reverts unit test structure and test_and_lint workflow

AllenNeuralDynamics · Jul 31, 2024 · 36ea0c9 · 36ea0c9
1 parent bcbc882
commit 36ea0c9
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Showing 78 changed files with 47 additions and 40 deletions.
diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml
@@ -0,0 +1,41 @@
+name: Run integration tests
+
+on:
+  push:
+    branches:
+      - feat-53-integration-testing
+
+jobs:
+  integration_tests:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    env:
+      AWS_METADATA_MAPPER_ROLE: ${{ secrets.AWS_METADATA_MAPPER_ROLE_DEV }}
+      AWS_METADATA_MAPPER_BUCKET: ${{ vars.AWS_METADATA_MAPPER_BUCKET_DEV }}
+      AWS_REGION: ${{ vars.AWS_REGION_DEV }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          python -m pip install -e .[all]
+          python -m pip install s3fs
+      - name: Configure aws credentials
+        uses: aws-actions/configure-aws-credentials@v2
+        with:
+          role-to-assume: ${{ env.AWS_METADATA_MAPPER_ROLE }}
+          role-session-name: github-integration-test-session
+          aws-region: ${{ env.AWS_REGION }}
+      - name: run integration tests
+        run:
+          python -m tests.integration.test_bergamo.test_session AWS_METADATA_MAPPER_BUCKET=${{ secrets.AWS_METADATA_MAPPER_BUCKET_DEV }}
+
+
+
+
+
diff --git a/.github/workflows/test_and_lint.yml b/.github/workflows/test_and_lint.yml
@@ -1,9 +1,9 @@
 name: Lint and run tests
 
 on:
-  push:
+  pull_request:
     branches:
-      - feat-53-integration-testing
+      - main
 
