cimsi 0.8.2__tar.gz → 0.8.2.dev1__tar.gz

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/.gitlab-ci.yml

@@ -21,9 +21,7 @@ before_script:
   - mkdir -p "${CI_JOB_RUN_DIR}"
   - git clone "${CI_REPOSITORY_URL}" "${CI_JOB_RUN_DIR}"
   - cd "${CI_JOB_RUN_DIR}"
-  # this will checkout the tag name if assigned
-  # if not, the SHA of this commit will be used
-  - git checkout "${CI_COMMIT_TAG:-$CI_COMMIT_SHA}"
+  - git checkout "${CI_COMMIT_SHA}"
     
 
 after_script:
@@ -125,9 +123,10 @@ deploy:
   script: |
     # make the deploy location
     mkdir -p ${IMSI_DEPLOY_PATH}/latest
+    cd ${IMSI_DEPLOY_PATH}
 
     # pass Python version, tag, and deploy path as arguments
-    source tests/deploy_imsi_env.sh "${IMSI_DEPLOYED_PYTHON_VER}" "${CI_COMMIT_TAG}" "${IMSI_DEPLOY_PATH}" "${CANESM_REF_REPO}"
+    source ${CI_JOB_RUN_DIR}/tests/deploy_imsi_env.sh "${IMSI_DEPLOYED_PYTHON_VER}" "${CI_COMMIT_TAG}" "${IMSI_DEPLOY_PATH}" "${CANESM_REF_REPO}"
   rules:
     # Only run these rules on gitlab.science.gc.ca
     - if: '$CI_SERVER_HOST != "gitlab.science.gc.ca"'
@@ -146,7 +145,6 @@ publish:
       when: never
 
     - if: $CI_COMMIT_TAG
-  allow_failure: true
 
 
 cleanup:

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/CONTRIBUTING.md

@@ -77,29 +77,4 @@ Integration Reviewers will:
 
  - [ ] The change is compatible with CCCma systems and operational pipelines.
  - [ ] Integration dependencies and environments are respected.
- - [ ] Broader model interactions have been considered.
-
-
-## Creating an Issue
-
-**Before you open an Issue**, search the issue tracker for similar entries. If you find an existing Issue is already open, upvote it or add context there is needed.
-
-### Opening an Issue
-
-- Open an Issue for bugs, requests, or documentation.
-- Use the appropriate Issue template.
-- Use the template to describe the Issue.
-- Do not open an Issue for general disussion or support.
-
-### Types of Issues
-
-All Issues must be opened as one of the following types:
-
-| Label   | Description |
-|:--      | :--         |
-| **bug** | Something is broken. |
-| **enhancement** | Improvement to an existing feature. |
-| **feature** | New additions or functionality. |
-| **docs** | Standalone changes or additions to documentation. |
-
-The Issue template you use will be pre-populated with one of these labels. **For Contributors, do not** add other labels to the Issue.
+ - [ ] Broader model interactions have been considered.

{cimsi-0.8.2/cimsi.egg-info → cimsi-0.8.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cimsi
-Version: 0.8.2
+Version: 0.8.2.dev1
 Summary: Integrated Modelling System Infrastructure (IMSI) is a comprehensive software project used to download, configure, build and run the suite of models in the CCCma Integrated Modelling System.
 Author: CCCma Technical Development Team
 License: OGL-Canada-2.0

{cimsi-0.8.2 → cimsi-0.8.2.dev1/cimsi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cimsi
-Version: 0.8.2
+Version: 0.8.2.dev1
 Summary: Integrated Modelling System Infrastructure (IMSI) is a comprehensive software project used to download, configure, build and run the suite of models in the CCCma Integrated Modelling System.
 Author: CCCma Technical Development Team
 License: OGL-Canada-2.0

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/cimsi.egg-info/SOURCES.txt

@@ -11,10 +11,6 @@ environment.yml
 logo.png
 pyproject.toml
 uv.lock
-.gitlab/issue_templates/bug.md
-.gitlab/issue_templates/documentation.md
-.gitlab/issue_templates/enhancement.md
-.gitlab/issue_templates/feature.md
 .gitlab/merge_request_templates/imsi_mr.md
 cimsi.egg-info/PKG-INFO
 cimsi.egg-info/SOURCES.txt
@@ -182,8 +178,6 @@ tests/test_ensemble/test_table_utils/test_yaml_table_vars.py
 tests/test_ensemble/test_table_utils/test_yaml_vars.py
 tests/test_list/test_list_cli.py
 tests/test_list/test_list_manager.py
-tests/test_override/test_apply_options_overrides.py
-tests/test_override/test_parse_override_cli.py
 tests/test_schema/test_compiler.py
 tests/test_schema/test_components.py
 tests/test_schema/test_experiment.py

