Release/1.0.2 (#2)

* type checking, ruff checking, and ruff formatting

* add in Changelog changes for this release

* finish with a newline

---------

Co-authored-by: Grant, Josh <grantjn@ornl.gov>

Author: sempervent

.github/workflows/lint.yml

@@ -19,3 +19,15 @@ jobs:
       - uses: astral-sh/ruff-action@v3
         with:
           args: format --check
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.7.3"
+      - name: Set up Python
+        run: uv python install
+      - name: Sync project, including dev dependencies
+        run: uv sync
+      - name: Build static content
+        run: |
+          uv run python ./scripts/gen_api_docs.py
+          uv run mkdocs build --clean

CHANGELOG.md

@@ -62,3 +62,14 @@ This project adheres to [Semantic Versioning](https://semver.org/).
 - 🗡️ Remove kwargs in `__init__` method of `BaseProbe`
 - 🗡️ Remove unused imports from many files
 - 🗡️ Remove commented-out code in some classes
+
+## [1.0.2] - 2025-05-12
+### Added
+- 🔥 `black` added as a dependency for auto-creation of probe types
+- 🔥 `ty` added as a dependency for type-checking
+
+### Fixed
+- 🩹 `ty` type checking errors addressed
+
+### Changed
+- ⚡ linting github action now confirms that the documentation can be built

opensampl/cli.py

@@ -8,7 +8,7 @@
 import json
 import sys
 from pathlib import Path
-from typing import Optional, Union
+from typing import Literal, Optional, Union
 
 import click
 import yaml
@@ -34,7 +34,7 @@
 
 env_file = find_dotenv()
 load_dotenv()
-level = ENV_VARS.LOG_LEVEL.get_value()
+level = str(ENV_VARS.LOG_LEVEL.get_value())
 logger.configure(handlers=[{"sink": sys.stderr, "level": level.upper()}])
 
 
@@ -128,7 +128,7 @@ def show(explain: bool, var: str):
 @config.command("set")
 @click.argument("name")
 @click.argument("value")
-def config_set(name: str, value: str, temp: Optional[bool] = None):
+def config_set(name: str, value: str):
     """
     Set the value of an environment variable.
 
@@ -140,7 +140,7 @@ def config_set(name: str, value: str, temp: Optional[bool] = None):
         opensampl config set BACKEND_URL http://localhost:8000
 
     """
-    set_env(name=name, value=value, temp=temp)
+    set_env(name=name, value=value)
 
 
 @cli.group(cls=CaseInsensitiveGroup)
@@ -188,7 +188,9 @@ def path_or_string(value: str) -> Union[dict, list]:
 )
 @click.argument("table_name", type=click.Choice(get_table_names()))
 @click.argument("filepath", type=path_or_string)
-def table_load(filepath: Union[dict, list], table_name: str, if_exists: str):
+def table_load(
+    filepath: Union[dict, list], table_name: str, if_exists: Literal["update", "error", "replace", "ignore"]
+):
     r"""
     Perform a Table load into the database.
 

opensampl/constants.py

@@ -1,8 +1,9 @@
 """Constants for accessing environment configurations"""
 
 import os
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any, Optional, Union
 
 from pydantic import BaseModel
 
@@ -12,23 +13,23 @@ class EnvVar(BaseModel):
 
     name: str
     description: str
-    type: type = str
+    type_: type = str
     default: Optional[Any] = None
 
-    def get_value(self):
+    def get_value(self) -> Optional[Union[str, bool, Path]]:
         """Get value of var in environment"""
         default = self.resolve_default()
-        if self.type is bool:
+        if self.type_ is bool:
             return os.getenv(self.name, default).lower() == "true"
-        if self.type is Path:
+        if self.type_ is Path:
             return Path(os.getenv(self.name, default))
         return os.getenv(self.name, default)
 
