fix: updates github action and broken test (#1009)

jtyoung84 · web-flow · commit d7d61bb1556d · 2024-08-03T00:04:29.000Z
diff --git a/examples/aibs_smartspim_instrument.py b/examples/aibs_smartspim_instrument.py
@@ -16,8 +16,6 @@
 )
 from aind_data_schema.core.instrument import Com, Instrument
 
-OUTPUT_PATH = "examples/"
-
 inst = Instrument(
     instrument_id="440_SmartSPIM2_20231004",
     modification_date=datetime.date(2023, 10, 4),
@@ -213,4 +211,4 @@
 )
 serialized = inst.model_dump_json()
 deserialized = Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="aibs_smartspim")
diff --git a/examples/aibs_smartspim_procedures.py b/examples/aibs_smartspim_procedures.py
@@ -6,8 +6,6 @@
 
 from aind_data_schema.core import procedures
 
-OUTPUT_PATH = "examples/"
-
 experimenter = "John Smith"
 # subject and specimen id can be the same?
 specimen_id = "651286"
@@ -163,4 +161,4 @@
 
 serialized = all_procedures.model_dump_json()
 deserialized = procedures.Procedures.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="aibs_smartspim")
diff --git a/examples/aind_smartspim_instrument.py b/examples/aind_smartspim_instrument.py
@@ -7,8 +7,6 @@
 from aind_data_schema.components.devices import Filter, Laser, MotorizedStage, OpticalTable, ScanningStage
 from aind_data_schema.core.instrument import Com, Detector, Instrument, Objective
 
-OUTPUT_PATH = "examples/"
-
 inst = Instrument(
     instrument_id="440_SmartSPIM1_20231004",
     instrument_type="SmartSPIM",
@@ -257,4 +255,4 @@
 
 serialized = inst.model_dump_json()
 deserialized = Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="aind_smartspim", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="aind_smartspim")
diff --git a/examples/bergamo_ophys_session.py b/examples/bergamo_ophys_session.py
@@ -15,8 +15,6 @@
     Stream,
 )
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -109,4 +107,4 @@
 
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="bergamo_ophys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="bergamo_ophys")
diff --git a/examples/data_description.py b/examples/data_description.py
@@ -9,8 +9,6 @@
 
 from aind_data_schema.core.data_description import Funding, RawDataDescription
 
-OUTPUT_PATH = "examples/"
-
 d = RawDataDescription(
     modality=[Modality.ECEPHYS, Modality.BEHAVIOR_VIDEOS],
     platform=Platform.ECEPHYS,
@@ -23,4 +21,4 @@
 
 serialized = d.model_dump_json()
 deserialized = RawDataDescription.model_validate_json(serialized)
-deserialized.write_standard_file(output_directory=OUTPUT_PATH)
+deserialized.write_standard_file()
diff --git a/examples/ephys_rig.py b/examples/ephys_rig.py
@@ -1,8 +1,6 @@
 """Generates an example JSON file for an ephys rig"""
 
-import os
 from datetime import date, datetime, timezone
-from pathlib import Path
 
 from aind_data_schema_models.harp_types import HarpDeviceType
 from aind_data_schema_models.modalities import Modality
@@ -30,8 +28,6 @@
 )
 from aind_data_schema.core.rig import Rig
 
-OUTPUT_PATH = Path(os.path.dirname(os.path.realpath(__file__)))
-
 # Describes a rig with running wheel, 2 behavior cameras, one Harp Behavior board,
 # one dual-color laser module, one stick microscope, and 2 Neuropixels probes
 
@@ -280,4 +276,4 @@
 )
 serialized = rig.model_dump_json()
 deserialized = Rig.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ephys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="ephys")
diff --git a/examples/ephys_session.py b/examples/ephys_session.py
@@ -1,8 +1,6 @@
 """Generates an example JSON file for an ephys session"""
 
-import os
 from datetime import datetime, timezone
-from pathlib import Path
 
 from aind_data_schema_models.modalities import Modality
 
@@ -19,8 +17,6 @@
     VisualStimulation,
 )
 
-OUTPUT_PATH = Path(os.path.dirname(os.path.realpath(__file__)))
-
 session = Session(
     experimenter_full_name=["Max Quibble", "Finn Tickle"],
     subject_id="664484",
@@ -204,4 +200,4 @@
 
 serialized = session.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ephys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="ephys")
diff --git a/examples/exaspim_acquisition.py b/examples/exaspim_acquisition.py
@@ -13,8 +13,6 @@
 from aind_data_schema.core import acquisition
 from aind_data_schema.core.procedures import Reagent
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -115,4 +113,4 @@
 
 serialized = acq.model_dump_json()
 deserialized = acquisition.Acquisition.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="exaspim", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="exaspim")
diff --git a/examples/exaspim_instrument.py b/examples/exaspim_instrument.py
@@ -7,8 +7,6 @@
 from aind_data_schema.components.devices import DAQChannel, DAQDevice, Detector, Filter, Laser
 from aind_data_schema.core import instrument
 
-OUTPUT_PATH = "examples/"
-
 inst = instrument.Instrument(
     instrument_id="440_exaSPIM1-20231004",
     instrument_type="exaSPIM",
@@ -207,4 +205,4 @@
 )
 serialized = inst.model_dump_json()
 deserialized = instrument.Instrument.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="exaspim", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="exaspim")
diff --git a/examples/fip_behavior_rig.py b/examples/fip_behavior_rig.py
@@ -8,8 +8,6 @@
 import aind_data_schema.components.devices as d
 import aind_data_schema.core.rig as r
 
-OUTPUT_PATH = "examples/"
-
 r = r.Rig(
     rig_id="447_FIP-Behavior_20000101",
     modification_date=date(2000, 1, 1),
@@ -342,4 +340,4 @@
     ],
 )
 
