Main (#1026)

* 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 --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
AllenNeuralDynamics · Aug 20, 2024 · 3b66c23 · 3b66c23
1 parent 26555a3
commit 3b66c23
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Showing 43 changed files with 39,734 additions and 31,708 deletions.
diff --git a/.github/workflows/tag_and_publish_main.yml b/.github/workflows/tag_and_publish_main.yml
@@ -38,7 +38,7 @@ jobs:
         password: ${{ secrets.AIND_PYPI_TOKEN }}
 
   upload_schemas_prod:
-    needs: publish
+    needs: tag_and_publish
     runs-on: ubuntu-latest
     permissions:
       id-token: write
@@ -71,7 +71,7 @@ jobs:
           aws s3 sync $TEMP_DIR s3://${AWS_DATA_SCHEMA_BUCKET}/$S3_PREFIX
 
   upload_diagrams:
-    needs: publish
+    needs: tag_and_publish
     runs-on: ubuntu-latest
     permissions:
       id-token: write

diff --git a/.github/workflows/update_docs.yml b/.github/workflows/update_docs.yml
@@ -12,6 +12,8 @@ jobs:
       OUTPUT_DIR: 'schemas'
     steps:
       - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.SERVICE_TOKEN }}
       - name: Set up Python 3.8
         uses: actions/setup-python@v3
         with:
@@ -47,6 +49,8 @@ jobs:
     continue-on-error: true
     steps:
       - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.SERVICE_TOKEN }}
       - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:

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": "0.10.28",
+   "schema_version": "0.10.29",
    "instrument_id": "440_SmartSPIM2_20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",
@@ -508,4 +508,4 @@
    ],
    "daqs": [],
    "notes": null
-}
+}
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": "0.13.14",
+   "schema_version": "0.13.15",
    "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": "0.10.28",
+   "schema_version": "0.10.29",
    "instrument_id": "440_SmartSPIM1_20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "SmartSPIM",
@@ -635,4 +635,4 @@
    ],
    "daqs": [],
    "notes": null
-}
+}
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": "0.3.4",
+   "schema_version": "0.3.5",
    "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": "0.13.11",
+   "schema_version": "0.13.12",
    "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": "0.5.4",
+   "schema_version": "0.5.5",
    "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": "0.3.4",
+   "schema_version": "0.3.5",
    "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": "0.6.20",
+   "schema_version": "0.6.21",
    "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": "0.10.28",
+   "schema_version": "0.10.29",
    "instrument_id": "440_exaSPIM1-20231004",
    "modification_date": "2023-10-04",
    "instrument_type": "exaSPIM",
@@ -457,4 +457,4 @@
       }
    ],
    "notes": null
-}
+}
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": "0.5.4",
+   "schema_version": "0.5.5",
    "rig_id": "447_FIP-Behavior_20000101",
    "modification_date": "2000-01-01",
    "mouse_platform": {
@@ -945,4 +945,4 @@
       }
    ],
    "notes": null
-}
+}
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": "0.5.4",
+   "schema_version": "0.5.5",
    "rig_id": "428_FIP1_20231003",
    "modification_date": "2023-10-03",
    "mouse_platform": {
@@ -899,4 +899,4 @@
       }
    ],
    "notes": null
-}
+}
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": "0.3.4",
+   "schema_version": "0.3.5",
    "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": "0.3.4",
+   "schema_version": "0.3.5",
    "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": "0.13.14",
+   "schema_version": "0.13.15",
    "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": "0.3.4",
+   "schema_version": "0.3.5",
    "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": "0.13.14",
+   "schema_version": "0.13.15",
    "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": "0.4.8",
+   "schema_version": "0.4.9",
    "processing_pipeline": {
       "data_processes": [
          {

diff --git a/examples/subject.json b/examples/subject.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/subject.py",
-   "schema_version": "0.5.9",
+   "schema_version": "0.5.10",
    "subject_id": "12345",
    "sex": "Male",
    "date_of_birth": "2022-11-22",