Prepare PyNWB 2.1.0 (#1492)

* Update changelog * Update requirements * Update submodule to 2.5.0 * Revert validation tests to python 3.8 because of allensdk incompat * See last commit * Update changelog * Update dandi req * Fix intersphinx * Fix missing crossref * Update release template * Increase timeout to reduce validation timeout errors * Improve comments * Temporarily run all CircleCI tests * Don't run ros3 examples in validation tests * Revert "Temporarily run all CircleCI tests" This reverts commit 5f6a9a5.
NeurodataWithoutBorders · Jul 7, 2022 · 2bf5d19 · 2bf5d19
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -314,7 +314,7 @@ jobs:
             python test.py --example-ros3
 
   test-validation:
-    <<: *py39
+    <<: *py38
     steps:
       - checkout
       - run: git submodule sync
@@ -326,7 +326,7 @@ jobs:
           command: |
             . ../venv/bin/activate
             pip install tox
-            tox -e validation-py39
+            tox -e validation-py38
           # Install is expected to be quick. Increase timeout in case there are some network issues.
           # While pip installing tox does not output by default. Circle thinks task is dead after 10 min.
           no_output_timeout: 30m

diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md
@@ -10,9 +10,9 @@ Prepare for release of PyNWB [version]
 - [ ] Update `README.rst` as needed
 - [ ] Update `src/pynwb/nwb-schema` submodule as needed. Check the version number and commit SHA manually
 - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed
-- [ ] Run tests locally including gallery tests and validation tests, and inspect all warnings and outputs
-  (`python test.py -v > out.txt`)
-- [ ] Test docs locally (`make apidoc`, `make html`)
+- [ ] Run tests locally including gallery, validation, and streaming tests, and inspect all warnings and outputs
+  (`python test.py -v -p -i -b -w -r > out.txt 2>&1`)
+- [ ] Test docs locally (`make clean`, `make html`)
 - [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged
 - [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and
   build docs for new branch): https://readthedocs.org/projects/pynwb/builds/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,9 +1,8 @@
 # PyNWB Changelog
 
-## PyNWB 2.1.0 (Upcoming)
+## PyNWB 2.1.0 (July 6, 2022)
 
 ### Breaking changes:
-- A warning is now raised if `SpatialSeries.data` has more than 3 columns. @bendichter, @rly (#1455, #1480)
 - Updated ``TimeIntervals`` to use the new  ``TimeSeriesReferenceVectorData`` type. This does not alter the overall
   structure of ``TimeIntervals`` in a major way aside from changing the value of the ``neurodata_type`` attribute of the
   ``TimeIntervals.timeseries`` column from ``VectorData`` to ``TimeSeriesReferenceVectorData``. This change facilitates
@@ -16,7 +15,9 @@
   behavior of the API is largely consistent with existing behavior. @oruebel, @rly (#1390)
 
 # Enhancements and minor changes
+- A warning is now raised if `SpatialSeries.data` has more than 3 columns. @bendichter, @rly (#1455, #1480)
 - The arguments x, y, z, imp, location, filtering are no longer required in the electrodes table.
+  @h-mayorquin, @rly (#1448)
 - Added `cell_id` attribute to `IntracellularElectrode`. @bendichter (#1459)
 - Added `offset` field to `TimeSeries` and its subtypes. @codycbakerphd (#1424)
 - Added support for NWB 2.5.0.
@@ -33,11 +34,11 @@
 
 ### Documentation and tutorial enhancements:
 - Added tutorial on annotating data via ``TimeIntervals``. @oruebel (#1390)
-- Added copy button to code blocks @weiglszonja (#1460)
-- Created behavioral tutorial @weiglszonja (#1464)
+- Added copy button to code blocks. @weiglszonja (#1460)
+- Created behavioral tutorial. @weiglszonja (#1464)
 - Enhanced display of icephys pandas tutorial by using ``dataframe_image`` to render and display large tables
   as images. @oruebel (#1469)
-- Created tutorial about reading and exploring an existing `NWBFile` @weiglszonja (#1453)
+- Created tutorial about reading and exploring an existing `NWBFile`. @weiglszonja (#1453)
 - Added new logo for PyNWB. @oruebel (#1461)
 - Minor text fixes. @oruebel @bendichter (#1443, #1462, #1463, #1466, #1472, #1473)
 