-    def resolve_default(self):
+    def resolve_default(self) -> Optional[Union[str, bool, Path]]:
         """Resolve default value for env var based on type"""
-        if self.type is bool:
+        if self.type_ is bool:
             return self.default or "false"
-        if self.type is Path and self.default is not None:
+        if self.type_ is Path and self.default is not None:
             return Path(self.default).resolve()
         return self.default
 
@@ -41,7 +42,7 @@ class ENV_VARS:  # noqa: N801
         description=(
             "Route all database operations through BACKEND_URL rather than applying directly using DATABASE_URL"
         ),
-        type=bool,
+        type_=bool,
     )
     BACKEND_URL = EnvVar(
         name="BACKEND_URL",
@@ -54,7 +55,7 @@ class ENV_VARS:  # noqa: N801
     ARCHIVE_PATH = EnvVar(
         name="ARCHIVE_PATH",
         description="Default path that files are moved to after they have been processed",
-        type=Path,
+        type_=Path,
         default="archive",
     )
     LOG_LEVEL = EnvVar(
@@ -68,7 +69,7 @@ class ENV_VARS:  # noqa: N801
     )
 
     @classmethod
-    def __iter__(cls) -> iter:
+    def __iter__(cls) -> Iterator[EnvVar]:
         """Get all EnvVar objects as iterable"""
         yield from (value for key, value in cls.__dict__.items() if isinstance(value, EnvVar))
 

opensampl/db/orm.py

@@ -2,7 +2,7 @@
 
 import uuid
 from datetime import datetime
-from typing import Any
+from typing import Any, Optional
 
 from geoalchemy2 import Geometry, WKTElement
 from geoalchemy2.shape import to_shape
@@ -101,7 +101,7 @@ class ProbeMetadata(Base):
     probe_data = relationship("ProbeData")
     adva_metadata = relationship("AdvaMetadata", back_populates="probe", uselist=False)
 
-    def __init__(self, **kwargs: dict):
+    def __init__(self, **kwargs: Any):
         """Initialize Probe Metadata object, dealing with converting location name into uuid"""
         location_name = kwargs.pop("location_name", None)
         test_name = kwargs.pop("test_name", None)
@@ -112,7 +112,7 @@ def __init__(self, **kwargs: dict):
         if test_name:
             self._test_name = test_name
 
-    def resolve_references(self, session: Session = None):
+    def resolve_references(self, session: Optional[Session] = None):
         """
         Resolve references.
 

opensampl/helpers/create_vendor.py

@@ -69,7 +69,7 @@ def generate_default_fields(cls, data: Any) -> Any:
         fields = []
         for field, sql_type in metadata_fields.items():
             if sql_type:
-                fields.append(MetadataField(name=field, type=sql_type))
+                fields.append(MetadataField(name=field, sqlalchemy_type=sql_type))
             else:
                 fields.append(MetadataField(name=field))
         data["metadata_fields"] = fields
@@ -239,7 +239,8 @@ def update_constants(self):
 
         file_text = constants_path.read_text()
         tree = ast.parse(file_text)
-
+        vm_lineno = None
+        vm_end_lineno = None
         for _, node in enumerate(tree.body):
             if (
                 isinstance(node, ast.Assign)

opensampl/helpers/source_writer.py

@@ -1,5 +1,7 @@
 """Helper for writing new source code based on new Vendor Configuration"""
 
+from typing import Any
+
 import astor
 import libcst as cst
 from black import FileMode, format_str
@@ -54,7 +56,7 @@ def leave_ClassDef(  # noqa: N802
         return updated_node.with_changes(body=updated_node.body.with_changes(body=body))
 
