PYTHON-4687: Make lint fixes provided by pre-commit

.evergreen/config.yml

@@ -187,7 +187,7 @@ buildvariants:
       - rhel87-small
     tasks:
       - name: test-llama-index
-  
+
   - name: test-docarray-rhel
     display_name: DocArray RHEL
     expansions:
@@ -210,4 +210,4 @@ buildvariants:
     run_on:
       - rhel87-small
     tasks:
-      - name: test-autogen
+      - name: test-autogen

.evergreen/provision-atlas.sh

@@ -7,9 +7,7 @@ PYTHON_BINARY=$(find_python3)
 # Should be called from src
 EVERGREEN_PATH=$(pwd)/.evergreen
 TARGET_DIR=$(pwd)/$DIR
-PING_ATLAS=$EVERGREEN_PATH/ping_atlas.py
 SCAFFOLD_SCRIPT=$EVERGREEN_PATH/scaffold_atlas.py
-DEPLOYMENT_NAME=$DIR
 
 set -ex
 mkdir atlas

.evergreen/scaffold_atlas.py

@@ -36,7 +36,7 @@ def upload_data(db: Database, filename: Path) -> None:
         loaded_collection = json.load(f)
 
     logger.info(
-        "Loading %s to Atlas database %s in colleciton %s",
+        "Loading %s to Atlas database %s in collection %s",
         filename.name,
         db.name,
         collection_name,

.evergreen/utils.sh

@@ -80,7 +80,7 @@ setup_local_atlas() {
             *)
             echo "Unrecognized state $STATE"
             sleep 1
-        esac      
+        esac
     done
 
     echo "container did not get healthy within 120 seconds, quitting"
@@ -92,14 +92,14 @@ setup_local_atlas() {
     wait "$CONTAINER_ID"
     EXPOSED_PORT=$(podman inspect --format='{{ (index (index .NetworkSettings.Ports "27017/tcp") 0).HostPort }}' "$CONTAINER_ID")
     export CONN_STRING="mongodb://127.0.0.1:$EXPOSED_PORT/?directConnection=true"
+    # shellcheck disable=SC2154
     echo "CONN_STRING=mongodb://127.0.0.1:$EXPOSED_PORT/?directConnection=true" > $workdir/src/.evergreen/.local_atlas_uri
 }
 
 fetch_local_atlas_uri() {
+    # shellcheck disable=SC2154
     . $workdir/src/.evergreen/.local_atlas_uri
 
     export CONN_STRING=$CONN_STRING
     echo "$CONN_STRING"
 }
-
-

.github/workflows/lint.yml

@@ -26,4 +26,4 @@ jobs:
           python -m pip install -U pip pre-commit
       - name: Run linters
         run: |
-          pre-commit run --hook-stage=manual --all-files
+          pre-commit run --hook-stage=manual --all-files

