Merge branch 'main' into feature/docker-integration

.github/workflows/build-docs.yaml

@@ -15,12 +15,12 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
       #----------------------------------------------
       #  -----  install & configure poetry  -----
       #----------------------------------------------
@@ -35,7 +35,7 @@ jobs:
       #----------------------------------------------
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}

.github/workflows/publish.yaml

@@ -17,12 +17,12 @@ jobs:
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       #----------------------------------------------
       #  -----  install & configure poetry  -----
       #----------------------------------------------

.github/workflows/pytest.yaml

@@ -9,7 +9,8 @@ jobs:
       matrix:
         python-version:
         - "3.10"  # Earliest version supported by ixmp4
-        - "3.11"  # Latest version supported by ixmp4
+        - "3.11"
+        - "3.12"  # Latest version supported by ixmp4
 
     runs-on: ubuntu-latest
     services:
@@ -34,7 +35,7 @@ jobs:
         uses: actions/checkout@v4
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       #----------------------------------------------
@@ -51,7 +52,7 @@ jobs:
       #----------------------------------------------
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
@@ -81,8 +82,8 @@ jobs:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       #----------------------------------------------
       #  -----  install & configure poetry  -----
       #----------------------------------------------
@@ -97,7 +98,7 @@ jobs:
       #----------------------------------------------
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}

.pre-commit-config.yaml

@@ -1,15 +1,13 @@
 repos:
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.6.1
+  rev: v1.8.0
   hooks:
   - id: mypy
     entry: bash -c "poetry run mypy ."
     language: system
-- repo: https://github.com/psf/black
-  rev: 23.12.1
-  hooks:
-  - id: black
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.11
+  rev: v0.2.1
   hooks:
-  - id: ruff
+  - id: ruff
+  - id: ruff-format
+    args: [ --check ]

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"

DEVELOPING.md

@@ -207,7 +207,7 @@ alembic revision -m "<message>" --autogenerate
 ```
 
 You will have to run all migrations before being able to create new ones in the development database.
-Be sure to run `black` and `isort` on newly created migrations!
+Be sure to run `ruff` on newly created migrations!
 
 ## Tests
 
@@ -322,7 +322,7 @@ It is overwritten on the fly by the poetry-dynamic-versioning plugin.
 
 Contributions to the code are always welcome! Please make sure your code follows our 
 code style so that the style is consistent. Each PR will be checked by a Code Quality 
-test that examines compliance with black, ruff, and mypy. 
+test that examines compliance with ruff and mypy. 
 
 ### Running pre-commit locally
 
@@ -340,7 +340,7 @@ on changed files, but if you want to run it on all files, you can run
 pre-commit run --all-files
 ```
 
-If you only want certain hooks to run, choose from `ruff`, `black`, and `mypy` as 
+If you only want certain hooks to run, choose from `ruff` and `mypy` as 
 `hook-ids` and run
 
 ```bash
@@ -354,16 +354,15 @@ are the same. You can, of course, run the code style tools manually. From within
 ixmp4 directory, this would look similar to this:
 
 ```bash
-black .
 mypy .
 ruff check .
+ruff format .
 
