📝 Update 06-semantic-segmentation notebook for the New API
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shaneahmed
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06-semantic-segmentation notebook for the New API
- Update `.readthedocs.yml` to Install CPU Version only for speed up readthedocs build
## Overview This PR addresses **issue #975** and introduces two major improvements: --- ### 1. Improved Index Usage Warning in `SQLiteStore` **Problem:** The previous logic for detecting index usage relied only on the first row of `EXPLAIN QUERY PLAN`. On macOS, this often corresponds to the `rtree` virtual table, so the check missed actual indexes and always warned. **Solution:** - Added a new helper method `_warn_if_query_not_using_index` that inspects **all rows** of the query plan. - The method now looks for any row containing `USING INDEX` or `USING COVERING INDEX` (macOS phrasing). - If no index is detected, a warning is logged; otherwise, it remains silent. **Impact:** More accurate performance warnings and better developer guidance for adding indexes. --- ### 2. Dynamic Port Allocation for Tile Server in Bokeh Tests **Problem:** macOS runs multiple daemons on well-known ports (e.g., `5000`). Tests hardcoded to `http://127.0.0.1:5000/...` often collided with other services, causing `HTML/403` responses and subsequent `JSONDecodeError` or `KeyError`. **Solution:** - Introduced dynamic port binding for the tile server: - At test session start, a free loopback port is reserved and exported as `TIATOOLBOX_TILESERVER_PORT`. - Both the Flask tile server and Bokeh client read this environment variable, ensuring consistent communication. - Updated all relevant tests (`test_app_bokeh.py`, `test_json_config_bokeh.py`, `test_server_bokeh.py`) and CLI launcher to use the dynamic port. - Added proxy bypass (`trust_env=False`) for local requests to avoid interference from system proxies. **Impact:** Eliminates port conflicts, stabilizes UI tests, and improves cross-platform reliability. --- ### Additional Changes - Updated Bokeh app hooks and main logic to respect dynamic port configuration. - Minor refactoring for clarity and maintainability. --- ✅ **Benefits:** - More robust query performance checks. - Reliable test execution across macOS and CI environments. - Cleaner integration between CLI, Bokeh app, and test harness. --- **Closes:** #975 --------- Co-authored-by: Jiaqi Lv <jiaqilv@Jiaqis-MacBook-Pro.local> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev-define-engines-abc #978 +/- ##
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Coverage 95.18% 95.18%
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Files 77 77
Lines 9689 9689
Branches 1255 1255
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Hits 9222 9222
Misses 431 431
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shaneahmed
reviewed
Dec 23, 2025
| bokeh>=3.1.1, <3.6.0 | ||
| Click>=8.1.3, <8.2.0 | ||
| dask>=2025.10.0 | ||
| dask-image>=2025.11.0 |
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As this is only used in Jupyter Notebook. I would suggest adding it to the bash cell in the notebook.
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View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2025-12-23T11:20:34Z You can add pip install dask_image here |
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View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2025-12-23T11:20:35Z Add a cell at the end to visualize the output using TIAViz. See this example https://app.reviewnb.com/TissueImageAnalytics/tiatoolbox/pull/977/discussion/#comment-3674742370 |
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Trying to update example notebook 06.