Common troubleshooting in PyCharm

Problem

Use this checklist if you see one or more of the following symptoms in PyCharm

Code insight and navigation

• The IDE shows red code / unresolved references, but the project runs successfully.
• Code completion, navigation (Go to Declaration), or Find Usages works incorrectly or uses clearly outdated information.
• Refactorings or file moves partially apply (old imports/paths are still used, wrong usages updated, etc.).

Indexing and performance

• The IDE keeps re-indexing the project, indexing never finishes, or is stuck on “Updating indices…”.
• The IDE becomes very slow or freezes during typing, completion, or basic editor actions in a particular project.

Errors and project-specific behavior

• The IDE randomly throws internal errors or exceptions, with stack traces that don’t obviously relate to your code.
• The problem is reproducible only in one specific project; other projects open and work normally.

UI, run/debug, and stability

• UI glitches: panels not updating, tool windows not showing expected content, editor view out of sync with the file on disk.
• Run/debug configurations that used to work suddenly fail in the IDE while still working from the command line.
• The IDE randomly crashes or becomes unresponsive without a clear pattern.

Cause

Most such issues are caused by corrupted caches, project configuration (.idea), or third-party plugins rather than a bug in PyCharm itself.

Resolution

Follow these steps in order. After each step, check whether the problem is gone.

1. Check if the issue is observed in the latest PyCharm version – If it disappears after updating, it was likely a known bug that has already been fixed.

2. Disable all non-bundled plugins (Settings | Plugins | click the cog icon | Disable All Downloaded Plugins). – If the problem goes away, re-enable plugins one by one to find the culprit.

3. Do File | Invalidate Caches with all options toggled. – Expect a one-time reindexing after restart; this should fix stale indexes and many “red code but runs fine” problems.

4. Check if the issue is reproducible in newly created projects. – If it is not reproducible in a new project, remove the .idea folder from the affected project and reopen it. – If it is reproducible in a new project as well, skip removing .idea and proceed to collecting logs.

Note about .idea: removing this folder resets project settings (run configurations, inspections, some UI layout) but does not touch your source code or virtualenv. If you have important custom run/debug configurations or code style, you may want to export or screenshot them first. Run/debug configurations will need to be recreated afterward.

5. If the issue persists after all steps above, collect logs and contact support. – Go to Help | Collect Logs and Diagnostic Data right after reproducing the issue and attach the archive to your support ticket or YouTrack issue.