Add conda env update command and file_bug_report Cursor command

.cursor/commands/file_bug_report.md

@@ -0,0 +1,132 @@
+# File Bug Report
+
+Transform a discovered bug into a well-documented GitHub issue.
+
+## Prerequisites Check
+
+Before starting, verify the GitHub CLI is available and authenticated:
+
+1. **Check `gh` is installed:**
+   ```bash
+   gh --version
+   ```
+   - If not found, guide the user to install it:
+     - macOS: `brew install gh`
+     - Linux: See https://github.com/cli/cli/blob/trunk/docs/install_linux.md
+     - Windows: `winget install --id GitHub.cli`
+
+2. **Check authentication:**
+   ```bash
+   gh auth status
+   ```
+   - If not authenticated, guide: `gh auth login`
+
+3. **Sandbox considerations:**
+   - GitHub CLI commands require access to credentials stored outside the workspace
+   - **Always use `required_permissions: ["all"]`** for any `gh` commands
+
+## Workflow
+
+### Phase 1: Bug Investigation
+
+1. **Gather initial information from the user:**
+   - Error message or unexpected behavior
+   - Steps to reproduce (if known)
+   - Relevant code or notebook
+
+2. **Investigate the bug:**
+   - Locate the relevant source code
+   - Reproduce the error if possible (write a minimal test case)
+   - Identify the root cause
+   - Check if this is a known issue:
+     ```bash
+     gh issue list --state open --search "<keywords>"
+     ```
+
+3. **If a solution is apparent:**
+   - Note the proposed fix in the issue body
+   - This helps future contributors (including yourself) address it quickly
+
+### Phase 2: Draft Issue
+
+1. **Create the issue markdown file:**
+   Save to `.github/issue_summaries/<short-description>.md` with this structure:
+
+   ```markdown
+   ## Description
+
+   <Clear, concise description of the bug>
+
+   ## Steps to Reproduce
+
+   1. <Step 1>
+   2. <Step 2>
+   3. ...
+
+   ## Expected Behavior
+
+   <What should happen>
+
+   ## Actual Behavior
+
+   <What actually happens, including error messages>
+
+   ## Environment
+
+   - CausalPy version: <version or commit>
+   - Python version: <version>
+   - OS: <operating system>
+
+   ## Proposed Solution (if known)
+
+   <Brief description of the fix, or remove this section if unknown>
+
+   ## Additional Context
+
+   <Any other relevant information, screenshots, or code snippets>
+   ```
+
+2. **Present the draft to the user:**
+   > "I've drafted the following bug report:
+   >
+   > **Title:** `<proposed title>`
+   >
+   > **Body:**
+   > <show the markdown content>
+   >
+   > Would you like to make any changes before filing?"
+
+   **Wait for user confirmation.**
+
+### Phase 3: File the Issue
+
+1. **Create the issue:**
+   ```bash
+   gh issue create --title "<descriptive title>" --body-file .github/issue_summaries/<short-description>.md --label "bug"
+   ```
+
+2. **Report success:**
+   > "✅ Bug report filed successfully!
+   >
+   > **Issue URL:** <link>
+   >
+   > **Issue Number:** #<number>"
+
+3. **Cleanup:**
+   Delete the markdown file (it's gitignored and no longer needed):
+   ```bash
+   rm .github/issue_summaries/<short-description>.md
+   ```
+
+## Guidelines
+
+- **Keep titles concise but descriptive:** Bad: "Error in code". Good: "KeyError when calling result.summary() with missing covariate"
+- **Include reproducible examples (if possible):** Minimal code that triggers the bug
+- **Don't speculate excessively:** If unsure about the cause, say so
+- **One bug per issue:** If multiple bugs are discovered, file separate issues
+
+## Error Handling
+
+- **Duplicate issue found:** Link to the existing issue instead of creating a new one
+- **Cannot reproduce:** File anyway with available information, note that reproduction failed
+- **Permission denied:** Check `gh auth status` and repository access (sandbox permissions covered in Prerequisites)

.gitignore

@@ -18,5 +18,6 @@ docs/source/api/generated/
 .cursor/plans
 .marimo/
 
-# PR summaries generated by issue2pr command
+# Temporary files generated by Cursor commands
 .github/pr_summaries/
+.github/issue_summaries/

CONTRIBUTING.md

@@ -78,6 +78,12 @@ For more instructions see the [Pull request checklist](#pull-request-checklist)
     conda activate CausalPy
     ```
 
+    To update an existing environment after changes to `environment.yml`:
+
+    ```bash
+    conda env update --file environment.yml --prune
+    ```
+
 1. Install the package and all development dependencies using the automated setup:
 
     ```bash