Summary

Fixes #2982. Maybe fixes #3527.

(削除) All tests pass locally. ⁸/₁₃ jobs pass on Travis. The Travis failures seem unrelated to the changes in this PR. (削除ここまで)
After rebase, all tests pass.

List of changes proposed in this PR (pull-request)

• Updates

  nipype/nipype/utils/draw_gantt_chart.py

  Line 391 in fa65caf

  def generate_gantt_chart(
  to handle changes to profiler
  • filter log file to include only logged nodes with timing information
  • convert datetime strings to datetime objects before doing datetime math
  • for nodes with timing information but no name, use id or an empty string for name instead of crashing
  • warn if a node is suspected of being included twice instead of raising an exception
  • skip nodes with non-timestamp start and finish values like "N/A" and "Unknown"
    

    nipype/nipype/utils/draw_gantt_chart.py

    Lines 144 to 147 in a08ee57

    try:

    all_res += float(event[resource])

    except ValueError:

    next
    
    

    nipype/nipype/utils/draw_gantt_chart.py

    Lines 151 to 154 in a08ee57

    try:

    all_res -= float(event[resource])

    except ValueError:

    next
• Adds a test

  nipype/nipype/pipeline/plugins/tests/test_callback.py

  Lines 66 to 98 in fa65caf

  @pytest.mark.parametrize("plugin", ["Linear", "MultiProc", "LegacyMultiProc"])

  def test_callback_gantt(tmpdir, plugin):

  import logging

  import logging.handlers

  from os import path

  from nipype.utils.profiler import log_nodes_cb

  from nipype.utils.draw_gantt_chart import generate_gantt_chart

  log_filename = path.join(tmpdir, "callback.log")

  logger = logging.getLogger("callback")

  logger.setLevel(logging.DEBUG)

  handler = logging.FileHandler(log_filename)

  logger.addHandler(handler)

  # create workflow

  wf = pe.Workflow(name="test", base_dir=tmpdir.strpath)

  f_node = pe.Node(

  niu.Function(function=func, input_names=[], output_names=[]), name="f_node"

  )

  wf.add_nodes([f_node])

  wf.config["execution"] = {"crashdump_dir": wf.base_dir, "poll_sleep_duration": 2}

  plugin_args = {"status_callback": log_nodes_cb}

  if plugin != "Linear":

  plugin_args["n_procs"] = 8

  wf.run(plugin=plugin, plugin_args=plugin_args)

  generate_gantt_chart(

  path.join(tmpdir, "callback.log"), 1 if plugin == "Linear" else 8

  )

  assert path.exists(path.join(tmpdir, "callback.log.html"))
  to make sure the Gantt chart HTML page generates without error
• Adds myself as a contributor to .zenodo.json

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.