Merge pull request #37 from AllenNeuralDynamics/feat-update-curriculu…

…m-dependency Update curriculum dependencies
AllenNeuralDynamics · Jun 17, 2024 · 57a6d9f · 57a6d9f
2 parents e68cf5e + f0b1098
commit 57a6d9f
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Showing 21 changed files with 300 additions and 112 deletions.
diff --git a/examples/aind_manipulator.py b/examples/aind_manipulator.py
@@ -1,4 +1,5 @@
 import datetime
+import os
 
 from aind_behavior_services.base import get_commit_hash
 from aind_behavior_services.calibration import aind_manipulator as m
@@ -41,6 +42,7 @@
 )
 
 seed_path = "local/aind_manipulator_{suffix}.json"
+os.makedirs(os.path.dirname(seed_path), exist_ok=True)
 with open(seed_path.format(suffix="calibration_logic"), "w") as f:
     f.write(calibration_logic.model_dump_json(indent=3))
 with open(seed_path.format(suffix="session"), "w") as f:

diff --git a/examples/load_cells.py b/examples/load_cells.py
@@ -1,4 +1,5 @@
 import datetime
+import os
 
 from aind_behavior_services.base import get_commit_hash
 from aind_behavior_services.calibration import load_cells as lc
@@ -42,6 +43,8 @@
 )
 
 seed_path = "local/load_cells_{suffix}.json"
+os.makedirs(os.path.dirname(seed_path), exist_ok=True)
+
 with open(seed_path.format(suffix="calibration_logic"), "w") as f:
     f.write(calibration_logic.model_dump_json(indent=3))
 with open(seed_path.format(suffix="session"), "w") as f:

diff --git a/examples/olfactometer.py b/examples/olfactometer.py
@@ -1,4 +1,5 @@
 import datetime
+import os
 
 from aind_behavior_services.base import get_commit_hash
 from aind_behavior_services.calibration import olfactometer as olf
@@ -65,6 +66,8 @@
 
 
 seed_path = "local/olfactometer_{suffix}.json"
+os.makedirs(os.path.dirname(seed_path), exist_ok=True)
+
 with open(seed_path.format(suffix="calibration_logic"), "w") as f:
     f.write(calibration_logic.model_dump_json(indent=3))
 with open(seed_path.format(suffix="session"), "w") as f:

diff --git a/examples/water_valve.py b/examples/water_valve.py
@@ -1,4 +1,5 @@
 import datetime
+import os
 
 from aind_behavior_services.base import get_commit_hash
 from aind_behavior_services.calibration import water_valve as wv
@@ -55,6 +56,8 @@ def linear_model(time, slope, offset):
 rig = wv.CalibrationRig(rig_name="WaterValveRig")
 
 seed_path = "local/water_valve_{suffix}.json"
+os.makedirs(os.path.dirname(seed_path), exist_ok=True)
+
 with open(seed_path.format(suffix="calibration_logic"), "w") as f:
     f.write(calibration_logic.model_dump_json(indent=3))
 with open(seed_path.format(suffix="session"), "w") as f:

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,7 @@ dependencies = [
     'gitpython>=3.1, <4.0',
     'scikit-learn',
     'semver',
-    'aind-behavior-curriculum@git+https://github.com/AllenNeuralDynamics/[email protected].2',
+    'aind-behavior-curriculum@git+https://github.com/AllenNeuralDynamics/[email protected].27',
 
 ]
 

diff --git a/src/DataSchemas/aind_behavior_services/__init__.py b/src/DataSchemas/aind_behavior_services/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.7.7"
+__version__ = "0.7.8"
 
 from .rig import AindBehaviorRigModel  # noqa: F401
 from .session import AindBehaviorSessionModel  # noqa: F401

diff --git a/src/DataSchemas/aind_behavior_services/launcher.py b/src/DataSchemas/aind_behavior_services/launcher.py
@@ -132,7 +132,9 @@ def _print_diagnosis(self) -> None:
         """
         Prints the diagnosis information for the launcher.
 
