From 5f8040242cca483a9c0ed5d81fa675b6c2982fb7 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 19 May 2023 09:43:42 -0400
Subject: [PATCH 1/2] Create inspecting_workflows.py

---
 .../nipype1/examples/inspecting_workflows.py  | 92 +++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 package/niflow/nipype1/examples/inspecting_workflows.py

diff --git a/package/niflow/nipype1/examples/inspecting_workflows.py b/package/niflow/nipype1/examples/inspecting_workflows.py
new file mode 100644
index 0000000..f2d6001
--- /dev/null
+++ b/package/niflow/nipype1/examples/inspecting_workflows.py
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+===========================
+Inspecting workflow results
+===========================
+
+It can be useful to investigate individual nodes' inputs and outputs in a workflow that has been run.
+For example, this can help developers write unit tests for their workflows.
+
+"""
+import os
+
+from nipype.interfaces import utility as niu
+from nipype.interfaces.base import (BaseInterfaceInputSpec, File,
+                                    SimpleInterface, TraitedSpec, traits)
+from nipype.pipeline import engine as pe
+
+# First, let's start by creating a simple interface to use in our workflow.
+# The WriteString interface just writes a string to a file.
+
+
+class _WriteStringInputSpec(BaseInterfaceInputSpec):
+    in_str = traits.Str(mandatory=True)
+
+
+class _WriteStringOutputSpec(TraitedSpec):
+    out_file = File(exists=True)
+
+
+class WriteString(SimpleInterface):
+    """Write a string to a file."""
+
+    input_spec = _WriteStringInputSpec
+    output_spec = _WriteStringOutputSpec
+
+    def _run_interface(self, runtime):
+        self._results["out_file"] = os.path.join(runtime.cwd, "out_file.txt")
+        with open(self._results["out_file"], "w") as fo:
+            fo.write(self.inputs.in_str)
+
+        return runtime
+
+
+# Now, we can create our workflow.
+# The workflow is very simple- an inputnode, a middle node, and an outputnode.
+wf = pe.Workflow(name="example_workflow")
+
+inputnode = pe.Node(
+    niu.IdentityInterface(fields=["in_str"]),
+    name="inputnode",
+)
+outputnode = pe.Node(
+    niu.IdentityInterface(fields=["out_file"]),
+    name="outputnode",
+)
+write_string = pe.Node(
+    WriteString(),
+    name="write_string",
+)
+
+# fmt:off
+wf.connect([
+    (inputnode, write_string, [("in_str", "in_str")]),
+    (write_string, outputnode, [("out_file", "out_file")]),
+])
+# fmt:on
+
+# At this point, we have our basic workflow structure, so we can set inputs and run it.
+wf.inputs.inputnode.in_str = "hello world"
+wf.base_dir = "."
+results = wf.run()
+
+# Here we define a simple function to make it easier to grab the nodes from the results object.
+
+
+def get_nodes(wf_results):
+    """Load nodes from a Nipype workflow's results."""
+    return {node.fullname: node for node in wf_results.nodes}
+
+
+# Let's grab the nodes and check their contents!
+nodes = get_nodes(results)
+out_file = nodes["example_workflow.write_string"].get_output("out_file")
+with open(out_file, "r") as fo:
+    print(fo.read())  # "hello world"
+
+# The same approach can be used to inspect inputs and outputs of individual nodes within a
+# workflow (except for identity interfaces),
+# so developers can write tests that check every element of a workflow,
+# rather than just the final product.

From f9906b8d3283a3d964d1f0987ab3f41da70945e3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo90@gmail.com>
Date: Fri, 19 May 2023 14:10:02 -0400
Subject: [PATCH 2/2] Apply suggestions from code review

Thanks for the suggestions!

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 package/niflow/nipype1/examples/inspecting_workflows.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/package/niflow/nipype1/examples/inspecting_workflows.py b/package/niflow/nipype1/examples/inspecting_workflows.py
index f2d6001..03c2404 100644
--- a/package/niflow/nipype1/examples/inspecting_workflows.py
+++ b/package/niflow/nipype1/examples/inspecting_workflows.py
@@ -17,11 +17,13 @@
                                     SimpleInterface, TraitedSpec, traits)
 from nipype.pipeline import engine as pe
 
-# First, let's start by creating a simple interface to use in our workflow.
-# The WriteString interface just writes a string to a file.
+"""
+First, let's start by creating a simple interface to use in our workflow.
+The WriteString interface just writes a string to a file.
+"""
 
 
-class _WriteStringInputSpec(BaseInterfaceInputSpec):
+class _WriteStringInputSpec(TraitedSpec):
     in_str = traits.Str(mandatory=True)