Move to a fully pyproject.toml based build (#878)

* Move pydocstyle config to pyproject.toml.

* Move mypy config to pyproject.toml.

* Remove unnecessary metadata section, see https://stackoverflow.com/questions/60084128/does-description-file-in-setup-cfg-section-metadata-have-any-effect

* Remove now unnecessary bdist_wheel section.

* Move pytest configuration to pyproject.toml.

* Move coverage config to pyproject.toml.

* Move flake8 and bumpversion configs to separate files.

* Move all project config to pyproject.toml.

* Specify build backend.

* Remove TODO.

* Remove editable install in CI.

* Revert "Remove editable install in CI."

This reverts commit 9e03309.

* Add minimum setuptools version.

* Update changelog.

* Make sure namespace packages aren't installed and try again.

* Explicitly disallow test installation and add an __init__.py for _vendor.

* Go back to an editable install for CI.

* Specify pydocstyle convention.

* Convert keywords to a proper list.

* Remove zip-safe.

* Point bumpversion to pyproject.toml.

* Update contributing docs.

* Apply suggestions from code review

Co-authored-by: Kelly Wang <47036428+klywang@users.noreply.github.com>
Co-authored-by: Bradley Dice <bdice@bradleydice.com>

* Update pyproject.toml

Co-authored-by: Kelly Wang <47036428+klywang@users.noreply.github.com>
Co-authored-by: Bradley Dice <bdice@bradleydice.com>
Co-authored-by: Brandon Butler <butlerbr@umich.edu>

.bumpversion

@@ -0,0 +1,15 @@
+[bumpversion]
+current_version = 1.8.0
+commit = True
+tag = False
+message = Bump up to version {new_version}.
+
+[bumpversion:file:pyproject.toml]
+
+[bumpversion:file:signac/version.py]
+
+[bumpversion:file:doc/conf.py]
+
+[bumpversion:file:CITATION.cff]
+
+[bumpversion:file:.zenodo.json]

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+max-line-length = 100
+exclude = _vendor
+select = E,F,W
+ignore = E123,E126,E203,E226,E241,E704,W503,W504

.github/workflows/run-pytest.yml

@@ -60,5 +60,5 @@ jobs:
       if: ${{ matrix.os == 'ubuntu-latest' && matrix.config.dependencies != 'minimal' }}
     - name: Test with pytest
       run: |
-        pytest --cov=signac --cov-config=setup.cfg --cov-report=xml tests/ -v
+        pytest --cov=signac --cov-config=pyproject.toml --cov-report=xml tests/ -v
     - uses: codecov/codecov-action@v2

.pre-commit-config.yaml

@@ -8,9 +8,7 @@ repos:
     rev: 'v4.3.0'
     hooks:
       - id: end-of-file-fixer
-        exclude: 'setup.cfg'
       - id: trailing-whitespace
-        exclude: 'setup.cfg'
       - id: check-builtin-literals
       - id: check-executables-have-shebangs
       - id: check-json
@@ -45,6 +43,8 @@ repos:
             ^doc/|
             ^tests/|
           )
+        additional_dependencies:
+          - toml
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: 'v0.981'
     hooks:

CONTRIBUTING.md

@@ -29,7 +29,7 @@ All contributors must agree to the Contributor Agreement ([ContributorAgreement.
 * Use the [OneFlow](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow) model of development:
   - Both new features and bug fixes should be developed in branches based on `master`.
   - Hotfixes (critical bugs that need to be released *fast*) should be developed in a branch based on the latest tagged release.
-* Write code that is compatible with all supported versions of Python (listed in [setup.py](https://github.com/glotzerlab/signac/blob/master/setup.py)).
+* Write code that is compatible with all supported versions of Python (listed in [pyproject.toml](https://github.com/glotzerlab/signac/blob/master/pyproject.toml)).
 * Avoid introducing dependencies -- especially those that might be harder to install in high-performance computing environments.
 * Create [unit tests](https://en.wikipedia.org/wiki/Unit_testing) and [integration tests](https://en.wikipedia.org/wiki/Integration_testing) that cover the common cases and the corner cases of the code.
 * Preserve backwards-compatibility whenever possible, and make clear if something must change.

