mdtraj 1.10 incompatibility #612
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mdtraj 1.10 removed TNGTrajectoryFile objects, which are used in the tests. This PR pins the mdtraj version between >=1.9.3, <1.10 in the environment.yml file.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description:
Pinning mdtraj version between >=1.9.3, <1.10 in environment.yml to address compatibility issues. mdtraj 1.10 was recently release and seems to not be fully backwards compatible.
Changes Made:
Updated environment.yml file to specify mdtraj version as >=1.9.3, <1.10 to address compatibility issues caused by recent updates.
Testing:
mdtraj 1.10 resulted in tests that relied on the TNGTrajectoryFile object in mdtraj to fail.
For example, tests/structure/test_trajectory.py
After pinning mdtraj to <1.10 all the tests passed successfully again.