Rename repo/package mom6_regional -> regional_mom6

.github/workflows/testing.yml

@@ -12,7 +12,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: psf/black@stable
         with:
-          src: "./mom6_regional ./tests"
+          src: "./regional_mom6 ./tests"
 
   testing:
     needs: formatting
@@ -42,7 +42,7 @@ jobs:
       - name: Test with pytest
         run: |
           if [[ "${{ matrix.python-version }}" == "3.10" ]]; then
-            python -m pytest --cov=mom6_regional --cov-report=xml tests/
+            python -m pytest --cov=regional_mom6 --cov-report=xml tests/
           else
             python -m pytest tests/
           fi

.gitignore

@@ -2,7 +2,7 @@ __pycache__
 .ipynb_checkpoints
 build
 _build
-mom6_regional/_version.py
-mom6_regional.egg-info
+regional_mom6/_version.py
+regional_mom6.egg-info
 .pytest_cache
 env

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Angus Gibson
+Copyright (c) 2023 COSIMA
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,9 +1,7 @@
-# A regional domain generator for Modular Ocean Model 6
+# regional_mom6: Python package for automatic generation of regional configurations for the Modular Ocean Model 6
 
-[![codecov](https://codecov.io/gh/COSIMA/mom6-regional/branch/master/graph/badge.svg?token=7OEZ1UZRY4)](https://codecov.io/gh/COSIMA/mom6-regional) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/mom6-regional/badge/?version=latest)](https://mom6-regional.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/COSIMA/regional-mom6/branch/master/graph/badge.svg?token=7OEZ1UZRY4)](https://codecov.io/gh/COSIMA/regional-mom6) [![Documentation Status](https://readthedocs.org/projects/regional-mom6/badge/?version=latest)](https://regional-mom6.readthedocs.io/en/latest/?badge=latest) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-`mom6_regional` contains functions and classes that do most of the legwork in setting up a regional domain in MOM6.
-Just provide it with some information about where, when and how big, and point it in the direction of your raw input files, and it'll sort out the boring details to create MOM6-friendly input files. Check out the [demo notebook](https://nbviewer.org/github/COSIMA/mom6-regional-scripts/blob/master/demo.ipynb)!
+Just provide some information about where, when and how big, and also where raw input forcing files live. The package will sort out all the boring details to create MOM6-friendly input files.
 
-### Python package
-This repository is being converted into a python package that will be distributed via `pip` and `conda`. At the moment, there are still som legacy stuff -- hold on to your chairs as we clean up the repo and the pipelines for generating regional MOM6 configurations.
+Check out the [demo notebook](https://nbviewer.org/github/COSIMA/regional-mom6/blob/m/demo.ipynb) and also the [documentation](https://readthedocs.org/projects/regional-mom6/badge/?version=latest)!

demos/model-forced.ipynb

@@ -453,10 +453,10 @@
     "import subprocess\n",
     "from scipy.ndimage import binary_fill_holes\n",
     "from importlib import reload\n",
-    "# os.chdir(\"/path/to/where/you/cloned/the/mom6-regional/repository\")\n",
-    "os.chdir(\"/home/149/ab8992/cosima_regional/mom6-regional-scripts/mom6_regional/\")\n",
+    "# os.chdir(\"/path/to/where/you/cloned/the/regional-mom6/repository\")\n",
+    "os.chdir(\"/home/149/ab8992/cosima_regional/regional-mom6/regional_mom6/\")\n",
     "\n",
-    "import mom6_regional as ml\n",
+    "import regional_mom6 as ml\n",
     "from dask.distributed import Client\n",
     "client = Client()\n",
     "client"
@@ -537,10 +537,10 @@
     "yextent = [-48,-38.95] ## latitude\n",
     "xextent = [143,150] ## longitude\n",
     "\n",
-    "daterange = [\"1990-01-01 00:00:00\", \"1990-01-05 00:00:00\"] ## 2003 is a good compimise for GLORYs and JRA forcing as they overlap. JRA ends in 2012, GLORYS starts in 1993\n",
+    "daterange = [\"1990-01-01 00:00:00\", \"1990-01-05 00:00:00\"] ## 2003 is a good compromise for GLORYs and JRA forcing as they overlap. JRA ends in 2012, GLORYS starts in 1993\n",
     "\n",
     "## Place where all your input files go\n",
-    "inputdir = f\"{scratch}/mom6_regional_configs/{expt_name}/\"\n",
+    "inputdir = f\"{scratch}/regional_mom6_configs/{expt_name}/\"\n",
     "\n",
     "## Directory where you'll run the experiment from\n",
     "rundir = f\"{home}/mom6_rundirs/{expt_name}/\"\n",

