Update Python Version and change mom6_bathy to mom6_forge

.github/workflows/ci-tests.yml

@@ -10,8 +10,12 @@ on:
 
 jobs:
   ci_tests:
-    name: visualCaseGen CI tests
+    name: visualCaseGen CI tests (Python ${{ matrix.python-version }})
     runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
     defaults:
       run:
         shell: bash -el {0}
@@ -56,6 +60,7 @@ jobs:
       - name: Create visualCaseGen conda env
         run: |
           cd CESM/visualCaseGen/
+          sed -i "s/python>=3.11.10/python=${{ matrix.python-version }}.*/" environment.yml
           conda env create --file environment.yml
           conda activate visualCaseGen
 

.gitmodules

@@ -1,6 +1,6 @@
-[submodule "external/mom6_bathy"]
-	path = external/mom6_bathy
-	url = https://github.com/NCAR/mom6_bathy.git
+[submodule "external/mom6_forge"]
+	path = external/mom6_forge
+	url = https://github.com/NCAR/mom6_forge.git
 [submodule "external/ipyfilechooser"]
 	path = external/ipyfilechooser
 	url = https://github.com/alperaltuntas/ipyfilechooser.git

docs/grid.rst

@@ -64,23 +64,23 @@ Ocean Grid
 For the ocean grid, if MOM6 is selected as the ocean model, you can either select a standard
 ocean grid or create a new MOM6 grid. When creating a new MOM6 grid, you'll specify parameters
 such as grid extent and resolution, after which you'll be directed to a separate notebook that
-uses the `mom6_bathy` tool to generate the new grid and bathymetry.
+uses the `mom6_forge` tool to generate the new grid and bathymetry.
 
 If using a standard ocean grid, select one from the list compatible with your chosen compset
 and atmosphere grid. If creating a new MOM6 grid, complete the required parameters, then proceed
-to launch the `mom6_bathy` tool for final customization.
+to launch the `mom6_forge` tool for final customization.
 
 .. image:: assets/Stage2_6.png
 
-After specifying all ocean grid parameters, click `Launch mom6_bathy`. This will open an 
+After specifying all ocean grid parameters, click `Launch mom6_forge`. This will open an 
 auto-generated Jupyter notebook where you can fine-tune the ocean grid, topography, and vertical grid.
 You can then generate the corresponding MOM6 input files, which will be saved under `ocnice` subdirectory
 within the directory you specified earlier for saving the new grid files.
-For more details on mom6_bathy, refer to its documentation: https://ncar.github.io/mom6_bathy/
+For more details on mom6_forge, refer to its documentation: https://ncar.github.io/mom6_forge/
 
-.. note:: If the `mom6_bathy` notebook doesn't open automatically, make sure that your browser allows
+.. note:: If the `mom6_forge` notebook doesn't open automatically, make sure that your browser allows
   pop-ups from visualCaseGen. If the notebook still doesn't open, you can manually launch it by
-  navigating to the `mom6_bathy_notebooks/` directory in your visualCaseGen installation and opening
+  navigating to the `mom6_forge_notebooks/` directory in your visualCaseGen installation and opening
   the notebook corresponding to your custom grid.
 
 Ocean Initial conditions

docs/ridge.rst

@@ -126,31 +126,31 @@ assign a unique name to your custom ocean grid.
 
 .. image:: assets/ridge7.png
 
-After specifying all ocean grid parameters, click the green **Launch mom6_bathy** button. This will open an auto-generated
+After specifying all ocean grid parameters, click the green **Launch mom6_forge** button. This will open an auto-generated
 Jupyter notebook where you can further customize the ocean bathymetry and generate all necessary grid input files.
 
