[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

README.md

@@ -1,6 +1,6 @@
 # Factory
 
-> **⚠️ This project is under active development.**  
+> **⚠️ This project is under active development.**
 
 A Python package for crystallographic data processing and analysis.
 

configs/config_example.yaml

@@ -22,7 +22,7 @@ model_settings:
   weight_decay: 0.000
   optimizer_eps: 1e-16
   weight_decouple: true
-  
+
   # Scheduler configuration
   # scheduler_step: 55
   scheduler_gamma: 0.1
@@ -41,18 +41,18 @@ model_settings:
   # scale_prior_variance: 6241.0
   # scale_distribution: FoldedNormalDistributionLayer
 
-  metadata_encoder: 
+  metadata_encoder:
     name: BaseMetadataEncoder
     params:
       depth: 10
 
-  # metadata_encoder: 
+  # metadata_encoder:
   #   name: SimpleMetadataEncoder
   #   params:
   #     hidden_dim: 256
   #     depth: 5
 
-  profile_encoder: 
+  profile_encoder:
     name: BaseShoeboxEncoder
     params:
       # in_channels: 1
@@ -91,7 +91,7 @@ model_settings:
     # params:
     #   concentration: 6.68
     #   rate: 0.001
-  
+
   background_prior_distribution:
     # name: TorchHalfNormal
     # params:
@@ -121,7 +121,3 @@ loss_settings:
 
 phenix_settings:
   r_values_reference_path: "/n/holylabs/LABS/hekstra_lab/Users/fgiehr/jobs/anomalous_peaks_files/pdb_model/refine_001.log"
-  
-
-
-

docs/Makefile

@@ -20,4 +20,4 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 watch:
-	sphinx-autobuild . _build/html --open-browser --watch examples 
+	sphinx-autobuild . _build/html --open-browser --watch examples

docs/_templates/layout.html

@@ -7,4 +7,4 @@
         <li class="toctree-l1"><a class="reference internal" href="{{ pathto('index') }}">Home</a></li>
         <li class="toctree-l1"><a class="reference internal" href="{{ pathto('api/index') }}">API Reference</a></li>
     </ul>
-{% endblock %} 
+{% endblock %}

docs/api/index.rst

@@ -7,4 +7,4 @@ API Reference
    model
    distributions
 
-This section provides detailed API documentation for Factory's modules and functions. 
+This section provides detailed API documentation for Factory's modules and functions.

docs/conf.py

@@ -227,4 +227,4 @@ def linkcode_resolve(domain, info):
 
     fn = os.path.relpath(fn, start=os.path.dirname("../factory"))
 
-    return f"https://github.com/rs-station/factory/blob/main/factory/{fn}{linespec}"  # noqa 
+    return f"https://github.com/rs-station/factory/blob/main/factory/{fn}{linespec}"  # noqa

docs/convert_favicon.py

@@ -1,4 +1,9 @@
 import cairosvg
 
 # Convert SVG to PNG
-cairosvg.svg2png(url='images/favicon.svg', write_to='images/favicon_32x32.png', output_width=32, output_height=32) 
+cairosvg.svg2png(
+    url="images/favicon.svg",
+    write_to="images/favicon_32x32.png",
+    output_width=32,
+    output_height=32,
+)

docs/images/favicon.svg

@@ -16,4 +16,4 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search` 
+* :ref:`search`

docs/index.rst

@@ -21,4 +21,4 @@ For development installation:
 
    git clone https://github.com/rs-station/factory.git
    cd factory
-   pip install -e ".[test,docs]" 
+   pip install -e ".[test,docs]"