-r.write_standard_file(prefix="fip_behavior", output_directory=OUTPUT_PATH)
+r.write_standard_file(prefix="fip_behavior")
diff --git a/examples/fip_ophys_rig.py b/examples/fip_ophys_rig.py
@@ -7,8 +7,6 @@
 import aind_data_schema.components.devices as d
 import aind_data_schema.core.rig as r
 
-OUTPUT_PATH = "examples/"
-
 rig = r.Rig(
     rig_id="428_FIP1_20231003",
     modification_date=date(2023, 10, 3),
@@ -286,4 +284,4 @@
 )
 serialized = rig.model_dump_json()
 deserialized = r.Rig.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="fip_ophys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="fip_ophys")
diff --git a/examples/mri_session.py b/examples/mri_session.py
@@ -8,8 +8,6 @@
 from aind_data_schema.components.devices import Scanner
 from aind_data_schema.core.session import MRIScan, MriScanSequence, ScanType, Session, Stream, SubjectPosition
 
-OUTPUT_PATH = "examples/"
-
 scan1 = MRIScan(
     scan_index="1",
     mri_scanner=Scanner(
@@ -76,4 +74,4 @@
 )
 serialized = sess.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="mri", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="mri")
diff --git a/examples/multiplane_ophys_session.py b/examples/multiplane_ophys_session.py
@@ -7,8 +7,6 @@
 
 from aind_data_schema.core.session import FieldOfView, LaserConfig, Session, Stream
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -204,4 +202,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="multiplane_ophys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="multiplane_ophys")
diff --git a/examples/ophys_procedures.py b/examples/ophys_procedures.py
@@ -22,8 +22,6 @@
     WaterRestriction,
 )
 
-OUTPUT_PATH = "examples/"
-
 t = datetime.datetime(2022, 7, 12, 7, 00, 00)
 t2 = datetime.datetime(2022, 9, 23, 10, 22, 00)
 
@@ -166,4 +164,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Procedures.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ophys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="ophys")
diff --git a/examples/ophys_session.py b/examples/ophys_session.py
@@ -6,8 +6,6 @@
 
 from aind_data_schema.core.session import DetectorConfig, FiberConnectionConfig, LaserConfig, Session, Stream
 
-OUTPUT_PATH = "examples/"
-
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
 
 s = Session(
@@ -62,4 +60,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Session.model_validate_json(serialized)
-deserialized.write_standard_file(prefix="ophys", output_directory=OUTPUT_PATH)
+deserialized.write_standard_file(prefix="ophys")
diff --git a/examples/procedures.py b/examples/procedures.py
@@ -13,8 +13,6 @@
     ViralMaterial,
 )
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 7, 12, 7, 00, 00, tzinfo=timezone.utc)
@@ -83,4 +81,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Procedures.model_validate_json(serialized)
-deserialized.write_standard_file(output_directory=OUTPUT_PATH)
+deserialized.write_standard_file()
diff --git a/examples/processing.py b/examples/processing.py
@@ -4,8 +4,6 @@
 
 from aind_data_schema.core.processing import AnalysisProcess, DataProcess, PipelineProcess, Processing, ProcessName
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -82,4 +80,4 @@
 )
 serialized = p.model_dump_json()
 deserialized = Processing.model_validate_json(serialized)
-p.write_standard_file(output_directory=OUTPUT_PATH)
+p.write_standard_file()
diff --git a/examples/subject.py b/examples/subject.py
@@ -7,8 +7,6 @@
 
 from aind_data_schema.core.subject import BreedingInfo, Housing, Sex, Subject
 
-OUTPUT_PATH = "examples/"
-
 # If a timezone isn't specified, the timezone of the computer running this
 # script will be used as default
 t = datetime(2022, 11, 22, 8, 43, 00, tzinfo=timezone.utc)
@@ -32,4 +30,4 @@
 )
 serialized = s.model_dump_json()
 deserialized = Subject.model_validate_json(serialized)
-deserialized.write_standard_file(output_directory=OUTPUT_PATH)
+deserialized.write_standard_file()
diff --git a/tests/resources/rig_session_compatibility/ephys_rig.py b/tests/resources/rig_session_compatibility/ephys_rig.py
diff --git a/tests/resources/rig_session_compatibility/ephys_session.py b/tests/resources/rig_session_compatibility/ephys_session.py
diff --git a/tests/resources/rig_session_compatibility/fip_ophys_rig.py b/tests/resources/rig_session_compatibility/fip_ophys_rig.py
diff --git a/tests/resources/rig_session_compatibility/fip_ophys_session.py b/tests/resources/rig_session_compatibility/fip_ophys_session.py
diff --git a/tests/test_rig_session_compatibility.py b/tests/test_rig_session_compatibility.py

Original file line number	Diff line number	Diff line change
`@@ -16,8 +16,6 @@`
`16`	`16`	`)`
`17`	`17`	`from aind_data_schema.core.instrument import Com, Instrument`
`18`	`18`
`19`		`-OUTPUT_PATH = "examples/"`
`20`		`-`
`21`	`19`	`inst = Instrument(`
`22`	`20`	`instrument_id="440_SmartSPIM2_20231004",`
`23`	`21`	`modification_date=datetime.date(2023, 10, 4),`
`@@ -213,4 +211,4 @@`
`213`	`211`	`)`
`214`	`212`	`serialized = inst.model_dump_json()`
`215`	`213`	`deserialized = Instrument.model_validate_json(serialized)`
`216`		`-deserialized.write_standard_file(prefix="aibs_smartspim", output_directory=OUTPUT_PATH)`
	`214`	`+deserialized.write_standard_file(prefix="aibs_smartspim")`