Update dev from main v1.1.0 (#1096)

* build: updates version number * feat: adds qc schema json * fix: updates schema version check to handle new core schemas * ci: adds service account token to github actions * bump schema version [skip actions] * fix: updates broken github action * bump schema version [skip actions] * build: increments version to 1.0.0 * build: sets core metadata schema to v1.0.0 * chore: version bump * bump schema version [skip actions] * chore: version bump for schemas (#1094) * chore: version bump for schemas * tests: example updates * bump schema version [skip actions] --------- Co-authored-by: Jon Young <104453205+jtyoung84@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
AllenNeuralDynamics · Oct 5, 2024 · 5a6c75b · 5a6c75b
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diff --git a/examples/aibs_smartspim_instrument.json b/examples/aibs_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "instrument_id": "440_SmartSPIM2_20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",

diff --git a/examples/aibs_smartspim_procedures.json b/examples/aibs_smartspim_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.1.1",
    "subject_id": "651286",
    "subject_procedures": [
       {

diff --git a/examples/aind_smartspim_instrument.json b/examples/aind_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "instrument_id": "440_SmartSPIM1_20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",

diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"

diff --git a/examples/data_description.json b/examples/data_description.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/data_description.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "license": "CC-BY-4.0",
    "platform": {
       "name": "Electrophysiology platform",

diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "rig_id": "323_EPHYS1_20231003",
    "modification_date": "2023-10-03",
    "mouse_platform": {

diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [],
    "experimenter_full_name": [
       "Max Quibble",

diff --git a/examples/exaspim_acquisition.json b/examples/exaspim_acquisition.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [],
    "experimenter_full_name": [
       "###"

diff --git a/examples/exaspim_instrument.json b/examples/exaspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/instrument.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "instrument_id": "440_exaSPIM1-20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "exaSPIM",

diff --git a/examples/fip_behavior_rig.json b/examples/fip_behavior_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "rig_id": "447_FIP-Behavior_20000101",
    "modification_date": "2000-01-01",
    "mouse_platform": {

diff --git a/examples/fip_ophys_rig.json b/examples/fip_ophys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "rig_id": "428_FIP1_20231003",
    "modification_date": "2023-10-03",
    "mouse_platform": {

diff --git a/examples/mri_session.json b/examples/mri_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [
       "dx.doi.org/10.57824/protocols.io.bh7kl4n6"
    ],

diff --git a/examples/multiplane_ophys_session.json b/examples/multiplane_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"

diff --git a/examples/ophys_procedures.json b/examples/ophys_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.1.1",
    "subject_id": "625100",
    "subject_procedures": [
       {

diff --git a/examples/ophys_session.json b/examples/ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.0.1",
    "protocol_id": [],
    "experimenter_full_name": [
       "John Doe"

diff --git a/examples/procedures.json b/examples/procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.1.1",
    "subject_id": "625100",
    "subject_procedures": [
       {

diff --git a/examples/processing.json b/examples/processing.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/processing.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.1.1",
    "processing_pipeline": {
       "data_processes": [
          {

diff --git a/examples/quality_control.json b/examples/quality_control.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/quality_control.py",
-   "schema_version": "1.0.0",
+   "schema_version": "1.1.1",
    "evaluations": [
       {
          "modality": {

