Comments (7)
With scijava/scijava-scripts@6cd677c, I finally updated travis-build.sh
to do things correctly. That is: conda's etc/profile.d/conda.sh
gets sourced as needed for conda 4.4+. I believe the code is good now. However, there is still an issue:
travis-build.sh: 7: /home/travis/miniconda/envs/travis-scijava/etc/conda/activate.d/openjdk_activate.sh: [[: not found
It seems like Travis must not use bash; this is not the first time I've seen it barf on bash-specific syntax. Unfortunately, the double bracket syntax is part of the openjdk package's activation script. Maybe we can find a way to run the rest of the travis-build script with bash specifically, instead of whatever Travis is using (probably dash?).
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@ctrueden wrote:
This issue is blocked by the openjdk activation script not working on Travis.
Is this still an issue? Maybe it can be fixed by replacing this in .travis.yml
:
- script: ".travis/build.sh"
+ script: bash ".travis/build.sh"
from tutorials.
Maybe it can be fixed by replacing this in .travis.yml
Unfortunately no.
Neither script: bash ".travis/build.sh"
(build #153) nor script: "bash .travis/build.sh"
(build #154) changed anything in the build.
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Dang it @kmader, I spent all day hacking on this. 😜 And it still doesn't work... 😞
The good news is: everything is in place for the SciJava travis-build.sh
script to support validating Jupyter notebooks. And this repository (imagej/tutorials) is configured to take advantage of it. Any other repository wanting to check their notebooks need only model their Travis config after the one here. It is largely automatic, installing conda for you when you have an environment.yml
, and running jupyter nbconvert --execute
on each .ipynb
file in the repo when the jupyter
executable is available afterwards.
The bad news is twofold: 1) The source activate travis-scijava
does not work, and various things I tried would not make it work; and 2) A couple of the notebooks here currently fail validation. And at least one (notebooks/3_-_Advanced_usage/2_-_Under_the_hood_-_ImgLib2.ipynb
) has a bunch of errors that strangely do not trigger a non-zero exit code from nbconvert
. Not sure what's up with that yet. I need to move on to other things for the moment, but at least the framework is here now.
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Sorry I didn't mean to make so much work for you, but the travis-build script is quite well done. The non-zero exit code issue is unfortunately quite common but we got around it by grepping for traceback (https://github.com/kmader/Quantitative-Big-Imaging-2018/blob/master/circleci/execute.sh#L20) maybe that would work here as well (at least with the python kernels)
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we got around it by grepping for traceback
Great idea. I'll do that in travis-build.sh
next time I work on this issue. We can grep for both Python- and Java-style stack traces.
Any idea why source activate travis-scijava
always says "source: not found" in the Travis output? (But it looks like you use CircleCI and not Travis?) I couldn't find others online reporting this problem. The source
command is bash-specific, so I thought maybe Travis wasn't running the script in bash—I had #!/bin/sh
at the top because I prefer to write POSIX-friendly scripts whenever possible—but when I explicitly changed it to #!/bin/bash
it still fails with the same error. So I'm stumped.
from tutorials.
This issue is blocked by the openjdk activation script not working on Travis. I made a fix that was supposed to address it (conda-forge/openjdk-feedstock#53) but after it was merged, it was pointed out that the fix is likely to be insufficient. I still have not had time to actually test it.
One way forward might be to have Travis run the conda stuff in a subshell with bash? Then we wouldn't have to make any more changes to the openjdk recipe upstream.
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Related Issues (20)
- Fix ExecuteCommands to work with fake format changes HOT 7
- some error massage
- Invalid service: net.imagej.legacy.LegacyService HOT 1
- Python kernel error (in Binder): PYJNIUS_JAR environment variable not defined. HOT 10
- Link to more awesome data science tutorials HOT 1
- Create tutorial about imglib2-roi and how to work with labelings HOT 2
- Useful Writing Plugin Setup Video HOT 2
- DynamicCommand: combobox in the example never gets updated HOT 2
- Include Maven installation of ImageJ and Fiji artifacts in postBuild for binder HOT 6
- Problems with %classpath HOT 3
- Consider using Jupytext for version control of Jupyter notebooks HOT 1
- A connection to the notebook server could not be established.
- "ImageJ with Python Kernel" section 6.2 doesn't work HOT 2
- HowTo wishlist HOT 15
- Move working-with-modules to howtos
- Address dependency skew in BeakerX notebooks
- Resolve BeakerX component version skew (kotlin, okio, maybe more)
- Tab completion isn't working in the Jupyter Notebooks
- Add -Djava.net.useSystemProxies=true tip to sections about proxy configuration
- Update to the latest version of ImageJ2
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