 jobs:
   ci:
@@ -24,36 +24,3 @@ jobs:
       run: flake8 . && interrogate --verbose .
     - name: Run tests and coverage
       run: coverage run -m unittest discover && coverage report
-  integration_tests:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    env:
-      AWS_METADATA_MAPPER_ROLE: ${{ secrets.AWS_METADATA_MAPPER_ROLE_DEV }}
-      AWS_METADATA_MAPPER_BUCKET: ${{ vars.AWS_METADATA_MAPPER_BUCKET_DEV }}
-      AWS_REGION: ${{ vars.AWS_REGION_DEV }}
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v3
-        with:
-          python-version: '3.10'
-      - name: Install dependencies
-        run: |
-          python -m pip install -e .[all]
-          python -m pip install s3fs
-      - name: Configure aws credentials
-        uses: aws-actions/configure-aws-credentials@v2
-        with:
-          role-to-assume: ${{ env.AWS_METADATA_MAPPER_ROLE }}
-          role-session-name: github-integration-test-session
-          aws-region: ${{ env.AWS_REGION }}
-      - name: run integration tests
-        run:
-          python -m tests.integration.test_bergamo.test_session AWS_METADATA_MAPPER_BUCKET=${{ secrets.AWS_METADATA_MAPPER_BUCKET_DEV }}
-
-
-
-
-
diff --git a/...ources/bergamo/cropped_neuron50_00001.tif → ...ources/bergamo/cropped_neuron50_00001.tif b/...ources/bergamo/cropped_neuron50_00001.tif → ...ources/bergamo/cropped_neuron50_00001.tif
diff --git a/...t/resources/bergamo/expected_session.json → ...s/resources/bergamo/expected_session.json b/...t/resources/bergamo/expected_session.json → ...s/resources/bergamo/expected_session.json
diff --git a/.../resources/bergamo/parsed_metadata.pkl.gz → .../resources/bergamo/parsed_metadata.pkl.gz b/.../resources/bergamo/parsed_metadata.pkl.gz → .../resources/bergamo/parsed_metadata.pkl.gz
diff --git a/...it/resources/bruker/example_scan_data.pkl → tests/resources/bruker/example_scan_data.pkl b/...it/resources/bruker/example_scan_data.pkl → tests/resources/bruker/example_scan_data.pkl
diff --git a/...resources/bruker/example_subject_data.pkl → ...resources/bruker/example_subject_data.pkl b/...resources/bruker/example_subject_data.pkl → ...resources/bruker/example_subject_data.pkl
diff --git a/...it/resources/bruker/expected_session.json → tests/resources/bruker/expected_session.json b/...it/resources/bruker/expected_session.json → tests/resources/bruker/expected_session.json
diff --git a/...namic_routing/base-missing-probe_rig.json → ...namic_routing/base-missing-probe_rig.json b/...namic_routing/base-missing-probe_rig.json → ...namic_routing/base-missing-probe_rig.json
diff --git a/...t/resources/dynamic_routing/base_rig.json → ...s/resources/dynamic_routing/base_rig.json b/...t/resources/dynamic_routing/base_rig.json → ...s/resources/dynamic_routing/base_rig.json
diff --git a/tests/unit/resources/dynamic_routing/mvr.ini → tests/resources/dynamic_routing/mvr.ini b/tests/unit/resources/dynamic_routing/mvr.ini → tests/resources/dynamic_routing/mvr.ini
diff --git a/...it/resources/dynamic_routing/mvr_rig.json → tests/resources/dynamic_routing/mvr_rig.json b/...it/resources/dynamic_routing/mvr_rig.json → tests/resources/dynamic_routing/mvr_rig.json
diff --git a/...s/unit/resources/dynamic_routing/sync.yml → tests/resources/dynamic_routing/sync.yml b/...s/unit/resources/dynamic_routing/sync.yml → tests/resources/dynamic_routing/sync.yml
diff --git a/...t/resources/dynamic_routing/sync_rig.json → ...s/resources/dynamic_routing/sync_rig.json b/...t/resources/dynamic_routing/sync_rig.json → ...s/resources/dynamic_routing/sync_rig.json
diff --git a/.../unit/resources/fip/000000_ophys_rig.json → tests/resources/fip/000000_ophys_rig.json b/.../unit/resources/fip/000000_ophys_rig.json → tests/resources/fip/000000_ophys_rig.json
diff --git a/...t/resources/fip/000000_ophys_session.json → ...s/resources/fip/000000_ophys_session.json b/...t/resources/fip/000000_ophys_session.json → ...s/resources/fip/000000_ophys_session.json