 # Or to enable ruff's automic fixes
 ruff check --fix .
 ```
 
 However, it is easy to forget running these commands manually. Therefore, we recommend 
-setting your editor up to run at least 
-[black](https://black.readthedocs.io/en/stable/integrations/editors.html) and 
-[ruff](https://docs.astral.sh/ruff/usage/#vs-code) automatically whenever you hit 
-`save`. A few minutes of configuration will save you time and nerves later on.
+setting your editor up to run at least [ruff](https://docs.astral.sh/ruff/usage/#vs-code) 
+automatically whenever you hit `save`. A few minutes of configuration will save you time 
+and nerves later on.

README.md

@@ -3,8 +3,8 @@
 Copyright (c) 2023-2024 IIASA - Energy, Climate, and Environment Program (ECE)
 
 [![license: MIT](https://img.shields.io/badge/license-MIT-brightgreen.svg)](https://github.com/iiasa/ixmp4/blob/main/LICENSE)
-[![python](https://img.shields.io/badge/python-3.10_|_3.11-blue?logo=python&logoColor=white)](https://github.com/iiasa/ixmp4)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![python](https://img.shields.io/badge/python-3.10_|_3.11_|_3.12-blue?logo=python&logoColor=white)](https://github.com/iiasa/ixmp4)
+[![Code style: ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 ## Overview
 

doc/source/index.rst

@@ -3,15 +3,15 @@ The ixmp4 package for scenario data management
 
 Copyright © 2023-2024 IIASA - Energy, Climate, and Environment Program (ECE)
 
-|license| |black| |python|
+|license| |ruff| |python|
 
 .. |license| image:: https://img.shields.io/badge/license-MIT-brightgreen
    :target: https://github.com/iiasa/ixmp4/blob/main/LICENSE
 
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-   :target: https://github.com/psf/black
+.. |ruff| image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json
+   :target: https://github.com/astral-sh/ruff
 
-.. |python| image:: https://img.shields.io/badge/python-3.10_|_3.11-blue?logo=python&logoColor=white
+.. |python| image:: https://img.shields.io/badge/python-3.10_|_3.11_|_3.12-blue?logo=python&logoColor=white
    :target: https://github.com/iiasa/ixmp4
 
 Overview

ixmp4/cli/platforms.py

@@ -97,8 +97,7 @@ def prompt_sqlite_removal(dsn: str):
     path = Path(dsn.replace("sqlite://", ""))
     path_str = typer.style(path, fg=typer.colors.CYAN)
     if typer.confirm(
-        "Do you want to remove the associated database file at "
-        f"{path_str} aswell?"  # type: ignore
+        "Do you want to remove the associated database file at " f"{path_str} as well?"  # type: ignore
     ):
         path.unlink()
         utils.echo("\nDatabase file deleted.")
@@ -110,7 +109,7 @@ def prompt_sqlite_removal(dsn: str):
 def remove(
     name: str = typer.Argument(
         ..., help="The string identifier of the platform to remove."
-    )
+    ),
 ):
     try:
         platform = settings.toml.get_platform(name)

ixmp4/data/api/iamc/datapoint.py

@@ -39,7 +39,7 @@ def list(
         self,
         join_parameters: bool | None = None,
         join_runs: bool | None = None,
-        **kwargs
+        **kwargs,
     ) -> list[DataPoint]:
         return super()._list(
             json=kwargs,
@@ -53,7 +53,7 @@ def tabulate(
         self,
         join_parameters: bool | None = None,
         join_runs: bool | None = None,
-        **kwargs
+        **kwargs,
     ) -> pd.DataFrame:
         return super()._tabulate(
             json=kwargs,

ixmp4/data/backend/base.py

@@ -40,3 +40,7 @@ def __init__(self, info: PlatformInfo) -> None:
         self.info = info
         self.iamc = IamcSubobject()
         self.optimization = OptimizationSubobject()
+
+    def close(self) -> None:
+        """Closes the connection to the database."""
+        ...

ixmp4/data/db/base.py

@@ -1,6 +1,6 @@
 import logging
 import sqlite3
-from datetime import datetime
+from datetime import datetime, timezone
 from typing import (
     TYPE_CHECKING,
     Any,
@@ -116,7 +116,10 @@ def get(self, *args, **kwargs) -> ModelType:
 
 class Creator(BaseRepository[ModelType], abstract.Creator):
     def get_creation_info(self) -> dict:
-        info = {"created_at": datetime.utcnow(), "created_by": "@unknown"}
+        info = {
+            "created_at": datetime.now(tz=timezone.utc),
+            "created_by": "@unknown",
+        }
         if self.backend.auth_context is not None:
             info["created_by"] = self.backend.auth_context.user.username
         return info
@@ -236,9 +239,7 @@ def tabulate(
 
         if self.session.bind is not None:
             with self.engine.connect() as con:
-                return (
-                    pd.read_sql(_exc, con=con).fillna(np.nan).replace([np.nan], [None])
-                )
+                return pd.read_sql(_exc, con=con).replace([np.nan], [None])
         else:
             raise ProgrammingError("Database session is closed.")
 

ixmp4/data/db/iamc/datapoint/repository.py

@@ -163,7 +163,7 @@ def select(
         join_runs: bool = False,
         _filter: DataPointFilter | None = None,
         _exc: db.sql.Select | None = None,
-        **kwargs: Any
+        **kwargs: Any,
     ) -> db.sql.Select:
         if _exc is not None:
             exc = _exc

ixmp4/data/db/timeseries.py

@@ -94,7 +94,7 @@ def select(
         *,
         _exc: db.sql.Select | None = None,
         join_parameters: bool | None = False,
-        **kwargs
+        **kwargs,
     ) -> db.sql.Select:
         if _exc is not None:
             exc = _exc

ixmp4/db/filters.py

@@ -192,11 +192,11 @@ def process_field(cls, namespace: dict, field_name: str, field_type: type):
                 )
         else:
             override_lookups = None
-        if override_lookups:
+        if isinstance(override_lookups, list):
             lookups = {k: v for k, v in lookups.items() if k in override_lookups}
         elif override_lookups is None:
             pass
-        else:
+        else:  # TODO (How) do we ensure the type of override_lookups?
             lookups = {}
         base_field_alias = str(field.alias) if field.alias else field_name
 

ixmp4/server/rest/__init__.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import datetime, timezone
 
 from fastapi import Depends, FastAPI, Path, Request
 from fastapi.encoders import jsonable_encoder
@@ -69,7 +69,7 @@ def root(
         version=version,
         is_managed=settings.managed,
         manager_url=str(settings.manager_url),
-        utcnow=datetime.utcnow(),
+        utcnow=datetime.now(tz=timezone.utc),
     )
 
 

ixmp4/server/rest/base.py

@@ -33,7 +33,7 @@ def __init__(
         __pydantic_self__,
         *args,
         results: pd.DataFrame | api.DataFrame | list[EnumeratedT],
-        **kwargs
+        **kwargs,
     ):
         if isinstance(results, pd.DataFrame):
             kwargs["results"] = api.DataFrame.model_validate(results)