Fix code formatting and linting issues

- Ran black formatter on clustrix/ and tests/ directories
- Fixed 31 flake8 errors in tests/ including:
  - Removed unused imports (F401 errors)
  - Converted lambda assignments to proper functions (E731 errors)
  - Fixed redefinition of unused imports (F811 errors)
  - Removed trailing whitespace
- All 223 tests continue to pass
- Documentation builds successfully (36 warnings about missing pages)
- Note: mypy has 45 type annotation errors that require extensive work

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: jeremymanning

clustrix/config.py

@@ -90,26 +90,26 @@ def save_to_file(self, config_path: str) -> None:
         """Save this configuration instance to a file."""
         config_path = Path(config_path)
         config_data = asdict(self)
-        
+
         with open(config_path, "w") as f:
             if config_path.suffix.lower() in [".yml", ".yaml"]:
                 yaml.dump(config_data, f, default_flow_style=False)
             else:
                 json.dump(config_data, f, indent=2)
-    
+
     @classmethod
     def load_from_file(cls, config_path: str) -> "ClusterConfig":
         """Load configuration from a file and return a new instance."""
         config_path = Path(config_path)
         if not config_path.exists():
             raise FileNotFoundError(f"Configuration file not found: {config_path}")
-        
+
         with open(config_path, "r") as f:
             if config_path.suffix.lower() in [".yml", ".yaml"]:
                 config_data = yaml.safe_load(f)
             else:
                 config_data = json.load(f)
-        
+
         return cls(**config_data)
 
 

docs/build/doctrees/api/config.doctree

@@ -219,7 +219,39 @@ <h1>Source code for clustrix.config</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">module_loads</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">module_loads</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pre_execution_commands</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">pre_execution_commands</span> <span class="o">=</span> <span class="p">[]</span></div>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pre_execution_commands</span> <span class="o">=</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="ClusterConfig.save_to_file">
+<a class="viewcode-back" href="../../api/config.html#clustrix.config.ClusterConfig.save_to_file">[docs]</a>
+    <span class="k">def</span> <span class="nf">save_to_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Save this configuration instance to a file.&quot;&quot;&quot;</span>
+        <span class="n">config_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config_path</span><span class="p">)</span>
+        <span class="n">config_data</span> <span class="o">=</span> <span class="n">asdict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_path</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">suffix</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;.yml&quot;</span><span class="p">,</span> <span class="s2">&quot;.yaml&quot;</span><span class="p">]:</span>
+                <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">config_data</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">config_data</span><span class="p">,</span> <span class="n">f</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="ClusterConfig.load_from_file">
+<a class="viewcode-back" href="../../api/config.html#clustrix.config.ClusterConfig.load_from_file">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">load_from_file</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">config_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;ClusterConfig&quot;</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Load configuration from a file and return a new instance.&quot;&quot;&quot;</span>
+        <span class="n">config_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">config_path</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">config_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+            <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Configuration file not found: </span><span class="si">{</span><span class="n">config_path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_path</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">suffix</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;.yml&quot;</span><span class="p">,</span> <span class="s2">&quot;.yaml&quot;</span><span class="p">]:</span>
+                <span class="n">config_data</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">config_data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">config_data</span><span class="p">)</span></div>
+</div>
 
 
 
@@ -351,7 +383,7 @@ <h1>Source code for clustrix.config</h1><div class="highlight"><pre>
                     &copy; Copyright 2025, Contextual Dynamics Laboratory
             </div>
             <div class="text-center text-white-50 font-italic mt-3">
-                <small>Last updated: Jun 25, 2025</small>
+                <small>Last updated: Jun 26, 2025</small>
                 <small>
                     Created using
                     <a class="text-white" href="https://github.com/wagtail/sphinx_wagtail_theme" rel="nofollow" target="_blank">

docs/build/doctrees/environment.pickle

@@ -160,7 +160,7 @@ <h1>All modules for which code is available</h1>
                     &copy; Copyright 2025, Contextual Dynamics Laboratory
             </div>
             <div class="text-center text-white-50 font-italic mt-3">
-                <small>Last updated: Jun 25, 2025</small>
+                <small>Last updated: Jun 26, 2025</small>
                 <small>
                     Created using
                     <a class="text-white" href="https://github.com/wagtail/sphinx_wagtail_theme" rel="nofollow" target="_blank">