-        This method prints the diagnosis information, including the computer name, data directory, and config library directory.
+        This method prints the diagnosis information,
+        including the computer name, data directory,
+        and config library directory.
 
         Parameters:
             None
@@ -171,11 +173,16 @@ def _print_header(self) -> None:
         print("-------------------------------")
         print(self._HEADER)
         print(
-            f"TaskLogic ({self.task_logic_schema.__name__}) Schema Version: {self.task_logic_schema.model_construct().version}"
+            f"TaskLogic ({self.task_logic_schema.__name__}) \
+                Schema Version: {self.task_logic_schema.model_construct().version}"
         )
-        print(f"Rig ({self.rig_schema.__name__}) Schema Version: {self.rig_schema.model_construct().version}")
         print(
-            f"Session ({self.session_schema.__name__}) Schema Version: {self.session_schema.model_construct().version}"
+            f"Rig ({self.rig_schema.__name__}) \
+              Schema Version: {self.rig_schema.model_construct().version}"
+        )
+        print(
+            f"Session ({self.session_schema.__name__}) \
+                Schema Version: {self.session_schema.model_construct().version}"
         )
         print("-------------------------------")
         if self._dev_mode:
@@ -187,8 +194,9 @@ def save_temp_model(self, model: Union[TRig, TSession, TTaskLogic], folder: Opti
 
         Args:
             model (BaseModel): The model to be saved.
-            folder (Optional[os.PathLike | str]): The folder where the model should be saved. If not provided, the default
-                temporary folder will be used.
+            folder (Optional[os.PathLike | str]):
+              The folder where the model should be saved.
+              If not provided, the default temporary folder will be used.
 
         Returns:
             str: The file path of the saved model.
@@ -221,7 +229,8 @@ def _validate_dependencies(self) -> None:
             raise FileNotFoundError(f"Config library not found! Expected {self.config_library_dir}.")
         if not (os.path.isdir(os.path.join(self.config_library_dir, "Rig", self.computer_name))):
             raise FileNotFoundError(
-                f"Rig configuration not found! Expected {os.path.join(self.config_library_dir, self.RIG_DIR, self.computer_name)}."
+                f"Rig configuration not found! \
+                    Expected {os.path.join(self.config_library_dir, self.RIG_DIR, self.computer_name)}."
             )
         if not (os.path.isfile(os.path.join(self.default_workflow))):
             raise FileNotFoundError(f"Bonsai workflow file not found! Expected {self.default_workflow}.")
@@ -519,43 +528,8 @@ def __init__(
         **launcher_kwargs,
     ) -> None:
 
-        parser = argparse.ArgumentParser()
-
-        parser.add_argument("--data_dir", help="Specify the data directory")
-        parser.add_argument("--remote_data_dir", help="Specify the remote data directory")
-        parser.add_argument("--repository_dir", help="Specify the repository directory")
-        parser.add_argument("--config_library_dir", help="Specify the configuration library directory")
-        parser.add_argument("--workflow", help="Specify the workflow")
-        parser.add_argument(
-            "--force_create_directories",
-            help="Specify whether to force create directories",
-            action="store_true",
-            default=False,
-        )
-        parser.add_argument("--dev_mode", help="Specify whether to run in dev mode", action="store_true", default=False)
-        parser.add_argument(
-            "--bonsai_is_editor_mode",
-            help="Specify whether to run in Bonsai editor mode",
-            action="store_false",
-            default=True,
-        )
-        parser.add_argument(
-            "--bonsai_is_start_flag",
-            help="Specify whether to start the Bonsai workflow",
-            action="store_false",
-            default=True,
-        )
-        parser.add_argument(
-            "--allow_dirty_repo", help="Specify whether to allow a dirty repository", action="store_true", default=False
-        )
-        parser.add_argument(
-            "--skip_hardware_validation",
-            help="Specify whether to skip hardware validation",
-            action="store_true",
-            default=False,
-        )
-
-        args = parser.parse_args()
+        parser = self._get_default_arg_parser()
+        args, _ = parser.parse_known_args()
 