diff --git a/...nit/resources/fip/example_from_teensy.txt → tests/resources/fip/example_from_teensy.txt b/...nit/resources/fip/example_from_teensy.txt → tests/resources/fip/example_from_teensy.txt
diff --git a/...ob/example_funding_multiple_response.json → ...ob/example_funding_multiple_response.json b/...ob/example_funding_multiple_response.json → ...ob/example_funding_multiple_response.json
diff --git a/...etadata_job/example_funding_response.json → ...etadata_job/example_funding_response.json b/...etadata_job/example_funding_response.json → ...etadata_job/example_funding_response.json
diff --git a/...data_job/example_procedures_response.json → ...data_job/example_procedures_response.json b/...data_job/example_procedures_response.json → ...data_job/example_procedures_response.json
diff --git a/...etadata_job/example_subject_response.json → ...etadata_job/example_subject_response.json b/...etadata_job/example_subject_response.json → ...etadata_job/example_subject_response.json
diff --git a/...adata_job/metadata_files/acquisition.json → ...adata_job/metadata_files/acquisition.json b/...adata_job/metadata_files/acquisition.json → ...adata_job/metadata_files/acquisition.json
diff --git a/..._job/metadata_files/data_description.json → ..._job/metadata_files/data_description.json b/..._job/metadata_files/data_description.json → ..._job/metadata_files/data_description.json
diff --git a/...tadata_job/metadata_files/instrument.json → ...tadata_job/metadata_files/instrument.json b/...tadata_job/metadata_files/instrument.json → ...tadata_job/metadata_files/instrument.json
diff --git a/...tadata_job/metadata_files/procedures.json → ...tadata_job/metadata_files/procedures.json b/...tadata_job/metadata_files/procedures.json → ...tadata_job/metadata_files/procedures.json
diff --git a/...tadata_job/metadata_files/processing.json → ...tadata_job/metadata_files/processing.json b/...tadata_job/metadata_files/processing.json → ...tadata_job/metadata_files/processing.json
diff --git a/...ther_metadata_job/metadata_files/rig.json → ...ther_metadata_job/metadata_files/rig.json b/...ther_metadata_job/metadata_files/rig.json → ...ther_metadata_job/metadata_files/rig.json
diff --git a/..._metadata_job/metadata_files/session.json → ..._metadata_job/metadata_files/session.json b/..._metadata_job/metadata_files/session.json → ..._metadata_job/metadata_files/session.json
diff --git a/..._metadata_job/metadata_files/subject.json → ..._metadata_job/metadata_files/subject.json b/..._metadata_job/metadata_files/subject.json → ..._metadata_job/metadata_files/subject.json
diff --git a/.../0123456789_Behavior_20240212T091443.json → .../0123456789_Behavior_20240212T091443.json b/.../0123456789_Behavior_20240212T091443.json → .../0123456789_Behavior_20240212T091443.json
diff --git a/...scope/0123456789_Eye_20240212T091443.json → ...scope/0123456789_Eye_20240212T091443.json b/...scope/0123456789_Eye_20240212T091443.json → ...scope/0123456789_Eye_20240212T091443.json
diff --git a/...cope/0123456789_Face_20240212T091444.json → ...cope/0123456789_Face_20240212T091444.json b/...cope/0123456789_Face_20240212T091444.json → ...cope/0123456789_Face_20240212T091444.json
diff --git a/.../resources/mesoscope/example_extract.json → .../resources/mesoscope/example_extract.json b/.../resources/mesoscope/example_extract.json → .../resources/mesoscope/example_extract.json
diff --git a/...resources/mesoscope/example_platform.json → ...resources/mesoscope/example_platform.json b/...resources/mesoscope/example_platform.json → ...resources/mesoscope/example_platform.json
diff --git a/...resources/mesoscope/expected_session.json → ...resources/mesoscope/expected_session.json b/...resources/mesoscope/expected_session.json → ...resources/mesoscope/expected_session.json
diff --git a/...ces/open_ephys/camstim_ephys_session.json → ...ces/open_ephys/camstim_ephys_session.json b/...ces/open_ephys/camstim_ephys_session.json → ...ces/open_ephys/camstim_ephys_session.json