     @classmethod
-    def format(cls, tree: cst.Module) -> cst.Module:
+    def format(cls, tree: Any) -> cst.Module:
         """Convert back to source, use black to format"""
         source = format_str(
             astor.to_source(tree),

opensampl/load_data.py

@@ -6,6 +6,7 @@
 
 import pandas as pd
 import requests
+import requests.exceptions
 from loguru import logger
 from sqlalchemy import UniqueConstraint, and_, create_engine, inspect, text
 from sqlalchemy.orm import Session, sessionmaker
@@ -32,7 +33,7 @@ def route_or_direct(route_endpoint: str, method: request_methods = "POST", send_
 
     def decorator(func: Callable) -> Callable:
         @wraps(func)
-        def wrapper(*args: list, **kwargs: dict) -> Callable:
+        def wrapper(*args: list, **kwargs: dict) -> Optional[Callable]:
             session = kwargs.pop("session", None)
             backend_url = ENV_VARS.BACKEND_URL.get_value()
             route_to_backend = ENV_VARS.ROUTE_TO_BACKEND.get_value()
@@ -80,7 +81,7 @@ def wrapper(*args: list, **kwargs: dict) -> Callable:
                             "Provide Session or Set DATABASE_URL env var to use direct database operations or set "
                             "ROUTE_TO_BACKEND to true and configure BACKEND_URL to use backend routing"
                         )
-                    session = sessionmaker(create_engine(database_url))()
+                    session = sessionmaker(create_engine(database_url))()  # ty: ignore[no-matching-overload]
 
                 return func(*args, **kwargs, session=session)
 
@@ -116,6 +117,8 @@ def write_to_table(
         SQLAlchemyError: For database errors
 
     """
+    if not isinstance(session, Session):
+        raise TypeError("Session must be a SQLAlchemy session")
     if if_exists not in ["error", "replace", "update", "ignore"]:
         raise ValueError("on_conflict must be one of: 'error', 'replace', 'update', 'ignore'")
 
@@ -202,7 +205,7 @@ def build_pk_conditions(
     return pk_conditions
 
 
-def extract_unique_constraints(inspector: inspect, data: dict[str, Any]):
+def extract_unique_constraints(inspector: Any, data: dict[str, Any]):
     """
     Identify unique constraints that can be used to match existing entries.
 
@@ -248,17 +251,19 @@ def find_existing_entry(
 
     """
     if pk_conditions:
-        existing = session.query(TableModel).filter(and_(*pk_conditions)).first()
+        existing = session.query(TableModel).filter(and_(*pk_conditions)).first()  # ty: ignore[missing-argument]
         if existing:
             return existing
 
     all_constraints = []
     for constraint_columns in unique_constraints:
-        constraint_condition = and_(*(getattr(TableModel, col) == val for col, val in constraint_columns))
+        constraint_condition = and_(  # ty: ignore[missing-argument]
+            *(getattr(TableModel, col) == val for col, val in constraint_columns)
+        )
         all_constraints.append(constraint_condition)
 
     if all_constraints:
-        return session.query(TableModel).filter(and_(*all_constraints)).first()
+        return session.query(TableModel).filter(and_(*all_constraints)).first()  # ty: ignore[missing-argument]
 
     return None
 
@@ -268,7 +273,7 @@ def handle_existing_entry(  # noqa: PLR0913
     TableModel,  # noqa: N803, ANN001
     data: dict[str, Any],
     pk_columns: list[str],
-    inspector: inspect,
+    inspector: Any,
     if_exists: conflict_actions,
     session: Optional[Session],
 ):
@@ -322,6 +327,8 @@ def handle_existing_entry(  # noqa: PLR0913
 @route_or_direct("load_time_data", send_file=True)
 def load_time_data(probe_key: ProbeKey, data: pd.DataFrame, session: Optional[Session] = None):
     """Load time series data"""
+    if not isinstance(session, Session):
+        raise TypeError("Session must be a SQLAlchemy session")
     route_to_backend = ENV_VARS.ROUTE_TO_BACKEND.get_value()
     if route_to_backend:
         csv_data = data.to_csv(index=False).encode("utf-8")
@@ -352,7 +359,7 @@ def load_time_data(probe_key: ProbeKey, data: pd.DataFrame, session: Optional[Se
         # Ensure correct dtypes
         df = df.astype({"time": "datetime64[ns]", "value": "float64", "probe_uuid": str})
 
