Merge pull request #20 from mcflugen/mcflugen/v0.2.3b0

Release v0.2.3

.pre-commit-config.yaml

@@ -35,7 +35,7 @@ repos:
   rev: 1.7.0
   hooks:
     - id: nbqa-pyupgrade
-      args: ["--py39-plus"]
+      args: ["--py310-plus"]
     - id: nbqa-isort
     - id: nbqa-flake8
       args: ["--extend-ignore=E402"]
@@ -55,7 +55,7 @@ repos:
   rev: v3.15.0
   hooks:
   - id: pyupgrade
-    args: [--py39-plus]
+    args: [--py310-plus]
 
 - repo: https://github.com/PyCQA/isort
   rev: 5.12.0

NEWS.md

@@ -3,3 +3,20 @@
 <!-- towncrier-draft-entries:: Not yet released -->
 
 <!-- towncrier release notes start -->
+
+## [0.2.3](https://github.com/mcflugen/compaction/tree/0.2.3) - 2023-11-21
+
+
+### Other Changes and Additions
+
+- Set up [towncrier](https://towncrier.readthedocs.io/en/stable/index.html)
+  to manage the changelog. [#16](https://github.com/mcflugen/compaction/issues/16)
+- Added a [pre-commit](https://pre-commit.com/) hook file for running
+  the linters. [#16](https://github.com/mcflugen/compaction/issues/16)
+- Added a [nox](https://nox.thea.codes/en/stable/) file for routine
+  project management like running the tests and linting. [#16](https://github.com/mcflugen/compaction/issues/16)
+- Added GitHub Actions for running the continuous integration tests, which
+  includes running the tests and linters. [#16](https://github.com/mcflugen/compaction/issues/16)
+- Moved static project metadata from *setup.py* to the now standard
+  *pyproject.toml*. [#16](https://github.com/mcflugen/compaction/issues/16)
+- Added support for Python 3.12 and dropped support for Python 3.9. [#19](https://github.com/mcflugen/compaction/issues/19)

README.md

@@ -1,24 +1,24 @@
 [![Test][test_badge]][test_workflow]
-[test_badge]: https://github.com/mcflugen/compaction/actions/workflows/test.yml/badge.svg
-[test_workflow]: https://github.com/mcflugen/compaction/actions/workflows/test.yml
 
 
 # compaction: Compact layers of sediment
 
 Compact a column of sediment following Bahr et al., 2001.
 
-Cite as::
-
-    @article{bahr2001exponential,
-      title={Exponential approximations to compacted sediment porosity profiles},
-      author={Bahr, David B and Hutton, Eric WH and Syvitski, James PM and Pratson, Lincoln F},
-      journal={Computers \& Geosciences},
-      volume={27},
-      number={6},
-      pages={691--700},
-      year={2001},
-      publisher={Pergamon}
-    }
+Cite as,
+
+```bibtex
+@article{bahr2001exponential,
+    title={Exponential approximations to compacted sediment porosity profiles},
+    author={Bahr, David B and Hutton, Eric WH and Syvitski, James PM and Pratson, Lincoln F},
+    journal={Computers \& Geosciences},
+    volume={27},
+    number={6},
+    pages={691--700},
+    year={2001},
+    publisher={Pergamon}
+}
+```
 
 ## Requirements
 
@@ -43,27 +43,35 @@ which *Compaction* will be installed. This, although not necessary, will
 isolate the installation so that there won't be conflicts with your
 base *Python* installation. This can be done with *conda* as:
 
-    $ conda create -n compaction python=3
-    $ conda activate compaction
+```bash
+conda create -n compaction python=3
+conda activate compaction
+```
 
 ## Stable Release
 
 *Compaction*, and its dependencies, can be installed either with *pip*
 or *conda*. Using *pip*:
 
-    $ pip install compaction
+```bash
+pip install compaction
+```
 
 Using *conda*:
 
-    $ conda install compaction -c conda-forge
+```bash
+conda install compaction -c conda-forge
+```
 
 ### From Source
 
 After downloading the *Compaction* source code, run the following from
 *Compaction*'s top-level folder (the one that contains *setup.py*) to
 install *Compaction* into the current environment:
 
-    $ pip install -e .
+```bash
+pip install -e .
+```
 
 ## Input Files
 
@@ -73,12 +81,17 @@ The main *Compaction* input file is a yaml-formatted text file that lists
 constants used by *Compaction*. Running the following will print a sample
 *Compaction* configuration file:
 
