Add python 3.12 to tests; remove lint

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v2
@@ -31,7 +31,3 @@ jobs:
       - name: Test
         run: |
           nox -s test
-
-      # - name: Test Notebooks
-      #   run: |
-      #     nox -s test-notebooks

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: 23.1.0
+  rev: 24.2.0
   hooks:
   - id: black
     name: black
@@ -23,16 +23,16 @@ repos:
     additional_dependencies: [".[jupyter]"]
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
+  rev: 1.7.1
   hooks:
     - id: nbqa-pyupgrade
-      args: ["--py38-plus"]
+      args: ["--py310-plus"]
     - id: nbqa-isort
     - id: nbqa-flake8
       args: ["--extend-ignore=E402"]
 
 - repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     additional_dependencies:
@@ -46,26 +46,26 @@ repos:
       )
 
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
+  rev: 0.7.1
   hooks:
     - id: nbstripout
       description: Strip output from jupyter notebooks
       args: [--drop-empty-cells]
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
+  rev: v3.15.1
   hooks:
   - id: pyupgrade
-    args: [--py36-plus]
+    args: [--py310-plus]
 
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
   hooks:
   - id: isort
-    files: \.py$
+    args: ["--force-single-line-imports"]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: check-builtin-literals
     - id: check-added-large-files
@@ -83,21 +83,3 @@ repos:
           .*requirements(-\w+)?.(in|txt)|
           MANIFEST.in
         )
-
-- repo: https://github.com/regebro/pyroma
-  rev: "4.1"
-  hooks:
-  - id: pyroma
-    args: ["-d", "--min=10", "."]
-    additional_dependencies:
-    - numpy
-    - cython
-
-- repo: https://github.com/mgedmin/check-manifest
-  rev: "0.49"
-  hooks:
-  - id: check-manifest
-    args: ["--ignore=.nox,build", "--no-build-isolation"]
-    additional_dependencies:
-    - numpy
-    - cython

README.md

@@ -1,4 +1,16 @@
-[![DOI](https://zenodo.org/badge/310435424.svg)](https://zenodo.org/doi/10.5281/zenodo.10003561)
+![[DOI][doi-link]][doi-badge]
+
+
+[barrier3d-github]:https://github.com/UNC-CECL/Barrier3D
+[brie-github]: https://github.com/UNC-CECL/brie
+[cascade-figure]: https://user-images.githubusercontent.com/57640439/226623608-d0c58437-d44f-4dca-8f43-0b92623fcda6.png
+[chom-github]: https://github.com/UNC-CECL/CHOM
+[doi-badge]: https://zenodo.org/badge/310435424.svg
+[doi-link]: https://zenodo.org/doi/10.5281/zenodo.10003561
+[nox-docs]: https://nox.thea.codes/
+[preprint-doi]: https://doi.org/10.31223/X5P947
+[zip-download]: https://github.com/UNC-CECL/CASCADE/archive/refs/heads/main.zip
+
 
 🌀 🌊 🏄‍♀️ 🏚️ 🌀 🌊 🏄‍♀️ 🏚️ 🌀 🌊 🏄‍♀️ 🏚️ 🌀 🌊 🏄‍♀️ 🏚️
 # cascade
@@ -15,10 +27,10 @@ are incorporated in *cascade* in two separate modules. The first module simulate
 pavement damage during overwashing events, including rebuilding roadways at sufficiently low elevations to allow for
 burial by overwash, constructing large dunes, and relocating the road into the barrier interior. The second module
 incorporates management strategies for maintaining a coastal community, including beach nourishment, dune construction,
-and overwash removal. For a full description of model dynamics, please see "The Future of Developed
-Barrier Systems - Part I: Pathways Toward Uninhabitability, Drowning, and Rebound" by Anarde et al., (2024, [Earth ArXiv preprint](https://doi.org/10.31223/X5P947)).
+and overwash removal. For a full description of model dynamics, please see *"The Future of Developed
+Barrier Systems - Part I: Pathways Toward Uninhabitability, Drowning, and Rebound" by Anarde et al., (2024, [Earth ArXiv preprint][preprint-doi])*.
 