         # optional parameters that override the defaults
         data_dir = args.data_dir if args.data_dir is not None else data_dir
@@ -600,3 +574,44 @@ def make_folder_structure(self) -> None:
 
     def _validate_dependencies(self) -> None:
         self.launcher._validate_dependencies()
+
+    @staticmethod
+    def _get_default_arg_parser() -> argparse.ArgumentParser:
+
+        parser = argparse.ArgumentParser()
+
+        parser.add_argument("--data_dir", help="Specify the data directory")
+        parser.add_argument("--remote_data_dir", help="Specify the remote data directory")
+        parser.add_argument("--repository_dir", help="Specify the repository directory")
+        parser.add_argument("--config_library_dir", help="Specify the configuration library directory")
+        parser.add_argument("--workflow", help="Specify the workflow")
+        parser.add_argument(
+            "--force_create_directories",
+            help="Specify whether to force create directories",
+            action="store_true",
+            default=False,
+        )
+        parser.add_argument("--dev_mode", help="Specify whether to run in dev mode", action="store_true", default=False)
+        parser.add_argument(
+            "--bonsai_is_editor_mode",
+            help="Specify whether to run in Bonsai editor mode",
+            action="store_false",
+            default=True,
+        )
+        parser.add_argument(
+            "--bonsai_is_start_flag",
+            help="Specify whether to start the Bonsai workflow",
+            action="store_false",
+            default=True,
+        )
+        parser.add_argument(
+            "--allow_dirty_repo", help="Specify whether to allow a dirty repository", action="store_true", default=False
+        )
+        parser.add_argument(
+            "--skip_hardware_validation",
+            help="Specify whether to skip hardware validation",
+            action="store_true",
+            default=False,
+        )
+
+        return parser
diff --git a/src/DataSchemas/aind_behavior_services/task_logic/__init__.py b/src/DataSchemas/aind_behavior_services/task_logic/__init__.py
@@ -13,6 +13,7 @@ class TaskParameters(curriculum_task.TaskParameters):
 class AindBehaviorTaskLogicModel(curriculum_task.Task):
 
     task_parameters: TaskParameters = Field(..., description="Parameters of the task logic", validate_default=True)
+    version: str = Field(..., pattern=curriculum_task.SEMVER_REGEX, description="task schema version")
 
     @field_validator("version", mode="before")
     @classmethod

diff --git a/src/DataSchemas/aind_behavior_services/utils.py b/src/DataSchemas/aind_behavior_services/utils.py
@@ -203,10 +203,17 @@ def bonsai_sgen(
         CompletedProcess: The result of running the command.
     Args:
         schema_path (PathLike): Target Json Schema file
-        output_path (PathLike): Specifies the name of the file containing the generated code.
-        namespace (Optional[str], optional): Specifies the namespace to use for all generated serialization classes. Defaults to DataSchema.
-        root_element (Optional[str], optional):  Specifies the name of the class used to represent the schema root element. If None, it will use the json schema root element. Defaults to None.
-        serializer (Optional[List[BonsaiSgenSerializers]], optional): Specifies the serializer data annotations to include in the generated classes. Defaults to None.
+        output_path (PathLike): Specifies the name of the
+          file containing the generated code.
+        namespace (Optional[str], optional): Specifies the
+          namespace to use for all generated serialization
+          classes. Defaults to DataSchema.
+        root_element (Optional[str], optional):  Specifies the
+          name of the class used to represent the schema root element.
+          If None, it will use the json schema root element. Defaults to None.
+        serializer (Optional[List[BonsaiSgenSerializers]], optional):
+          Specifies the serializer data annotations to include in the generated classes.
+          Defaults to None.
     """
 
     if serializer is None:

