Migrate to pyproject.toml + cleanup (#1158)

* Migrate to pyproject.toml + cleanup

* Remove more instances of python setup.py ...

* release.rst entry

* Move changes to unreleased section

* Remove pre-commit checks from workflows

* Update `jupyter` dependencies

Co-authored-by: jakirkham <jakirkham@gmail.com>

* Lower pin setuptools

* Document installing `build`

Co-authored-by: jakirkham <jakirkham@gmail.com>

* Add docs for twine and pre-commit

* Add pre-commit badge to readme.

* add .readthedocs.yaml

Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>

.github/workflows/python-package.yml

@@ -83,9 +83,3 @@ jobs:
           #name: codecov-umbrella # optional
           #fail_ci_if_error: true # optional (default = false)
         verbose: true # optional (default = false)
-    - name: Linting
-      shell: "bash -l {0}"
-      run: |
-        conda activate zarr-env
-        flake8 zarr
-        mypy zarr

.gitignore

@@ -67,6 +67,9 @@ zarr/version.py
 # emacs
 *~
 
+# VSCode
+.vscode/
+
 # test data
 #*.zarr
 #*.zip

.pre-commit-config.yaml

@@ -1,3 +1,6 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
 default_stages: [commit, push]
 default_language_version:
   python: python3.9
@@ -11,7 +14,21 @@ repos:
       ]
       exclude: ^(venv/|docs/)
       types: ['python']
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        args: ["-L", "ba,ihs,kake,nd,noe,nwo,te"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
     - id: check-yaml
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.981
+    hooks:
+      - id: mypy
+        files: zarr
+        args: []
+        additional_dependencies:
+          - types-redis
+          - types-setuptools

.readthedocs.yaml

@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: requirements_rtfd.txt
+    - method: pip
+      path: .

README.md

@@ -40,10 +40,19 @@
   <td>Build Status</td>
   <td>
     <a href="https://github.com/zarr-developers/zarr-python/blob/main/.github/workflows/python-package.yml">
-    <img src="https://github.com/zarr-developers/zarr-python/actions/workflows/python-package.yml/badge.svg" alt="license" />
+    <img src="https://github.com/zarr-developers/zarr-python/actions/workflows/python-package.yml/badge.svg" alt="build status" />
     </a>
   </td>
 </tr>
+<tr>
+  <td>Pre-commit Status</td>
+  <td>
+    <a href=""https://github.com/zarr-developers/zarr-python/blob/main/.pre-commit-config.yaml">
+    <img src="https://results.pre-commit.ci/badge/github/zarr-developers/zarr-python/main.svg" alt="pre-commit status" />
+    </a>
+  </td>
+</tr>
+
 <tr>
   <td>Coverage</td>
   <td>

docs/contributing.rst

@@ -179,14 +179,33 @@ also collected automatically via the Codecov service, and total
 coverage over all builds must be 100% (although individual builds
 may be lower due to Python 2/3 or other differences).
 
-Code standards
-~~~~~~~~~~~~~~
+Code standards - using pre-commit
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 All code must conform to the PEP8 standard. Regarding line length, lines up to 100
 characters are allowed, although please try to keep under 90 wherever possible.
-Conformance can be checked by running::
 
-    $ python -m flake8 --max-line-length=100 zarr
+``Zarr`` uses a set of ``pre-commit`` hooks and the ``pre-commit`` bot to format,
+type-check, and prettify the codebase. ``pre-commit`` can be installed locally by
+running::
+
+    $ python -m pip install pre-commit
+
+The hooks can be installed locally by running::
+
+    $ pre-commit install
+
+This would run the checks every time a commit is created locally. These checks will also run
+on every commit pushed to an open PR, resulting in some automatic styling fixes by the
+``pre-commit`` bot. The checks will by default only run on the files modified by a commit,
+but the checks can be triggered for all the files by running::
+
+    $ pre-commit run --all-files
+
+If you would like to skip the failing checks and push the code for further discussion, use
+the ``--no-verify`` option with ``git commit``.
+
+
 
