Update tests, infrastructure

.gitignore

@@ -1,11 +1,8 @@
+# output NWB files
+*.nwb
+
 # generated docs
-docs/_build
 docs/source/_format_auto_docs
-docs/source/_static
-!docs/source/_static/theme_overrides.css
-
-# copied spec files
-src/pynwb/ndx_events/spec/*.yaml
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -29,6 +26,7 @@ parts/
 sdist/
 var/
 wheels/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -47,14 +45,18 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
+*.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
+.ruff_cache/
 
 # Translations
 *.mo
@@ -64,6 +66,7 @@ coverage.xml
 *.log
 local_settings.py
 db.sqlite3
+db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -76,16 +79,49 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# pyenv
-.python-version
+# IPython
+profile_default/
+ipython_config.py
 
-# celery beat schedule file
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
 celerybeat-schedule
+celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
@@ -111,6 +147,24 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
 
 # Mac finder
 .DS_Store

CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog for ndx-events
+
+## 0.3.0 (Upcoming)
+
+

LICENSE.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Ryan Ly
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -22,8 +22,8 @@ subtype of `DynamicTable`, where each row corresponds to a different event type.
 Unlike for the other event types, users can add their own custom columns to annotate each event type or event time.
 This can be useful for storing event metadata related to data preprocessing and analysis, such as marking bad events.
 
-This extension was developed by Ryan Ly, Ben Dichter, Oliver Rübel, and Andrew Tritt. Information about the rationale,
-background, and alternative approaches to this extension can be found here:
+This extension was developed by Ryan Ly, Oliver Rübel, and the NWB Technical Advisory Board.
+Information about the rationale, background, and alternative approaches to this extension can be found here:
 https://docs.google.com/document/d/1qcsjyFVX9oI_746RdMoDdmQPu940s0YtDjb1en1Xtdw
 
 ## Installation

pyproject.toml

@@ -0,0 +1,112 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "ndx-events"
+version = "0.3.0"
+authors = [
+    { name="Ryan Ly", email="[email protected]" }
+]
+description = "NWB extension for storing timestamped event and TTL pulse data"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "BSD-3"}
+classifiers = [
+    # TODO: add classifiers before release
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+]
+keywords = [
+    'NeurodataWithoutBorders',
+    'NWB',
+    'nwb-extension',
+    'ndx-extension',
+]
+dependencies = [
+    "pynwb>=2.5.0",
+    "hdmf>=3.10.0",
+]
+
+# TODO: add URLs before release
+[project.urls]
+"Homepage" = "https://github.com/rly/ndx-events"
+# "Documentation" = "https://package.readthedocs.io/"
+"Bug Tracker" = "https://github.com/rly/ndx-events/issues"
+"Discussions" = "https://github.com/rly/ndx-events/discussions"
+"Changelog" = "https://github.com/rly/ndx-events/CHANGELOG.md"
+
+[tool.hatch.build]
+include = [
+    "src/pynwb",
+    "spec/ndx-events.extensions.yaml",
+    "spec/ndx-events.namespace.yaml",
+]
+exclude = [
+    "src/pynwb/tests",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = [
+    "src/pynwb/ndx_events",
+    "spec"
+]
+
+[tool.hatch.build.targets.wheel.sources]
+"spec" = "ndx_events/spec"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/pynwb",
+    "spec/ndx-events.extensions.yaml",
+    "spec/ndx-events.namespace.yaml",
+    "docs",
+]
+exclude = []
+
+[tool.pytest.ini_options]
+addopts = "--cov --cov-report html"
+
+[tool.codespell]
+skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,hdmf-common-schema,./docs/_build/*,*.ipynb"
+
+[tool.coverage.run]
+branch = true
+source = ["src/pynwb"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "@abstract"
+]
+
+[tool.black]
+line-length = 120
+preview = true
+exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb|docs/"
+
+[tool.ruff]
+select = ["E", "F", "T100", "T201", "T203"]
+exclude = [
+  ".git",
+  ".tox",
+  "__pycache__",
+  "build/",
+  "dist/",
+]
+line-length = 120
+
+[tool.ruff.per-file-ignores]
+"src/spec/create_extension_spec.py" = ["T201"]
+"src/pynwb/tests/test_example_usage.py" = ["T201"]
+
+[tool.ruff.mccabe]
+max-complexity = 17

requirements-dev.txt

@@ -0,0 +1,15 @@
+# pinned dependencies to reproduce an entire development environment to
+# run tests, check code style, and generate documentation
+black==23.9.1
+codespell==2.2.6
+coverage==7.3.2
+hdmf==3.10.0
+hdmf-docutils==0.4.5
+pre-commit==3.4.0
+pynwb==2.5.0
+pytest==7.4.2
+pytest-cov==4.1.0
+python-dateutil==2.8.2
+pytest-subtests==0.6.0
+ruff==0.0.292
+tox==4.11.3

requirements-min.txt

@@ -0,0 +1,5 @@
+# minimum versions of package dependencies for installation
+# these should match the minimum versions specified in pyproject.toml
+# NOTE: it may be possible to relax these minimum requirements
+pynwb==2.5.0
+hdmf==3.10.0