Use stdin for PythonTA document linting

[PraneethS42]

Proposed Changes

This PR updates the language server to lint the contents supplied by VS Code through standard input instead of rereading the saved file from disk.

Using document.source ensures PythonTA analyzes the document content known to the language server. PythonTA 2.13.1 introduced the required --stdin support.

Language server changes

• bundled/tool/lsp_server.py
  • Enables stdin mode from _linting_helper
  • Passes --stdin to PythonTA instead of the document filename
  • When stdin mode is disabled, continues support of filename-based execution
  • Handles PythonTA’s temporary stdin_*.py URI. Since each stdin invocation analyzes one document, the server extracts diagnostics from that result and republishes them using the actual VS Code document URI
• bundled/tool/lsp_jsonrpc.py
  • Ensures empty document contents ("") are forwarded when PythonTA runs through the alternate-interpreter JSON-RPC path
  • Previously, empty strings were treated as missing values and omitted from the RPC message

Dependency changes

• pyproject.toml
  • As per discussion, replaces the moving/unstable PythonTA dependency with the stable python-ta==2.13.1 release, which includes stdin support
• uv.lock
  • Regenerated with uv sync to lock PythonTA 2.13.1 and its package metadata

Test changes

• src/test/python_tests/test_server.py
  • Adds an end-to-end test where the editor content differs from the file on disk. Confirms diagnostics correspond to document.source: proves PythonTA reads from stdin
• src/test/python_tests/test_lsp_server_helpers.py
  • Adds unit coverage for PythonTA output containing a temporary stdin URI. Confirms diagnostics are still returned for publication against the real document.
• src/test/python_tests/test_lsp_jsonrpc.py
  • Adds coverage ensuring an empty source string is preserved in JSON-RPC messages
• src/test/python_tests/test_notebook.py
  • Updates the notebook-close test to wait specifically for the empty diagnostic notification.
  • This prevents a delayed notebook-open diagnostic notification from ending the test prematurely now that notebook contents are successfully linted through stdin.

Screenshots of your changes (if applicable)

Type of Change

(Write an X or a brief description next to the type or types that best describe your changes.)

Type	Applies?
🚨 Breaking change (fix or feature that would cause existing functionality to change)
✨ New feature (non-breaking change that adds functionality)	X
🐛 Bug fix (non-breaking change that fixes an issue)
🎨 User interface change (change to user interface; provide screenshots)
♻️ Refactoring (internal change to codebase, without changing functionality)
🚦 Test update (change that only adds or modifies tests)
📦 Dependency update (change that updates a dependency)	x
📖 Documentation update (change that updates documentation)
🔧 Internal (change that only affects developers or continuous integration)

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[coveralls]

Coverage Report for CI Build 37417097920

Coverage decreased (-15.0%) to 62.402%

Details

• Coverage decreased (-15.0%) from the base build.
• Patch coverage: 4 uncovered changes across 1 file (12 of 16 lines covered, 75.0%).
• No coverage regressions found.

Uncovered Changes

File	Changed	Covered	%
bundled/tool/lsp_server.py	15	11	73.33%
Total (2 files)	16	12	75.0%

Coverage Regressions

No coverage regressions found.

---

Coverage Stats

Relevant Lines:	1293
Covered Lines:	805
Line Coverage:	62.26%
Relevant Branches:	106
Covered Branches:	68
Branch Coverage:	64.15%
Branches in Coverage %:	Yes
Coverage Strength:	1.19 hits per line

---

💛 - Coveralls

[david-yz-liu]

Hi @PraneethS42, the changes look okay to me, but I don't think this is working properly. When I run this with the example in the README, here's what I see (after expanding the error):

This is not the expected error message, and seems to indicate that some junk characters are being sent to PythonTA.

[PraneethS42]

That's interesting, I'll take a look at this shortly. When I was testing, I was running it on some other personal Python files as opposed to the README example. I'll make sure to test that first in the future.

[PraneethS42]

Could you take another look and see if it's working on your system as intended?

[david-yz-liu]

Works great, thanks @PraneethS42!