changelog.txt

@@ -36,6 +36,7 @@ Changed
  - The ``calc_id`` function has been moved from the ``hashing`` module to the ``job`` module (#873).
  - Tests are run with all warnings treated as errors (#871).
  - The contents of the ``syncutil`` module have been moved into ``sync`` (#869).
+ - The project now leverages a fully pyproject.toml-driven build (#878).
 
 Removed
 +++++++

doc/installation.rst

@@ -53,13 +53,18 @@ Consider installing :ref:`optional dependencies <optional_dependencies>`.
 Source Code Installation
 ========================
 
-Alternatively you can clone the `git repository <https://github.com/glotzerlab/signac>`_ and execute the ``setup.py`` script to install the package.
+Alternatively you can clone the `git repository <https://github.com/glotzerlab/signac>`_ and pip install it directly (Option 1), or install directly from git (Option 2).
 
 .. code:: bash
 
+  # Option 1
   git clone https://github.com/glotzerlab/signac.git
   cd signac
-  python setup.py install --user
+  pip install .
+
+  # Option 2
+  pip install git+https://github.com/glotzerlab/signac.git
+
 
 Consider installing :ref:`optional dependencies <optional_dependencies>`.
 

pyproject.toml

@@ -1,3 +1,60 @@
+# Copyright (c) 2020 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=64.0.0"]
+
+[project]
+name = "signac"
+version = "1.8.0"
+description = "Manage large and heterogeneous data spaces on the file system."
+readme = "README.md"
+# Supported versions are determined according to NEP 29.
+# https://numpy.org/neps/nep-0029-deprecation_policy.html
+requires-python = ">=3.8"
+license = { file = "LICENSE.txt" }
+maintainers = [{ name = "signac Developers", email = "signac-support@umich.edu" }]
+authors = [{ name = "Carl Simon Adorf et al.", email = "csadorf@umich.edu" }]
+keywords = ["simulation", "database", "index", "collaboration", "workflow"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Topic :: Database",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = [
+    # Platform-independent file locking
+    "filelock>=3.0",
+    # Used for version parsing and comparison
+    "packaging>=15.0",
+    # Progress bars
+    "tqdm>=4.10.0",
+]
+
+[project.optional-dependencies]
+h5 = ["h5py"]
+
+[project.scripts]
+signac = "signac.__main__:main"
+
+[project.urls]
+Homepage = "https://signac.io"
+Documentation = "https://docs.signac.io"
+Download = "https://pypi.org/project/signac/"
+Source = "https://github.com/glotzerlab/signac"
+Issues = "https://github.com/glotzerlab/signac/issues"
+
+[tools.setuptools.packages.find]
+namespaces = false
+exclude = ["tests*", "benchmarks*"]
+
 [tool.black]
 target-version = ['py38']
 include = '\.pyi?$'
@@ -19,3 +76,24 @@ force-exclude = '''
 [tool.isort]
 profile = 'black'
 skip_glob = 'signac/_vendor/*'
+
+[tool.pydocstyle]
+convention = "numpy"
+match = "^((?!\\.sync-zenodo-metadata|setup).)*\\.py$"
+match-dir = "^((?!\\.|tests|_vendor).)*$"
+ignore-decorators = "deprecated"
+add-ignore = "D105, D107, D203, D204, D213"
+
+[tool.mypy]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+xfail_strict = true
+filterwarnings = "error"
+
+[tool.coverage.run]
+branch = true
+concurrency = ["thread", "multiprocessing"]
+parallel = true
+source = [ "signac" ]
+omit = [ "*/signac/_vendor/*" ]

signac/_vendor/__init__.py

@@ -0,0 +1,4 @@
+# Copyright (c) 2022 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Vendored packages."""