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/docs/developing_configurations.rst

@@ -87,7 +87,6 @@ interconnected nature between:
 - models & experiments, which dictate:
    - what jobs you want to run
    - how many simulated years you might want
-   - the explicit `flow` that you might want to use and configure
 - machines, which dictates:
    - what sequencers are available
    - what resource configurations are allowed (i.e. how many days can be simulated in the allowable wall-clock?)
@@ -179,7 +178,7 @@ To define what jobs will run and with what resources, ``imsi`` relies on the
 key path.
 
 Specifically, ``imsi`` will look for ``sequencing:sequencing_flow:FLOW_NAME``, where
-the flow name is determined by one of three methods:
+the flow name is determined by one of two methods:
 
 1. **automatically via the** ``machine`` **and sequencer specific configuration**
 
@@ -191,27 +190,7 @@ the flow name is determined by one of three methods:
    4. extracts the `non-machine specific` ``FLOW_NAME`` from ``sequencing:sequencers:SEQUENCER_NAME:baseflows:model_type``
    5. appends ``default_sequencing_suffix`` to the `non-machine specific` ``FLOW_NAME`` such that ``FLOW_NAME=${FLOW_NAME}-${default_sequencing_suffix}``
 
-2. **from the** ``flow: FLOW_NAME`` **entry in the experiment/model configuration**
-   
-   This is an extension of the above automatic method, but allows users to explicitly
-   define what `non-machine specific` flow they want to use for this experiment/model. The machine specific suffixing
-   still occurs as per the automatic method. For example, if a user wanted to use the
-   ``basic`` flow for a ``ESM`` model type on a machine with a ``-maestro`` suffix, they would
-   add the following to their experiment/model configuration:
-
-   .. code-block:: yaml
-      models:
-        some_canesm_model:
-          flow: basic
-
-   and to their sequencing flow configuration, ``imsi`` would look for
-   ``sequencing:sequencing_flow:canesm_split_job_flow-basic-hallN``.
-
-   If the user does not provide a ``flow: FLOW_NAME`` entry in the experiment/model configuration,
-   ``imsi`` will fall back to the automatic method described in (1) above. If ``flow`` is specified under 
-   both ``model`` and ``experiment``, the experiment definition takes precedence.
-
-3. **from the** ``--flow`` **argument to** ``imsi setup``
+2. **from the** ``--flow`` **argument to** ``imsi setup``
 
 With this in mind, modifications/development of sequencer flows can be achieved via:
 

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/docs/imsi_tracking.rst

@@ -79,7 +79,6 @@ By default, ``imsi`` only logs the above information for certain ``cli`` command
 
 * ``imsi config``
 * ``imsi reload``
-* ``imsi override``
 * ``imsi set``
 * ``imsi build```
 * ``imsi submit``

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/docs/usage.rst

@@ -257,30 +257,34 @@ on the workflow.
       >> imsi set -s model=model-x -s exp=exp-y
 
 
-4\. Apply blocks of pre-defined modifications using ``imsi override --option``
+4\. Apply blocks of pre-defined modifications using ``imsi set --options``
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
+   .. warning::
+
+      imsi |version|: this command is a WIP and there may be unexpected behaviour.
 
    +------------------+------------------------------------------------------------------+
    | **Command**      | .. code-block:: bash                                             |
    |                  |                                                                  |
-   |                  |     >> imsi override --option <option_block>/<option_file>       |
+   |                  |     >> imsi set --options <option_block>=<option_key>            |
    |                  |                                                                  |
    +------------------+------------------------------------------------------------------+
    | **Steps**        | Run the command above. The options are defined in the imsi       |
-   |                  | Configuration Files for the source, nominally in YAML files      |
-   |                  | under ``imsi-config/options/<option_block>/<option_file>``.      |
+   |                  | Configuration Files for the source, nominally in                 |
+   |                  | ``model_options.yaml``.                                          |
    +------------------+------------------------------------------------------------------+
    | **Purpose**      | Apply pre-defined sets of modifications to the run               |
-   |                  | configuration. The directory ``<option_block>`` and its contents |
-   |                  | can be generally thought of as common modifications to           |
-   |                  | configuration that are not otherwise captured in the structured  |
-   |                  | configuration system.                                            |
+   |                  | configuration. The ``option_block`` and contents can be generally|
+   |                  | thought of as common modifications to configuration that are not |
+   |                  | otherwise captured in the structured imsi Configuration Files.   |
+   +------------------+------------------------------------------------------------------+
+   | **Caveats**      | **This command is currently under development**                  |
    +------------------+------------------------------------------------------------------+
 