.gitignore

@@ -49,4 +49,3 @@ xunit-results/
 
 # Miscellaneous
 .DS_Store
-

README.md

@@ -30,7 +30,7 @@ Within each subdirectory you should expect to have:
 The general layout of this repo looks like this:
 
 ```bash
-├── LICENSE                                     # License Agreeement
+├── LICENSE                                     # License Agreement
 ├── README.md                                   # This Document
 ├── langchain-python                            # Folder scoped for one Integration
 │   └── run.sh                                  # Script that executes test

autogen/run.sh

@@ -6,18 +6,20 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 PYTHON_BINARY=$(find_python3)
 $PYTHON_BINARY -c "import sys; print(f'Python version found: {sys.version_info}')"
 
 # Create and activate an isolated python venv environment
 $PYTHON_BINARY -m venv venv
-source venv/bin/activate
+. venv/bin/activate
 #  Install autogen with extras
 $PYTHON_BINARY -m pip install .[test,"retrievechat-mongodb"]
 
 
 # Run tests. Sensitive variables in Evergreen come from Evergreen project: ai-ml-pipeline-testing/
+# shellcheck disable=SC2154
 MONGODB_URI=$autogen_mongodb_uri \
 MONGODB_DATABASE="autogen_test_db" \
 $PYTHON_BINARY -m pytest -v test/agentchat/contrib/vectordb/test_mongodb.py

chatgpt-retrieval-plugin/run.sh

@@ -4,6 +4,7 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 
 PYTHON_BINARY=$(find_python3)
@@ -14,13 +15,14 @@ $PYTHON_BINARY -m pip install -U pip poetry
 # Create a package specific poetry environment
 $PYTHON_BINARY -m poetry env use $PYTHON_BINARY
 # Activate the poetry env, which itself does not include poetry
-source $($PYTHON_BINARY -m poetry env info --path)/bin/activate
+. "$($PYTHON_BINARY -m poetry env info --path)/bin/activate"
 # Recreate the poetry lock file
 $PYTHON_BINARY -m poetry lock --no-update
 # Install from pyproject.toml into package specific environment
 $PYTHON_BINARY -m poetry install --with dev
 
 # Run tests. Sensitive variables in Evergreen come from Evergeen project: ai-ml-pipeline-testing/
+# shellcheck disable=SC2154
 OPENAI_API_KEY=$openai_api_key \
 DATASTORE="mongodb-atlas" \
 BEARER_TOKEN="staylowandkeepmoving" \

docarray/run.sh

@@ -5,13 +5,14 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 PYTHON_BINARY=$(find_python3)
 $PYTHON_BINARY -c "import sys; print(f'Python version found: {sys.version_info}')"
 
 # Create and activate an isolated python venv environment
 $PYTHON_BINARY -m venv venv
-source venv/bin/activate
+. venv/bin/activate
 # Install Poetry
 pip install -U pip poetry
 # Recreate the poetry lock file
@@ -21,6 +22,7 @@ poetry install --with dev --extras mongo
 
 
 # Run tests. Sensitive variables in Evergreen come from Evergeen project: ai-ml-pipeline-testing/
+# shellcheck disable=SC2154
 MONGODB_URI=$docarray_mongodb_uri \
 MONGODB_DATABASE="docarray_test_db" \
-pytest -v tests/index/mongo_atlas
+pytest -v tests/index/mongo_atlas

langchain-python/run.sh

@@ -3,10 +3,12 @@
 # WORKING_DIR = src/langchain-python/langchain
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 
 PYTHON_BINARY=$(find_python3)
 
+# shellcheck disable=SC2164
 cd libs/partners/mongodb
 
  $PYTHON_BINARY -m venv venv_pipeline
@@ -18,7 +20,10 @@ poetry lock --no-update
 
 poetry install --with test --with test_integration
 
-export MONGODB_ATLAS_URI=$(fetch_local_atlas_uri)
+MONGODB_ATLAS_URI=$(fetch_local_atlas_uri)
+
+export MONGODB_ATLAS_URI
+# shellcheck disable=SC2154
 export OPENAI_API_KEY=$openai_api_key
 
 make test

llama-index-python-kvstore/run.sh

@@ -2,21 +2,23 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 
 CONN_STRING=$(fetch_local_atlas_uri)
 PYTHON_BINARY=$(find_python3)
 $PYTHON_BINARY -c "import sys; print(f'Python version found: {sys.version_info}')"
 
