Upgrade requirements and generate test files workflow (#1550)

Co-authored-by: Oliver Ruebel <[email protected]>
NeurodataWithoutBorders · Sep 1, 2022 · 46627b5 · 46627b5
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -60,10 +60,10 @@ body:
     attributes:
       label: Python Version
       options:
-        - 3.7
-        - 3.8
-        - 3.9
-        - 3.10
+        - "3.7"
+        - "3.8"
+        - "3.9"
+        - "3.10"
     validations:
       required: true
   - type: textarea

diff --git a/.github/workflows/generate_test_files.yml b/.github/workflows/generate_test_files.yml
@@ -39,4 +39,4 @@ jobs:
         with:
           name: test-files-${{ matrix.name }}
           path: |
-            tests/back_compat/*.nwb
+            src/pynwb/testing/*.nwb
diff --git a/.gitignore b/.gitignore
@@ -69,5 +69,8 @@ tests/coverage/htmlcov
 # vscode
 .vscode/
 
-#mypy
+# mypy
 .mypy_cache/
+
+# macos
+.DS_Store
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,27 +1,39 @@
 # PyNWB Changelog
 
-## PyNWB 2.1.1 (Upcoming)
+## PyNWB 2.1.1 (September 1, 2022)
 
 ### 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 images tutorial. @weiglszonja (#1470)
-- Add example code for s3fs in the streaming tutorial. @bdichter (#1499)
+- Added support for explicit ordering of sphinx gallery tutorials in the docs. @oruebel 
+  [#1504](https://github.com/NeurodataWithoutBorders/pynwb/pull/1504), @bdichter
+  [#1495](https://github.com/NeurodataWithoutBorders/pynwb/pull/1495)
+- Added developer guide on how to create a new tutorial. @oruebel
+  [#1504](https://github.com/NeurodataWithoutBorders/pynwb/pull/1504)
+- Added images tutorial. @weiglszonja
+  [#1470](https://github.com/NeurodataWithoutBorders/pynwb/pull/1470)
+- Added example code for fsspec in the streaming tutorial. @bdichter
+  [#1499](https://github.com/NeurodataWithoutBorders/pynwb/pull/1499)
 
 ### Enhancements and minor changes
-- Update coverage workflow, report separate unit vs integration coverage. @rly (#1509)
-- 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
+- Updated coverage workflow, report separate unit vs integration coverage. @rly
+  [#1509](https://github.com/NeurodataWithoutBorders/pynwb/pull/1509)
+- Deleted test files generated from running sphinx gallery examples. @rly
+  [#1517](https://github.com/NeurodataWithoutBorders/pynwb/pull/1517)
+- Enabled 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".
-  @bendichter (#1499)
+  @bendichter
+  [#1499](https://github.com/NeurodataWithoutBorders/pynwb/pull/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`
   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)
+  the user from creating new instances when these checks are violated. @weiglszonja
+  [#1516](https://github.com/NeurodataWithoutBorders/pynwb/pull/1516)
 - Created a GitHub Actions workflow to generate test files for testing backward compatibility. @rly
   [#1548](https://github.com/NeurodataWithoutBorders/pynwb/pull/1548)
-- Enhanced docs for ``LabMetaData`` to clarify its usage @oruebel [#1546](https://github.com/NeurodataWithoutBorders/pynwb/pull/1546)
+- Updated requirements, including allowing numpy 1.23. @rly
+  [#1550](https://github.com/NeurodataWithoutBorders/pynwb/pull/1550)
+- Enhanced docs for ``LabMetaData`` to clarify its usage. @oruebel 
+  [#1546](https://github.com/NeurodataWithoutBorders/pynwb/pull/1546)
 
 ## PyNWB 2.1.0 (July 6, 2022)
 

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,11 +1,11 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB, run PyNWB tests, check code style,
 # compute coverage, and create test environments
 codecov==2.1.12
-coverage==6.3.2
-flake8==4.0.1
+coverage==6.4.2
+flake8==5.0.4
 flake8-debugger==4.1.2
 flake8-print==5.0.0
 importlib-metadata==4.2.0
 pytest==7.1.2
 pytest-cov==3.0.0
-tox==3.25.0
+tox==3.25.1
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
-h5py==3.6.0
-hdmf==3.4.0
+h5py==3.7.0
+hdmf==3.4.2
 numpy==1.21.5  # note that numpy 1.22 dropped python 3.7 support
 pandas==1.3.5  # note that pandas 1.4 dropped python 3.7 support
 python-dateutil==2.8.2
-setuptools==62.2.0
+setuptools==63.4.1
diff --git a/setup.cfg b/setup.cfg
@@ -25,16 +25,16 @@ exclude =
   src/pynwb/_version.py
   src/pynwb/_due.py
 per-file-ignores =
-  docs/gallery/*:E402,T001
-  docs/source/tutorials/*:E402,T001
+  docs/gallery/*:E402,E501,T201
+  docs/source/tutorials/*:E402,T201
   src/pynwb/io/__init__.py:F401
   src/pynwb/legacy/io/__init__.py:F401
   tests/integration/__init__.py:F401
   src/pynwb/testing/__init__.py:F401
-  src/pynwb/validate.py:T001
-  setup.py:T001
-  test.py:T001
-  scripts/*:T001
+  src/pynwb/validate.py:T201
+  setup.py:T201
+  test.py:T201
+  scripts/*:T201
 extend-ignore = E203
 
