sl-shared-assets 4.0.0__tar.gz → 4.0.1__tar.gz

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sl-shared-assets
-Version: 4.0.0
+Version: 4.0.1
 Summary: Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries.
 Project-URL: Homepage, https://github.com/Sun-Lab-NBB/sl-shared-assets
 Project-URL: Documentation, https://sl-shared-assets-api-docs.netlify.app/
@@ -713,16 +713,21 @@ Requires-Dist: ruff==0.12.7; extra == 'conda'
 Requires-Dist: sphinx-autodoc-typehints==3.2.0; extra == 'conda'
 Requires-Dist: sphinx-click==6.0.0; extra == 'conda'
 Requires-Dist: sphinx==8.2.3; extra == 'conda'
+Requires-Dist: tox-uv==1.26.2; extra == 'conda'
+Requires-Dist: tox==4.28.4; extra == 'conda'
 Requires-Dist: twine==6.1.0; extra == 'conda'
 Requires-Dist: types-appdirs==1.4.3.5; extra == 'conda'
 Requires-Dist: types-filelock==3.2.7; extra == 'conda'
 Requires-Dist: types-paramiko==3.5.0.20250801; extra == 'conda'
+Requires-Dist: types-pytz==2025.2.0.20250516; extra == 'conda'
 Requires-Dist: types-tqdm==4.67.0.20250516; extra == 'conda'
+Requires-Dist: uv==0.8.4; extra == 'conda'
 Provides-Extra: condarun
 Requires-Dist: appdirs==1.4.4; extra == 'condarun'
 Requires-Dist: filelock==3.18.0; extra == 'condarun'
 Requires-Dist: natsort==8.4.0; extra == 'condarun'
 Requires-Dist: numpy==2.2.6; extra == 'condarun'
+Requires-Dist: polars==1.32.0; extra == 'condarun'
 Requires-Dist: pyarrow==21.0.0; extra == 'condarun'
 Requires-Dist: pytz==2025.2; extra == 'condarun'
 Requires-Dist: tqdm==4.67.1; extra == 'condarun'
@@ -752,10 +757,6 @@ Requires-Dist: ataraxis-automation==5.0.0; extra == 'noconda'
 Requires-Dist: build==1.3.0; extra == 'noconda'
 Requires-Dist: sphinx-rtd-dark-mode==1.3.0; extra == 'noconda'
 Requires-Dist: sphinx-rtd-theme==3.0.2; extra == 'noconda'
-Requires-Dist: tox-uv==1.26.2; extra == 'noconda'
-Requires-Dist: tox==4.28.4; extra == 'noconda'
-Requires-Dist: types-pytz==2025.2.0.20250516; extra == 'noconda'
-Requires-Dist: uv==0.8.4; extra == 'noconda'
 Description-Content-Type: text/markdown
 
 # sl-shared-assets

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/envs/slsa_dev_lin.yml

@@ -135,6 +135,8 @@ dependencies:
   - pip=25.2=pyh145f28c_0
   - platformdirs=4.3.8=pyhe01879c_0
   - pluggy=1.6.0=pyhd8ed1ab_0
+  - polars=1.32.0=default_h9382660_0
+  - polars-default=1.32.0=py39hf521cc8_0
   - prometheus-cpp=1.3.0=ha5d0236_0
   - psutil=7.0.0=py313h536fd9c_0
   - pyarrow=21.0.0=py313h78bf25f_0
@@ -145,6 +147,7 @@ dependencies:
   - pysocks=1.7.1=pyha55dd90_7
   - python=3.13.5=hec9711d_102_cp313
   - python-gil=3.13.5=h4df99d1_102
+  - python-uv=0.8.4=pyhe01879c_0
   - python_abi=3.13=8_cp313
   - pytz=2025.2=pyhd8ed1ab_0
   - re2=2025.07.22=h5a314c3_0
@@ -172,12 +175,14 @@ dependencies:
   - tk=8.6.13=noxft_hd72426e_102
   - tomli=2.2.1=pyhe01879c_2
   - tox=4.28.4=pyhe01879c_0
+  - tox-uv=1.26.2=pyhd8ed1ab_0
   - tqdm=4.67.1=pyhd8ed1ab_1
   - trove-classifiers=2025.5.9.12=pyhd8ed1ab_0
   - twine=6.1.0=pyh29332c3_0
   - types-appdirs=1.4.3.5=pyhd8ed1ab_1
   - types-filelock=3.2.7=pyhd8ed1ab_1
   - types-paramiko=3.5.0.20250801=pyhd8ed1ab_0
+  - types-pytz=2025.2.0.20250516=pyhd8ed1ab_0
   - types-requests=2.32.4.20250611=pyhd8ed1ab_0
   - types-tqdm=4.67.0.20250516=pyhd8ed1ab_0
   - typing_extensions=4.14.1=pyhe01879c_0
@@ -202,7 +207,6 @@ dependencies:
     - invoke==2.2.0
     - loguru==0.7.3
     - paramiko==4.0.0
-    - polars==1.32.0
     - pyarrow==21.0.0
     - pyproject_hooks==1.2.0
     - simple_slurm==0.3.6
@@ -210,8 +214,5 @@ dependencies:
     - sphinx-rtd-dark-mode==1.3.0
     - sphinx-rtd-theme==3.0.2
     - sphinxcontrib-jquery==4.1
-    - tox-uv==1.26.2
-    - types-pytz==2025.2.0.20250516
-    - uv==0.8.4
     - xxhash==3.5.0
 

