logging improvements and version bump

[parashardhapola]

Version bump: 0.19.3 → 0.19.4

API URL migration: prod.cytetype.nygen.io → cytetype.nygen.io (across main.py, README.md, and integration tests)

Progress display rewrite (cytetype/api/progress.py):

• Replaced the per-cluster progress bar (individual cluster status with colored symbols) with a simpler single-line job-level status (queued / running / waiting)
• Added Jupyter notebook support — detects ZMQInteractiveShell and uses an IPython DisplayHandle to update a single output cell in-place instead of printing repeated lines
• Added elapsed time display (MM:SS) in interactive terminals
• Spinner animation still updates in TTY mode; plain/non-TTY mode deduplicates repeated status lines
• finalize() now accepts an explicit final_status string (completed, failed, timed_out) and only shows failed cluster details on failure
• Constructor accepts an optional stream parameter for testability

Polling loop improvements (cytetype/api/client.py):

• _sleep_with_spinner now receives job_status: str instead of the full cluster_status dict, matching the simplified progress display
• New _log_report_cta() helper that logs the report URL prominently under a [TRACK PROGRESS] heading
• Report URL is logged before the initial polling delay (so users see it immediately)
• Log messages simplified: removed the job ID from the "submitted" message, rewrote the disconnect recovery hint
• Report URL is also logged on failure and timeout paths

Post-annotation report link (cytetype/main.py):

• After annotate() completes, the report URL is logged from adata.uns["{prefix}_jobDetails"]["report_url"]
• Minor formatting fix in validate_adata call arguments

Tests:

• New tests/test_api_client.py — unit tests for ProgressDisplay (plain output dedup, notebook display handle updates) and wait_for_completion (verifies report CTA is logged before polling begins)
• tests/test_cytetype_integration.py — updated default API URL assertion
• tests/test_validation.py — reformatted @pytest.mark.parametrize calls (style-only, no logic changes)

[qodo-code-review]

Review Summary by Qodo

Progress display rewrite with notebook support and logging improvements

✨ Enhancement 🐞 Bug fix

Walkthroughs

Description

• Simplified progress display from per-cluster to job-level status
• Added Jupyter notebook support with in-place output updates
• Improved logging with prominent report URL tracking before polling
• Enhanced API URL migration and version bump to 0.19.4
• Added comprehensive unit tests for progress display and polling

Diagram

flowchart LR
  A["Job Submission"] --> B["Log Report URL"]
  B --> C["Start Polling"]
  C --> D["Update Progress Display"]
  D --> E{Display Mode}
  E -->|TTY| F["Spinner + Elapsed Time"]
  E -->|Notebook| G["Single Output Cell"]
  E -->|Plain| H["Deduplicated Lines"]
  F --> I["Job Completion"]
  G --> I
  H --> I
  I --> J["Finalize with Status"]
  J --> K["Show Failed Clusters if needed"]

Loading

File Changes

1. cytetype/__init__.py ⚙️ Configuration changes +1/-1

Version bump to 0.19.4

• Version bumped from 0.19.3 to 0.19.4

cytetype/init.py

---

2. cytetype/api/progress.py ✨ Enhancement +138/-88

Complete rewrite of progress display system

• Replaced per-cluster progress bar with simplified job-level status display
• Added Jupyter notebook detection and in-place output cell updates via DisplayHandle
• Implemented elapsed time display (MM:SS format) for interactive terminals
• Added spinner animation for TTY mode and plain text deduplication for non-TTY
• Refactored finalize() to accept explicit final_status parameter and show failed clusters only
 on failure
• Added stream parameter to constructor for testability
• Simplified status messages and removed colored cluster symbols

cytetype/api/progress.py

---

3. cytetype/api/client.py ✨ Enhancement +27/-21

Polling loop improvements and report URL tracking

• Changed _sleep_with_spinner() to receive job_status: str instead of full cluster_status dict
• Added _log_report_cta() helper function to log report URL under [TRACK PROGRESS] heading
• Moved report URL logging before initial polling delay for immediate user visibility
• Simplified job submission log message and improved disconnect recovery hint
• Added report URL logging on failure and timeout paths
• Updated finalize() calls to pass explicit final_status parameter
• Initialize job_status and cluster_status variables at start of polling loop

cytetype/api/client.py

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View more (5)

4. cytetype/main.py ✨ Enhancement +10/-3

API URL migration and post-annotation report logging

• Updated default API URL from prod.cytetype.nygen.io to cytetype.nygen.io
• Added report URL logging after annotate() completion from adata.uns metadata
• Reformatted validate_adata() call arguments for better readability

cytetype/main.py

---

5. tests/test_api_client.py 🧪 Tests +140/-0

New unit tests for progress display and polling

• New unit test file with comprehensive tests for ProgressDisplay and wait_for_completion
• Tests verify plain output deduplication avoids repeated status lines
• Tests verify notebook display handle updates single output cell instead of printing multiple lines
• Tests verify report CTA is logged before polling begins
• Includes helper classes for mocking logger, streams, and display handles

tests/test_api_client.py

---

6. tests/test_cytetype_integration.py 🧪 Tests +1/-1

Update API URL in integration test

• Updated default API URL assertion from prod.cytetype.nygen.io to cytetype.nygen.io

tests/test_cytetype_integration.py

---

7. tests/test_validation.py Formatting +63/-44

Reformat parametrize decorators for consistency

• Reformatted @pytest.mark.parametrize decorators for improved code style
• Expanded multi-line parameter lists with proper indentation
• No logic changes, style-only formatting updates

tests/test_validation.py

---

8. README.md 📝 Documentation +1/-1

Update example report URL

• Updated example report URL from prod.cytetype.nygen.io to cytetype.nygen.io

README.md

---

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📎 Requirement gaps (0)

1. TTY progress line artifacts ☑ 🐞 Bug ⚙ Maintainability

Description

ProgressDisplay.update()/finalize() rewrite the current terminal line using '\r' but never clear the
remainder of the previous line, so when a shorter status replaces a longer one, leftover characters
remain visible. This produces confusing/garbled progress output in interactive TTY sessions
(cosmetic but user-facing).

Code

cytetype/api/progress.py[R65-68]

+        if self._interactive:
+            message = self._build_running_line(job_status)
+            print(f"\r{message}", end="", file=self.stream, flush=True)
+        elif self._use_notebook_display:

Evidence

Interactive rendering uses a carriage return to overwrite the current line but does not clear to
end-of-line. Since status strings have different lengths (e.g., “Waiting for CyteType job to
start...” vs “CyteType job running...”), switching from a longer to a shorter message will leave
trailing characters from the previous message on the screen; finalize() has the same pattern for the
last render.

cytetype/api/progress.py[60-74]
cytetype/api/progress.py[93-99]
cytetype/api/progress.py[133-142]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

### Issue description
In TTY mode, `ProgressDisplay` redraws the same line using `\r` but does not clear the rest of the line. When a shorter message replaces a longer one, trailing characters from the previous message remain visible.

### Issue Context
This affects interactive terminals (`stream.isatty() == True`). The status text varies in length depending on job state.

### Fix Focus Areas
- cytetype/api/progress.py[65-68]
- cytetype/api/progress.py[93-96]

### Suggested fix
When printing in interactive mode, append an ANSI clear-to-end-of-line sequence, e.g.:
- `print(f"\r{message}\033[K", end="", ...)` for `update()`
- `print(f"\r{message}\033[K", ...)` for `finalize()`

(Alternative: track the previous rendered length and right-pad with spaces.)

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

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