-![ModelTimeLoop-01](https://user-images.githubusercontent.com/57640439/226623608-d0c58437-d44f-4dca-8f43-0b92623fcda6.png)
+![ModelTimeLoop-01][cascade-figure]
 
 In development: *cascade* represents decisions about coastal land-use (e.g., housing markets) and community-level
 mitigation measures using an empirically-grounded agent-based real estate model – the Coastal Home Ownership Model (*chom*).
@@ -42,19 +54,23 @@ on local wave and sediment characteristics as well as the offshore wave climate
 Lorenzo-Trueba & Ashton, 2014; Ortiz & Ashton, 2016). For ease of model coupling, *brie* and *chom* were rewritten in Python
 and all models (*barrier3d*, *brie*, *chom*) were appended with a basic-model interface with the help of the
 Community Surface Dynamics Modeling System. The repositories for the models coupled within *cascade* are noted here:
-- *barrier3d*: [GitHub Python Repository - Version 2.0 (BMI)](https://github.com/UNC-CECL/Barrier3D)
-- *brie*: [GitHub Python Repository - Version 1.0 (BMI)](https://github.com/UNC-CECL/brie)
-- *chom*: [GitHub Python Repository - Version 0.0.1.dev0 (BMI)](https://github.com/UNC-CECL/CHOM)
+- *barrier3d*: [GitHub Python Repository - Version 2.0 (BMI)][barrier3d-github]
+- *brie*: [GitHub Python Repository - Version 1.0 (BMI)][brie-github]
+- *chom*: [GitHub Python Repository - Version 0.0.1.dev0 (BMI)][chom-github]
 
 ## Installation
 
 To install the latest release of *cascade* using *pip*, simply run the following in your terminal of choice:
 
-      pip install coastal-cascade
+```bash
+pip install coastal-cascade
+```
 
 You can also use `conda`:
 
-      conda install coastal-cascade
+```bash
+conda install coastal-cascade
+```
 
 ### From Source
 
@@ -64,51 +80,61 @@ need to get *cascade*'s source code, and then install *cascade* from that code.
 
 To get the source code you can either clone the repository with *git*:
 
-      git clone git@github.com/UNC-CECL/cascade
+```bash
+git clone git@github.com:UNC-CECL/cascade
+```
 
-or download a [zip file](https://github.com/UNC-CECL/CASCADE/archive/refs/heads/main.zip):
+or download a [zip file][zip-download]:
 
-      curl -OL https://github.com/UNC-CECL/CASCADE/archive/refs/heads/main.zip
+```bash
+curl -OL https://github.com/UNC-CECL/CASCADE/archive/refs/heads/main.zip
+```
 
 Once you have a copy of the source code, you can install it into your current
 environment,
 
-      pip install -e .
+```bash
+pip install -e .
+```
 
-We use [nox] to automate routine maintenance tasks like running the tests,
-removing lint, etc. Install [nox] with *pip*::
+We use [nox-docs] to automate routine maintenance tasks like running the tests,
+removing lint, etc. Install [nox-docs] with *pip*::
 
-      pip install nox
+```bash
+pip install nox
+```
 
-When you're done making changes, you can now run [nox] to check that the tests
+When you're done making changes, you can now run [nox-docs] to check that the tests
 pass and that there isn't any lint:
 
-      nox -s test  # run the unit tests
-      nox -s test-notebooks  # test that the notebooks run successfully
-      nox -s lint  # find and, where possible, remove lint (black, flake8, etc.)
+```bash
+nox -s test  # run the unit tests
+nox -s test-notebooks  # test that the notebooks run successfully
+nox -s lint  # find and, where possible, remove lint (black, flake8, etc.)
+```
 
 To run all of the above in a single command:
 
-      nox
-
-[nox]: https://nox.thea.codes/
+```bash
+nox
+```
 
 ## Example simulations
-This ReadMe corresponds to the version of *cascade* used for the simulations detailed in 
-*"The Future of Developed Barrier Systems - Part I: Pathways Toward Uninhabitability, Drowning, and Rebound" by 
-Anarde et al., (2024, [Earth ArXiv preprint](https://doi.org/10.31223/X5P947))* -- namely, v1.0.0. For a more complete 
+This ReadMe corresponds to the version of *cascade* used for the simulations detailed in
+*"The Future of Developed Barrier Systems - Part I: Pathways Toward Uninhabitability, Drowning, and Rebound" by
+Anarde et al., (2024, [Earth ArXiv preprint][preprint-doi])* -- namely, v1.0.0. For a more complete
 set of example model runs and description of module functionality, we direct the use to the examples
 provided in `notebooks`.
 