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/envs/slsa_dev_lin_spec.txt

@@ -145,7 +145,8 @@ https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.45-hc749103_0.conda
 https://conda.anaconda.org/conda-forge/noarch/pip-25.2-pyh145f28c_0.conda
 https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.8-pyhe01879c_0.conda
 https://conda.anaconda.org/conda-forge/noarch/pluggy-1.6.0-pyhd8ed1ab_0.conda
-
+https://conda.anaconda.org/conda-forge/linux-64/polars-1.32.0-default_h9382660_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/polars-default-1.32.0-py39hf521cc8_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/prometheus-cpp-1.3.0-ha5d0236_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/psutil-7.0.0-py313h536fd9c_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/pyarrow-21.0.0-py313h78bf25f_0.conda
@@ -157,6 +158,7 @@ https://conda.anaconda.org/conda-forge/noarch/pyproject-api-1.9.1-pyhe01879c_0.c
 https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
 https://conda.anaconda.org/conda-forge/linux-64/python-3.13.5-hec9711d_102_cp313.conda
 https://conda.anaconda.org/conda-forge/noarch/python-gil-3.13.5-h4df99d1_102.conda
+https://conda.anaconda.org/conda-forge/noarch/python-uv-0.8.4-pyhe01879c_0.conda
 https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda
 https://conda.anaconda.org/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/linux-64/re2-2025.07.22-h5a314c3_0.conda
@@ -189,14 +191,14 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.
 https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhe01879c_2.conda
 https://conda.anaconda.org/conda-forge/noarch/tox-4.28.4-pyhe01879c_0.conda
-
+https://conda.anaconda.org/conda-forge/noarch/tox-uv-1.26.2-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.1-pyhd8ed1ab_1.conda
 https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2025.5.9.12-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/twine-6.1.0-pyh29332c3_0.conda
 https://conda.anaconda.org/conda-forge/noarch/types-appdirs-1.4.3.5-pyhd8ed1ab_1.conda
 https://conda.anaconda.org/conda-forge/noarch/types-filelock-3.2.7-pyhd8ed1ab_1.conda
 https://conda.anaconda.org/conda-forge/noarch/types-paramiko-3.5.0.20250801-pyhd8ed1ab_0.conda
-
+https://conda.anaconda.org/conda-forge/noarch/types-pytz-2025.2.0.20250516-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/types-requests-2.32.4.20250611-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/types-tqdm-4.67.0.20250516-pyhd8ed1ab_0.conda
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.14.1-pyhe01879c_0.conda

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "hatchling.build"
 # Project metdata section. Provides the genral ID information about the project.
 [project]
 name = "sl-shared-assets"
-version = "4.0.0"
+version = "4.0.1"
 description = "Provides data acquisition and processing assets shared between Sun (NeuroAI) lab libraries."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -74,6 +74,7 @@ condarun = [
     "appdirs==1.4.4",
     "tqdm==4.67.1",
     "natsort==8.4.0",
+    "polars==1.32.0",
     "pyarrow==21.0.0",
     "filelock==3.18.0",
     "pytz==2025.2",
@@ -81,6 +82,11 @@ condarun = [
 