-The mom6_bathy tool
+The mom6_forge tool
 ~~~~~~~~~~~~~~~~~~~
 
-.. important:: If the `mom6_bathy` notebook doesn't open automatically, make sure that your browser allows
+.. important:: If the `mom6_forge` notebook doesn't open automatically, make sure that your browser allows
   pop-ups from visualCaseGen. If the notebook still doesn't open, you can manually launch it by
-  navigating to the `mom6_bathy_notebooks/` directory in your visualCaseGen installation and opening
+  navigating to the `mom6_forge_notebooks/` directory in your visualCaseGen installation and opening
   the notebook corresponding to your custom grid.
 
-Once the auto-generated `mom6_bathy` notebook is open, you will see a series of cells that guide you through
+Once the auto-generated `mom6_forge` notebook is open, you will see a series of cells that guide you through
 the process of creating your custom ocean bathymetry. Before proceeding, make sure that the appropriate
 kernel is selected in the top right corner of the notebook. Then, execute the first two cells to import
 the necessary libraries and to instantiate the `Grid` object. Notice that the `Grid` object is initialized
 with the parameters you specified in visualCaseGen.
 
 .. image:: assets/ridge8.png
 
-The third section of mom6_bathy is where a custom bathymetry may be defined. The default option is to produce
+The third section of mom6_forge is where a custom bathymetry may be defined. The default option is to produce
 a flat ocean bottom of depth 2000m. We are going to instead generate an ocean that
 resembles the ridge world case of `Wu et al (2021) <https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GL093966>`_ ,
 which has a depth 4000m with some sinusoidal fluctuations, a land ridge of width 1 degree longitude and
 the furthest poleward 10 degrees latitude at the poles set to land. We will specify this analytically with python
-code within mom6_bathy.
+code within mom6_forge.
 
 First, instantiate the topo object by running the cell below. Note that the `min_depth` parameter, which
 is set to 10.0m by default determines the minimum bathymetric depth for a cell to be considered ocean.
@@ -199,7 +199,7 @@ You can plot the bathymetry to see the results by running the cell below:
 Vertical Grid
 ~~~~~~~~~~~~~
 
-Next, you will need to set up the vertical grid. In the `mom6_bathy` notebook, 
+Next, you will need to set up the vertical grid. In the `mom6_forge` notebook, 
 a default vertical grid is provided, which consists of 20 layers, and a ratio of 10,
 which means that the thicknesses of layers gradually increase with depth, and the thickness
 of the bottom layer is 10 times thicker than the top layer.
@@ -222,7 +222,7 @@ vertical grid files (needed by MOM6), CICE grid file (needed by the sea ice mode
 (needed by the CESM coupler).
 
 .. warning:: The paths specified in the cell below are for illustrative purposes only. Do not modify the paths
-    in your auto-generated `mom6_bathy` notebook. The paths are unique to the user's system and should not be changed,
+    in your auto-generated `mom6_forge` notebook. The paths are unique to the user's system and should not be changed,
     since doing so will prevent visualCaseGen from confirming that the grid files have been successfully generated
     and will prevent configuring CESM accurately.
 

docs/troubleshooting.rst

@@ -23,13 +23,13 @@ Commonly Encountered Issues
   right corner of the welcome dialog to see if any error messages are displayed. If so, submit an issue on the
   visualCaseGen GitHub repository with the error messages.
 
-- **mom6_bathy notebook doesn't open automatically:** If the `mom6_bathy` notebook doesn't open automatically, 
+- **mom6_forge notebook doesn't open automatically:** If the `mom6_forge` notebook doesn't open automatically, 
   make sure that your browser allows
   pop-ups from visualCaseGen. If the notebook still doesn't open, you can manually launch it by
-  navigating to the `mom6_bathy_notebooks/` directory in your visualCaseGen installation and opening
+  navigating to the `mom6_forge_notebooks/` directory in your visualCaseGen installation and opening
   the notebook corresponding to your custom grid.
 
-- **The mom6_bathy interactive point-and-click feature is not working on JupyterHub.**
+- **The mom6_forge interactive point-and-click feature is not working on JupyterHub.**
   If you are experiencing issues with interactive features, such as point-and-click highlighting of individual 
   cells, you may need to (re)install the ipympl extension. Steps to (re)install the ipympl extension: (1) Open 
   JupyterHub. (2) Locate the *Extension Manager* tab on the left sidebar: Look for an icon that resembles a puzzle

environment.yml

@@ -5,11 +5,11 @@ channels:
   - anaconda
 
 dependencies:
-  - python>=3.11.10,<3.12
-  - libxml2>=2.13,<2.14
-  - xesmf>=0.8.10,<0.9
+  - python>=3.11.10,<3.13.0
+  - libxml2>=2.13,<2.16
+  - xesmf>=0.8.10,<0.10.0
   - pip
   - pip:
-    - -e ./external/mom6_bathy/
+    - -e ./external/mom6_forge/
     - -e ./external/ipyfilechooser/
     - -e ./ # visualCaseGen

internal/README.md

@@ -1 +1 @@
-This subdirectory is internally used by visualCaseGen to exchange information with mom6_bathy and other tools. Manually interfering with files in this directory may disrupt any active visualCaseGen session.
+This subdirectory is internally used by visualCaseGen to exchange information with mom6_forge and other tools. Manually interfering with files in this directory may disrupt any active visualCaseGen session.

