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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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[0.5.38] Missing tiny-queue.js file on conda installation make `cbImportScanpy` fail #123

Closed pcm32 closed 5 years ago

pcm32 commented 5 years ago

On running cbImportScanpy I get the following failure due to missing tiny-queue.js file in the ext folder (there are other files in there that are getting installed correctly):

Traceback (most recent call last):
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/bin/cbImportScanpy", line 12, in <module>
    sys.exit(cbImportScanpyCli())
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/convert.py", line 529, in cbImportScanpyCli
    build(outDir, options.htmlDir, port=options.port)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cellbrowser.py", line 3465, in build
    cbUpgrade(outDir, datasets)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cellbrowser.py", line 4084, in cbUpgrade
    makeIndexHtml(webDir, datasets, outDir, devMode=devMode)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cellbrowser.py", line 4032, in makeIndexHtml
    writeVersionedLink(ofh, '<script src="%s"></script>', baseDir, jsFname, addVersion=addVersion)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cellbrowser.py", line 3916, in writeVersionedLink
    md5 = md5WithPython(filePath)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cellbrowser.py", line 2906, in md5WithPython
    with open(fname, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.5.38/lib/python3.7/site-packages/cellbrowser/cbWeb/ext/tiny-queue.js'

Files currently available on a fresh install are on ext are:

Chart.bundle.min.js         introjs.2.4.0.min.css           papaparse.min.js
FastBitSet.js               jquery-ui-1.12.1.css            select2.4.0.4.min.css
FileSaver.1.1.20151003.min.js       jquery-ui.min.js            select2.min.js
OverlayScrollbars.min.css       jquery.3.1.1.min.js         selectize.bootstrap3.css
bootstrap-dropmenu.min.css      jquery.contextMenu.css          selectize.js
bootstrap-submenu.js            jquery.contextMenu.js           slick.cellrangedecorator.js
bootstrap-submenu.min.css       jquery.event.drag-2.3.0.js      slick.cellrangeselector.js
bootstrap.3.3.7.min.css         jquery.overlayScrollbars.min.js     slick.cellselectionmodel.js
bootstrap.min.css           jquery.sparkline.min.js         slick.core.js
bootstrap.min.js            jquery.tipsy.1.0.3.min.css      slick.editors.js
chartjs-chart-box-and-violin-plot.js    jquery.tipsy.min.js         slick.examples.css
chosen-sprite.png           jquery.ui.position.min.js       slick.formatters.js
chosen.1.8.2.min.css            jsurl2.js               slick.grid.css
chosen.jquery.min.js            lz-string.js                slick.grid.js
font-awesome.css            materialIcons.woff          spectrum-1.8.0.css
googleMaterialIcons.css         mousetrap.min.js            spectrum.min.js
hamster.js              normalizeWheel.js           split.js
images                  pako_inflate.min.js         tablesort.js
intro.min.js                palette.js              tablesort.number.min.js
pcm32 commented 5 years ago

I guess this is because the file is not present in https://github.com/maximilianh/cellBrowser/tree/master/src/cbPyLib/cellbrowser/cbWeb/ext.

maximilianh commented 5 years ago

Oh oh, darn, my mistake, sorry, will fix this immediately.

On Tue, Jul 30, 2019 at 1:02 PM Pablo Moreno notifications@github.com wrote:

I guess this is because the file is not present in https://github.com/maximilianh/cellBrowser/tree/master/src/cbPyLib/cellbrowser/cbWeb/ext .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/123?email_source=notifications&email_token=AACL4TLYPJCI45BFMIY5SVDQCANVNA5CNFSM4IH3CCO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3DTMHA#issuecomment-516371996, or mute the thread https://github.com/notifications/unsubscribe-auth/AACL4TKK2QQCRKMLFRKP4PDQCANVNANCNFSM4IH3CCOQ .

maximilianh commented 5 years ago

ok, I've released 0.5.41 now, sorry for such a stupid bug! Something like this should not happen, but even CI wouldn't really help. I just need to be more careful with my commits.

On Tue, Jul 30, 2019 at 1:16 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Oh oh, darn, my mistake, sorry, will fix this immediately.

On Tue, Jul 30, 2019 at 1:02 PM Pablo Moreno notifications@github.com wrote:

I guess this is because the file is not present in https://github.com/maximilianh/cellBrowser/tree/master/src/cbPyLib/cellbrowser/cbWeb/ext .

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/123?email_source=notifications&email_token=AACL4TLYPJCI45BFMIY5SVDQCANVNA5CNFSM4IH3CCO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3DTMHA#issuecomment-516371996, or mute the thread https://github.com/notifications/unsubscribe-auth/AACL4TKK2QQCRKMLFRKP4PDQCANVNANCNFSM4IH3CCOQ .

pcm32 commented 5 years ago

Thanks @maximilianh. I switched the bioconda package to install from the pip hosted file instead of github, as you seem to release more often there, but installation fails because https://github.com/maximilianh/cellBrowser/blob/master/LICENSE doesn't get included in the pip package:

13:21:24 BIOCONDA INFO (OUT) ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml)
13:21:26 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /private/var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmp0f2b3v1s/build_script.bash:/opt/build_script.bash -v /tmp/miniconda/miniconda/conda-bld/:/opt/host-conda-bld -v /Users/pmoreno/Development/bioconda-recipes/recipes/ucsc-cell-browser:/opt/recipe -e LANG=en_GB.UTF-8 -e HOST_USER_ID=502 bioconda/bioconda-utils-build-env:latest /bin/bash /opt/build_script.bash

Could you either add the LICENSE to the pip package and re-release 0.5.41 or make a release on github? If you fix the pip one, then I won't bother you anymore with github releases ;-).

maximilianh commented 5 years ago

Ah, weird that this is suddenly a problem but used to work just fine until now. I had no idea conda requires this file. Sure, I've added the file now, can you try 0.5.42 ?

pcm32 commented 5 years ago

Thanks for fixing this @maximilianh, please see issue #124 with other problems I get with the newest version.