diff --git a/...t/resources/open_ephys/ephys_session.json → ...s/resources/open_ephys/ephys_session.json b/...t/resources/open_ephys/ephys_session.json → ...s/resources/open_ephys/ephys_session.json
diff --git a/...it/resources/open_ephys/newscale_main.csv → tests/resources/open_ephys/newscale_main.csv b/...it/resources/open_ephys/newscale_main.csv → tests/resources/open_ephys/newscale_main.csv
diff --git a/...s/open_ephys/newscale_surface_finding.csv → ...s/open_ephys/newscale_surface_finding.csv b/...s/open_ephys/newscale_surface_finding.csv → ...s/open_ephys/newscale_surface_finding.csv
diff --git a/...s/open_ephys/open-ephys-inferred_rig.json → ...s/open_ephys/open-ephys-inferred_rig.json b/...s/open_ephys/open-ephys-inferred_rig.json → ...s/open_ephys/open-ephys-inferred_rig.json
diff --git a/.../resources/open_ephys/open-ephys_rig.json → .../resources/open_ephys/open-ephys_rig.json b/.../resources/open_ephys/open-ephys_rig.json → .../resources/open_ephys/open-ephys_rig.json
diff --git a/...en_ephys/settings.mislabeled-probes-0.xml → ...en_ephys/settings.mislabeled-probes-0.xml b/...en_ephys/settings.mislabeled-probes-0.xml → ...en_ephys/settings.mislabeled-probes-0.xml
diff --git a/...en_ephys/settings.mislabeled-probes-1.xml → ...en_ephys/settings.mislabeled-probes-1.xml b/...en_ephys/settings.mislabeled-probes-1.xml → ...en_ephys/settings.mislabeled-probes-1.xml
diff --git a/tests/unit/resources/open_ephys/settings.xml → tests/resources/open_ephys/settings.xml b/tests/unit/resources/open_ephys/settings.xml → tests/resources/open_ephys/settings.xml
diff --git a/...it/resources/open_ephys/settings_main.xml → tests/resources/open_ephys/settings_main.xml b/...it/resources/open_ephys/settings_main.xml → tests/resources/open_ephys/settings_main.xml
diff --git a/...s/open_ephys/settings_surface_finding.xml → ...s/open_ephys/settings_surface_finding.xml b/...s/open_ephys/settings_surface_finding.xml → ...s/open_ephys/settings_surface_finding.xml
diff --git a/...artspim/example_ASI_logging_afternoon.txt → ...artspim/example_ASI_logging_afternoon.txt b/...artspim/example_ASI_logging_afternoon.txt → ...artspim/example_ASI_logging_afternoon.txt
diff --git a/...smartspim/example_ASI_logging_morning.txt → ...smartspim/example_ASI_logging_morning.txt b/...smartspim/example_ASI_logging_morning.txt → ...smartspim/example_ASI_logging_morning.txt
diff --git a/.../unit/resources/smartspim/local_json.json → tests/resources/smartspim/local_json.json b/.../unit/resources/smartspim/local_json.json → tests/resources/smartspim/local_json.json
diff --git a/tests/unit/test_bergamo/__init__.py → tests/test_bergamo/__init__.py b/tests/unit/test_bergamo/__init__.py → tests/test_bergamo/__init__.py
diff --git a/tests/unit/test_bergamo/test_session.py → tests/test_bergamo/test_session.py b/tests/unit/test_bergamo/test_session.py → tests/test_bergamo/test_session.py
diff --git a/tests/unit/test_bruker/__init__.py → tests/test_bruker/__init__.py b/tests/unit/test_bruker/__init__.py → tests/test_bruker/__init__.py
diff --git a/tests/unit/test_bruker/test_session.py → tests/test_bruker/test_session.py b/tests/unit/test_bruker/test_session.py → tests/test_bruker/test_session.py
diff --git a/tests/unit/test_dynamic_routing/__init__.py → tests/test_dynamic_routing/__init__.py b/tests/unit/test_dynamic_routing/__init__.py → tests/test_dynamic_routing/__init__.py
diff --git a/...unit/test_dynamic_routing/test_mvr_rig.py → tests/test_dynamic_routing/test_mvr_rig.py b/...unit/test_dynamic_routing/test_mvr_rig.py → tests/test_dynamic_routing/test_mvr_rig.py
@@ -8,7 +8,7 @@
 from aind_metadata_mapper.dynamic_routing.mvr_rig import (  # type: ignore
     MvrRigEtl,
 )
-from tests.unit.test_dynamic_routing import test_utils as test_utils
+from tests.test_dynamic_routing import test_utils as test_utils
 