mom6_bathy_notebooks/README.md → mom6_forge_notebooks/README.md

@@ -1,2 +1,2 @@
-This directory is for storing mom6_bathy notebooks generated by visualCaseGen.
+This directory is for storing mom6_forge notebooks generated by visualCaseGen.
 When you are done with a notebook, you may manually remove or store it for documentation purposes.

pyproject.toml

@@ -13,21 +13,21 @@ classifiers = [
   "Programming Language :: Python",
   "Framework :: Jupyter"
 ]
-requires-python = ">=3.11.10,<3.12"
+requires-python = ">=3.11.10,<3.13.0"
 dependencies = [
-  "ipykernel>=6.29,<6.30",
-  "ipython>=8.2,<8.3",
-  "jupyterlab>=4.0,<4.1",
-  "jupyterlab_server>=2.25,<2.26",
-  "ipywidgets>=8.1.1,<8.2",
-  "PyYAML>=6.0,<6.1",
-  "z3-solver>=4.12.3,<4.13",
-  "networkx>=3.3,<3.4",
-  "netcdf4>=1.6,<1.7",
-  "xarray>=2023.12,<2024",
-  "black>=24.1,<24.2",
-  "pytest>=8.0,<8.1",
-  "hypothesis>=6.125.1,<6.126"
+  "ipykernel>=6.29,<7.3.0",
+  "ipython>=8.2,<9.13",
+  "jupyterlab>=4.0,<4.6.0",
+  "jupyterlab_server>=2.25,<2.29.0",
+  "ipywidgets>=8.1.1,<8.2.0",
+  "PyYAML>=6.0,<6.1.0",
+  "z3-solver>=4.12.3,<4.17.0",
+  "networkx>=3.3,<3.7.0",
+  "netcdf4>=1.6,<1.8.0",
+  "xarray>=2023.12,<2026.3.0",
+  "black>=24.1,<26.4.0",
+  "pytest>=8.0,<9.1.0",
+  "hypothesis>=6.125.1,<6.152.0"
 ]
 
 [build-system]

tests/3_system/test_custom_compset_std_grid.py

@@ -16,7 +16,7 @@
 from visualCaseGen.initialize_stages import initialize_stages
 from visualCaseGen.specs.options import set_options
 from visualCaseGen.specs.relational_constraints import get_relational_constraints
-from visualCaseGen.custom_widget_types.mom6_bathy_launcher import MOM6BathyLauncher
+from visualCaseGen.custom_widget_types.mom6_forge_launcher import MOM6ForgeLauncher
 from visualCaseGen.custom_widget_types.case_creator_widget import CaseCreatorWidget
 from tests.utils import safe_create_case
 

tests/3_system/test_custom_mom6_grid.py

@@ -16,7 +16,7 @@
 from visualCaseGen.initialize_stages import initialize_stages
 from visualCaseGen.specs.options import set_options
 from visualCaseGen.specs.relational_constraints import get_relational_constraints
-from visualCaseGen.custom_widget_types.mom6_bathy_launcher import MOM6BathyLauncher
+from visualCaseGen.custom_widget_types.mom6_forge_launcher import MOM6ForgeLauncher
 from visualCaseGen.custom_widget_types.case_creator_widget import CaseCreatorWidget
 from tests.utils import safe_create_case
 
@@ -90,24 +90,24 @@ def test_custom_mom6_grid():
         cvars["OCN_LENY"].value = 160.0
         cvars["CUSTOM_OCN_GRID_NAME"].value = "custom_ocn_grid"
 
-        # now launch the mom6_bathy notebook
+        # now launch the mom6_forge notebook
 
-        mom6_bathy_launcher_widget = Stage.active()._widget._main_body.children[-1]
-        assert isinstance(mom6_bathy_launcher_widget, MOM6BathyLauncher)
+        mom6_forge_launcher_widget = Stage.active()._widget._main_body.children[-1]
+        assert isinstance(mom6_forge_launcher_widget, MOM6ForgeLauncher)
 