diff --git a/src/DataSchemas/schemas/aind_manipulator_calibration_logic.json b/src/DataSchemas/schemas/aind_manipulator_calibration_logic.json
@@ -47,19 +47,32 @@
       "title": "Description",
       "type": "string"
     },
+    "task_parameters": {
+      "allOf": [
+        {
+          "$ref": "#/definitions/CalibrationParameters"
+        }
+      ],
+      "title": "Task parameters"
+    },
     "version": {
       "const": "0.2.0",
       "default": "0.2.0",
       "title": "Version",
       "type": "string"
     },
-    "task_parameters": {
-      "allOf": [
+    "stage_name": {
+      "default": null,
+      "description": "Optional stage name the `Task` object instance represents.",
+      "oneOf": [
         {
-          "$ref": "#/definitions/CalibrationParameters"
+          "type": "string"
+        },
+        {
+          "type": "null"
         }
       ],
-      "title": "Task parameters"
+      "title": "Stage Name"
     }
   },
   "required": [

diff --git a/src/DataSchemas/schemas/load_cells_calibration_logic.json b/src/DataSchemas/schemas/load_cells_calibration_logic.json
@@ -76,19 +76,32 @@
       "title": "Description",
       "type": "string"
     },
+    "task_parameters": {
+      "allOf": [
+        {
+          "$ref": "#/definitions/CalibrationParameters"
+        }
+      ],
+      "title": "Task parameters"
+    },
     "version": {
       "const": "0.4.0",
       "default": "0.4.0",
       "title": "Version",
       "type": "string"
     },
-    "task_parameters": {
-      "allOf": [
+    "stage_name": {
+      "default": null,
+      "description": "Optional stage name the `Task` object instance represents.",
+      "oneOf": [
         {
-          "$ref": "#/definitions/CalibrationParameters"
+          "type": "string"
+        },
+        {
+          "type": "null"
         }
       ],
-      "title": "Task parameters"
+      "title": "Stage Name"
     }
   },
   "required": [

diff --git a/src/DataSchemas/schemas/olfactometer_calibration_logic.json b/src/DataSchemas/schemas/olfactometer_calibration_logic.json
@@ -156,19 +156,32 @@
       "title": "Description",
       "type": "string"
     },
+    "task_parameters": {
+      "allOf": [
+        {
+          "$ref": "#/definitions/CalibrationParameters"
+        }
+      ],
+      "title": "Task parameters"
+    },
     "version": {
       "const": "0.4.0",
       "default": "0.4.0",
       "title": "Version",
       "type": "string"
     },
-    "task_parameters": {
-      "allOf": [
+    "stage_name": {
+      "default": null,
+      "description": "Optional stage name the `Task` object instance represents.",
+      "oneOf": [
         {
-          "$ref": "#/definitions/CalibrationParameters"
+          "type": "string"
+        },
+        {
+          "type": "null"
         }
       ],
-      "title": "Task parameters"
+      "title": "Stage Name"
     }
   },
   "required": [

diff --git a/src/DataSchemas/schemas/water_valve_calibration_logic.json b/src/DataSchemas/schemas/water_valve_calibration_logic.json
@@ -75,19 +75,32 @@
       "title": "Description",
       "type": "string"
     },
+    "task_parameters": {
+      "allOf": [
+        {
+          "$ref": "#/definitions/CalibrationParameters"
+        }
+      ],
+      "title": "Task parameters"
+    },
     "version": {
       "const": "0.4.0",
       "default": "0.4.0",
       "title": "Version",
       "type": "string"
     },
-    "task_parameters": {
-      "allOf": [
+    "stage_name": {
+      "default": null,
+      "description": "Optional stage name the `Task` object instance represents.",
+      "oneOf": [
         {
-          "$ref": "#/definitions/CalibrationParameters"
+          "type": "string"
+        },
+        {
+          "type": "null"
         }
       ],
-      "title": "Task parameters"
+      "title": "Stage Name"
     }
   },
   "required": [