Update pyproject.toml

.github/workflows/ci-tests.yml

@@ -10,13 +10,20 @@ 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}
     steps:
-
+      - name: Configure Git Identity
+        run: |
+          git config --global user.name "github-actions"
+          git config --global user.email "github-actions@github.com"
       - name: Install xmllint
         run: sudo apt-get install -y libxml2-utils
       - name: Checkout VisualCaseGen to temp folder
@@ -29,7 +36,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: alperaltuntas/CESM
-          ref: cesm3_0_beta03_gui
+          ref: cesm3_0_beta08_gui
           path: CESM
           #submodules: recursive
 
@@ -53,6 +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

CONTRIBUTING.md

@@ -0,0 +1,37 @@
+# Contributing to visualCaseGen
+
+Thank you for your interest in contributing to visualCaseGen!
+
+We welcome contributions that fix bugs, introduce new features, and enhance the usability, robustness, or performance of the tool. Here's how you can get involved:
+
+## Getting Started
+
+Fork the repository and clone your fork.
+
+Follow the instructions in the visualCaseGen documentation to set up your local visualCaseGen environment: https://esmci.github.io/visualCaseGen/
+
+Create a new branch for your feature or bugfix.
+
+## What You Can Contribute
+
+- Bug fixes and issue resolutions
+- Enhancements to the GUI or core functionality
+- Improved documentation or examples
+- Code cleanup and test coverage
+
+## Guidelines
+
+- Follow the existing code style and structure.
+- Include clear commit messages.
+- Test your changes before submitting.
+- Add tests if you introduce new features.
+- Open a Pull Request with a short summary of your changes.
+- If addressing an open issue, mention it in your PR (e.g., Closes #42).
+
+## Reporting Issues
+
+Please use the GitHub Issues page to report bugs or suggest features. When reporting:
+
+- Include the version of visualCaseGen you used and details about your system environment.
+- Provide clear steps to reproduce the issue.
+- Include screenshots or logs if helpful.

ProConPy/config_var.py

@@ -334,6 +334,11 @@ def update_options_validities(self):
 
         return validities_changed
 
+    @property
+    def valid_options(self):
+        """Returns the list of valid options for this variable."""
+        return [opt for opt in self._options if self._options_validities.get(opt, False)]
+
     def _refresh_widget_options(self):
         """Refresh the widget options list based on information in the current self._options_validities."""
 

ProConPy/stage.py

@@ -352,7 +352,7 @@ def _proceed(self):
             return
 
         # Display the child stage and its siblings by appending them to the current stage's widget
-        if self.has_children():
+        if self.has_children() and next_stage.is_descendant_of(self):
             self._widget.add_child_stages(first_child=next_stage)
 
         # Proceed the csp solver before enabling the next stage
@@ -378,20 +378,24 @@ def get_next(self, full_dfs=False):
             The next stage to visit, if found. Otherwise, None.
         """
 
-        if self.has_children():
-            return self._get_child_to_enable(full_dfs)
-        elif self._right is not None:
+        # First try to get a child stage to enable
+        if (child_to_enable := self._get_child_to_enable(full_dfs)) is not None:
+            return child_to_enable
+
+        # No child stage to enable. Try to get the right sibling.
+        if self._right is not None:
             return self._right
-        else:  # Backtrack
-            ancestor = self._parent
-            while ancestor is not None:
-                if ancestor._right is not None and (
-                    full_dfs or not ancestor.has_condition()
-                ):
-                    return ancestor._right
-                else:
-                    ancestor = ancestor._parent
-            return None
+
+        # No child or right sibling. Backtrack to find the next stage.
+        ancestor = self._parent
+        while ancestor is not None:
+            if ancestor._right is not None and (
+                full_dfs or not ancestor.has_condition()
+            ):
+                return ancestor._right
+            else:
+                ancestor = ancestor._parent
+        return None
 
     def _get_child_to_enable(self, full_dfs):
         """Determine the child stage to activate.
@@ -401,6 +405,9 @@ def _get_child_to_enable(self, full_dfs):
         full_dfs : bool
             If True, visit all the stages in the stage tree. Otherwise, skip stages whose guards
             are not satisfied."""
+
+        if self.has_children() is False:
+            return None
 
         child_to_activate = None
 
@@ -412,18 +419,19 @@ def _get_child_to_enable(self, full_dfs):
                         child_to_activate is None
                     ), "Only one child stage can be activated at a time."
                     child_to_activate = child
+
+            if child_to_activate is None:
+                # No child guard's condition is satisfied.
+                # Let the caller handle this case (by backtracking).
+                return None
         else:
             # If children are not guards, the first child is activated.
             # Note the remaining children will be activated in sequence by their siblings.
             child_to_activate = self._children[0]
 
         # If the child to activate is a Guard, return it's first child
         if child_to_activate.has_condition():
-            return child_to_activate._children[0]
-
-        assert (
-            child_to_activate is not None
-        ), "At least one child stage must be activated."
+            child_to_activate = child_to_activate._children[0]
 
         return child_to_activate
 

README.md

@@ -1,3 +1,5 @@
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.09130/status.svg)](https://doi.org/10.21105/joss.09130)
+
 # visualCaseGen
 
 Welcome to **visualCaseGen**, an intuitive graphical user interface (GUI) designed to simplify the workflow of creating Community Earth System Model v.3 (CESM3) cases. With visualCaseGen, users can effortlessly explore and define component sets (compsets), select or customize grid resolutions, and prepare their CESM cases, all through an interactive and user-friendly platform that runs on Jupyter notebooks.

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/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ======================================
 
-visualCaseGen is presently bundled with a CESM distribution (fork) based on cesm3_0_beta06. The following
+visualCaseGen is presently bundled with a CESM distribution (fork) based on cesm3_0_beta08. The following
 instructions guide you through obtaining and installing this specific CESM distribution with visualCaseGen.
 
 Prerequisite
@@ -31,8 +31,8 @@ CESM may take some time.
 
 .. code-block:: bash
 
-    git clone https://github.com/alperaltuntas/cesm.git -b cesm3_0_beta06_gui cesm3_0_beta06_gui
-    cd cesm3_0_beta06_gui
+    git clone https://github.com/alperaltuntas/cesm.git -b cesm3_0_beta08_gui cesm3_0_beta08_gui
+    cd cesm3_0_beta08_gui
     ./bin/git-fleximod update
 
 This will download the required CESM version, including visualCaseGen.

docs/open.rst

@@ -64,7 +64,7 @@ To access the GUI on a remote machine, set up SSH tunneling with port forwarding
 .. code-block:: bash
 
     conda activate visualCaseGen
-    cd [PATH_TO_visualCaseGen] # e.g., ~/cesm3_0_beta03_gui/visualCaseGen
+    cd [PATH_TO_visualCaseGen] # e.g., ~/cesm3_0_beta08_gui/visualCaseGen
     jupyter-lab GUI.ipynb --no-browser
 
 If the above steps are successful, the command line will display a URL that you can copy and paste into your web browser

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

@@ -5,10 +5,11 @@ channels:
   - anaconda
 
 dependencies:
-  - python>=3.11.10,<3.12
-  #- xesmf
+  - 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.