 [metadata]

diff --git a/setup.py b/setup.py
@@ -20,8 +20,8 @@
 
 reqs = [
     'h5py>=2.10,<4',
-    'hdmf>=3.3.2,<4',
-    'numpy>=1.16,<1.23',
+    'hdmf>=3.4.2,<4',
+    'numpy>=1.16,<1.24',
     'pandas>=1.0.5,<2',
     'python-dateutil>=2.7,<3',
     'setuptools'

diff --git a/src/pynwb/testing/make_test_files.py b/src/pynwb/testing/make_test_files.py
@@ -1,4 +1,5 @@
 import numpy as np
+from pathlib import Path
 
 from datetime import datetime
 from pynwb import NWBFile, NWBHDF5IO, __version__, TimeSeries
@@ -11,8 +12,7 @@
 
 
 def _write(test_name, nwbfile):
-    filename = 'tests/back_compat/%s_%s.nwb' % (__version__, test_name)
-
+    filename = str("%s/%s_%s.nwb") % (Path(__file__).parent, __version__, test_name)
     with NWBHDF5IO(filename, 'w') as io:
         io.write(nwbfile)
 
@@ -83,7 +83,7 @@ def _make_imageseries_no_data():
     image_series = ImageSeries(
         name='test_imageseries',
         external_file=['external_file'],
-        starting_frame=[1, 2, 3],
+        starting_frame=[1],
         format='external',
         timestamps=[1., 2., 3.]
     )
@@ -152,6 +152,8 @@ def _make_imageseries_nonmatch_starting_frame():
 if __name__ == '__main__':
     # install these versions of PyNWB and run this script to generate new files
     # python src/pynwb/testing/make_test_files.py
+    # files will be made in src/pynwb/testing/
+    # files should be moved to tests/back_compat/
 
     if __version__ == '1.1.2':
         _make_empty()

diff --git a/tests/back_compat/1.5.1_imageseries_no_data.nwb b/tests/back_compat/1.5.1_imageseries_no_data.nwb
diff --git a/tests/back_compat/1.5.1_imageseries_no_unit.nwb b/tests/back_compat/1.5.1_imageseries_no_unit.nwb
diff --git a/tests/back_compat/1.5.1_timeseries_no_data.nwb b/tests/back_compat/1.5.1_timeseries_no_data.nwb
diff --git a/tests/back_compat/1.5.1_timeseries_no_unit.nwb b/tests/back_compat/1.5.1_timeseries_no_unit.nwb
diff --git a/tests/back_compat/2.1.0_imageseries_no_data.nwb b/tests/back_compat/2.1.0_imageseries_no_data.nwb
diff --git a/tests/back_compat/2.1.0_imageseries_non_external_format.nwb b/tests/back_compat/2.1.0_imageseries_non_external_format.nwb
diff --git a/tests/back_compat/2.1.0_imageseries_nonmatch_starting_frame.nwb b/tests/back_compat/2.1.0_imageseries_nonmatch_starting_frame.nwb
diff --git a/tests/back_compat/test_read.py b/tests/back_compat/test_read.py
@@ -9,6 +9,17 @@
 
 class TestReadOldVersions(TestCase):
 
+    expected_warnings = {
+        ''
+        '2.1.0_imageseries_non_external_format.nwb': [(
+            "ImageSeries 'test_imageseries': Format must be 'external' when external_file is specified."
+        )],
+        '2.1.0_imageseries_nonmatch_starting_frame.nwb': [(
+            "ImageSeries 'test_imageseries': The number of frame indices in 'starting_frame' should have the same "
+            "length as 'external_file'."
+        )],
+    }
+
     expected_errors = {
         '1.0.2_str_experimenter.nwb': [("root/general/experimenter (general/experimenter): incorrect shape - expected "
                                         "an array of shape '[None]', got non-array data 'one experimenter'")],
@@ -20,17 +31,6 @@ class TestReadOldVersions(TestCase):
                                "- expected an array of shape '[None]', got non-array data 'one publication'")],
     }
 
-    @classmethod
-    def setUpClass(cls):
-        cls.image_series_warnings = [
-            "ImageSeries 'test_imageseries': Either external_file or data must be "
-            "specified (not None), but not both.",
-            "ImageSeries 'test_imageseries': The number of frame indices in "
-            "'starting_frame' should have the same length as 'external_file'.",
-            "ImageSeries 'test_imageseries': Format must be 'external' when "
-            "external_file is specified.",
-        ]
-
     def test_read(self):
         """Test reading and validating all NWB files in the same folder as this file.
 
