Merge remote-tracking branch 'origin/main' into 173-refactor-levels

Author: harryswift01

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,73 @@
+
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+# Bug Report
+
+**Describe the bug**  
+<!-- A clear and concise description of the issue. -->
+
+---
+
+## To Reproduce  
+<!-- Provide the YAML configuration and the exact CLI command that reproduces the issue. -->
+
+### YAML configuration
+<!-- Paste the YAML file or the smallest excerpt that reproduces the issue.  
+Remove unrelated fields to make it minimal. -->
+```yaml
+# Paste the YAML snippet here
+```
+
+### CLI command used
+<!-- Write the exact command used, for example:   -->
+```bash
+# Paste the CLI command here
+```
+
+### Actual output
+<!-- Paste the output, logs, or error messages here -->
+```bash
+# Paste the output, logs, or error messages here
+```
+
+### Expected output
+<!-- Describe what you expected to see instead -->
+
+---
+
+## Environment and Versions
+
+- Operating System:
+- CodeEntropy Version:
+- Python Version:
+- Package list:
+  - If using conda, run: `conda list > packages.txt` and paste the contents here.
+    
+    ``` bash
+    # Paste packages.txt here
+    ```
+
+  - If using venv/pip, run: `pip list > packages.txt` and paste the contents here.
+
+    ``` bash
+    # Paste packages.txt here
+    ```
+
+---
+
+## Screenshots or Logs
+
+Attach any relevant screenshots, logs, or stack traces.
+
+---
+
+## Additional Context
+
+Include anything else that might help reproduce or understand the bug, such as changes from a previously working version.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,29 @@
+
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+---
+
+# Feature Request
+
+## Problem / Motivation
+<!-- Describe the problem you want to solve or the motivation for this feature. -->
+
+## Proposed Solution
+<!-- Describe the feature you would like to see implemented. Include examples if applicable. -->
+
+## Alternatives Considered
+- <!-- Alternative 1 -->
+- <!-- Alternative 2 -->
+
+## Expected Impact
+<!-- How this feature would affect the codebase or workflow -->
+- <!-- Impact 1 -->
+- <!-- Impact 2 -->
+
+## Additional Context
+<!-- Add any other context, screenshots, or references for the feature request here. -->
+- <!-- Further context -->

CITATION.cff

@@ -76,5 +76,5 @@ keywords:
   - biomolecular simulations
   - protein flexibility
 license: MIT
-version: 1.0.6
-date-released: '2025-11-27'
+version: 1.0.7
+date-released: '2026-01-09'

CodeEntropy/__init__.py

@@ -8,4 +8,4 @@
 and statistical mechanics.
 """
 
-__version__ = "1.0.6"
+__version__ = "1.0.7"