-   **What does** ``imsi override --option`` **do?**
+   **What does** ``imsi set -o`` **do?**
 
-   In simple terms, ``imsi override --option`` is analogous to manually modifying the Resolved
+   In simple terms, ``imsi set -o`` is analogous to manually modifying the Resolved
    Configuration File and running ``imsi config``.
 
 .. warning::
@@ -348,6 +352,11 @@ Any further modifications to the upstream Configuration File for ``exp-B``
 can be applied by using ``imsi reload`` for simplicity thereafter.
 
 
+.. warning::
+
+   ``imsi set --options`` is a WIP.
+
+
 Validating imsi configuration files with ``imsi validate``
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.8.2'
-__version_tuple__ = version_tuple = (0, 8, 2)
+__version__ = version = '0.8.2.dev1'
+__version_tuple__ = version_tuple = (0, 8, 2, 'dev1')
 
-__commit_id__ = commit_id = 'ge9cd69fb8'
+__commit_id__ = commit_id = 'g904569cbb'

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/cli/core_cli.py

@@ -300,38 +300,30 @@ def reload(ctx):
     help="""A key-value pair for a setup parameter and it's value.
     [Example: exp=exp_y]"""
 )
-@click.pass_context
-@log_cli
-def set(ctx, selections):
-    import imsi.user_interface.ui_manager as uim
-
-    force_dirs(Path("src"))
-    uim.validate_version_reqs()
-    # tmp disabling parm_file -> None
-    uim.set_selections(None, selections, force=ctx.obj["FORCE"])
-
-
-@click.command(
-    short_help="Override settings.",
-    help="Override configuration options from imsi-config."
-)
 @click.option(
-    "-o", "--option",
-    metavar="PATH/FILE.yaml",
+    "-o",
+    "--options",
+    metavar="OPTION_BLOCK=VALUE",
     multiple=True,
-    help="File paths under imsi-config/options. If specifying multiple paths, options are applied in the order provided."
+    help="""A key-value pair for an option block and it's value, as
+    stored in the *_options.yaml files of the imsi Configuration Files.
+    [Example: block_a=option_1]""",
 )
 @click.pass_context
 @log_cli
-def override(ctx, option):
+def set(ctx, selections, options):
     import imsi.user_interface.ui_manager as uim
 
     force_dirs(Path("src"))
     uim.validate_version_reqs()
-    if option:
-        uim.parse_override(option, force=ctx.obj["FORCE"])
+    if any([selections, options]):
+        # tmp disabling parm_file -> None
+        uim.set_selections(None, selections, options, force=ctx.obj["FORCE"])
     else:
-        click.echo("Error: Provide at least one --option.", err=True)
+        click.echo(
+            "Error: Must provide at least one --selections or --options",
+            err=True,
+        )
 
 
 @click.command(

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/cli/entry.py

@@ -73,7 +73,6 @@ cli.add_lazy_command("imsi.cli.core_cli.status")
 cli.add_lazy_command("imsi.cli.core_cli.reload")
 cli.add_lazy_command("imsi.cli.core_cli.set")
 cli.add_lazy_command("imsi.cli.core_cli.get_src", name='get-src')
-cli.add_lazy_command("imsi.cli.core_cli.override")
 cli.add_lazy_command("imsi.tools.disk_tools.disk_tools_cli.clean")
 cli.add_lazy_command("imsi.tools.list.list_cli.list")
 cli.add_lazy_command("imsi.tools.menu.menu_cli.setup_menu", name="setup-menu")

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/config_manager/config_manager.py

