fix: fix errors when running pre-commit run --all-files & unify mypy testing (queens-py#225)

Author: leahaeusel

.github/pull_request_template.md

@@ -17,4 +17,4 @@ If there's anyone you think should be looped in on this pull request,
 feel free to @mention them here!
 -->
 
-> Note: More information on the merge request procedure in QUEENS can be found in the [*Submit a pull request*](../CONTRIBUTING.md#5-submit-a-pull-request) section in the [CONTRIBUTING.md](../CONTRIBUTING.md) file.
+> Note: More information on the merge request procedure in QUEENS can be found in the [*Submit a pull request*](../CONTRIBUTING.md#5-submit-a-pull-request) section in the [CONTRIBUTING.md](../CONTRIBUTING.md) file.

.pre-commit-config.yaml

@@ -95,16 +95,12 @@ repos:
         pass_filenames: true
         # Delete modules once type hinting has been introduced there
         exclude: |
-          (?x)^(
-          ^docs/|
-          ^tests/|
-          ^test_utils/|
-          ^src/example_simulator_functions/|
-          ^src/queens_interfaces/|
+          (?x)(
+          ^(.gitlab|.github|config|doc|tests|test_utils)/|
+          ^src/(example_simulator_functions|queens_interfaces)/|
           ^src/queens/(data_processors|distributions|drivers|iterators|models|parameters)/|
           ^src/queens/(schedulers|stochastic_optimizers|variational_distributions|visualization)/|
-          ^src/queens/main.py|
-          ^src/queens/global_settings.py
+          ^src/queens/(main.py|global_settings.py)
           ).*$
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.1

doc/source/faq/directories.md

@@ -1,6 +1,6 @@
 ## What is the Output Directory in QUEENS?
 
-The output directory, commonly referred to as `output_dir`, is a designated space where all results from iterators are stored. You must specify this directory within the `GlobalSettings` object. 
+The output directory, commonly referred to as `output_dir`, is a designated space where all results from iterators are stored. You must specify this directory within the `GlobalSettings` object.
 
 > **Note:** This directory does **not** include the outputs from model simulations, such as simulation data. While this distinction might seem confusing at first, remember that analysis outputs are consistently stored locally, whereas model outputs can reside on remote machines. For more information, consult *[Where are my simulations?](#where-are-my-simulations)* and *[How is the output of a simulation model structured?](#how-is-the-output-of-a-simulation-model-structured)*.
 
@@ -44,4 +44,4 @@ Here’s a breakdown of each component:
 - `metadata.yaml`: Provides metadata from the simulation run, detailing timings, inputs, outputs, and additional information.
 - `output`: Includes the actual output files generated by the solver, including the log file created by QUEENS.
 
-The specific `job_dir` is assigned by a scheduler. For more details, refer to *[Where are my simulations?](#where-are-my-simulations)*.
+The specific `job_dir` is assigned by a scheduler. For more details, refer to *[Where are my simulations?](#where-are-my-simulations)*.

pyproject.toml

@@ -164,27 +164,14 @@ disallow_untyped_calls = false  # Change to true once all functions are typed
 disallow_untyped_decorators = true
 disallow_untyped_defs = true
 ignore_missing_imports = true
-exclude = [
-    "config/",
-    "doc/",
-    "tests/",
-    # Delete the following line by line once type hinting has been introduced in the respective module
-    "test_utils/",
-    "src/example_simulator_functions/",
-    "src/queens_interfaces/",
-    "src/queens/data_processors/",
-    "src/queens/distributions/",
-    "src/queens/drivers/",
-    "src/queens/iterators/",
-    "src/queens/models/",
-    "src/queens/parameters/",
-    "src/queens/schedulers/",
-    "src/queens/stochastic_optimizers/",
-    "src/queens/variational_distributions/",
-    "src/queens/visualization/",
-    "src/queens/main.py",
-    "src/queens/global_settings.py",
-]
+# Delete modules once type hinting has been introduced there
+exclude = '''(?x)(
+    ^(.gitlab|.github|config|doc|tests|test_utils)/|
+    ^src/(example_simulator_functions|queens_interfaces)/|
+    ^src/queens/(data_processors|distributions|drivers|iterators|models|parameters)/|
+    ^src/queens/(schedulers|stochastic_optimizers|variational_distributions|visualization)/|
+    ^src/queens/(main.py|global_settings.py)
+).*$'''
 [[tool.mypy.overrides]]
 module = ["yaml"]
 follow_untyped_imports = true