diff --git a/schemas/acquisition_schema.json b/schemas/acquisition_schema.json
@@ -613,11 +613,7 @@
                "type": "integer"
             },
             "imaging_angle_unit": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AngleUnit"
-                  }
-               ],
+               "$ref": "#/$defs/AngleUnit",
                "default": "degrees",
                "title": "Imaging angle unit"
             },
@@ -1261,21 +1257,13 @@
                "type": "string"
             },
             "input": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AindGeneric"
-                  }
-               ],
+               "$ref": "#/$defs/AindGeneric",
                "default": {},
                "description": "Calibration input",
                "title": "inputs"
             },
             "output": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AindGeneric"
-                  }
-               ],
+               "$ref": "#/$defs/AindGeneric",
                "default": {},
                "description": "Calibration output",
                "title": "outputs"
@@ -1342,11 +1330,7 @@
                "type": "integer"
             },
             "excitation_wavelength_unit": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/SizeUnit"
-                  }
-               ],
+               "$ref": "#/$defs/SizeUnit",
                "default": "nanometer",
                "title": "Laser wavelength unit"
             },
@@ -1356,11 +1340,7 @@
                "type": "number"
             },
             "excitation_power_unit": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/PowerUnit"
-                  }
-               ],
+               "$ref": "#/$defs/PowerUnit",
                "default": "milliwatt",
                "title": "Laser power unit"
             },
@@ -1381,11 +1361,7 @@
                "title": "Dilation (pixels)"
             },
             "dilation_unit": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/SizeUnit"
-                  }
-               ],
+               "$ref": "#/$defs/SizeUnit",
                "default": "pixel",
                "title": "Dilation unit"
             },
@@ -2182,19 +2158,11 @@
          "description": "Description of an image axis",
          "properties": {
             "name": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AxisName"
-                  }
-               ],
+               "$ref": "#/$defs/AxisName",
                "title": "Name"
             },
             "direction": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AnatomicalDirection"
-                  }
-               ],
+               "$ref": "#/$defs/AnatomicalDirection",
                "description": "Tissue direction as the value of axis increases. If Other describe in notes."
             },
             "dimension": {
@@ -2203,11 +2171,7 @@
                "type": "integer"
             },
             "unit": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/SizeUnit"
-                  }
-               ],
+               "$ref": "#/$defs/SizeUnit",
                "default": "micrometer",
                "title": "Axis physical units"
             }
@@ -2225,11 +2189,7 @@
          "description": "Description of immersion medium",
          "properties": {
             "medium": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/ImmersionMedium"
-                  }
-               ],
+               "$ref": "#/$defs/ImmersionMedium",
                "title": "Immersion medium"
             },
             "refractive_index": {
@@ -4662,11 +4622,7 @@
                "title": "URL to commit being used"
             },
             "parameters": {
-               "allOf": [
-                  {
-                     "$ref": "#/$defs/AindGeneric"
-                  }
-               ],
+               "$ref": "#/$defs/AindGeneric",
                "default": {},
                "title": "Software parameters"
             }
@@ -5144,10 +5100,10 @@
          "type": "string"
       },
       "schema_version": {
-         "const": "1.0.0",
-         "default": "1.0.0",
+         "const": "1.0.1",
+         "default": "1.0.1",
          "enum": [
-            "1.0.0"
+            "1.0.1"
          ],
          "title": "Schema Version",
          "type": "string"
@@ -5244,11 +5200,7 @@
          "type": "array"
       },
       "chamber_immersion": {
-         "allOf": [
-            {
-               "$ref": "#/$defs/Immersion"
-            }
-         ],
+         "$ref": "#/$defs/Immersion",
          "title": "Acquisition chamber immersion data"
       },
       "sample_immersion": {

diff --git a/schemas/data_description_schema.json b/schemas/data_description_schema.json
@@ -1775,10 +1775,10 @@
          "type": "string"
       },
       "schema_version": {
-         "const": "1.0.0",
-         "default": "1.0.0",
+         "const": "1.0.1",
+         "default": "1.0.1",
          "enum": [
-            "1.0.0"
+            "1.0.1"
          ],
          "title": "Schema Version",
          "type": "string"
@@ -1954,11 +1954,7 @@
          "type": "array"
       },
       "data_level": {
-         "allOf": [
-            {
-               "$ref": "#/$defs/DataLevel"
-            }
-         ],
+         "$ref": "#/$defs/DataLevel",
          "description": "level of processing that data has undergone",
          "title": "Data Level"
       },