@@ -90,8 +90,6 @@ class SequencingFactory:
     def create_from_database(
         db: ConfigDatabase,
         machine: Machine,
-        experiment: Experiment,
-        model: Model,
         sequencer_name: str,
         flow_name: str = None,
         model_type: str = None,
@@ -118,10 +116,8 @@ class SequencingFactory:
             model_type,
             sequencer_name,
             sequencing_config["sequencer"].get("baseflows"),
-            machine_specific_flows=sequencing_configs["sequencing_flow"],
+            flows=sequencing_configs["sequencing_flow"],
             machine=machine,
-            experiment=experiment,
-            model=model
         )
 
         sequencing_config["sequencing_flow"] = SequencingFactory.set_flow_config(
@@ -164,10 +160,8 @@ class SequencingFactory:
         model_type: str,
         sequencer_name: str,
         sequencer_baseflows: dict,
-        machine_specific_flows,
+        flows,
         machine: Machine,
-        experiment: Experiment,
-        model: Model,
     ):
         """Get the default sequencing flow, which handles the selected model_type, and
         also has configuration support for the selected sequencer and machine.
@@ -189,24 +183,17 @@ class SequencingFactory:
         # The platform/machine specific implementation of baseflows is denoted with a suffix on baseflow
         # This will return the first baseflow/machine specific flow in the list (which is constrain to be
         # only those suppoting the specific model_type)
-        # Prefer explicit 'experiment' field, fall back to 'model'; error if neither present
-        experiment_or_model_flow = experiment.flow or model.flow
-
         for baseflow in base_flows:
-            if experiment_or_model_flow is not None:
-                machine_specific_flow = f"{baseflow}-{experiment_or_model_flow}-{machine.default_sequencing_suffix}"
-            else:
-                machine_specific_flow = f"{baseflow}-{machine.default_sequencing_suffix}"
-            if machine_specific_flow in machine_specific_flows:
+            machine_specific_flow = f"{baseflow}-{machine.default_sequencing_suffix}"  # convention for the naming
+            if machine_specific_flow in flows:
                 return machine_specific_flow
-
         supported_base_flows = ", ".join(base_flows)
         raise KeyError(
-            f"Could not determine a default sequencing flow for sequencer '{sequencer_name}' "
-            f"on machine '{machine.name}' (suffix '{machine.default_sequencing_suffix}'), "
-            f"for model_type '{model_type}' and experiment or model flow '{experiment_or_model_flow}'. "
-            f"Supported baseflows for this model_type are: {supported_base_flows}. "
-            "Machine-specific versions for this combination are not implemented but required."
+            f"Could not determine a default sequencing flow for sequencer: {sequencer_name} "
+            f"on machine: {machine.name}/{machine.default_sequencing_suffix} that supports model_type: {model_type}. "
+            f"Support baseflows found for {model_type} are: {supported_base_flows}. "
+            f"Machine specific version(s) for {machine.default_sequencing_suffix} are "
+            "not implemented but required."
         )
 
     @staticmethod
@@ -427,7 +414,7 @@ class ConfigManager:
         setup_params = self.create_SetupParams(setup_params, machine)  # improvable
         utilities = self.create_utilities()
         (SEQ_N, FLOW_N), sequencing = self.create_sequencing(
-            machine, experiment, model, setup_params.sequencer_name, flow_name
+            machine, setup_params.sequencer_name, flow_name, experiment
         )
         POST_N, postproc = self.create_postproc(model, experiment, postproc_profile)
 
@@ -496,16 +483,13 @@ class ConfigManager:
     def create_sequencing(
         self,
         machine: Machine,
-        experiment: Experiment,
-        model: Model,
         sequencer_name: str,
         flow_name: str,
+        experiment: Experiment,
     ) -> Sequencing:
         return SequencingFactory.create_from_database(
             self.db,
             machine=machine,
-            experiment=experiment,
-            model=model,
             sequencer_name=sequencer_name,
             flow_name=flow_name,
             model_type=experiment.model_type,

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/config_manager/schema/experiment.py

@@ -25,7 +25,6 @@ class Experiment(BaseModel):
     parent_branch_time: str
     inherits_from: Optional[str] = None
     supported_models: List[str]
-    flow: Optional[str] = None # overrides flow specified in model
 
     def validate_model_name(self, model_name: str):
         if model_name not in self.supported_models:

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/config_manager/schema/model.py

@@ -19,4 +19,3 @@ class Model(BaseModel):
     prefix: Optional[str] = None
     model_filename_prefix: Optional[str] = None
     model_rs_filename_prefix: Optional[str] = None
-    flow: Optional[str] = None

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/sequencer_interface/maestro_cap.py

@@ -133,7 +133,7 @@ class MaestroSequencerInterface(Sequencer):
         maestro_dst = maestro_config['SEQ_EXP_HOME']            # destination for setup
         modules_provided = exp_flow['flow_definitions'].keys()  # ie folder names
 
