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/main/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 rm\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",
@@ -866,19 +866,19 @@
     "ic = om2_input.isel(time = 0)\n",
     "\n",
     "## Nicer Slicer handles seams in longitude and different grids. Ensures that the output matches our 'xextent'\n",
-    "ic = ml.nicer_slicer(ic,[xextent[0],xextent[1]],[\"xu_ocean\",\"xt_ocean\"])\n",
+    "ic = rm.nicer_slicer(ic,[xextent[0],xextent[1]],[\"xu_ocean\",\"xt_ocean\"])\n",
     "ic.to_netcdf(tmpdir + \"/ic_unprocessed\")\n",
     "\n",
     "## Cut out East and West segments. Does lat slice first then uses nicer slicer for lon slice\n",
     "eastwest = om2_input.sel(    \n",
     "    yu_ocean = slice(yextent[0] - 0.2,yextent[1] + 0.2),\n",
     "    yt_ocean = slice(yextent[0] - 0.2,yextent[1] + 0.2)\n",
     ")\n",
-    "ml.nicer_slicer(eastwest,[xextent[1],xextent[1]],[\"xu_ocean\",\"xt_ocean\"]).to_netcdf(tmpdir + \"/east_unprocessed\")\n",
-    "ml.nicer_slicer(eastwest,[xextent[0],xextent[0]],[\"xu_ocean\",\"xt_ocean\"]).to_netcdf(tmpdir + \"/west_unprocessed\")\n",
+    "rm.nicer_slicer(eastwest,[xextent[1],xextent[1]],[\"xu_ocean\",\"xt_ocean\"]).to_netcdf(tmpdir + \"/east_unprocessed\")\n",
+    "rm.nicer_slicer(eastwest,[xextent[0],xextent[0]],[\"xu_ocean\",\"xt_ocean\"]).to_netcdf(tmpdir + \"/west_unprocessed\")\n",
     "\n",
     "## Cut out North and South segments\n",
-    "northsouth = ml.nicer_slicer(om2_input,[xextent[0],xextent[1]],[\"xu_ocean\",\"xt_ocean\"])\n",
+    "northsouth = rm.nicer_slicer(om2_input,[xextent[0],xextent[1]],[\"xu_ocean\",\"xt_ocean\"])\n",
     "northsouth.sel(\n",
     "    yu_ocean = slice(yextent[1] - 0.2,yextent[1] + 0.2),\n",
     "    yt_ocean = slice(yextent[1] - 0.2,yextent[1] + 0.2)\n",
@@ -935,7 +935,7 @@
    ],
    "source": [
     "reload(ml)\n",
-    "expt = ml.experiment(\n",
+    "expt = rm.experiment(\n",
     "    xextent,\n",
     "    yextent,\n",
     "    daterange,\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 rm\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",
@@ -486,7 +486,7 @@
     "usr = \"YOUR COPERNICUS USERNAME\"  \n",
     "file = open(f\"{tmpdir}/get_oceanfiles.sh\",\"w\")\n",
     "file.write(\n",
-    "        ml.motu_requests(xextent, yextent, daterange, tmpdir, usr, pwd,[\"north\",\"south\",\"east\",\"west\"])\n",
+    "        rm.motu_requests(xextent, yextent, daterange, tmpdir, usr, pwd,[\"north\",\"south\",\"east\",\"west\"])\n",
     ")\n",
     "file.close()\n",
     "\n",
@@ -529,7 +529,7 @@
    "outputs": [],
    "source": [
     "reload(ml)\n",
-    "expt = ml.experiment(\n",
+    "expt = rm.experiment(\n",
     "    xextent,\n",
     "    yextent,\n",
     "    daterange,\n",
@@ -837,7 +837,7 @@
     "for fname , vname in zip([\"2t\",\"10u\",\"10v\",\"sp\",\"2d\"] , [\"t2m\",\"u10\",\"v10\",\"sp\",\"d2m\"]):\n",
     "\n",
     "    ## Cut out this variable to our domain size\n",
-    "    rawdata[fname] = ml.nicer_slicer(\n",
+    "    rawdata[fname] = rm.nicer_slicer(\n",
     "        xr.open_mfdataset(f\"{erapath}/{fname}/{daterange[0].split('-')[0]}/{fname}*\",decode_times = False,chunks = {\"longitude\":100,\"latitude\":100}),\n",
     "        xextent,\n",
     "        \"longitude\"\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

@@ -1,7 +1,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "MOM6 Regional"
+project = "Regional MOM6"
 copyright = "2023, Ashley Barnes & COSIMA Contributors"
 author = "Ashley Barnes & COSIMA Contributors"
 
@@ -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.

docs/index.rst

@@ -1,5 +1,8 @@
-Welcome to MOM6 Regional's documentation!
-=========================================
+Regional MOM6 Documentation
+===========================
+
+``regional_mom6`` is a Python package for automatic generation of regional
+configurations for the Modular Ocean Model 6
 
 .. toctree::
    :maxdepth: 2

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

tests/test_trivial.py

@@ -1,5 +1,5 @@
 import numpy as np
-from mom6_regional import angle_between
+from regional_mom6 import angle_between
 
 
 # placeholder trivial test test