 # Dependencies known to be installable with conda for all development platforms (OSX ARM64, WIN AMD64, LIN AMD64).
 conda = [
+    # Tox
+    "tox==4.28.4",
+    "tox-uv==1.26.2",
+    "uv==0.8.4",
+
     # Documentation
     "sphinx==8.2.3",
     "importlib_metadata==8.7.0",
@@ -101,20 +107,13 @@ conda = [
     "types-appdirs==1.4.3.5",
     "types-tqdm==4.67.0.20250516",
     "types-paramiko==3.5.0.20250801",
-    "types-filelock==3.2.7"
+    "types-filelock==3.2.7",
+    "types-pytz==2025.2.0.20250516",
 ]
 
 # Dependencies known to not be installable with conda for at least one supported development platform
 # (OSX ARM64, WIN AMD64, LIN AMD64).
 noconda = [
-    # Tox
-    "tox==4.28.4",
-    "tox-uv==1.26.2",
-    "uv==0.8.4",
-
-    # Types
-    "types-pytz==2025.2.0.20250516",
-
     # Documentation
     "sphinx-rtd-dark-mode==1.3.0",
     "sphinx-rtd-theme==3.0.2",

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/src/sl_shared_assets/cli.py

@@ -21,6 +21,7 @@ from .data_classes import SessionData, TrackerFileNames, get_processing_tracker
 @click.option(
     "-id",
     "--manager_id",
+    type=int,
     required=True,
     default=0,
     show_default=True,

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/src/sl_shared_assets/data_classes/surgery_data.py

@@ -65,7 +65,7 @@ class ImplantData:
     """The descriptive name of the implant."""
     implant_target: str
     """The name of the brain region or cranium section targeted by the implant."""
-    implant_code: int
+    implant_code: str
     """The manufacturer code or internal reference code for the implant. This code is used to identify the implant in 
     additional datasheets and lab ordering documents."""
     implant_ap_coordinate_mm: float
@@ -89,7 +89,7 @@ class InjectionData:
     """The name of the brain region targeted by the injection."""
     injection_volume_nl: float
     """The volume of substance, in nanoliters, delivered during the injection."""
-    injection_code: int
+    injection_code: str
     """The manufacturer code or internal reference code for the injected substance. This code is used to identify the 
     substance in additional datasheets and lab ordering documents."""
     injection_ap_coordinate_mm: float
@@ -108,22 +108,22 @@ class DrugData:
 
     lactated_ringers_solution_volume_ml: float
     """Stores the volume of Lactated Ringer's Solution (LRS) administered during surgery, in ml."""
-    lactated_ringers_solution_code: int
+    lactated_ringers_solution_code: str
     """Stores the manufacturer code or internal reference code for Lactated Ringer's Solution (LRS). This code is used 
     to identify the LRS batch in additional datasheets and lab ordering documents."""
     ketoprofen_volume_ml: float
     """Stores the volume of ketoprofen diluted with saline administered during surgery, in ml."""
-    ketoprofen_code: int
+    ketoprofen_code: str
     """Stores the manufacturer code or internal reference code for ketoprofen. This code is used to identify the 
     ketoprofen batch in additional datasheets and lab ordering documents."""
     buprenorphine_volume_ml: float
     """Stores the volume of buprenorphine diluted with saline administered during surgery, in ml."""
-    buprenorphine_code: int
+    buprenorphine_code: str
     """Stores the manufacturer code or internal reference code for buprenorphine. This code is used to identify the 
     buprenorphine batch in additional datasheets and lab ordering documents."""
     dexamethasone_volume_ml: float
     """Stores the volume of dexamethasone diluted with saline administered during surgery, in ml."""
-    dexamethasone_code: int
+    dexamethasone_code: str
     """Stores the manufacturer code or internal reference code for dexamethasone. This code is used to identify the 
     dexamethasone batch in additional datasheets and lab ordering documents."""
 

