Delete test files generated from running sphinx gallery examples (#1517)

* Close gallery test files so they can be deleted on Windows

* Delete test files generated from running sphinx gallery examples

* Add coverage files from testing to gitignore

* Update changelog

* Temp

* Update make a tutorial

* Clean up text

* Do not remove coverage files after validate tests

* Remove more test files

* Fix flake8

.gitignore

@@ -58,6 +58,7 @@ docs/tmpl.index.rst
 # coverage output
 tests/coverage/htmlcov
 .coverage
+.coverage.*
 
 # duecredit output
 .duecredit.p

CHANGELOG.md

@@ -4,18 +4,19 @@
 
 ### Documentation and tutorial enhancements:
 - Support explicit ordering of sphinx gallery tutorials in the docs. @oruebel (#1504), @bdichter (#1495)
-- Add developer guide on how to create a new tutorial. @oruebel (#1504) 
+- Add developer guide on how to create a new tutorial. @oruebel (#1504)
 - Add images tutorial. @weiglszonja (#1470)
 - Add example code for s3fs in the streaming tutorial. @bdichter (#1499)
 
 ### Enhancements and minor changes
 - Update coverage workflow, report separate unit vs integration coverage. @rly (#1509)
-- Enable passing an S3File created through s3fs, which provides a method for reading an NWB file directly 
+- Delete test files generated from running sphinx gallery examples. @rly (#1517)
+- Enable passing an S3File created through s3fs, which provides a method for reading an NWB file directly
   from s3 that is an alternative to ros3. This required relaxing of `NWBHDF5IO` input validation. The `path`
-  arg is not needed if `file` is provided. `mode` now has a default value of "r". 
+  arg is not needed if `file` is provided. `mode` now has a default value of "r".
   @bendichter (#1499)
 - Added a method to `NWBMixin` that only raises an error when a check is violated on instance creation,
-  otherwise throws a warning when reading from a file. The new checks in `ImageSeries` when `external_file` 
+  otherwise throws a warning when reading from a file. The new checks in `ImageSeries` when `external_file`
   is provided is used with this method to ensure that that files with invalid data can be read, but prohibits
   the user from creating new instances when these checks are violated. @weiglszonja (#1516)
 

docs/gallery/advanced_io/h5dataio.py

@@ -160,9 +160,8 @@
 
 from pynwb import NWBHDF5IO
 
-io = NWBHDF5IO('advanced_io_example.nwb', 'w')
-io.write(nwbfile)
-io.close()
+with NWBHDF5IO('advanced_io_example.nwb', 'w') as io:
+    io.write(nwbfile)
 
 ####################
 # Reading the data
@@ -182,7 +181,7 @@
                                                                v.data.chunks,
                                                                v.data.compression,
                                                                v.data.maxshape))
-
+io.close()
 ####################
 #
 # .. code-block:: python

docs/gallery/advanced_io/iterative_write.py

@@ -542,16 +542,16 @@ def iter_largearray(filename, shape, dtype='float64'):
 # Read the NWB file
 from pynwb import NWBHDF5IO  # noqa: F811
 
-io = NWBHDF5IO('basic_sparse_iterwrite_largearray.nwb', 'r')
-nwbfile = io.read()
-data = nwbfile.get_acquisition('synthetic_timeseries').data
-# Compare all the data values of our two arrays
-data_match = np.all(arrdata == data[:])   # Don't do this for very large arrays!
-# Print result message
-if data_match:
-    print("Success: All data values match")
-else:
-    print("ERROR: Mismatch between data")
+with NWBHDF5IO('basic_sparse_iterwrite_largearray.nwb', 'r') as io:
+    nwbfile = io.read()
+    data = nwbfile.get_acquisition('synthetic_timeseries').data
+    # Compare all the data values of our two arrays
+    data_match = np.all(arrdata == data[:])   # Don't do this for very large arrays!
+    # Print result message
+    if data_match:
+        print("Success: All data values match")
+    else:
+        print("ERROR: Mismatch between data")
 
 
 ####################

docs/gallery/advanced_io/linking_data.py

@@ -175,6 +175,7 @@
 io4.write(nwbfile4,
           link_data=True)     # <-------- Specify default behavior to link rather than copy data
 io4.close()
+io1.close()
 
 #####################
 # .. note::
@@ -240,6 +241,8 @@
 io3 = NWBHDF5IO(filename3, 'w', manager=manager)
 io3.write(nwbfile3)
 io3.close()
+io1.close()
+io2.close()
 
 
 ####################

docs/gallery/domain/icephys.py

@@ -194,3 +194,6 @@
 # consisting of acquisition and stimulus, from sweep 1.
 
 series = nwbfile.sweep_table.get_series(1)
+
+# close the file
+io.close()

docs/gallery/general/extensions.py

@@ -237,8 +237,8 @@ def __init__(self, **kwargs):
 # explicitly specify this. This behavior is enabled by the *load_namespaces*
 # argument to the :py:class:`~pynwb.NWBHDF5IO` constructor.
 
