DOC: IDaRS Algorithm #331
DOC: IDaRS Algorithm #331
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move cell, so that one can run "this cell and all below"
Avoid evidence of crash when not using GPU
This is very difficult because jupyter notebook markdown for indentation, essential for explaining algorithms, is rubbish. Solution was to use fullstops instead of spaces.
Improve many of the text cells Set up a tmp directory for storing downloaded files or newly created files, and change the code accouringly. Check by a complete run with GPU on Colab.
Colab version has no end-of-line markers. Do not run the notebook again, but do "jupyter notebook idars.ipynb" in order to get a version with conventianal end-of-line markers.
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Codecov Report
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## develop #331 +/- ##
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Coverage 99.84% 99.84%
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Files 54 54
Lines 5168 5168
Branches 887 887
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Hits 5160 5160
Misses 2 2
Partials 6 6 Continue to review full report at Codecov.
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Explain in text cells how to react to a crash due to memory overflow Save notebook in Google Drive; run notebook in Colab; save to Drive Download Restore end-of-line markers with command "jupyter notebook idars.py" but do not run. Save
'make html' in the docs directory failed with nbsphinx
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I finally got 'make html' in docs to work, and found that readthedocs version of the text cells was horrible, although it looks fine with the standard notebook rendering. I converted to draft in order to use sphinx in the jupyter notebook. It seems quite complicated, so I may take some time. |
…eadthedocs 1. Some clickable links were not clickable in rtd. 2. Allow indentation in markdown cells in jnb 3. Allow indentation in rtd rendereing of markdown cells 4. Minor edits to improve working
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View / edit / reply to this conversation on ReviewNB mostafajahanifar commented on 2022-04-22T10:07:52Z Because publication link have "()" characters in it, we should use html tags to include a hyperlink. like below: <a href="https://www.thelancet.com/journals/landig/article/PIIS2589-7500(2100180-1/fulltext">original publication</a>
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This branch was started in order to include, in a text cell, pseudo-code for the IDaRS algorithm. The algorithm actually used in the experiments described in the paper by Bilal et al is included here. One reason this is important is that the algorithm listed in the Supplementary Materials for Bilal et al is not correct, and does not correctly describe what was actually done in that work.
Running the notebook on a Macbook revealed a bug, resulting in a crash, as described in Issue #325. This is now fixed, and the notebook completes overnight on a Macbook. Clean-up of files downloaded by the notebook has also been improved.
Many minor changes have been made to text cells, to make them clearer or eliminate unnecessary words.