.00% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
plantcv/parallel/multiprocess.py	100.00% <ø> (ø)
plantcv/parallel/__init__.py	100.00% <100.00%> (ø)
plantcv/parallel/job_builder.py	100.00% <100.00%> (ø)
plantcv/parallel/parsers.py	100.00% <100.00%> (ø)
plantcv/parallel/process_results.py	100.00% <100.00%> (ø)
plantcv/parallel/workflow_inputs.py	100.00% <100.00%> (ø)
plantcv/utils/converters.py	100.00% <100.00%> (ø)

[HaleySchuhl]

Error handling for "images" input in Workflow Image when input is not a list.

[nfahlgren]

@JorgeGtz found an issue with the other_args configuration property. In the new workflow_inputs function other is an input keyword argument but other_args are individual arguments and values that are appended to the workflow but are not parsed by the workflow_inputs function.

I think I can refactor other_args to be a dictionary and then have workflow_inputs parse the keywords and values so that they are available in the argparse object.