 RESOURCES_DIR = (
     Path(os.path.dirname(os.path.realpath(__file__)))

diff --git a/...t_dynamic_routing/test_neuropixels_rig.py → ...t_dynamic_routing/test_neuropixels_rig.py b/...t_dynamic_routing/test_neuropixels_rig.py → ...t_dynamic_routing/test_neuropixels_rig.py
diff --git a/...nit/test_dynamic_routing/test_sync_rig.py → tests/test_dynamic_routing/test_sync_rig.py b/...nit/test_dynamic_routing/test_sync_rig.py → tests/test_dynamic_routing/test_sync_rig.py
@@ -8,7 +8,7 @@
 from aind_metadata_mapper.dynamic_routing.sync_rig import (  # type: ignore
     SyncRigEtl,
 )
-from tests.unit.test_dynamic_routing import test_utils as test_utils
+from tests.test_dynamic_routing import test_utils as test_utils
 
 RESOURCES_DIR = (
     Path(os.path.dirname(os.path.realpath(__file__)))

diff --git a/...s/unit/test_dynamic_routing/test_utils.py → tests/test_dynamic_routing/test_utils.py b/...s/unit/test_dynamic_routing/test_utils.py → tests/test_dynamic_routing/test_utils.py
diff --git a/tests/unit/test_fip/__init__.py → tests/test_fip/__init__.py b/tests/unit/test_fip/__init__.py → tests/test_fip/__init__.py
diff --git a/tests/unit/test_fip/test_session.py → tests/test_fip/test_session.py b/tests/unit/test_fip/test_session.py → tests/test_fip/test_session.py
diff --git a/tests/unit/test_gather_metadata.py → tests/test_gather_metadata.py b/tests/unit/test_gather_metadata.py → tests/test_gather_metadata.py
diff --git a/tests/unit/test_legacy_core.py → tests/test_legacy_core.py b/tests/unit/test_legacy_core.py → tests/test_legacy_core.py
diff --git a/tests/unit/test_mesoscope/__init__.py → tests/test_mesoscope/__init__.py b/tests/unit/test_mesoscope/__init__.py → tests/test_mesoscope/__init__.py
diff --git a/tests/unit/test_mesoscope/test_session.py → tests/test_mesoscope/test_session.py b/tests/unit/test_mesoscope/test_session.py → tests/test_mesoscope/test_session.py
diff --git a/tests/unit/test_open_ephys/__init__.py → tests/test_open_ephys/__init__.py b/tests/unit/test_open_ephys/__init__.py → tests/test_open_ephys/__init__.py
diff --git a/tests/unit/test_open_ephys/test_rig.py → tests/test_open_ephys/test_rig.py b/tests/unit/test_open_ephys/test_rig.py → tests/test_open_ephys/test_rig.py
diff --git a/tests/unit/test_open_ephys/test_session.py → tests/test_open_ephys/test_session.py b/tests/unit/test_open_ephys/test_session.py → tests/test_open_ephys/test_session.py
diff --git a/tests/test_open_ephys/test_utils/__init__.py b/tests/test_open_ephys/test_utils/__init__.py
diff --git a/...n_ephys/test_utils/test_behavior_utils.py → ...n_ephys/test_utils/test_behavior_utils.py b/...n_ephys/test_utils/test_behavior_utils.py → ...n_ephys/test_utils/test_behavior_utils.py
diff --git a/...pen_ephys/test_utils/test_naming_utils.py → ...pen_ephys/test_utils/test_naming_utils.py b/...pen_ephys/test_utils/test_naming_utils.py → ...pen_ephys/test_utils/test_naming_utils.py
diff --git a/...t_open_ephys/test_utils/test_pkl_utils.py → ...t_open_ephys/test_utils/test_pkl_utils.py b/...t_open_ephys/test_utils/test_pkl_utils.py → ...t_open_ephys/test_utils/test_pkl_utils.py
diff --git a/..._open_ephys/test_utils/test_stim_utils.py → ..._open_ephys/test_utils/test_stim_utils.py b/..._open_ephys/test_utils/test_stim_utils.py → ..._open_ephys/test_utils/test_stim_utils.py
diff --git a/..._open_ephys/test_utils/test_sync_utils.py → ..._open_ephys/test_utils/test_sync_utils.py b/..._open_ephys/test_utils/test_sync_utils.py → ..._open_ephys/test_utils/test_sync_utils.py
diff --git a/tests/unit/test_smartspim/__init__.py → tests/test_smartspim/__init__.py b/tests/unit/test_smartspim/__init__.py → tests/test_smartspim/__init__.py
diff --git a/...s/unit/test_smartspim/example_metadata.py → tests/test_smartspim/example_metadata.py b/...s/unit/test_smartspim/example_metadata.py → tests/test_smartspim/example_metadata.py
diff --git a/...s/unit/test_smartspim/test_acquisition.py → tests/test_smartspim/test_acquisition.py b/...s/unit/test_smartspim/test_acquisition.py → tests/test_smartspim/test_acquisition.py
@@ -12,7 +12,7 @@
     JobSettings,
     SmartspimETL,
 )
-from tests.unit.test_smartspim.example_metadata import (
+from tests.test_smartspim.example_metadata import (
     example_filter_mapping,
     example_metadata_info,
     example_processing_manifest,

diff --git a/tests/unit/test_smartspim/test_utils.py → tests/test_smartspim/test_utils.py b/tests/unit/test_smartspim/test_utils.py → tests/test_smartspim/test_utils.py
@@ -9,7 +9,7 @@
 from aind_data_schema.components.coordinates import AnatomicalDirection
 
 from aind_metadata_mapper.smartspim import utils
-from tests.unit.test_smartspim.example_metadata import (
+from tests.test_smartspim.example_metadata import (
     example_filter_mapping,
     example_metadata_info,
 )

diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py