Repository clean up before v0.6 release

.github/workflows/docs.yml

@@ -26,7 +26,7 @@ jobs:
               micromamba-version: latest
               environment-name: testing
               create-args: >-
-                python=3.12
+                python=3.11
                 mamba
                 pandoc
                 nox

.github/workflows/notebooks.yml

@@ -23,7 +23,7 @@ jobs:
           - uses: conda-incubator/setup-miniconda@v2
             with:
               auto-update-conda: true
-              python-version: "3.12"
+              python-version: "3.11"
               channels: conda-forge
               channel-priority: true
 

.pre-commit-config.yaml

@@ -53,11 +53,11 @@ repos:
   -   id: pyupgrade
       args: [--py38-plus]
 
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/asottile/reorder-python-imports
+  rev: v3.12.0
   hooks:
-    - id: isort
-      files: \.py$
+  - id: reorder-python-imports
+    args: [--py310-plus, --add-import, "from __future__ import annotations"]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
@@ -79,15 +79,12 @@ repos:
         )
     - id: name-tests-test
 
-- repo: https://github.com/PyCQA/pydocstyle
-  rev: 6.3.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.1.8
   hooks:
-    - id: pydocstyle
+    - id: ruff
       files: sequence/.*\.py$
-      args:
-        - --convention=numpy
-        - --add-select=D417
-      additional_dependencies: [".[toml]"]
+      args: [--fix]
 
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v1.7.0
@@ -105,10 +102,4 @@ repos:
   rev: "4.2"
   hooks:
   - id: pyroma
-    args: ["-d", "--min=9", "."]
-
-- repo: https://github.com/mgedmin/check-manifest
-  rev: "0.49"
-  hooks:
-  - id: check-manifest
-    args: ["--ignore=.nox,build", "--no-build-isolation"]
+    args: ["-d", "--min=10", "."]

docs/conf.py

@@ -11,12 +11,13 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
-
 # If extensions (or modules to document with autodoc) are in another
 # directory, add these directories to sys.path here. If the directory is
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
 #
+from __future__ import annotations
+
 import os
 import pathlib
 

docs/tutorials/notebooks/example.ipynb

@@ -31,7 +31,9 @@
    "source": [
     "import tqdm\n",
     "\n",
-    "from sequence import Sequence, SequenceModelGrid, processes"
+    "from sequence import processes\n",
+    "from sequence.grid import SequenceModelGrid\n",
+    "from sequence.sequence import Sequence"
    ]
   },
   {

news/82.misc

@@ -0,0 +1,2 @@
+
+Updated *Sequence* annotations to python 3.10+.

noxfile.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 import pathlib
 import shutil
@@ -74,7 +76,7 @@ def test_cli(session: nox.Session) -> None:
 def lint(session: nox.Session) -> None:
     """Look for lint."""
     session.install("pre-commit")
-    session.run("pre-commit", "run", "--all-files", "--verbose")
+    session.run("pre-commit", "run", "--all-files")
 
 
 @nox.session

pyproject.toml

@@ -1,84 +1,80 @@
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
 [project]
-name = "sequence-model"
+name = "sequence_model"
+requires-python = ">=3.10"
 description = "Python version of the Steckler Sequence model built with landlab"
+keywords = [
+    "landlab",
+    "sequence",
+    "stratigraphy",
+]
 authors = [
-  {email = "mcflugen@gmail.com"},
-  {name = "Eric Hutton"}
+    { email = "mcflugen@gmail.com" },
+    { name = "Eric Hutton" },
 ]
 maintainers = [
-  {email = "mcflugen@gmail.com"},
-  {name = "Eric Hutton"}
+    { email = "mcflugen@gmail.com" },
+    { name = "Eric Hutton" },
 ]
-keywords = ["sequence", "stratigraphy", "landlab"]
-license = {text = "MIT"}
 classifiers = [
-  "Development Status :: 2 - Pre-Alpha",
-  "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
-  "Natural Language :: English",
-  "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
-requires-python = ">=3.10"
 dependencies = [
-  "compaction",
-  "landlab",
-  "netcdf4",
-  "numpy >=1.22",
-  "pyyaml",
-  "rich-click",
-  "scipy",
-  "tomlkit",
-  "tqdm",
-]
-dynamic = ["readme", "version"]
+    "compaction",
+    "landlab",
+    "netcdf4",
+    "numpy >=1.22",
+    "pyyaml",
+    "rich-click",
+    "scipy",
+    "tomlkit",
+    "tqdm",
+]
+dynamic = [
+    "readme",
+    "version",
+]
+
+[project.license]
+text = "MIT"
 
 [project.urls]
-homepage = "https://github.com/sequence-dev/sequence"
+changelog = "https://github.com/sequence-dev/sequence/blob/develop/CHANGES.md"
 documentation = "https://sequence.readthedocs.io"
+homepage = "https://github.com/sequence-dev/sequence"
 repository = "https://github.com/sequence-dev/sequence"
-changelog = "https://github.com/sequence-dev/sequence/blob/develop/CHANGES.md"
 
