Merge pull request #1848 from danforthcenter/exclude-plot-image

Exclude plot image

Author: nfahlgren

docs/parallel_jupyterconfig.md

@@ -4,7 +4,7 @@ The `jupyterconfig` class is very similar to the [`WorkflowConfig` class](parall
 
 ### Quick Start
 
-Initializing a `jupyterconfig` object in a Jupyter notebook will immediately use `nbconvert` to create a python script version of the workflow. When the python script is generated notebook cells marked with `@ignore` as the start of a comment (`# @ignore`) are excluded, which may be useful to avoid making diagnostic plots in parallel or otherwise in keeping your notebook reproducible. Similar to `WorkflowConfig` objects you can overwrite default attributes to meet your particular needs. Once your edits are done the `run` method will run the workflow in parallel. Note that you will need to specify arguments with [`workflow_inputs`](parallel_workflow_inputs.md) how you would when using `WorkflowConfig` to run a script in parallel.
+Initializing a `jupyterconfig` object in a Jupyter notebook will immediately use `nbconvert` to create a python script version of the workflow. When the python script is generated notebook cells marked with `@ignore` as the start of a comment (`# @ignore`) are excluded, which may be useful to avoid making diagnostic plots in parallel or otherwise in keeping your notebook reproducible. Any calls to `plot_image` will also be removed. Similar to `WorkflowConfig` objects you can overwrite default attributes to meet your particular needs. Once your edits are done the `run` method will run the workflow in parallel. Note that you will need to specify arguments with [`workflow_inputs`](parallel_workflow_inputs.md) how you would when using `WorkflowConfig` to run a script in parallel.
 
 ```python
 from plantcv import parallel as pcvpar

plantcv/parallel/jupyterconfig.py

@@ -143,7 +143,8 @@ def notebook2script(self):
             source, _ = exporter.from_notebook_node(nb)
             # Write the output to a Python file
             with open(self.workflow, 'w') as fh:
-                fh.writelines(source)
+                pattern = pattern = r".*?(.*?[.])?plot_image\(.*?\).*\n?|.*get_ipython\(\).*\n?"
+                fh.writelines(re.sub(pattern, "", source))
             # return boolean for if self.script exists
         return os.path.exists(self.workflow)