Introduce pylint & other improvements on the CI (#2130)

* Make mypy check also ui and rest_api, fix ui

* Remove explicit type packages from extras, mypy now downloads them

* Make pylint and mypy run on every file except tests

* Rename tasks

* Change cache key

* Fix mypy errors in rest_api

* Normalize python versions to avoid cache misses

* Add all exclusions to make pylint pass

* Run mypy on rest_api and ui as well

* test if installing the package really changes outcome

* Comment out installation of packages

* Experiment: randomize tests

* Add fallback installation steps on cache misses

* Remove randomization

* Add comment on cache

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

.github/workflows/linux_ci.yml

@@ -15,6 +15,42 @@ on:
 
 jobs:
 
+  type-check:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          # Mypy can't run properly on 3.7 as it misses support for Literal types.
+          # FIXME once we drop support for 3.7, use the cache.
+          python-version: 3.8
+      - name: Setup mypy
+        run: |
+          # FIXME installing the packages before running mypy raises
+          # a lot of errors which were never detected before!
+          # pip install .
+          # pip install rest_api/
+          # pip install ui/
+
+          # FIXME --install-types does not work properly yet, see https://github.com/python/mypy/issues/10600
+          # Hotfixing by installing type packages explicitly. 
+          # Run mypy --install-types haystack locally to ensure the list is still up to date
+          # mypy --install-types --non-interactive .
+
+          pip install mypy pydantic types-Markdown types-PyYAML types-requests types-setuptools types-six types-tabulate types-chardet types-emoji types-protobuf
+
+      - name: Test with mypy
+        run: |
+          echo "=== haystack/ ==="
+          mypy haystack
+
+          echo "=== rest_api/ ==="
+          mypy rest_api --exclude=rest_api/build/ --exclude=rest_api/test/
+
+          echo "=== ui/ ==="
+          mypy ui --exclude=ui/build/ --exclude=ui/test/
+
+
   build-cache:
     runs-on: ubuntu-20.04
     steps:
@@ -31,7 +67,7 @@ jobs:
         with:
           path: ${{ env.pythonLocation }}
           # The cache will be rebuild every day and at every change of the dependency files
-          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github') }}
+          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}
 
       - name: Install dependencies
         if: steps.cache-python-env.outputs.cache-hit != 'true'
@@ -41,17 +77,9 @@ jobs:
           pip install rest_api/
           pip install ui/
           pip install torch-scatter -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
+          echo "=== pip freeze ==="
+          pip freeze
 
-  prepare-build:
-    needs: build-cache
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v2
-      - id: set-matrix
-        run: |
-          echo "::set-output name=matrix::$(find $(find . -type d -name test -not -path "./*env*/*") -type f -name test_*.py | jq -SR . | jq -cs .)"
-    outputs:
-      matrix: ${{ steps.set-matrix.outputs.matrix }}
 
   code-and-docs-updates:
     needs: build-cache
@@ -75,11 +103,24 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github') }}
+          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}
+
+      - name: Install Dependencies (on cache miss only)
+        # The cache might miss during the execution of an action: there should always be a fallback step to
+        # rebuild it in case it goes missing
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pip install --upgrade pip
+          pip install .[test]
+          pip install rest_api/
+          pip install ui/
+          pip install torch-scatter -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
+          echo "=== pip freeze ==="
+          pip freeze
           
-      # Apply black on the entire codebase
+      # Apply Black on the entire codebase
       - name: Blacken
-        run: python3 -m black .
+        run: black .
 
       # Convert the Jupyter notebooks into markdown tutorials
       - name: Generate Tutorials
@@ -120,7 +161,8 @@ jobs:
           git status
           git push
 
-  type-check:
+
+  linter:
     needs: code-and-docs-updates
     runs-on: ubuntu-20.04
     steps:
@@ -129,23 +171,53 @@ jobs:
       - run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.7
 
       - name: Cache Python
         uses: actions/cache@v2
         with:
           path: ${{ env.pythonLocation }}
-          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github') }}
+          key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}
 