 [project.optional-dependencies]
-dev = ["nox"]
+dev = [
+    "nox",
+]
 
 [project.scripts]
 sequence = "sequence.cli:sequence"
 
+[build-system]
+requires = [
+    "setuptools",
+]
+build-backend = "setuptools.build_meta"
+
 [tool.setuptools]
-packages = ["sequence"]
+packages = [
+    "sequence",
+]
 
-[tool.setuptools.dynamic]
-readme = {file = ["README.md", "AUTHORS.md"], content-type="text/markdown"}
-version = {attr = "sequence._version.__version__"}
+[tool.setuptools.dynamic.version]
+attr = "sequence._version.__version__"
 
-[tool.pytest.ini_options]
-minversion = "6.0"
-testpaths = ["notebooks", "sequence", "tests"]
-norecursedirs = [".*", "*.egg*", "build", "dist", "examples"]
-addopts = """
-  --ignore setup.py
-  --tb native
-  --strict
-  --durations 16
-  --doctest-modules
-  -vvv
-"""
-doctest_optionflags = [
-  "NORMALIZE_WHITESPACE",
-  "IGNORE_EXCEPTION_DETAIL",
-  "ALLOW_UNICODE"
-]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-    "notebook: marks tests as notebook (deselect with '-m \"not notebook\"')"
-]
+[tool.setuptools.dynamic.readme]
+file = "README.md"
+content-type = "text/markdown"
 
 [tool.isort]
 multi_line_output = 3
@@ -90,38 +86,69 @@ line_length = 88
 [tool.mypy]
 ignore_missing_imports = true
 
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = [
+    "notebooks",
+    "sequence",
+    "tests",
+]
+norecursedirs = [
+    ".*",
+    "*.egg*",
+    "build",
+    "dist",
+    "examples",
+]
+addopts = [
+    "--ignore=setup.py",
+    "--tb=native",
+    "--strict",
+    "--durations=16",
+    "--doctest-modules",
+    "-vvv",
+]
+doctest_optionflags = [
+    "NORMALIZE_WHITESPACE",
+    "IGNORE_EXCEPTION_DETAIL",
+    "ALLOW_UNICODE",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "notebook: marks tests as notebook (deselect with '-m \"not notebook\"')",
+]
+
+[tool.ruff.lint]
+select = [
+    "D",
+]
+extend-select = [
+    "D417",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
 [tool.towncrier]
 directory = "news"
 package = "sequence"
 filename = "CHANGES.md"
 single_file = true
-underlines = ["", "", ""]
-start_string = "<!-- towncrier release notes start -->\n"
+underlines = [
+    "",
+    "",
+    "",
+]
+start_string = """
+<!-- towncrier release notes start -->
+"""
 template = "news/changelog_template.jinja"
 issue_format = "[#{issue}](https://github.com/sequence-dev/sequence/issues/{issue})"
 title_format = "## {version} ({project_date})"
-
-[[tool.towncrier.type]]
-directory = "notebook"
-name = "📚 New Tutorial Notebooks"
-showcontent = true
-
-[[tool.towncrier.type]]
-directory = "feature"
-name = "🍰 New Features"
-showcontent = true
-
-[[tool.towncrier.type]]
-directory = "bugfix"
-name = "🛠️ Bug Fixes"
-showcontent = true
-
-[[tool.towncrier.type]]
-directory = "docs"
-name = "📖 Documentation Enhancements"
-showcontent = true
-
-[[tool.towncrier.type]]
-directory = "misc"
-name = "🔩 Other Changes and Additions"
-showcontent = true
+type = [
+    { directory = "notebook", name = "📚 New Tutorial Notebooks", showcontent = true },
+    { directory = "feature", name = "🍰 New Features", showcontent = true },
+    { directory = "bugfix", name = "🛠️ Bug Fixes", showcontent = true },
+    { directory = "docs", name = "📖 Documentation Enhancements", showcontent = true },
+    { directory = "misc", name = "🔩 Other Changes and Additions", showcontent = true },
+]

sequence/__init__.py

@@ -1,12 +1,6 @@
 """A sequence-stratigraphic model of a 1D profile written with *Landlab*."""
-from ._grid import SequenceModelGrid
-from ._version import __version__
-from .sequence import Sequence
-from .sequence_model import SequenceModel
+from __future__ import annotations
 
-__all__ = [
-    "__version__",
-    "Sequence",
-    "SequenceModel",
-    "SequenceModelGrid",
-]
+from sequence._version import __version__
+
+__all__ = ["__version__"]

sequence/_version.py

@@ -1 +1,3 @@
+from __future__ import annotations
+
 __version__ = "0.5.2.dev0"