 # cd to the MongoDB integration. It has its own project
+# shellcheck disable=SC2164
 cd llama-index-integrations/storage/kvstore/llama-index-storage-kvstore-mongodb
- 
+
 # Install Poetry into base python
 $PYTHON_BINARY -m pip install -U pip poetry
 # Create a package specific poetry environment
 $PYTHON_BINARY -m poetry env use $PYTHON_BINARY
 # Activate the poetry env, which itself does not include poetry
-source $($PYTHON_BINARY -m poetry env info --path)/bin/activate
+. "$($PYTHON_BINARY -m poetry env info --path)/bin/activate"
 # PYTHON-4522: Will fix requirement in llama-index repo
 $PYTHON_BINARY -m poetry add motor
 # Recreate the poetry lock file
@@ -25,6 +27,7 @@ $PYTHON_BINARY -m poetry lock --no-update
 $PYTHON_BINARY -m poetry install --with dev
 
 # Run tests. Sensitive variables in Evergreen come from Evergreen project: ai-ml-pipeline-testing/
+# shellcheck disable=SC2154
 OPENAI_API_KEY=$openai_api_key \
 MONGODB_URI=$CONN_STRING \
 MONGODB_DATABASE="llama_index_test_db" \

llama-index-python-vectorstore/run.sh

@@ -2,26 +2,29 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 
 PYTHON_BINARY=$(find_python3)
 $PYTHON_BINARY -c "import sys; print(f'Python version found: {sys.version_info}')"
 
 # cd to the MongoDB integration. It has its own project
+# shellcheck disable=SC2164
 cd llama-index-integrations/vector_stores/llama-index-vector-stores-mongodb
 
 # Install Poetry into base python
 $PYTHON_BINARY -m pip install -U pip poetry
 # Create a package specific poetry environment
 $PYTHON_BINARY -m poetry env use $PYTHON_BINARY
 # Activate the poetry env, which itself does not include poetry
-source $($PYTHON_BINARY -m poetry env info --path)/bin/activate
+. "$($PYTHON_BINARY -m poetry env info --path)/bin/activate"
 # Recreate the poetry lock file
 $PYTHON_BINARY -m poetry lock --no-update
 # Install from pyproject.toml into package specific environment
 $PYTHON_BINARY -m poetry install --with dev
 
 # Run tests. Sensitive variables in Evergreen come from Evergreen project: ai-ml-pipeline-testing/
+# shellcheck disable=SC2154
 MONGODB_URI=$(fetch_local_atlas_uri) \
 OPENAI_API_KEY=$openai_api_key \
 MONGODB_DATABASE="llama_index_test_db" \

semantic-kernel-csharp/run.sh

@@ -2,6 +2,7 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 # WORKING_DIR = src/semantic-kernel-csharp/semantic-kernel
 
@@ -20,4 +21,4 @@ sed -i -e 's/"MongoDB Atlas cluster is required"/null/g' dotnet/src/IntegrationT
 # Run tests
 echo "Running MongoDBMemoryStoreTests"
 MongoDB__ConnectionString=$(fetch_local_atlas_uri) \
-$DOTNET_SDK_PATH/dotnet test dotnet/src/IntegrationTests/IntegrationTests.csproj --filter SemanticKernel.IntegrationTests.Connectors.MongoDB.MongoDBMemoryStoreTests
+$DOTNET_SDK_PATH/dotnet test dotnet/src/IntegrationTests/IntegrationTests.csproj --filter SemanticKernel.IntegrationTests.Connectors.MongoDB.MongoDBMemoryStoreTests

semantic-kernel-python/run.sh

@@ -2,12 +2,14 @@
 
 set -x
 
+# shellcheck disable=SC2154
 . $workdir/src/.evergreen/utils.sh
 
 CONN_STRING=$(fetch_local_atlas_uri)
 PYTHON_BINARY=$(find_python3)
 
 # WORKING_DIR = src/semantic-kernel-python/semantic-kernel
+# shellcheck disable=SC2164
 cd python
 
 # Temporary solution until https://github.com/microsoft/semantic-kernel/issues/9067 resolves
@@ -19,6 +21,7 @@ make install-python
 make install-sk
 make install-pre-commit
 
+# shellcheck disable=SC2154
 OPENAI_API_KEY=$openai_api_key \
     OPENAI_ORG_ID="" \
     AZURE_OPENAI_DEPLOYMENT_NAME="" \
@@ -28,6 +31,7 @@ OPENAI_API_KEY=$openai_api_key \
     Python_Integration_Tests=1 \
     uv run pytest tests/integration/connectors/memory/test_mongodb_atlas.py -k test_collection_knn
 
+# shellcheck disable=SC2154
 OPENAI_API_KEY=$openai_api_key \
     OPENAI_ORG_ID="" \
     AZURE_OPENAI_DEPLOYMENT_NAME="" \