pytest fails - dataframe mismatch?

[nathanlyons]

@kbarnhart I installed Dakota and the repo on MacOS, and then created an environment as described in the install instructions. The stuff below was printed after only a few seconds running pytest.

(dakota_clinic) mm77:calibration_with_dakota_clinic njlyons$ pytest
======================================= test session starts ========================================
platform darwin -- Python 3.7.3, pytest-4.5.0, py-1.8.0, pluggy-0.11.0
rootdir: /Users/njlyons/Code/calibration_with_dakota_clinic, inifile: setup.cfg, testpaths: heat, tests
collected 6 items

heat/heat.py .. [ 33%]
tests/test_all_notebooks.py F [ 50%]
tests/test_frame_equal.py FFF [100%]

============================================= FAILURES ==============================================
_ test_notebook[/Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb] _
Traceback (most recent call last):
File "/Users/njlyons/Code/calibration_with_dakota_clinic/tests/test_all_notebooks.py", line 65, in test_notebook
nb, errors = _notebook_run(notebook)
File "/Users/njlyons/Code/calibration_with_dakota_clinic/tests/test_all_notebooks.py", line 48, in _notebook_run
subprocess.check_call(args)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['jupyter', 'nbconvert', '--to', 'notebook', '--execute', '--ExecutePreprocessor.kernel_name=python', '--ExecutePreprocessor.timeout=None', '--output', '/var/folders/f4/hg6s0z510jx0kwbqsfhbc62c0000gn/T/tmp3hetj8lc.ipynb', '--output-dir=.', '/Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb']' returned non-zero exit status 1.
--------------------------------------- Captured stderr call ----------------------------------------
[NbConvertApp] Converting notebook /Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb to notebook
[NbConvertApp] Executing notebook with kernel: python

Error reading restart file 'dakota_02_nl2sol.rst' (empty or corrupt file).
Details (Boost archive exception): input stream error

Error reading restart file 'dakota_03_ego.rst' (empty or corrupt file).
Details (Boost archive exception): input stream error
[NbConvertApp] ERROR | Error while converting '/Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb'
Traceback (most recent call last):
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 408, in export_single_notebook
output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
return self.from_file(f, resources=resources, **kw)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 197, in from_file
return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/exporters/notebook.py", line 32, in from_notebook_node
nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 139, in from_notebook_node
nb_copy, resources = self._preprocess(nb_copy, resources)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 316, in _preprocess
nbc, resc = preprocessor(nbc, resc)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/preprocessors/base.py", line 47, in call
return self.preprocess(nb, resources)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 381, in preprocess
nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/preprocessors/base.py", line 69, in preprocess
nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 424, in preprocess_cell
raise CellExecutionError.from_cell_and_msg(cell, out)
nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:

files = glob.glob(os.path.join(TOP_DIR, "analysis", "*.dat"))
dfs = []
for file in files:
df = pd.read_csv(file, engine="python", delim_whitespace=True)
df["method"] = file.split(".")[0].split("_")[-1]
dfs.append(df)

df = pd.concat(dfs, ignore_index=True)
method_cats = CategoricalDtype(categories=["grid", "nl2sol", "ego"], ordered=True)
df["method"] = df["method"].astype(method_cats)
df = df.set_index(["method", "deltaT", "duration_years"]).drop(columns=["interface"])

(
ggplot(df.reset_index(), aes(x="deltaT", y="duration_years", color="%eval_id"))
+ geom_point()
+ scale_color_cmap(name="jet")
+ facet_wrap("~method")
)

---

PlotnineError Traceback (most recent call last)
~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/IPython/core/formatters.py in call(self, obj)
700 type_pprinters=self.type_printers,
701 deferred_pprinters=self.deferred_printers)
--> 702 printer.pretty(obj)
703 printer.flush()
704 return stream.getvalue()

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/IPython/lib/pretty.py in pretty(self, obj)
400 if cls is not object
401 and callable(cls.dict.get('repr')):
--> 402 return _repr_pprint(obj, self, cycle)
403
404 return _default_pprint(obj, self, cycle)

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/IPython/lib/pretty.py in repr_pprint(obj, p, cycle)
695 """A pprint that just redirects to the normal repr function."""
696 # Find newlines and replace them with p.break()
--> 697 output = repr(obj)
698 for idx,output_line in enumerate(output.splitlines()):
699 if idx:

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/ggplot.py in repr(self)
93 # in the jupyter notebook.
94 if not self.figure:
---> 95 self.draw()
96 plt.show()
97 return '<ggplot: (%d)>' % self.hash()