-io = NWBHDF5IO('cache_spec_example.nwb', mode='r', load_namespaces=True)
-nwbfile = io.read()
+with NWBHDF5IO('cache_spec_example.nwb', mode='r', load_namespaces=True) as io:
+    nwbfile = io.read()
 
 ####################
 # .. _MultiContainerInterface:
@@ -345,16 +345,14 @@ class PotatoSack(MultiContainerInterface):
 
 load_namespaces(ns_path)
 # from xxx import PotatoSack, Potato
-io = NWBHDF5IO('test_multicontainerinterface.nwb', 'r')
-nwb = io.read()
-print(nwb.get_processing_module()['potato_sack'].get_potato('big_potato').weight)
+with NWBHDF5IO('test_multicontainerinterface.nwb', 'r') as io:
+    nwb = io.read()
+    print(nwb.get_processing_module()['potato_sack'].get_potato('big_potato').weight)
 # note: you can call get_processing_module() with or without the module name as
 # an argument. however, if there is more than one module, the name is required.
 # here, there is more than one potato, so the name of the potato is required as
 # an argument to get get_potato
 
-io.close()
-
 ####################
 # Example: Cortical Surface Mesh
 # -----------------------------------------------------

docs/gallery/general/plot_timeintervals.py

@@ -238,7 +238,8 @@
 with NWBHDF5IO('example_timeintervals_file.nwb', 'w') as io:
     io.write(nwbfile)
 # read the file
-io = NWBHDF5IO('example_timeintervals_file.nwb', 'r')
-nwbfile_in = io.read()
-# plot the sleep stages TimeIntervals table
-nwbfile.get_time_intervals('sleep_stages').to_dataframe()
+with NWBHDF5IO('example_timeintervals_file.nwb', 'r') as io:
+    nwbfile_in = io.read()
+
+    # plot the sleep stages TimeIntervals table
+    nwbfile_in.get_time_intervals('sleep_stages').to_dataframe()

docs/gallery/general/scratch.py

@@ -171,3 +171,8 @@
 #    .. note::
 #       We recommend writing scratch data into copies of files only. This will make it easier to
 #       isolate and discard scratch data and avoids updating files that store precious data.
+
+# close the IO objects
+raw_io.close()
+proc_io.close()
+scratch_io.close()

docs/source/make_a_tutorial.rst

@@ -18,6 +18,10 @@ Create a new tutorial
    include the prefix ``plot_`` as part of the name of tutorial file. Tutorials
    without the prefix will render just the code cells and text.
 
+2. Add the names of any files created by running the python file to the
+   ``files_to_remove`` variable in ``clean_up_tests()`` in ``test.py``. This function
+   will remove the created output files after the sphinx-gallery tests are completed.
+
 2. **Optional:** To specify an explicit position for your tutorial in the subsection of the
    gallery, update the ``GALLERY_ORDER`` variable of the ``CustomSphinxGallerySectionSortKey``
    class defined in ``docs/source/conf.py``. If you skip this step, the tutorial will

test.py

@@ -170,6 +170,9 @@ def get_namespaces(nwbfile):
                 cmds += [["python", "-m", "pynwb.validate", "--no-cached-namespace", nwb]]
 
                 for ns in namespaces:
+                    # for some reason, this logging command is necessary to correctly printing the namespace in the
+                    # next logging command
+                    logging.info("Namespace found: %s" % ns)
                     cmds += [["python", "-m", "pynwb.validate", "--cached-namespace", "--ns", ns, nwb]]
 
                 for cmd in cmds:
@@ -228,6 +231,51 @@ def run_integration_tests(verbose=True):
     run_test_suite("tests/validation", "validation CLI tests", verbose=verbose)
 
 
+def clean_up_tests():
+    # remove files generated from running example files
+    files_to_remove = [
+        "advanced_io_example.nwb",
+        "basic_alternative_custom_write.nwb",
+        "basic_iterwrite_example.nwb",
+        "basic_sparse_iterwrite_*.nwb",
+        "basic_sparse_iterwrite_*.npy",
+        "basics_tutorial.nwb",
+        "behavioral_tutorial.nwb",
+        "brain_observatory.nwb",
+        "cache_spec_example.nwb",
+        "ecephys_tutorial.nwb",
+        "ecog.extensions.yaml",
+        "ecog.namespace.yaml",
+        "ex_test_icephys_file.nwb",
+        "example_timeintervals_file.nwb",
+        "exported_nwbfile.nwb",
+        "external_linkcontainer_example.nwb",
+        "external_linkdataset_example.nwb",
+        "external1_example.nwb",
+        "external2_example.nwb",
+        "icephys_example.nwb",
+        "icephys_pandas_testfile.nwb",
+        "images_tutorial.nwb",
+        "manifest.json",
+        "mylab.extensions.yaml",
+        "mylab.namespace.yaml",
+        "nwbfile.nwb",
+        "ophys_tutorial.nwb",
+        "processed_data.nwb",
+        "raw_data.nwb",
+        "scratch_analysis.nwb",
+        "test_cortical_surface.nwb",
+        "test_icephys_file.nwb",
+        "test_multicontainerinterface.extensions.yaml",
+        "test_multicontainerinterface.namespace.yaml",
+        "test_multicontainerinterface.nwb",
+    ]
+    for f in files_to_remove:
+        for name in glob.glob(f):
+            if os.path.exists(name):
+                os.remove(name)
+
+
 def main():
     # setup and parse arguments
     parser = argparse.ArgumentParser('python test.py [options]')
@@ -303,6 +351,10 @@ def main():
     if flags['ros3'] in args.suites:
         run_test_suite("tests/integration/ros3", "pynwb ros3 streaming tests", verbose=args.verbosity)
 
+    # Delete files generated from running example tests above
+    if flags['example'] in args.suites or flags['validation'] in args.suites:
+        clean_up_tests()
+
     final_message = 'Ran %s tests' % TOTAL
     exitcode = 0
     if ERRORS > 0 or FAILURES > 0: