Update pyproject.toml and remove setup.py (#143)

* Update pyproject.toml and remove setup.py - Update version control to hatch backend - Update pytest, coverage, and ruff via pyproject.toml * Update __init__.py * Delete versioneer.py * Update .gitignore * Create .git_archival.txt * Update .gitattributes * Create codespell.yml * Create ruff.yml * Update conf.py * Update conf.py * Update test_io_convert.py * Update CHANGELOG.md * Update base_tests_zarrio.py * Update test_fsspec_streaming.py * Update overview.rst * Update storage.rst * Update _version.py * Update utils.py * Update backend.py * Update backend.py * Update CHANGELOG.md * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml * Update pyproject.toml Co-authored-by: Ryan Ly <[email protected]> * Delete setup.cfg * Delete setup.py * Delete src/hdmf_zarr/_version.py * Delete .github/workflows/run_flake8.yml --------- Co-authored-by: Ryan Ly <[email protected]>
hdmf-dev · Dec 7, 2023 · 5e48ab5 · 5e48ab5
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diff --git a/.git_archival.txt b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
@@ -1 +1 @@
-src/hdmf_zarr/_version.py export-subst
+.git_archival.txt export-subst
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,14 @@
+name: Codespell
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,11 @@
+name: Ruff
+on: pull_request
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Run ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_flake8.yml b/.github/workflows/run_flake8.yml
diff --git a/.gitignore b/.gitignore
@@ -142,3 +142,6 @@ dmypy.json
 
 # DS_Store
 .DS_Store
+
+# Version
+_version.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Enhancements
 * Added a new default to consolidate metadata in order more efficeintly traverse storage contents. @mavaylon1 [#142](https://github.com/hdmf-dev/hdmf-zarr/pull/142)
 * Fix linking for FSSpec and support passing of `storage_options` required reading data from S3 #138. @alejoe91 [#120](https://github.com/hdmf-dev/hdmf-zarr/pull/138)
+* Updated versioning to hatch-vcs and deprecated setup.py in full transition to `pyproject.toml`. @mavaylon1 [#143](https://github.com/hdmf-dev/hdmf-zarr/pull/143)
 
 ## 0.4.0 (October 3, 2023)
 
@@ -65,7 +66,7 @@
   links/reference when moving Zarr files @oruebel [#46](https://github.com/hdmf-dev/hdmf-zarr/pull/46)
 * Fixed bugs in requirements defined in setup.py @oruebel [#46](https://github.com/hdmf-dev/hdmf-zarr/pull/46)
 * Fixed bug regarding Sphinx external links @mavaylon1 [#53](https://github.com/hdmf-dev/hdmf-zarr/pull/53)
-* Updated gallery tests to use test_gallery.py and necessary package dependcies 
+* Updated gallery tests to use test_gallery.py and necessary package dependencies 
   @mavaylon1 [#53](https://github.com/hdmf-dev/hdmf-zarr/pull/53)
 * Updated dateset used in conversion tutorial, which caused warnings 
   @oruebel [#56](https://github.com/hdmf-dev/hdmf-zarr/pull/56)

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -30,8 +30,8 @@
 # This lets us ensure that the source package is imported, and that its
 # version is used.
 sys.path.insert(0, os.path.join(project_root, 'src'))
-from hdmf_zarr._version import get_versions
 
+import hdmf_zarr
 
 # -- Autodoc configuration -----------------------------------------------------
 autoclass_content = 'both'
@@ -46,9 +46,9 @@
 author = 'Oliver Ruebel, Matthew Avaylon'
 
 # The short X.Y version.
-version = '{}'.format(get_versions()['version'])
+version = hdmf_zarr.__version__
 # The full version, including alpha/beta/rc tags.
-release = '{}'.format(get_versions()['version'])
+release = hdmf_zarr.__version__
 
 # -- General configuration ---------------------------------------------------
 

diff --git a/docs/source/overview.rst b/docs/source/overview.rst
@@ -24,7 +24,7 @@ Supported features
 - Iterative data write using :py:class:`~hdmf.data_utils.AbstractDataChunkIterator` 
 - Parallel write with :py:class:`~hdmf.data_utils.GenericDataChunkIterator` (since v0.4)
 - Lazy load of datasets
-- Lazy load of datasets containing object refernces (since v0.4)
+- Lazy load of datasets containing object references (since v0.4)
 