 Test coverage
 ~~~~~~~~~~~~~

docs/installation.rst

@@ -23,7 +23,7 @@ To work with Zarr source code in development, install from GitHub::
 
     $ git clone --recursive https://github.com/zarr-developers/zarr-python.git
     $ cd zarr-python
-    $ python setup.py install
+    $ python -m pip install -e .
 
 To verify that Zarr has been fully installed, run the test suite::
 

docs/release.rst

@@ -6,14 +6,20 @@ Release notes
     # to document your changes. On releases it will be
     # re-indented so that it does not show up in the notes.
 
-    .. _unreleased:
+.. _unreleased:
 
-    Unreleased
-    ----------
+Unreleased
+----------
 ..
     # .. warning::
     #    Pre-release! Use :command:`pip install --pre zarr` to evaluate this release.
 
+Maintenance
+~~~~~~~~~~~
+
+* Migrate to ``pyproject.toml`` and remove redundant infrastructure.
+  By :user:`Saransh Chopra <Saransh-cpp>` :issue:`1158`.
+
 .. _release_2.13.3:
 
 2.13.3

pyproject.toml

@@ -1,3 +1,80 @@
 [build-system]
-requires = ["setuptools>=40.8.0", "wheel"]
+requires = ["setuptools>=40.8.0", "setuptools-scm", "wheel"]
 build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "zarr"
+description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+readme = { file = "README.md", content-type = "text/markdown" }
+maintainers = [
+    { name = "Alistair Miles", email = "alimanfoo@googlemail.com" }
+]
+requires-python = ">=3.8"
+dependencies = [
+    'asciitree',
+    'numpy>=1.7',
+    'fasteners',
+    'numcodecs>=0.10.0',
+]
+dynamic = [
+  "version",
+]
+classifiers = [
+    'Development Status :: 6 - Mature',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Information Technology',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python',
+    'Topic :: Software Development :: Libraries :: Python Modules',
+    'Operating System :: Unix',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+]
+
+[project.optional-dependencies]
+jupyter = [
+    'notebook',
+    'ipytree>=0.2.2',
+    'ipywidgets>=8.0.0',
+]
+
+[project.urls]
+"Bug Tracker" = "https://github.com/zarr-developers/zarr-python/issues"
+Changelog = "https://zarr.readthedocs.io/en/stable/release.html"
+Discussions = "https://github.com/zarr-developers/zarr-python/discussions"
+Documentation = "https://zarr.readthedocs.io/"
+Homepage = "https://github.com/zarr-developers/zarr-python"
+
+
+[tool.setuptools]
+packages = ["zarr", "zarr._storage", "zarr.tests"]
+
+[tool.setuptools_scm]
+version_scheme = "guess-next-dev"
+local_scheme = "dirty-tag"
+write_to = "zarr/version.py"
+
+[tool.mypy]
+python_version = "3.8"
+ignore_missing_imports = true
+follow_imports = "silent"
+
+[tool.pytest.ini_options]
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "ELLIPSIS", 
+    "IGNORE_EXCEPTION_DETAIL",
+]
+addopts = [
+    "--durations=10",
+]
+filterwarnings = [
+    "error:::zarr.*",
+    "ignore:Not all N5 implementations support blosc compression.*:RuntimeWarning",
+    "ignore:PY_SSIZE_T_CLEAN will be required.*:DeprecationWarning",
+    "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
+]

release.txt

@@ -3,5 +3,9 @@ tox
 echo $version
 git tag -a v$version -m v$version
 git push --tags
-python setup.py register sdist
+# Install `build` if not present with `python -m pip install build` or similar
+# for building Zarr
+python -m build
+# Install `twine` if not present with `python -m pip install twine` or similar
+# for publishing Zarr to PyPI
 twine upload dist/zarr-${version}.tar.gz