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/ggplot.py in draw(self, return_ggplot)
186 # new frames knowing that they are separate from the original.
187 with pd.option_context('mode.chained_assignment', None):
--> 188 return self._draw(return_ggplot)
189
190 def _draw(self, return_ggplot=False):

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/ggplot.py in _draw(self, return_ggplot)
193 # assign a default theme
194 self = deepcopy(self)
--> 195 self._build()
196
197 # If no theme we use the default

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/ggplot.py in _build(self)
286 # Initialise panels, add extra data for margins & missing
287 # facetting variables, and add on a PANEL variable to data
--> 288 layout.setup(layers, self)
289
290 # Compute aesthetics to produce data with generalised

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/facets/layout.py in setup(self, layers, plot)
56 # Generate panel layout
57 data = self.facet.setup_data(data)
---> 58 self.layout = self.facet.compute_layout(data)
59 self.layout = self.coord.setup_layout(self.layout)
60 self.check_layout()

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/facets/facet_wrap.py in compute_layout(self, data)
68
69 base = combine_vars(data, self.plot.environment,
---> 70 self.vars, drop=self.drop)
71 n = len(base)
72 dims = wrap_dims(n, self.nrow, self.ncol)

~/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/plotnine/facets/facet.py in combine_vars(data, environment, vars, drop)
602 if len(base) == 0:
603 raise PlotnineError(
--> 604 "Faceting variables must have at least one value")
605
606 base = base.reset_index(drop=True)

PlotnineError: 'Faceting variables must have at least one value'
PlotnineError: 'Faceting variables must have at least one value'

____________________________ test_dat_equiv[analysis/dakota_03_ego.dat] _____________________________
Traceback (most recent call last):
File "/Users/njlyons/Code/calibration_with_dakota_clinic/tests/test_frame_equal.py", line 20, in test_dat_equiv
check_less_precise=2)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1458, in assert_frame_equal
'{shape!r}'.format(shape=right.shape))
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1094, in raise_assert_detail
raise AssertionError(msg)
AssertionError: DataFrame are different

DataFrame shape mismatch
[left]: (0, 5)
[right]: (63, 5)
____________________________ test_dat_equiv[analysis/dakota_01_grid.dat] ____________________________
Traceback (most recent call last):
File "/Users/njlyons/Code/calibration_with_dakota_clinic/tests/test_frame_equal.py", line 20, in test_dat_equiv
check_less_precise=2)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1458, in assert_frame_equal
'{shape!r}'.format(shape=right.shape))
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1094, in raise_assert_detail
raise AssertionError(msg)
AssertionError: DataFrame are different

DataFrame shape mismatch
[left]: (0, 5)
[right]: (100, 5)
___________________________ test_dat_equiv[analysis/dakota_02_nl2sol.dat] ___________________________
Traceback (most recent call last):
File "/Users/njlyons/Code/calibration_with_dakota_clinic/tests/test_frame_equal.py", line 20, in test_dat_equiv
check_less_precise=2)
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1458, in assert_frame_equal
'{shape!r}'.format(shape=right.shape))
File "/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/pandas/util/testing.py", line 1094, in raise_assert_detail
raise AssertionError(msg)
AssertionError: DataFrame are different

DataFrame shape mismatch
[left]: (0, 5)
[right]: (50, 5)
========================================= warnings summary ==========================================
/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbformat/notebooknode.py:4
/Users/njlyons/anaconda3/envs/dakota_clinic/lib/python3.7/site-packages/nbformat/notebooknode.py:4: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Mapping

-- Docs: https://docs.pytest.org/en/latest/warnings.html
===================================== slowest 16 test durations =====================================
47.37s call tests/test_all_notebooks.py::test_notebook[/Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb]
0.07s call heat/heat.py::heat.heat.solve_1d
0.02s call heat/heat.py::heat.heat.Heat
0.01s call tests/test_frame_equal.py::test_dat_equiv[analysis/dakota_03_ego.dat]
0.01s call tests/test_frame_equal.py::test_dat_equiv[analysis/dakota_02_nl2sol.dat]
0.01s call tests/test_frame_equal.py::test_dat_equiv[analysis/dakota_01_grid.dat]
0.01s setup tests/test_all_notebooks.py::test_notebook[/Users/njlyons/Code/calibration_with_dakota_clinic/Clinic_Notes_and_Tutorial.ipynb]

(0.00 durations hidden. Use -vv to show these durations.)
========================== 4 failed, 2 passed, 1 warnings in 48.53 seconds ==========================

[kbarnhart]

@nathanlyons thanks for reporting this. This error is consistent with Dakota not running.
A couple of follow up questions:

1. What is your OS?
2. Is there anything inside of the file dakota_01_grid.log?