 Known Limitations
 -----------------

diff --git a/docs/source/storage.rst b/docs/source/storage.rst
@@ -174,7 +174,7 @@ as JSON. Each dict (i.e., element) in the list defines a link, with each dict co
   pointing to an object within the same Zarr file, the value of source will be ``"."``. For external
   links that point to object in another Zarr file, the value of source will be the path to
   the other Zarr file relative to the root path of the Zarr file containing the link.
-* ``path`` : Path to the linked object within the Zarr file idenfied by the ``source`` key
+* ``path`` : Path to the linked object within the Zarr file identified by the ``source`` key
 * ``object_id``: Object id of the reference object. May be None in case the referenced object
   does not have an assigned object_id (e.g., in the case we reference a dataset with a fixed
   name but without and assigned ``data_type`` (or ``neurodata_type`` in the case of NWB).

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,87 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "hdmf_zarr"
+authors = [
+  { name="Oliver Ruebel", email="[email protected]" },
+  { name="Matthew Avaylon", email="[email protected]" },
+]
+description = "A package defining a Zarr I/O backend for HDMF"
+readme = "README.rst"
+requires-python = ">=3.8"
+license = {text = "BSD"}
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: BSD License",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: MacOS",
+    "Operating System :: Unix",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
+]
+dependencies = [
+    'hdmf>=3.9.0',
+    'zarr>=2.11.0',
+    'numpy>=1.24',
+    'numcodecs>=0.9.1',
+    'numcodecs==0.11.0',
+    'pynwb>=2.5.0',
+    'threadpoolctl>=3.1.0',
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tqdm = ["tqdm>=4.41.0"]
+fsspec = ["fsspec"]
+s3fs = ["s3fs"]
+
+[project.urls]
+"Homepage" = "https://github.com/hdmf-dev/hdmf-zarr"
+"Bug Tracker" = "https://github.com/hdmf-dev/hdmf-zarr/issues"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+# this file is created/updated when the package is installed and used in
+# src/hdmf_zarr/__init__.py to set `hdmf_zarr.__version__`
+# this allows the version to be accessible from python
+version-file = "src/hdmf_zarr/_version.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = [".git_archival.txt"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/hdmf_zarr"]
+
+[tool.pytest.ini_options]
+addopts = "--cov --cov-report html"
+
+[tool.codespell]
+skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb"
+ignore-words-list = "datas"
+
+[tool.coverage.run]
+branch = true
+source = ["src/"]
+omit = [
+    "src/hdmf_zarr/_due.py",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "@abstract"
+]
+
 [tool.black]
 line-length = 120
 target-version = ['py38']
@@ -25,3 +109,26 @@ force-exclude = '''
    /docs/*
 )\
 '''
+
+[tool.ruff]
+select = ["E", "F", "T100", "T201", "T203"]
+exclude = [
+  ".git",
+  ".tox",
+  "__pycache__",
+  "build/",
+  "dist/",
+  "docs/source/conf.py",
+  "src/hdmf_zarr/_due.py",
+  "docs/source/tutorials/",
+  "docs/_build/",
+]
+line-length = 120
+
+[tool.ruff.per-file-ignores]
+"docs/gallery/*" = ["E402", "T201"]
+"src/*/__init__.py" = ["F401"]
+"test_gallery.py" = ["T201"]
+
+[tool.ruff.mccabe]
+max-complexity = 17
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/src/hdmf_zarr/__init__.py b/src/hdmf_zarr/__init__.py
@@ -2,9 +2,15 @@
 from .utils import ZarrDataIO
 from .nwb import NWBZarrIO
 
-from ._version import get_versions  # noqa: E402
-__version__ = get_versions()['version']
-del get_versions
+try:
+    # see https://effigies.gitlab.io/posts/python-packaging-2023/
+    from ._version import __version__
+except ImportError:  # pragma: no cover
+    # this is a relatively slower method for getting the version string
+    from importlib.metadata import version  # noqa: E402
+
+    __version__ = version("hdmf")
+    del version
 
 # Duecredit definitions
 from ._due import due, BibTeX  # noqa: E402