diff --git a/docs/gallery/general/plot_timeintervals.py b/docs/gallery/general/plot_timeintervals.py
@@ -69,6 +69,8 @@
 # tables for :py:meth:`~pynwb.file.NWBFile.epochs`, :py:meth:`~pynwb.file.NWBFile.trials`, and
 # :py:meth:`~pynwb.file.NWBFile.invalid_times`.
 #
+# .. _basic_trials:
+#
 # Trials
 # ^^^^^^
 #

diff --git a/docs/gallery/general/read_basics.py b/docs/gallery/general/read_basics.py
@@ -183,7 +183,8 @@
 #
 #     (200, 400, 300, 3)
 #
-# This :py:class:`~pynwb.image.OpticalSeries` data contains 200 images of size 400x300 pixels with three channels (red, green, and blue).
+# This :py:class:`~pynwb.image.OpticalSeries` data contains 200 images of size 400x300 pixels with three channels
+# (red, green, and blue).
 #
 # Slicing datasets
 # ----------------

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -74,9 +74,9 @@
 }
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.8', None),
+    'python': ('https://docs.python.org/3.9', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
-    'matplotlib': ('https://matplotlib.org', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
     'h5py': ('https://docs.h5py.org/en/latest/', None),
     'hdmf': ('https://hdmf.readthedocs.io/en/latest/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),

diff --git a/environment-ros3.yml b/environment-ros3.yml
@@ -6,10 +6,10 @@ channels:
 dependencies:
   - python=3.9
   - h5py==3.6.0
-  - hdmf==3.3.1
+  - hdmf==3.3.2
   - matplotlib==3.5.1
-  - numpy==1.21.0
-  - pandas==1.3.0
-  - python-dateutil==2.8.1
+  - numpy==1.21.5
+  - pandas==1.3.5
+  - python-dateutil==2.8.2
   - setuptools
-  - dandi==0.39.4
+  - dandi==0.43.0
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,9 +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==2.1.11
-coverage==5.5
-flake8==3.9.2
-flake8-debugger==4.0.0
-flake8-print==4.0.0
-importlib-metadata==4.6.1
-tox==3.23.1
+codecov==2.1.12
+coverage==6.3.2
+flake8==4.0.1
+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
diff --git a/requirements-doc.txt b/requirements-doc.txt
@@ -1,7 +1,8 @@
-# dependencies to generate the documentation for PyNWB
-sphinx
+# dependencies to generate the documentation for PyNWB and test run the sphinx gallery examples that do not require
+# ROS3 support in h5py. For those examples, use the conda env specified in environment-ros3.yml
+sphinx>=4  # improved support for docutils>=0.17
+sphinx_rtd_theme>=1  # <1 does not work with docutils>=0.17
 matplotlib
-sphinx_rtd_theme
 sphinx-gallery
 allensdk>=2.11.0  # python 3.8 is not supported in allensdk<2.11
 MarkupSafe==2.0.1  # resolve incompatibility between jinja2 and markupsafe: https://github.com/AllenInstitute/AllenSDK/issues/2308

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,6 +1,6 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.3.1
+hdmf==3.3.2
 numpy==1.16
 pandas==1.0.5
 python-dateutil==2.7

diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
-h5py==3.3.0
-hdmf==3.3.1
-numpy==1.21.0
-pandas==1.3.0
-python-dateutil==2.8.1
-setuptools==57.1.0
+h5py==3.6.0
+hdmf==3.3.2
+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
diff --git a/setup.py b/setup.py
@@ -19,9 +19,9 @@
 schema_dir = 'nwb-schema/core'
 
 reqs = [
-    'h5py>=2.9,<4',
-    'hdmf>=3.1.1,<4',
-    'numpy>=1.16,<1.22',
+    'h5py>=2.10,<4',
+    'hdmf>=3.3.2,<4',
+    'numpy>=1.16,<1.23',
     'pandas>=1.0.5,<2',
     'python-dateutil>=2.7,<3',
     'setuptools'