-        setup_maestro_from_src(maestro_src, maestro_dst, modules_provided, runid=runid)
+        setup_maestro_from_src(maestro_src, maestro_dst, modules_provided, runid=runid, force=force)
 
     def config(self, configuration: Configuration, **kwargs):
         """Configure maestro experiment."""
@@ -467,7 +467,7 @@ def config_hub(seq_exp_home, experiment):
     try:
         proc = subprocess.run(cmd, cwd=seq_exp_home, env=maestro_env, capture_output=True)
         proc.check_returncode()
-    except subprocess.CalledProcessError:
+    except subprocess.CalledProcessError as e:
         raise Exception("Failed call: '{cmd}': {err}".format(cmd=' '.join(proc.args), err=proc.stderr))
 
 def copy_default_main_config(src: str, dst: str):
@@ -505,7 +505,7 @@ def init_maestro_module_folders(path: str, entry_module: str = 'module', modules
     if modules is None:
         modules = [entry_module]
 
-    if entry_module not in modules:
+    if not entry_module in modules:
         raise ValueError('entry_module must match one of modules provided')
 
     for m in modules:
@@ -1134,7 +1134,7 @@ def validate_maestro_exp(seq_exp_home: str):
         try:
             proc = subprocess.run(cmd, cwd=seq_exp_home, env=maestro_env, capture_output=True)
             proc.check_returncode()
-        except subprocess.CalledProcessError:
+        except subprocess.CalledProcessError as e:
             stdout = proc.stdout.decode().strip()
             stderr = proc.stderr.decode().strip()
             if not stderr.startswith(err_startswith):

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/tools/disk_tools/disk_tools_cli.py

@@ -9,6 +9,7 @@ import click
     )
 @click.option(
     "--runid_path",
+    default=None,
     required=True,
     type=click.Path(),
     help="Path to a valid run setup directory.",

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/user_interface/ui_manager.py

@@ -1,20 +1,20 @@
 import os
 import copy
+import glob
 from omegaconf import OmegaConf
 from pathlib import Path
 import subprocess
 import shlex
 import shutil
 from typing import Dict
-from pydantic import BaseModel, field_validator
-from typing import Iterable
 
 from imsi.config_manager import config_manager as cm
 from imsi.sequencer_interface.sequencers import create_sequencer
 from imsi.shell_interface import shell_interface_manager
 from imsi.shell_interface.config_hooks_manager import call_hooks
 from imsi.utils.dict_tools import parse_vars, update, load_json
-from imsi.user_interface.ui_utils import save_setup_configuration, load_run_config, apply_options_overrides
+from imsi.user_interface.ui_utils import save_setup_configuration, load_run_config
+from imsi.sequencer_interface.sequencers import create_sequencer
 from imsi.utils.general import is_broken_symlink, _return_with_message
 from imsi.utils.git_tools import is_repo_clean
 from imsi import __version__
@@ -53,7 +53,6 @@ def validate_version_reqs(source_config_path: Path = Path("src/imsi-config"), ve
             See https://imsi.readthedocs.io/en/main/config_breaking_changes.html for more information"""
         )
 
-
 def create_imsi_configuration(
     imsi_config_path: str, setup_params: Dict
 ) -> (cm.Configuration, cm.ConfigDatabase):
@@ -138,55 +137,7 @@ def update_config_from_state(force=False):
     )
     build_run_config_on_disk(state_configuration, db, force=force)
 
-
-class Override(BaseModel):
-    options: str
-
-    @field_validator("options")
-    def validate_options(cls, v):
-        if "/" not in v:
-            raise ValueError("Option must be in the format <group>/<option>")
-        return v
-
-
-def parse_override_options(options: Iterable[str]) -> list[dict]:
-    return [Override(options=o).model_dump() for o in options]
-
-
-def parse_override(options: Iterable[str], force=False):
-    """Parse and apply command-line option overrides to the current IMSI run configuration.
-
-    Parameters:
-    - options: An iterable of option identifier strings. Each string must contain
-        a '/' separating the group and option name (e.g. "group/option" or
-        "group/option=value").
-    - force: If True, forces rebuilding of on-disk run artifacts
-        and other actions performed by build_run_config_on_disk even if not strictly
-        necessary. Defaults to False.
-    """
-
-    # get existing simulation config
-    configuration = load_run_config()
-    db = cm.database_factory(configuration.get_unique_key_value("imsi_config_path"))
-
-    print(f"Overriding configuration with: {options}")
-    options_list = parse_override_options(options)
-
-    configuration_with_overrides = apply_options_overrides(
-        config_dictionary=configuration.model_dump(), options=options_list
-    )
-    new_configuration = cm.Configuration(**configuration_with_overrides)
-
-    # Update the saved configuration file accordingly
-    # (including triggering rebuilding of /sequencer folder too, running
-    # hooks, etc):
-    build_run_config_on_disk(new_configuration, db, force=force)
-
-    # Update the saved configuration file accordingly
-    save_setup_configuration(new_configuration, save_config=True)
-
-
-def set_selections(parm_file=None, selections=None, force=False):
+def set_selections(parm_file=None, selections=None, options=None, force=False):
     """Parse key=value pairs of selection given on the command line
     Try to apply these to the imsi selections for the sim.
     """
@@ -229,6 +180,14 @@ def set_selections(parm_file=None, selections=None, force=False):
     # Create a new simulation that we imbue with these properties
     new_configuration = config_manager.create_configuration(**updated_setup_params.model_dump())
 