         # After setting all the required parameters, the launch button should be enabled
-        assert mom6_bathy_launcher_widget._btn_launch_mom6_bathy.disabled is False
+        assert mom6_forge_launcher_widget._btn_launch_mom6_forge.disabled is False
 
         # *Click* the launch button
-        mom6_bathy_launcher_widget._on_btn_launch_clicked(b=None)
+        mom6_forge_launcher_widget._on_btn_launch_clicked(b=None)
 
         # The confirm button should be visible:
         assert (
-            mom6_bathy_launcher_widget._btn_confirm_completion.layout.display != "none"
+            mom6_forge_launcher_widget._btn_confirm_completion.layout.display != "none"
         )
 
         # *Click* the confirm button
-        mom6_bathy_launcher_widget._on_btn_confirm_completion_clicked(b=None)
+        mom6_forge_launcher_widget._on_btn_confirm_completion_clicked(b=None)
 
         # Since the notebook wasn't fully executed, we should remain in the same stage
         assert Stage.active().title.startswith("Custom Ocean")
@@ -116,10 +116,10 @@ def test_custom_mom6_grid():
         import nbformat
         from nbconvert.preprocessors import ExecutePreprocessor, CellExecutionError
 
-        # find the only mom6_bathy_*.ipynb file in the mom6_bathy_notebooks directory
+        # find the only mom6_forge_*.ipynb file in the mom6_forge_notebooks directory
         ocn_grid_name = cvars['CUSTOM_OCN_GRID_NAME'].value
-        nb_files = list(Path("mom6_bathy_notebooks").glob(f"mom6_bathy_{ocn_grid_name}*.ipynb"))
-        assert len(nb_files) == 1, "Expected only one mom6_bathy notebook file"
+        nb_files = list(Path("mom6_forge_notebooks").glob(f"mom6_forge_{ocn_grid_name}*.ipynb"))
+        assert len(nb_files) == 1, "Expected only one mom6_forge notebook file"
         nb_path = nb_files[0]
 
         with open(nb_path, "r") as f:
@@ -173,7 +173,7 @@ def test_custom_mom6_grid():
                 # If the error is not related to machine porting, raise it
                 raise e
 
-        # remove mom6_bathy notebook belonging to the test_grid:
+        # remove mom6_forge notebook belonging to the test_grid:
         if os.path.exists(nb_path):
             os.remove(nb_path)
 

tests/3_system/test_f2000_custom_grid.py

@@ -18,7 +18,7 @@
 from visualCaseGen.specs.relational_constraints import get_relational_constraints
 from visualCaseGen.custom_widget_types.clm_modifier_launcher import MeshMaskModifierLauncher, FsurdatModifierLauncher
 from visualCaseGen.custom_widget_types.case_creator_widget import CaseCreatorWidget
-from visualCaseGen.custom_widget_types.mom6_bathy_launcher import MOM6BathyLauncher
+from visualCaseGen.custom_widget_types.mom6_forge_launcher import MOM6ForgeLauncher
 from tests.utils import safe_create_case
 
 
@@ -308,30 +308,30 @@ def construct_custom_res_from_new_mom6_grid_modified_clm_grid(cime):
         cvars["OCN_LENY"].value = 160.0
         cvars["CUSTOM_OCN_GRID_NAME"].value = "custom_ocn_grid"
 
-        # now launch the mom6_bathy notebook
+        # now launch the mom6_forge notebook
 
-        mom6_bathy_launcher_widget = Stage.active()._widget._main_body.children[-1]
-        assert isinstance(mom6_bathy_launcher_widget, MOM6BathyLauncher)
+        mom6_forge_launcher_widget = Stage.active()._widget._main_body.children[-1]
+        assert isinstance(mom6_forge_launcher_widget, MOM6ForgeLauncher)
 
         # After setting all the required parameters, the launch button should be enabled
-        assert mom6_bathy_launcher_widget._btn_launch_mom6_bathy.disabled is False
+        assert mom6_forge_launcher_widget._btn_launch_mom6_forge.disabled is False
 
         # *Click* the launch button
-        mom6_bathy_launcher_widget._on_btn_launch_clicked(b=None)
+        mom6_forge_launcher_widget._on_btn_launch_clicked(b=None)
 
         # The confirm button should be visible:
         assert (
-            mom6_bathy_launcher_widget._btn_confirm_completion.layout.display != "none"
+            mom6_forge_launcher_widget._btn_confirm_completion.layout.display != "none"
         )
 
