MDAnalysis/mdanalysis release-1.1.1

MDAnalysis 1.1.1

on GitHub

Final bugfix release for 1.0.x

Python support is kept the same as 1.0.0, with python 3.9 not supported.

Supported python versions:

• 2.7, 3.5, 3.6, 3.7, 3.8

Please note that python 2.7 and 3.5 support will be dropped in the upcoming 2.0.0 release.

Major changes:

Bug fixes

• Re-enables support for Windows (Issue #3129)
• NSGrid distance search backend is re-enabled, with a brand new code fixing previously seen issues (Issues #2670 #2229 #2345 #2919)
• Adds support for numpy 1.20 for compatible python versions
• Fixes bug where the exclusion matrix of hbond_autocorrel was not applied correctly (Issue #2987 PR #3242)

Deprecations:

• NCDFWriter scale_factor writing behaviour will change in 2.x (Issue #2327)
• PDBWriter will no longer use the last letter of SegID for the chainID in 2.x (Issue #3144)
• In 2.x, the universe attributes tempfactors and bfactors will stop being separate (Issue #1901)
• MDAnalysis.analysis.hbonds.WaterBridgeAnalysis will be moved to MDAnalysis.analysis.hydrogenbonds.WaterBridgeAnalysis in 2.x (PR #3111)
• In 2.x the TPRParser will index residues from 1 instead of 0. The tpr_resid_from_one keyword has been added to modify this behaviour (Issue #2364)

Enhancements:

• The get_connections method has been added to more easily get bonds, angles, dihedrals, etc.. for a group (Issues #1264 #2821)

See the CHANGELOG for more changes and details.

Known issues:

• Windows builds
  • For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the MDAnalysisTests.lib.test_augment tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.0.
  • For python 3.5 only, extra tests failures are seen. These mostly relate to deprecations and warnings being raised upstream (primarily by os.path). As far as we know they do not affect the validity of the code. The following tests are affected:
    • MDAnalysisTests.analysis.test_base::test_analysis_class_decorator
    • MDAnalysisTests.analysis.test_dihedrals::TestRamachandran::test_protein_ends
    • MDAnalysisTests.analysis.test_helanal::test_warnings
    • MDAnalysisTests.coordinates.test_chainreader::TestChainReaderContinuous::test_easy_trigger_warning
    • MDAnalysisTests.utils.test_streamio::TestNamedStream_filename_behaviour::test_func[abspath]

Notes:

• Release 1.1.1 fixes an installation issue with 1.1.0. There is no published release for version 1.1.0.
• As detailed in the 1.0.0 release, the 1.x releases only include bug fix changes. New features are being developed for MDAnalysis 2.x.