Closed kenza12 closed 2 years ago
Hi @kenza12 , and thanks in advance for working on the conda packaging. We appreciate your help.
I think I see two different issues here. I've broken them apart into:
java
executable pathIf I've missed something, please let me know.
The java
settings are a very recent addition by @jakebeal . I had some concerns about /usr/bin/java
at the time and we didn't have enough use to require a change. I think if you want to change the default value of JAVA_LOCATION
from /usr/bin/java
to java
, and @jakebeal agrees to the change, we can incorporate that. I would appreciate it if you could open a specific issue for that change, and submit a pull request for it so that @jakebeal can test in his environment.
We use unittest for pySBOL2. It succeeds in my environment and it succeeds in the GitHub action we have set up for this package. I don't understand why pytest
fails when unittest
succeeds on some of these tests. I suggest you stick with unittest unless you want to debug pytest-specific issues with our unit tests. We would welcome a contribution for that, and do not plan to undertake that effort ourselves. You can see the unittest invocation in our GitHub build/test action:
python -m unittest discover -s test
Hi @tcmitchell ,
Thank you for your detailed answer.
For Java, I just opened a specific issue and submitted a PR.
For unit tests, I used your command line with unittest and it's indeed working. Unfortunately I don't have enough time to debug the pytest errors. So, I will use unittest instead of pytest.
Thank you very much.
PR #418 has been merged, and switching to python3 -m unittest
avoids the problem of the missing URIs. I think this issue is complete. If I'm mistaken, please reopen this issue. If new issues arise, please file new issues. And once again, thank you very much for doing the conda packaging!
Nice ! Thanks a lot ! Just one last thing, can you add (or update) a tag like v1.4: https://github.com/SynBioDex/pySBOL2/releases/tag/v1.4 including the JAVA modification. Conda use a tagged source code (as an archive) to ensure that it can be verified.
@kenza12 I have released version 1.4.1 with your java path bug fix. The tag is "v1.4.1".
Ok perfect, thank you @tcmitchell !
Hi, I'm trying to update the conda package of pysbol2 to the latest tagged version (v1.4) which is a dependency for sbol-utilities (already discussed here: https://github.com/SynBioDex/SBOL-utilities/issues/121). I got some errors while running the tests with pytest. Some links are not found and the tool path
'/usr/bin/java'
is not found too. In my tests, I added java (openjdk) to the dependencies and I changed'/usr/bin/java'
to'java'
insbol2/config.py
, in this lineConfigOptions.JAVA_LOCATION.value: '/usr/bin/java'
to make it work.Is it possible for you to check these tests in order to update these not found links (e.g. http://sd2e.org/parent/child/1 and https://sbols.org/CRISPR_Example/foo) and the java error by replacing
/usr/bin/java
byjava
. Finally, to add a new tag or update to the latest version v1.5 (according to the setup.py) including these modifications.Thank you.
Best wishes,
Kenza BAZI-KABBAJ