diff --git a/src/pynwb/nwb-schema b/src/pynwb/nwb-schema
diff --git a/test.py b/test.py
@@ -73,6 +73,7 @@ def _import_from_file(script):
 
 
 def run_example_tests():
+    """Run the Sphinx gallery example files, excluding ROS3-dependent ones, to check for errors."""
     logging.info('running example tests')
     examples_scripts = list()
     for root, dirs, files in os.walk(os.path.join(os.path.dirname(__file__), "docs", "gallery")):
@@ -88,6 +89,7 @@ def run_example_tests():
 
 
 def run_example_ros3_tests():
+    """Run the Sphinx gallery example files that depend on ROS3 to check for errors."""
     logging.info('running example ros3 tests')
     examples_scripts = list()
     for root, dirs, files in os.walk(os.path.join(os.path.dirname(__file__), "docs", "gallery")):
@@ -149,7 +151,7 @@ def validate_nwbs():
                 def get_namespaces(nwbfile):
                     comp = run(["python", "-m", "pynwb.validate",
                                "--list-namespaces", "--cached-namespace", nwb],
-                               stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=20)
+                               stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=30)
 
                     if comp.returncode != 0:
                         return []
@@ -172,7 +174,7 @@ def get_namespaces(nwbfile):
 
                 for cmd in cmds:
                     logging.info("Validating with \"%s\"." % (" ".join(cmd[:-1])))
-                    comp = run(cmd, stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=20)
+                    comp = run(cmd, stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=30)
                     TOTAL += 1
 
                     if comp.returncode != 0:
@@ -273,17 +275,17 @@ def main():
         run_test_suite("tests/unit", "pynwb unit tests", verbose=args.verbosity)
 
     # Run example tests
-    if flags['example'] in args.suites:
+    if flags['example'] in args.suites or flags['validation'] in args.suites:
         run_example_tests()
 
     # Run example tests with ros3 streaming examples
+    # NOTE this requires h5py to be built with ROS3 support and the dandi package to be installed
+    # this is most easily done by creating a conda environment using environment-ros3.yml
     if flags['example-ros3'] in args.suites:
         run_example_ros3_tests()
 
-    # Run validation tests
+    # Run validation tests on the example NWB files generated above
     if flags['validation'] in args.suites:
-        run_example_tests()
-        run_example_ros3_tests()
         validate_nwbs()
 
     # Run integration tests

diff --git a/tox.ini b/tox.ini
@@ -99,7 +99,7 @@ commands = {[testenv:build]commands}
 deps = null
 commands = python -c "import hdmf"
 
-# Envs that will execute gallery tests
+# Envs that will execute gallery tests that do not require ROS3
 [testenv:gallery]
 install_command =
     pip install -U {opts} {packages}
@@ -110,7 +110,7 @@ deps =
 
 commands =
     pip install -r requirements-doc.txt
-    # installing allensdk may downgrade certain requirements so
+    # NOTE: installing allensdk may downgrade certain requirements so
     # reinstall the repo with its requirements
     pip install -r requirements-dev.txt -r requirements.txt
     pip install -U -e .
@@ -143,7 +143,7 @@ deps =
 
 commands =
     pip install -r requirements-doc.txt
-    # installing allensdk may downgrade certain requirements so
+    # NOTE: installing allensdk may downgrade certain requirements so
     # reinstall the repo with its requirements
     pip install -r requirements-dev.txt -r requirements.txt
     pip install -U -e .
@@ -161,7 +161,7 @@ deps =
 
 commands =
     pip install -r requirements-doc.txt
-    # installing allensdk may downgrade certain requirements so
+    # NOTE: installing allensdk may downgrade certain requirements so
     # reinstall the repo with its requirements
     pip install -r requirements-dev.txt -r requirements.txt
     pip install -U --pre -e .
@@ -175,8 +175,8 @@ deps =
     -rrequirements-min.txt
 commands = {[testenv:gallery]commands}
 
-[testenv:validation-py39]
-basepython = python3.9
+[testenv:validation-py38]
+basepython = python3.8
 install_command =
     pip install -U {opts} {packages}
 deps =