demos/reanalysis-forced.ipynb

@@ -331,10 +331,10 @@
     "import subprocess\n",
     "from scipy.ndimage import binary_fill_holes\n",
     "from importlib import reload\n",
-    "# os.chdir(\"/path/to/where/you/cloned/the/mom6-regional/repository\")\n",
-    "os.chdir(\"/home/149/ab8992/cosima_regional/mom6-regional-scripts/mom6_regional/\")\n",
+    "# os.chdir(\"/path/to/where/you/cloned/the/regional-mom6/repository\")\n",
+    "os.chdir(\"/home/149/ab8992/cosima_regional/regional-mom6/regional_mom6/\")\n",
     "\n",
-    "import mom6_regional as ml\n",
+    "import regional_mom6 as ml\n",
     "from dask.distributed import Client\n",
     "client = Client()\n",
     "client"
@@ -417,7 +417,7 @@
     "daterange = [\"2003-01-01 00:00:00\", \"2003-01-05 00:00:00\"] ## 2003 is a good compimise for GLORYs and JRA forcing as they overlap. JRA ends in 2012, GLORYS starts in 1993\n",
     "\n",
     "## Place where all your input files go\n",
-    "inputdir = f\"{scratch}/mom6_regional_configs/{expt_name}/\"\n",
+    "inputdir = f\"{scratch}/regional_mom6_configs/{expt_name}/\"\n",
     "\n",
     "## Directory where you'll run the experiment from\n",
     "rundir = f\"{home}/mom6_rundirs/{expt_name}/\"\n",

docs/api.rst

@@ -2,6 +2,6 @@
  API reference
 ===============
 
-.. automodule:: mom6_regional.mom6_regional
+.. automodule:: regional_mom6.regional_mom6
    :members:
    :undoc-members:

docs/conf.py

@@ -23,6 +23,6 @@
 html_theme = "sphinx_book_theme"
 html_static_path = ["_static"]
 html_theme_options = {
-    "repository_url": "https://github.com/COSIMA/mom6-regional",
+    "repository_url": "https://github.com/COSIMA/regional-mom6",
     "use_repository_button": True,
 }

docs/contributing.md

@@ -1,7 +1,7 @@
 Instructions for Contributors
 =============================
 
-Before you submit a [pull request](https://github.com/COSIMA/mom6-regional/pulls) it's always a
+Before you submit a [pull request](https://github.com/COSIMA/regional-mom6/pulls) it's always a
 good idea to run the tests locally and catch any potential bugs/errors that might have been
 introduced. Also, sometimes it's also a good idea to build the documentation locally to see
 how new docstrings or any new bits of documentation that you may have added look like.

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "mom6_regional"
+name = "regional_mom6"
 description = "Automatic generation of regional configurations for Modular Ocean Model 6"
 keywords = ["mom6", "regional", "ocean modeling"]
 authors = [
@@ -21,7 +21,7 @@ requires = ["setuptools", "setuptools_scm[toml]"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
-packages = ["mom6_regional"]
+packages = ["regional_mom6"]
 
 [tool.setuptools_scm]
-write_to = "mom6_regional/_version.py"
+write_to = "regional_mom6/_version.py"

mom6_regional/__init__.py → regional_mom6/__init__.py

@@ -3,4 +3,4 @@
 except ImportError:
     __version__ = "unknown"
 
-from .mom6_regional import *  # noqa
+from .regional_mom6 import *  # noqa