-        dtype = {column.name: column.type for column in ProbeData.__table__.columns}
+        dtype = {column.name: column.type_ for column in ProbeData.__table__.columns}
 
         # Write directly to database using pandas
         df.to_sql(
@@ -380,6 +387,8 @@ def load_probe_metadata(
     session: Optional[Session] = None,
 ):
     """Write object to table"""
+    if not isinstance(session, Session):
+        raise TypeError("Session must be a SQLAlchemy session")
     route_to_backend = ENV_VARS.ROUTE_TO_BACKEND.get_value()
     if route_to_backend:
         return {
@@ -419,6 +428,8 @@ def load_probe_metadata(
 @route_or_direct("create_new_tables", method="GET")
 def create_new_tables(create_schema: bool = True, session: Optional[Session] = None):
     """Use the ORM definition to create all tables, optionally creating the schema as well"""
+    if not isinstance(session, Session):
+        raise TypeError("Session must be a SQLAlchemy session")
     route_to_backend = ENV_VARS.ROUTE_TO_BACKEND.get_value()
     if route_to_backend:
         return {"create_schema": create_schema}

opensampl/server/cli.py

@@ -7,6 +7,7 @@
 import shlex
 import subprocess
 import sys
+from typing import TextIO, cast
 
 import click
 from dotenv import load_dotenv
@@ -51,7 +52,7 @@ def get_cast_compose_file():
         with pkg_resources.path("opensampl.server", filename) as path:
             return str(path)
     except ImportError:
-        click.echo("Error: docker-compose.yaml file not found in package.", error=True)
+        click.echo("Error: docker-compose.yaml file not found in package.", err=True)
         sys.exit(1)
 
 
@@ -89,10 +90,10 @@ def up(env_file: click.Path | str, extra_args: list):
 
     logger.debug(f"Running: {command}")
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)  # noqa: S603
-
-    for line in process.stdout:
-        print(line, end="")  # noqa: T201 Print each line as it arrives
-
+    stdout = cast("TextIO", process.stdout)
+    if stdout:
+        for line in stdout:
+            print(line, end="")  # noqa: T201 Print each line as it arrives
     process.wait()
 
     set_env(name="BACKEND_URL", value="http://localhost:8015")
@@ -122,9 +123,10 @@ def down(env_file: click.Path, extra_args: list) -> None:
     if extra_args:
         command.extend(extra_args)
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)  # noqa: S603
-
-    for line in process.stdout:
-        print(line, end="")  # noqa: T201 Print each line as it arrives
+    stdout = cast("TextIO", process.stdout)
+    if stdout:
+        for line in stdout:
+            print(line, end="")  # noqa: T201 Print each line as it arrives
 
     process.wait()
 
@@ -155,10 +157,10 @@ def ps(env_file: click.Path) -> None:
     command = build_docker_compose_base(env_file)
     command.extend(["ps"])
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)  # noqa: S603
-
-    for line in process.stdout:
-        print(line, end="")  # noqa: T201 Print each line as it arrives
-
+    stdout = cast("TextIO", process.stdout)
+    if stdout:
+        for line in stdout:
+            print(line, end="")  # noqa: T201 Print each line as it arrives
     process.wait()
 
 
@@ -178,9 +180,10 @@ def run(env_file: click.Path, run_commands: list) -> None:
     command.extend(list(run_commands))
     logger.info(command)
     process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)  # noqa: S603
-
-    for line in process.stdout:
-        print(line, end="")  # noqa: T201  Print each line as it arrives
+    stdout = cast("TextIO", process.stdout)
+    if stdout:
+        for line in stdout:
+            print(line, end="")  # noqa: T201  Print each line as it arrives
 
     process.wait()