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/src/sl_shared_assets/data_classes/surgery_data.pyi

@@ -37,7 +37,7 @@ class ImplantData:
 
     implant: str
     implant_target: str
-    implant_code: int
+    implant_code: str
     implant_ap_coordinate_mm: float
     implant_ml_coordinate_mm: float
     implant_dv_coordinate_mm: float
@@ -52,7 +52,7 @@ class InjectionData:
     injection: str
     injection_target: str
     injection_volume_nl: float
-    injection_code: int
+    injection_code: str
     injection_ap_coordinate_mm: float
     injection_ml_coordinate_mm: float
     injection_dv_coordinate_mm: float
@@ -64,13 +64,13 @@ class DrugData:
     """
 
     lactated_ringers_solution_volume_ml: float
-    lactated_ringers_solution_code: int
+    lactated_ringers_solution_code: str
     ketoprofen_volume_ml: float
-    ketoprofen_code: int
+    ketoprofen_code: str
     buprenorphine_volume_ml: float
-    buprenorphine_code: int
+    buprenorphine_code: str
     dexamethasone_volume_ml: float
-    dexamethasone_code: int
+    dexamethasone_code: str
 
 @dataclass
 class SurgeryData(YamlConfig):

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/src/sl_shared_assets/data_classes/runtime_data.py

@@ -104,9 +104,6 @@ class LickTrainingDescriptor(YamlConfig):
     dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter replaces this field with their 
-    notes made during runtime."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
@@ -116,6 +113,9 @@ class LickTrainingDescriptor(YamlConfig):
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter replaces this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -160,9 +160,6 @@ class RunTrainingDescriptor(YamlConfig):
     dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
-    notes made during runtime."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
@@ -172,6 +169,9 @@ class RunTrainingDescriptor(YamlConfig):
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -191,9 +191,6 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     dispensed during the paused (idle) state."""
     pause_dispensed_water_volume_ml: float = 0.0
     """Stores the total water volume, in milliliters, dispensed during the paused (idle) state."""
-    experimenter_notes: str = "Replace this with your notes."
-    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
-    notes made during runtime."""
     experimenter_given_water_volume_ml: float = 0.0
     """The additional volume of water, in milliliters, administered by the experimenter to the animal after the session.
     """
@@ -203,6 +200,9 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     incomplete: bool = False
     """If this field is set to True, the session is marked as 'incomplete' and automatically excluded from all further 
     Sun lab automated processing and analysis."""
+    experimenter_notes: str = "Replace this with your notes."
+    """This field is not set during runtime. It is expected that each experimenter will replace this field with their 
+    notes made during runtime."""
 
 
 @dataclass()
@@ -217,14 +217,14 @@ class WindowCheckingDescriptor(YamlConfig):
 
     experimenter: str
     """The ID of the experimenter running the session."""
-    experimenter_notes: str = "Replace this with your notes."
-    """The notes on the quality of the cranial window and animal's suitability for the target project."""
     surgery_quality: int = 0
     """The quality of the cranial window and surgical intervention on a scale from 0 (non-usable) to 
     3 (high-tier publication grade) inclusive."""
     incomplete: bool = True
     """Window checking sessions are always considered 'incomplete', as they do not contain the full range of 
     information collected as part of a 'standard' behavior training or experiment session."""
+    experimenter_notes: str = "Replace this with your notes."
+    """The notes on the quality of the cranial window and animal's suitability for the target project."""
 
 
 @dataclass()

{sl_shared_assets-4.0.0 → sl_shared_assets-4.0.1}/src/sl_shared_assets/data_classes/runtime_data.pyi

@@ -56,10 +56,10 @@ class LickTrainingDescriptor(YamlConfig):
     maximum_unconsumed_rewards: int = ...
     dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
-    experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class RunTrainingDescriptor(YamlConfig):
@@ -80,10 +80,10 @@ class RunTrainingDescriptor(YamlConfig):
     maximum_idle_time_s: float = ...
     dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
-    experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class MesoscopeExperimentDescriptor(YamlConfig):
@@ -94,10 +94,10 @@ class MesoscopeExperimentDescriptor(YamlConfig):
     maximum_unconsumed_rewards: int = ...
     dispensed_water_volume_ml: float = ...
     pause_dispensed_water_volume_ml: float = ...
-    experimenter_notes: str = ...
     experimenter_given_water_volume_ml: float = ...
     preferred_session_water_volume_ml: float = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class WindowCheckingDescriptor(YamlConfig):
@@ -110,9 +110,9 @@ class WindowCheckingDescriptor(YamlConfig):
     """
 
     experimenter: str
-    experimenter_notes: str = ...
     surgery_quality: int = ...
     incomplete: bool = ...
+    experimenter_notes: str = ...
 
 @dataclass()
 class ZaberPositions(YamlConfig):