#2741 Image missing stereochemistry information when using abbreviations

[jblack-mestre]

Generic request

• PR name follows the pattern #1234 – issue name
• branch name does not contain '#'
• base branch (master or release/xx) is correct
• PR is linked with the issue
• task status changed to "Code review"
• code follows product standards
• regression tests updated

[jblack-mestre]

Is is possible to write a unit test in api/cpp/tests/rendering/basic.cpp for this bug and others? These changes affect render_internal.cpp

[AlexanderSavelyev]

I guess in this particular case it is not render issue. It is just missing stereocenter, which is worth to test using just stereo information (e.g. number of stereo bonds down)

[jblack-mestre]

Unfortunately we can't count the up and down bonds for the unit test; in this case, indigo correctly assigns the stereocenters with the correct bond directions, but when the molecule is passed through MoleculeRenderInternal::_prepareSGroups(), the stereocenter to the super atom is forgotten.
Can you suggest another place for a unit test?

[AlexanderSavelyev]

for render tests we use regression test with pixel comparison
e.g. https://github.com/epam/Indigo/blob/master/api/tests/integration/tests/rendering/render_reactions.py#L108
in order to execute regression tests need to build indigo-python target

cmake --build . --config Release --target indigo-python
# copy
python -m pip install ..\dist\epam.indigo-1.29.0.dev1-py3-none-win_amd64.whl
# run tests by mask
python3 ..\api\tests\integration\test.py -p render_reactions

also, there are some requirements should be installed to python

python3 -m pip install Pillow

[AlexanderSavelyev]

please also merge latest changes from master branch

[jblack-mestre]

thanks for the info, I've added a test to render_reactions.py.

I merged the changes from master yesterday. Git merge upstream/master is telling me I am up to date

[jblack-mestre]

Do you know what the problem is? My fork is in sync with indigo/master and my branch is up to date with my fork's master and the indigo/master branches

[AlexanderSavelyev]

I just verified, your branch is not up-to-date
please do
git fetch upstream
git merge upstream/master

[jblack-mestre]

[AlexanderSavelyev]

oh, I see, Indigo team didn't backmerge to master the changes about github actions. Will fix it and let you know

[AlexanderSavelyev]

please take the latest changes from master

[jblack-mestre]

I don't have access to a linx/mac machine in order to generate the reference files for the regression test. How is this normally done?

The windows tests fail due to a diff in the output - do I need to update a output reference file?

[AlexanderSavelyev]

• no need to merge from master anymore. It was just one issue with checkout github action upgrade. There is no need to PR to be up-to-date with master branch (and in general it is not possible)
• for windows it seems that the test is running ok, but the console output is different. please replace the expected output from "out" folder into "api/tests/integration/ref/rendering/render_reactions.py.out"
• you can check if test is passed by running python3 api\tests\integration\test.py -p render_reactions locally
• the image from win folder should be copied into linux and mac. Usually the images are the same, but if there are difference - the test will print out the expected result

[jblack-mestre]

thanks for the info - I've made the changes

[AlexanderSavelyev]

all tests passed, merged, thanks so much for the fix!