-      - name: Test with mypy
-        run: mypy haystack
+      - name: Install Dependencies (on cache miss only)
+        # The cache might miss during the execution of an action: there should always be a fallback step to
+        # rebuild it in case it goes missing
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pip install --upgrade pip
+          pip install .[test]
+          pip install rest_api/
+          pip install ui/
+          pip install torch-scatter -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
+          echo "=== pip freeze ==="
+          pip freeze
 
-  build:
-    needs: prepare-build
+      - name: Linter
+        run: |
+          pylint -ry haystack/
+          pylint -ry rest_api/
+          pylint -ry ui/
+
+
+  prepare-matrix:
+    needs: build-cache
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - id: set-matrix
+        run: |
+          find $(find . -type d -name test -not -path "./*env*/*") -type f -name test_*.py | jq -SR . | jq -cs .
+          echo "::set-output name=matrix::$(find $(find . -type d -name test -not -path "./*env*/*") -type f -name test_*.py | jq -SR . | jq -cs .)"
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+
+
+  tests:
+    needs: prepare-matrix
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        test-path: ${{fromJson(needs.prepare-build.outputs.matrix)}}
+        test-path: ${{fromJson(needs.prepare-matrix.outputs.matrix)}}
       fail-fast: false
 
     steps:
@@ -161,7 +233,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.pythonLocation }}
-        key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}-${{ hashFiles('.github') }}
+        key: linux-${{ env.date }}-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/setup.cfg') }}-${{ hashFiles('**/pyproject.toml') }}
 
     - name: Run Elasticsearch
       run: docker run -d -p 9200:9200 -e "discovery.type=single-node" -e "ES_JAVA_OPTS=-Xms128m -Xmx128m" elasticsearch:7.9.2
@@ -190,11 +262,26 @@ jobs:
     - name: Install tesseract
       run: sudo apt-get install tesseract-ocr libtesseract-dev poppler-utils
 
+    - name: Install Dependencies (on cache miss only)
+      # The cache might miss during the execution of an action: there should always be a fallback step to
+      # rebuild it in case it goes missing
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: |
+        pip install --upgrade pip
+        pip install .[test]
+        pip install rest_api/
+        pip install ui/
+        pip install torch-scatter -f https://data.pyg.org/whl/torch-1.10.0+cpu.html
+        echo "=== pip freeze ==="
+        pip freeze
+
+    # Haystack needs to be reinstalled at this stage to make sure the current commit's version is the one getting tested.
+    # The cache can last way longer than a specific action's run, so older Haystack version could be carried over.
     - name: Reinstall Haystack
       run: |
         pip install .[test]
         pip install rest_api/
-        pip install eager ui/
+        pip install ui/
 
     - name: Run tests
       run: pytest -s ${{ matrix.test-path }}

pyproject.toml

@@ -20,7 +20,93 @@ disable = [
   "fixme",
   "protected-access",
   "too-few-public-methods",
-  "raise-missing-from"
+  "raise-missing-from",
+
+  "invalid-name",
+  "logging-fstring-interpolation",
+  "wrong-import-position",
+  "too-many-locals",
+  "duplicate-code",
+  "too-many-arguments",
+  "arguments-differ",
+  "wrong-import-order",
+  "consider-using-f-string",
+  "no-else-return",
+  "unused-variable",
+  "attribute-defined-outside-init",
+  "too-many-instance-attributes",
+  "no-self-use",
+  "super-with-arguments",
+  "anomalous-backslash-in-string",
+  "redefined-builtin",
+  "logging-format-interpolation",
+  "f-string-without-interpolation",
+  "abstract-method",
+  "too-many-branches",
+  "trailing-whitespace",
+  "unspecified-encoding",
+  "unidiomatic-typecheck",
+  "no-name-in-module",
+  "dangerous-default-value",
+  "unused-import",
+  "consider-using-with",
+  "redefined-outer-name",
+  "cyclic-import",
+  "arguments-renamed",
+  "unnecessary-pass",
+  "ungrouped-imports",
+  "broad-except",
+  "unnecessary-comprehension",
+  "subprocess-run-check",
+  "singleton-comparison",
+  "no-else-raise",
+  "import-outside-toplevel",
+  "consider-iterating-dictionary",
+  "too-many-nested-blocks",
+  "undefined-loop-variable",
+  "too-many-statements",
+  "consider-using-in",
+  "bare-except",
+  "too-many-lines",
+  "unexpected-keyword-arg",
+  "simplifiable-if-expression",
+  "use-list-literal",
+  "reimported",
+  "no-else-continue",
+  "deprecated-method",
+  "consider-using-dict-items",
+  "use-a-generator",
+  "simplifiable-if-statement",
+  "import-error",
+  "consider-using-from-import",
+  "useless-object-inheritance",
+  "use-dict-literal",
+  "unsubscriptable-object",
+  "too-many-return-statements",
+  "superfluous-parens",
+  "no-value-for-parameter",
+  "no-else-break",
+  "inconsistent-return-statements",
+  "consider-using-set-comprehension",
+  "c-extension-no-member",
+  "useless-super-delegation",
+  "useless-else-on-loop",
+  "used-before-assignment",
+  "unsupported-membership-test",
+  "unneeded-not",
+  "unnecessary-lambda",
+  "trailing-newlines",
+  "too-many-boolean-expressions",
+  "super-init-not-called",
+  "pointless-string-statement",
+  "non-parent-init-called",
+  "invalid-sequence-index",
+  "import-self",
+  "deprecated-argument",
+  "access-member-before-definition",
+
+  "invalid-envvar-default",
+  "logging-too-many-args",
 ]
 [tool.pylint.'DESIGN']
 max-args=7