-    $ compact show config
-    c: 5.0e-08
-    porosity_max: 0.5
-    porosity_min: 0.0
-    rho_grain: 2650.0
-    rho_void: 1000.0
+```
+compact show config
+```
+
+```yaml
+c: 5.0e-08
+porosity_max: 0.5
+porosity_min: 0.0
+rho_grain: 2650.0
+rho_void: 1000.0
+```
 
 ### Porosity File
 
@@ -87,11 +100,16 @@ sediment layers to be compacted as a two-column CSV file. The first
 column is layer thickness (in meters) and the second the porosity of
 the sediment in that layer. A sample porosity file can be obtained with:
 
-    $ compact show porosity
-    # Layer Thickness [m], Porosity [-]
-    100.0,0.5
-    100.0,0.5
-    100.0,0.5
+```bash
+compact show porosity
+```
+
+```
+# Layer Thickness [m], Porosity [-]
+100.0,0.5
+100.0,0.5
+100.0,0.5
+```
 
 ## Output File
 
@@ -103,13 +121,26 @@ the input porosity file - a CSV file of layer thickness and porosity.
 To run a simulation using the sample input files described above, you first
 need to create a set of sample files:
 
-    $ sequence setup example
-    example/sequence.yaml
+```
+sequence setup example
+```
+
+```
+example/sequence.yaml
+```
 
 You can now run the simulation:
 
-    $ sequence run example/sequence.yaml
-    # Layer Thickness [m], Porosity [-]
-    100.0,0.5
-    96.18666488709239,0.4801774231522433
-    92.78860257194452,0.4611407154102571
+```bash
+sequence run example/sequence.yaml
+```
+
+```
+# Layer Thickness [m], Porosity [-]
+100.0,0.5
+96.18666488709239,0.4801774231522433
+92.78860257194452,0.4611407154102571
+```
+
+[test_badge]: https://github.com/mcflugen/compaction/actions/workflows/test.yml/badge.svg
+[test_workflow]: https://github.com/mcflugen/compaction/actions/workflows/test.yml

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["cython~=3.0.0b3", "numpy", "setuptools", "wheel"]
+requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -19,7 +19,7 @@ keywords = [
   "numerical modeling",
   "sediment compaction",
 ]
-license = {file = "LICENSE.md"}
+license = {text = "MIT"}
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
@@ -43,13 +43,13 @@ dependencies = [
 	"tomlkit",
 	"scipy",
 ]
-dynamic = ["readme", "version"]
+dynamic = ["readme" , "version"]
 
 [project.urls]
 homepage = "https://github.com/mcflugen/compaction"
 documentation = "https://compaction.readthedocs.io"
 repository = "https://github.com/mcflugen/compaction"
-changelog = "https://github.com/mcflugen/compaction/blob/develop/CHANGES.rst"
+changelog = "https://github.com/mcflugen/compaction/blob/master/NEWS.md"
 
 [project.optional-dependencies]
 dev = ["nox"]
@@ -71,8 +71,11 @@ compaction = "compaction.cli:compaction"
 [tool.setuptools]
 include-package-data = true
 
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.setuptools.dynamic]
-readme = {file = ["README.md", "AUTHORS.md"]}
+readme = {file = ["README.md", "AUTHORS.md"], content-type="text/markdown"}
 version = {attr = "compaction._version.__version__"}
 
 [tool.pytest.ini_options]

setup.cfg

@@ -7,7 +7,7 @@ select = B,C,E,F,W,T4,B9
 
 [zest.releaser]
 tag-format = v{version}
-python-file-with-version = compaction/_version.py
+python-file-with-version = src/compaction/_version.py
 
 [coverage:run]
 relative_files = True

src/compaction/_version.py

@@ -1 +1 @@
-__version__ = "v0.3.0.dev0"
+__version__ = "0.2.4.dev0"

src/compaction/cli.py

@@ -4,7 +4,7 @@
 import warnings
 from functools import partial
 from io import StringIO
-from typing import Optional, TextIO
+from typing import TextIO
 
 import click
 import numpy as np  # type: ignore
@@ -88,7 +88,7 @@ def _tomlkit_to_popo(d):
     return result
 
 
-def load_config(stream: Optional[TextIO] = None):
+def load_config(stream: TextIO | None = None):
     """Load compaction config file.
 
     Parameters

src/compaction/compaction.py

@@ -1,6 +1,4 @@
 #! /usr/bin/env python
-from typing import Optional
-
 import numpy as np  # type: ignore
 from scipy.constants import g  # type: ignore
 
@@ -15,7 +13,7 @@ def compact(
     porosity_max: float = 1.0,
     rho_void: float = 1000.0,
     gravity: float = g,
-    return_dz: Optional[np.ndarray] = None,
+    return_dz: np.ndarray | None = None,
 ) -> np.ndarray:
     """Compact a column of sediment.