fix logging (#80)

* Update logging code

* Update CHANGELOG

* Fix changelog

CHANGELOG.md

@@ -10,24 +10,29 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+### Fixes
+
+-   Do not change the configuration of the root logger, only the `dso` logger. Changing the root logger
+    had side-effects on other libraries when importing `dso` in Python ([#80](https://github.com/Boehringer-Ingelheim/dso/pull/80)).
+
 ### New Features
 
-- Python API that mirrors `dso-r` functionality (e.g. to be used from Jupyter notebooks) ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
+-   Python API that mirrors `dso-r` functionality (e.g. to be used from Jupyter notebooks) ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
 
 ### Chore
 
-- Refactor CLI into separate module ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
-- Defer imports in CLI until they are actually needed to speed up CLI ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
-- Make all modules explicitly private that are not part of the public API ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
-- Relicense the package as LGPL-3.0-or-later, with an exception for the templates ([#76](https://github.com/Boehringer-Ingelheim/dso/pull/76))
+-   Refactor CLI into separate module ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
+-   Defer imports in CLI until they are actually needed to speed up CLI ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
+-   Make all modules explicitly private that are not part of the public API ([#30](https://github.com/Boehringer-Ingelheim/dso/pull/30))
+-   Relicense the package as LGPL-3.0-or-later, with an exception for the templates ([#76](https://github.com/Boehringer-Ingelheim/dso/pull/76))
 
 ## v0.10.1
 
 ### Fixes
 
 -   Take comments into account when linting for `DSO001` ([#69](https://github.com/Boehringer-Ingelheim/dso/pull/69))
 -   Make it possible to override watermarks/disclaimers with a simple `null` ([#69](https://github.com/Boehringer-Ingelheim/dso/pull/69)).
--   Compile *all* configs on `dso repro`, not just the ones relvant to the specified stage. This is required because we don't
+-   Compile _all_ configs on `dso repro`, not just the ones relvant to the specified stage. This is required because we don't
     know which other stages dvc might compile ([#69](https://github.com/Boehringer-Ingelheim/dso/pull/69)).
 -   Make `get-config` compatible with dvc matrix stages ([#69](https://github.com/Boehringer-Ingelheim/dso/pull/69)).
 
@@ -39,17 +44,19 @@ and this project adheres to [Semantic Versioning][].
 ## v0.10.0
 
 ### Template updates
+
 -   Improve instruction text in quarto template to get users started more quickly ([#40](https://github.com/Boehringer-Ingelheim/dso/pull/40))
 -   Add `.gitignore` catch-all clauses for `output` and `report` folders in stages to not pick up data and repots being tracked via git ([#46](https://github.com/Boehringer-Ingelheim/dso/issues/46)).
 -   Every dso project is now also a [uv project](https://docs.astral.sh/uv/concepts/projects/#building-projects) declaring Python dependencies in `pyproject.toml`. This makes it possible to
     use a different dso version per project and makes it easy to work with virtual Python environments ([#52](https://github.com/Boehringer-Ingelheim/dso/pull/52))
 -   bash templates now include `-euo pipefail` settings, ensuring that stages fail early and return a nonzero error code if something failed ([#59](https://github.com/Boehringer-Ingelheim/dso/pull/59)).
 
 ### Fixes
+
 -   Remove vendored `hiyapyco` code since required changes were released upstream in v0.7.0 ([#45](https://github.com/Boehringer-Ingelheim/dso/pull/45)).
 -   `None` values in `params.in.yaml` can now be used to override anything, e.g. to disable watermarking only in a specific stage ([#45](https://github.com/Boehringer-Ingelheim/dso/pull/45)).
 -   Clean up existing `*.rmarkdown` files in quarto stage before running `quarto render`. This fixes issues with re-running quarto stages that failed in the previous attempt ([#57](https://github.com/Boehringer-Ingelheim/dso/pull/57)).
--   DSO now respects a `DSO_SKIP_CHECK_ASK_PRE_COMMIT` environment variable.  If it is set
+-   DSO now respects a `DSO_SKIP_CHECK_ASK_PRE_COMMIT` environment variable. If it is set
     to anything that evaluates as `True`, we skip the check if pre-commit is installed. This was a
     requirement introduced by the R API package, see [#50](https://github.com/Boehringer-Ingelheim/dso/issues/50) ([#58](https://github.com/Boehringer-Ingelheim/dso/pull/58)).
 -   Improve logging for "missing path" warning during `compile-config` ([#59](https://github.com/Boehringer-Ingelheim/dso/pull/59)).

src/dso/_logging.py

@@ -1,13 +1,12 @@
-from logging import basicConfig, getLogger
+from logging import Formatter, getLogger
 
 from rich.console import Console
 from rich.logging import RichHandler
 
 console_stderr = Console(stderr=True)
 console = Console(stderr=False)
 log = getLogger("dso")
-basicConfig(
-    level="INFO",
-    format="%(message)s",
-    handlers=[RichHandler(markup=True, console=console_stderr, show_path=False, show_time=True)],
-)
+log.setLevel("INFO")
+handler = RichHandler(markup=True, console=console_stderr, show_path=False, show_time=True)
+handler.setFormatter(Formatter("%(message)s"))
+log.addHandler(handler)