+    if options:
+        print(f"set options: {options}")
+        options_config = db.get_config("model_options")
+        selected_option_names = parse_vars(options)
+        new_configuration = apply_options(
+            options_config, configuration, selected_option_names
+        )
+
     # Update the saved configuration file accordingly
     # (including triggering rebuilding of /sequencer folder too, running
     # hooks, etc):
@@ -237,6 +196,43 @@ def set_selections(parm_file=None, selections=None, force=False):
     # Update the saved configuration file accordingly
     save_setup_configuration(new_configuration, save_config=True)
 
+def apply_options(
+    options_config: Dict, configuration: cm.Configuration, selected_option_names: Dict
+) -> cm.Configuration:
+    """
+    Take a set of options or 'patches' and apply them to the simulation configuration and
+    return an updated configuration.
+
+    Input:
+    ------
+    selected_options : dict
+       k-v pairs of option name and selection
+    """
+    # Check first the option is valid
+    for option, selection in selected_option_names.items():
+        if option in options_config.keys():
+            if selection in options_config[option].keys():
+                for target_config, target_values in options_config[option][
+                    selection
+                ].items():
+                    # Add to list of applied options
+                    # self.options[option] = selection
+                    # Set the options in the simulations internal state
+                    new_config_dict = configuration.model_dump()
+                    update(new_config_dict[target_config], target_values)
+                print(f"Updated {option} with {selection}")
+            else:
+                raise ValueError(
+                    f"\n**ERROR**: there is no valid selection {selection} under the option named {option}. "
+                    + f"Available selections are {list(options_config[option]['options'].keys())}"
+                )
+        else:
+            raise ValueError(
+                f"\n**ERROR**: there is no option named {option}. Available options are {list(options_config.keys())}"
+            )
+        return cm.Configuration(**new_config_dict)
+
+
 def compile_model_execs(args, force=False):
     """
     Builds all component executables by calling an upstream script from the

{cimsi-0.8.2 → cimsi-0.8.2.dev1}/imsi/user_interface/ui_utils.py

@@ -3,9 +3,6 @@ import shutil
 from pathlib import Path
 import warnings
 
-import yaml
-
-from imsi.utils.dict_tools import update
 from imsi.config_manager.config_manager import Configuration, ConfigManager
 
 
@@ -57,32 +54,6 @@ def _get_config_filename(serialized=False) -> str:
     return guessed
 
 
-def apply_options_overrides(config_dictionary: dict, options: list) -> dict:
-    """Merge YAML option files into config_dictionary.
-
-    Each item in options must be a single-key dict mapping a subdirectory name to
-    a filename (without suffix). Example: [{"some_dir": "option_name"}, ...].
-
-    If any loaded YAML defines keys whose full key-paths overlap with existing
-    keys in config_dictionary, a warning is emitted listing the overlapping paths.
-    """
-    options_root = Path(config_dictionary["setup_params"]["work_dir"]) / "src" / "imsi-config"
-
-    for option in options:
-        parent_dir, filename = next(iter(option.items()))
-        option_file = (options_root / parent_dir / filename).with_suffix(".yaml")
-
-        if not option_file.exists():
-            raise FileNotFoundError(f"Option file not found: {option_file}")
-
-        with option_file.open() as stream:
-            cfg = yaml.safe_load(stream) or {}
-
-        config_dictionary = update(config_dictionary, cfg)
-
-    return config_dictionary
-
-
 def load_run_config(serialized=True):
     # relative to cwd/pwd
     config_file = _get_config_filename(serialized=serialized)