rest_api/application.py

@@ -42,11 +42,11 @@ def get_openapi_specs() -> dict:
     """
     app = get_application()
     return get_openapi(
-        title=app.title if app.title else None,
-        version=app.version if app.version else None,
-        openapi_version=app.openapi_version if app.openapi_version else None,
-        description=app.description if app.description else None,
-        routes=app.routes if app.routes else None,
+        title=app.title,
+        version=app.version,
+        openapi_version=app.openapi_version,
+        description=app.description,
+        routes=app.routes,
     )
 
 

rest_api/controller/feedback.py

@@ -1,3 +1,5 @@
+from typing import Dict, Union, Optional
+
 import json
 import logging
 
@@ -40,8 +42,8 @@ def get_feedback():
 @router.post("/eval-feedback")
 def get_feedback_metrics(filters: FilterRequest = None):
     """
-    This endpoint returns basic accuracy metrics based on user feedback, 
-    e.g., the ratio of correct answers or correctly identified documents. 
+    This endpoint returns basic accuracy metrics based on user feedback,
+    e.g., the ratio of correct answers or correctly identified documents.
     You can filter the output by document or label.
 
     Example:
@@ -51,13 +53,14 @@ def get_feedback_metrics(filters: FilterRequest = None):
     """
 
     if filters:
-        filters = filters.filters
-        filters["origin"] = ["user-feedback"]
+        filters_content = filters.filters or {}
+        filters_content["origin"] = ["user-feedback"]
     else:
-        filters = {"origin": ["user-feedback"]}
+        filters_content = {"origin": ["user-feedback"]}
 
-    labels = DOCUMENT_STORE.get_all_labels(filters=filters)
+    labels = DOCUMENT_STORE.get_all_labels(filters=filters_content)
 
+    res: Dict[str, Optional[Union[float, int]]]
     if len(labels) > 0:
         answer_feedback = [1 if l.is_correct_answer else 0 for l in labels]
         doc_feedback = [1 if l.is_correct_document else 0 for l in labels]

rest_api/controller/file_upload.py

@@ -1,10 +1,11 @@
+from typing import Optional, List, Union
+
 import json
 import logging
 import os
 import shutil
 import uuid
 from pathlib import Path
-from typing import Optional, List
 
 from fastapi import APIRouter, UploadFile, File, Form, HTTPException, Depends
 from pydantic import BaseModel
@@ -48,7 +49,8 @@ except KeyError:
     logger.warning("Indexing Pipeline not found in the YAML configuration. File Upload API will not be available.")
 