         # now, programmatically run the notebook
         import nbformat
         from nbconvert.preprocessors import ExecutePreprocessor, CellExecutionError
 
-        # find the only mom6_bathy_*.ipynb file in the mom6_bathy_notebooks directory
+        # find the only mom6_forge_*.ipynb file in the mom6_forge_notebooks directory
         ocn_grid_name = cvars['CUSTOM_OCN_GRID_NAME'].value
-        nb_files = list(Path("mom6_bathy_notebooks").glob(f"mom6_bathy_{ocn_grid_name}*.ipynb"))
-        assert len(nb_files) == 1, "Expected only one mom6_bathy notebook file"
+        nb_files = list(Path("mom6_forge_notebooks").glob(f"mom6_forge_{ocn_grid_name}*.ipynb"))
+        assert len(nb_files) == 1, "Expected only one mom6_forge notebook file"
         nb_path = nb_files[0]
 
         with open(nb_path, "r") as f:
@@ -393,7 +393,7 @@ def construct_custom_res_from_new_mom6_grid_modified_clm_grid(cime):
         # sleep for a bit to allow the case to be created
         time.sleep(5)
 
-        # remove mom6_bathy notebook belonging to the test_grid:
+        # remove mom6_forge notebook belonging to the test_grid:
         os.remove(nb_path)
 
         # remove the caseroot directory

visualCaseGen/config_vars/grid_vars.py

@@ -53,7 +53,7 @@ def initialize_custom_grid_variables(cime):
     ConfigVarInt("OCN_NY")  # number of cells in y-direction
     ConfigVarReal("OCN_LENX")  # grid length in x-direction
     ConfigVarReal("OCN_LENY")  # grid length in y-direction
-    ConfigVarStr('MB_ATTEMPT_ID') # latest mom6_bathy attempt id (auxiliary variable)
+    ConfigVarStr('MB_ATTEMPT_ID') # latest mom6_forge attempt id (auxiliary variable)
     ConfigVarStr(
         "MOM6_BATHY_STATUS", widget_none_val=""
     )  # a status variable to prevent the completion of the stage

visualCaseGen/custom_widget_types/case_creator.py

@@ -9,7 +9,7 @@
 import math 
 
 from ProConPy.config_var import cvars
-from visualCaseGen.custom_widget_types.mom6_bathy_launcher import MOM6BathyLauncher
+from visualCaseGen.custom_widget_types.mom6_forge_launcher import MOM6ForgeLauncher
 from visualCaseGen.custom_widget_types.dummy_output import DummyOutput
 from visualCaseGen.custom_widget_types.case_tools import xmlchange, run_case_setup, append_user_nl, is_ccs_config_writeable
 
@@ -435,7 +435,7 @@ def _update_component_grids(
                 new_domain,
                 "desc",
             )
-            desc.text = f"New ocean grid {ocn_grid} generated by mom6_bathy"
+            desc.text = f"New ocean grid {ocn_grid} generated by mom6_forge"
 
             if not do_exec:
                 return
@@ -642,10 +642,10 @@ def _apply_mom_namelist_changes(self, do_exec):
                 ocn_grid_mode == "Create New"
             ), f"Unknown ocean grid mode: {ocn_grid_mode}"
 
-        supergrid_file_path = MOM6BathyLauncher.supergrid_file_path()
-        topo_file_path = MOM6BathyLauncher.topo_file_path()
-        vgrid_file_path = MOM6BathyLauncher.vgrid_file_path()
-        ocn_grid_path = MOM6BathyLauncher.get_custom_ocn_grid_path()
+        supergrid_file_path = MOM6ForgeLauncher.supergrid_file_path()
+        topo_file_path = MOM6ForgeLauncher.topo_file_path()
+        vgrid_file_path = MOM6ForgeLauncher.vgrid_file_path()
+        ocn_grid_path = MOM6ForgeLauncher.get_custom_ocn_grid_path()
 
         # read in min and max depth from the MOM6 topo file:
         ds_topo = xr.open_dataset(topo_file_path)
@@ -752,7 +752,7 @@ def _apply_cice_namelist_changes(self, do_exec):
         if not comp_ice.startswith("cice"):
             return
 
-        cice_grid_file_path = MOM6BathyLauncher.cice_grid_file_path()
+        cice_grid_file_path = MOM6ForgeLauncher.cice_grid_file_path()
         self._apply_user_nl_changes(
             "cice",
             [