 Example (default) data inputs for cascade are provided in the `data` directory:
-```
+```python
 from cascade.cascade import Cascade
 
 datadir = "data/"
 ```
 To initialize an instance of *cascade* with no human dynamics, 3 barrier segments (each 500-m long), and
 default *barrier3d* and *brie* parameters:
-```
+```python
 cascade = Cascade(
     datadir,
     name="no_human_dynamics_3_barrier_segments",
@@ -120,7 +146,7 @@ cascade = Cascade(
 )
 ```
 To initialize an instance of *cascade* with roadway barrier management on 1 barrier segment:
-```
+```python
 cascade = Cascade(
     datadir,
     name="roadway_mgmt_1_barrier_segments",
@@ -132,7 +158,7 @@ cascade = Cascade(
 )
 ```
 To initialize *cascade* with community barrier management on 1 barrier segment:
-```
+```python
 cascade = Cascade(
     datadir,
     name="community_mgmt_1_barrier_segments",
@@ -144,7 +170,7 @@ cascade = Cascade(
 )
 ```
 Once initialized, a *cascade* time loop can be completed as follows:
-```
+```python
 for time_step in range(cascade.time_step_count - 1):
     cascade.update()
     if cascade.b3d_break:

cascade/beach_dune_manager.py

@@ -39,12 +39,14 @@
 initial beach slope defined in Barrier3D to develop the storm series. This beach
 width is then modified dynamically via nourishment and shoreface dynamics.
 """
+
 import copy
 import math
 
 import numpy as np
 
-from .roadway_manager import rebuild_dunes, set_growth_parameters
+from .roadway_manager import rebuild_dunes
+from .roadway_manager import set_growth_parameters
 
 dm3_to_m3 = 1000  # convert from cubic decameters to cubic meters
 
@@ -292,9 +294,9 @@ def filter_overwash(
     else:
         # spread overwash removed from roadway equally over the adjacent dune cells
         total_overwash_removal_dune_volume = sum(overwash_removal_dune)  # array of dam
-        total_overwash_removal_dune_volume[
-            total_overwash_removal_dune_volume < 0
-        ] = 0  # don't let it erode a dune
+        total_overwash_removal_dune_volume[total_overwash_removal_dune_volume < 0] = (
+            0  # don't let it erode a dune
+        )
         number_dune_cells = np.size(post_storm_yxz_dune_grid, 1)
         overwash_volume_to_dune = np.transpose(
             [total_overwash_removal_dune_volume / number_dune_cells] * number_dune_cells
@@ -304,9 +306,9 @@ def filter_overwash(
 
     # don't allow dunes to exceed a maximum height (limits 10-m dunes after big
     # storms...yikes!); assume the rest of the sand disappears
-    new_dune_domain[
-        new_dune_domain > artificial_maximum_dune_height
-    ] = artificial_maximum_dune_height
+    new_dune_domain[new_dune_domain > artificial_maximum_dune_height] = (
+        artificial_maximum_dune_height
+    )
 
     # dam^3
     total_overwash_removal = (
@@ -499,9 +501,9 @@ def abandonment_cleanup_tasks(
 
         # turn dune migration back on
         barrier3d.dune_migration_on = True
-        self._dune_migration_on[
-            self._time_index - 1
-        ] = barrier3d.dune_migration_on  # keep track!
+        self._dune_migration_on[self._time_index - 1] = (
+            barrier3d.dune_migration_on
+        )  # keep track!
 
         # set the shoreline change aggregate to the dam (cell) fraction
         barrier3d.SCRagg[self._time_index - 1] = (barrier3d.x_s % 1) * -1

cascade/brie_coupler.py

@@ -27,13 +27,15 @@
 In future versions, the coupled model will incorporate tidal inlet dynamics
 within BRIE (i.e., the inlet model will be turned on).
 """
+
 import math
 import pathlib
 
 import numpy as np
 from barrier3d import Barrier3d
 from brie import Brie
-from yaml import dump, full_load
+from yaml import dump
+from yaml import full_load
 
 
 def set_yaml(var_name, new_vals, file_name):