 
-os.makedirs(FILE_UPLOAD_PATH, exist_ok=True)  # create directory for uploading files
+# create directory for uploading files
+os.makedirs(FILE_UPLOAD_PATH, exist_ok=True)
 
 
 @as_form
@@ -75,9 +77,10 @@ class Response(BaseModel):
 @router.post("/file-upload")
 def upload_file(
     files: List[UploadFile] = File(...),
-    meta: Optional[str] = Form("null"),  # JSON serialized string
-    fileconverter_params: FileConverterParams = Depends(FileConverterParams.as_form),
-    preprocessor_params: PreprocessorParams = Depends(PreprocessorParams.as_form),
+    # JSON serialized string
+    meta: Optional[str] = Form("null"),  # type: ignore
+    fileconverter_params: FileConverterParams = Depends(FileConverterParams.as_form),  # type: ignore
+    preprocessor_params: PreprocessorParams = Depends(PreprocessorParams.as_form),  # type: ignore
 ):
     """
     You can use this endpoint to upload a file for indexing
@@ -88,7 +91,7 @@ def upload_file(
 
     file_paths: list = []
     file_metas: list = []
-    meta = json.loads(meta) or {}
+    meta_form = json.loads(meta)  # type: ignore
 
     for file in files:
         try:
@@ -97,8 +100,8 @@ def upload_file(
                 shutil.copyfileobj(file.file, buffer)
 
             file_paths.append(file_path)
-            meta["name"] = file.filename
-            file_metas.append(meta)
+            meta_form["name"] = file.filename
+            file_metas.append(meta_form)
         finally:
             file.file.close()
 

rest_api/controller/utils.py

@@ -44,6 +44,6 @@ def as_form(cls: Type[BaseModel]):
 
     sig = inspect.signature(_as_form)
     sig = sig.replace(parameters=new_params)
-    _as_form.__signature__ = sig
+    _as_form.__signature__ = sig  # type: ignore
     setattr(cls, "as_form", _as_form)
     return cls

rest_api/schema.py

@@ -35,7 +35,7 @@ class AnswerSerialized(Answer):
 @pydantic_dataclass
 class DocumentSerialized(Document):
     content: str
-    embedding: Optional[List[float]]
+    embedding: Optional[List[float]]  # type: ignore
 
 
 @pydantic_dataclass

rest_api/setup.py

@@ -3,7 +3,7 @@ import logging
 from pathlib import Path
 
 
-VERSION = None
+VERSION = "0.0.0"
 try:
     VERSION = open(Path(__file__).parent.parent / "VERSION.txt", "r").read()
 except Exception as e:

rest_api/test/test_rest_api.py

@@ -42,7 +42,6 @@ def exclude_no_answer(responses):
     return responses
 
 
-@pytest.mark.elasticsearch
 @pytest.fixture(scope="session")
 def client() -> TestClient:
     os.environ["PIPELINE_YAML_PATH"] = str(
@@ -55,7 +54,6 @@ def client() -> TestClient:
     client.post(url="/documents/delete_by_filters", data='{"filters": {}}')
 
 
-@pytest.mark.elasticsearch
 @pytest.fixture(scope="session")
 def populated_client(client: TestClient) -> TestClient:
     client.post(url="/documents/delete_by_filters", data='{"filters": {}}')

setup.cfg

@@ -154,9 +154,7 @@ colab =
 dev = 
     # Type check
     mypy
-    types-Markdown 
-    types-requests 
-    types-PyYAML 
+    typing_extensions; python_version < '3.8'
     # Test
     pytest
     responses

ui/setup.py

@@ -3,7 +3,7 @@ import logging
 from pathlib import Path
 
 
-VERSION = None
+VERSION = "0.0.0"
 try:
     # After git clone, VERSION.txt is in the root folder
     VERSION = open(Path(__file__).parent.parent / "VERSION.txt", "r").read()

ui/utils.py

@@ -1,4 +1,4 @@
-from typing import List, Dict, Any, Tuple
+from typing import List, Dict, Any, Tuple, Optional
 
 import os
 import logging
@@ -112,7 +112,7 @@ def upload_doc(file):
     return response
 
 
-def get_backlink(result) -> Tuple[str, str]:
+def get_backlink(result) -> Tuple[Optional[str], Optional[str]]:
     if result.get("document", None):
         doc = result["document"]
         if isinstance(doc, dict):