@@ -41,15 +41,29 @@ def test_read(self):
         nwb_files = dir_path.glob('*.nwb')
         for f in nwb_files:
             with self.subTest(file=f.name):
-                with NWBHDF5IO(str(f), 'r') as io:
-                    errors = validate(io)
-                    io.read()
-                    if errors:
-                        for e in errors:
-                            if f.name in self.expected_errors and str(e) not in self.expected_errors[f.name]:
-                                warnings.warn('%s: %s' % (f.name, e))
-                        # TODO uncomment below when validation errors have been fixed
-                        # raise Exception('%d validation error(s). See warnings.' % len(errors))
+                with warnings.catch_warnings(record=True) as warnings_on_read:
+                    with NWBHDF5IO(str(f), 'r') as io:
+                        errors = validate(io)
+                        io.read()
+                        for w in warnings_on_read:
+                            if f.name in self.expected_warnings:
+                                if str(w.message) not in self.expected_warnings[f.name]:
+                                    pass
+                                    # will replace above with below after the test file is updated
+                                    # raise Exception("Unexpected warning: %s: %s" % (f.name, str(w.message)))
+                            else:
+                                pass
+                                # will replace above with below after the test file is updated
+                                # raise Exception("Unexpected warning: %s: %s" % (f.name, str(w.message)))
+                        if errors:
+                            for e in errors:
+                                if f.name in self.expected_errors:
+                                    if str(e) not in self.expected_errors[f.name]:
+                                        warnings.warn('%s: %s' % (f.name, e))
+                                else:
+                                    raise Exception("Unexpected validation error: %s: %s" % (f.name, e))
+                            # TODO uncomment below when validation errors have been fixed
+                            # raise Exception('%d validation error(s). See warnings.' % len(errors))
 
     def test_read_timeseries_no_data(self):
         """Test that a TimeSeries written without data is read with data set to the default value."""
@@ -72,36 +86,29 @@ def test_read_imageseries_no_data(self):
             read_nwbfile = io.read()
             np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].data, ImageSeries.DEFAULT_DATA)
 
-    def test_read_imageseries_no_data_warns_when_checks_are_violated(self):
-        """Test that warnings are raised when an ImageSeries is read that was created
-        incorrectly."""
-        f = Path(__file__).parent / "1.5.1_imageseries_no_data.nwb"
-        with warnings.catch_warnings(record=True) as warnings_on_read:
-            with NWBHDF5IO(str(f), "r") as io:
-                io.read()
-                warning_msgs = [warning.message.args[0] for warning in warnings_on_read]
-                self.assertEqual(len(warning_msgs), 2)
-                self.assertTrue(
-                    all(msg in warning_msgs for msg in self.image_series_warnings[1:])
-                )
-                assert self.image_series_warnings[0] not in warning_msgs
-
     def test_read_imageseries_no_unit(self):
         """Test that an ImageSeries written without unit is read with unit set to the default value."""
         f = Path(__file__).parent / '1.5.1_imageseries_no_unit.nwb'
         with NWBHDF5IO(str(f), 'r') as io:
             read_nwbfile = io.read()
             self.assertEqual(read_nwbfile.acquisition['test_imageseries'].unit, ImageSeries.DEFAULT_UNIT)
 
-    def test_read_imageseries_no_unit_warns_when_checks_are_violated(self):
-        """Test that warnings are raised when an ImageSeries is read that was created
-        incorrectly."""
-        f = Path(__file__).parent / "1.5.1_imageseries_no_unit.nwb"
-        with warnings.catch_warnings(record=True) as warnings_on_read:
-            with NWBHDF5IO(str(f), "r") as io:
-                io.read()
-                warning_msgs = [warning.message.args[0] for warning in warnings_on_read]
-                self.assertEqual(len(warning_msgs), 3)
-                self.assertTrue(
-                    all(msg in warning_msgs for msg in self.image_series_warnings)
-                )
+    def test_read_imageseries_non_external_format(self):
+        """Test that reading an ImageSeries with an inconsistent format does not change the value."""
+        fbase = "2.1.0_imageseries_non_external_format.nwb"
+        f = Path(__file__).parent / fbase
+        expected_warning = self.expected_warnings[fbase][0]
+        with self.assertWarnsWith(UserWarning, expected_warning):
+            with NWBHDF5IO(str(f), 'r') as io:
+                read_nwbfile = io.read()
+                self.assertEqual(read_nwbfile.acquisition['test_imageseries'].format, "tiff")
+
+    def test_read_imageseries_nonmatch_starting_frame(self):
+        """Test that reading an ImageSeries with an inconsistent starting_frame does not change the value."""
+        fbase = "2.1.0_imageseries_nonmatch_starting_frame.nwb"
+        f = Path(__file__).parent / fbase
+        expected_warning = self.expected_warnings[fbase][0]
+        with self.assertWarnsWith(UserWarning, expected_warning):
+            with NWBHDF5IO(str(f), 'r') as io:
+                read_nwbfile = io.read()
+                np.testing.assert_array_equal(read_nwbfile.acquisition['test_imageseries'].starting_frame, [1, 2, 3])