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Release 2023.4.0#184

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lohedges merged 183 commits intomainOpenBioSim/biosimspace:mainfrom release_2023.4.0OpenBioSim/biosimspace:release_2023.4.0Copy head branch name to clipboardOct 13, 2023

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Commits

Commits on Jun 29, 2023

• Update Sire requirement to 2023.4.0.dev. [ci skip]

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Commits on Jun 30, 2023

• Merge branch 'main' into devel [ci skip]

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Commits on Jul 3, 2023

• Check for non-periodic cartesian space. [closes #124]

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• Update Python variants for development builds.

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• Exclude all but the latest Python from all but Linux.

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• Merge pull request #125 from OpenBioSim/fix_124

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Commits on Jul 7, 2023

• Allow user to specify backend in process.getTrajectory()

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• Update search.

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• Blacken.

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• Fix PLUMED version check. [closes OpenBioSim/BioSimSpaceTutorials#35]

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• Pass work_dir to Plumed constructor as a string.

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• Merge pull request #128 from OpenBioSim/fix_tutorials

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Commits on Jul 10, 2023

• Import correct alchemlyb extract function. [closes #132]

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• Increase distance tolerance in test.

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Commits on Jul 11, 2023

• Reduce box vectors using OpenMM code to avoid rounding issue.

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• Merge pull request #133 from OpenBioSim/fix_132

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• Merge pull request #135 from OpenBioSim/fix_134

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Commits on Jul 13, 2023

• Fixed OpenMM compatibility in BSSEqBoundNode.ipynb. [ci skip]

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• Fix the extract in the gmx.process

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Commits on Jul 14, 2023

• Merge pull request #17 from Exscientia/feat_2023.3

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• Merge pull request #138 from OpenBioSim/fix_137

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Commits on Jul 25, 2023

• Update issue template. [ci skip]

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• Add support for aligning principal axes of system to solvent box.

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Commits on Jul 26, 2023

• Merge pull request #143 from OpenBioSim/feature_139

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Commits on Jul 31, 2023

• Fixed squash and unsquash in the case of explicit dummies (#18)

  

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Commits on Aug 1, 2023

• Fix use of totalSteps in OpenMM StateDataReporter.

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• Fix totalSteps for minimisation protocol.

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• Need to use totalSteps=1.

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• Merge pull request #146 from OpenBioSim/fix_145

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• Add support for trajectory RMSD calculations with Sire.

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• Modify test so that it passes for debugging purposes.

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• Just align to first molecule for now. Make molecules whole on load.

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Commits on Aug 2, 2023

• Update water topology for Gro87 format. [ref #148]

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• Add parameter to allow user to optionally match water naming convention.

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• Optimise by avoiding duplication of water topology check.

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• Make sure property map is passed using keyword formatting.

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• Further optimisations by avoiding duplicate water topology checks.

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Commits on Aug 3, 2023

• Use new Sire trajectory RMSD API.

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• Update test to use atoms spanning multiple molecules as a reference.

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• Exclude crystal waters from genion and allow user to preserve water.

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• Merge branch 'fix_148' into feature_crystal_water

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Commits on Aug 4, 2023

• Allow user to preserve water topology on solvation and write.

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• Add charged example system to ensure crystal waters aren't removed.

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• Use property map to specify crystal water residue name and skip flag.

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Commits on Aug 7, 2023

• Remove debug statement.

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• Try to disable MDAnalysis logging, although this doesn't appear to work.

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• Remove redundant attributes and imports. [closes #150]

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• Merge pull request #151 from OpenBioSim/fix_150

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• Merge branch 'devel' into feature_crystal_water

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• Allow user to choose topology compatibility during parameterisation.

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Commits on Aug 8, 2023

• Merge branch 'devel' into feature_sire_trajectory_rmsd

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• Only return incompatible molecule if makeCompatibleWith fails.

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• Merge pull request #152 from OpenBioSim/feature_sire_trajectory_rmsd

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• Merge branch 'devel' into feature_crystal_water

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Commits on Aug 9, 2023

• Don't disable MDAnalysis logging. It doesn't work and is confusing.

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• Merge branch 'devel' into feature_crystal_water

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• Add tutorial section for crystal waters.

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• Pass property map as a keyword argument.

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Commits on Aug 10, 2023

• First pass at porting @annamherz's analysis code.

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• Assert alchemlyb is imported when used as analysis method.

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• Use internal command_split utility function.

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• Expose threshold to instance checkOverlap method.

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• Remove debug pickle file.

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• Fix indentation of conditional block.

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• Fix case in string comparison.

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• Fix extraction of SOMD TI data.

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• Handle different data type for alchemlyb 2+.

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• Fix use of alchemlyb extract functions following refactor.

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• Grammar tweak.

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Commits on Aug 11, 2023

• Reorder member functions.

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• Silence excessive pymbar warnings on startup.

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• Add FEP analysis unit test.

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• Unpin alchemlyb requirement.

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• Add alchemlyb requirement.

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• Change dictionary name.

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• Formatting tweak.

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• Remove GROMACS version check since meaningless in a staticmethod.

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• Check GROMACS is installed when performing native analysis.

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• Fix ridiculous Copilot case adjustments. (What was it doing?)

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• Use pathlib for OS agnostic file globbing.

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• No need to wrap partial in a staticmethod.

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• Blacken.

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Commits on Aug 14, 2023

• Refactor to provide separate u_nk and dhdl extraction functions.

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Commits on Aug 15, 2023

• Fix comments. [ci skip]

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Commits on Aug 16, 2023

• Make the saveMetric method more robust (#19)

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Commits on Aug 21, 2023

• Remove end state connectivy properties if they are the same.

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• Add test to make sure only a single connectivity property is present.

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• Handle different connectivity in either end state.

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• Add @annamherz's suggestions. [ci skip]

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• Relative class isn't private. [ci skip]

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Commits on Aug 22, 2023

• Allow support for different engines for analysis only.

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• Make sure np.matrix is used for all overlap objects.

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• Use try/except on NumPy array conversion.

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Commits on Aug 23, 2023

• Merge pull request #157 from OpenBioSim/fix_merge_connectivity

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• Use a shared property for file format.

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• Handle shared properties on read.

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• Add shared space property when converting to OpenMM format. [ref #159]

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• No need to set and add property.

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Commits on Aug 24, 2023

• Merge pull request #160 from OpenBioSim/fix_159

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Commits on Sep 1, 2023

• Ensure that SOMD pert files are always correct for ABFE

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  Finlay Clark

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• Merge some recent bugfixes (#24)

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• Add support for generating SOMD2 input. [ci skip]

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• Merge pull request #164 from fjclark/bugfix_somd_pert_files

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• Simplify SOMD data to dataframe conversion. [ci skip]

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• Add initial support for SOMD2 FEP analysis. [ci skip]

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Commits on Sep 2, 2023

• Fix reduced potential calculation. [ci skip]

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• Convert dataframe column index to float. [ci skip]

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• Drop NaN values from returned dataframes. [ci skip]

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Commits on Sep 4, 2023

• Revert "Merge some recent bugfixes (#24)"

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  Miroslav Suruzhon

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Commits on Sep 7, 2023

• Remove note regarding reduction rounding bias.

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• Update expected box angles in test.

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• Add methods to rotate and reduce box vectors.

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• Allow user to rotate and/or reduce box on read.

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• Use correct property name to avoid confusion.

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• Update space property in system following rotation.

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• Grammar tweak.

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Commits on Sep 12, 2023

• Allow user to specify the box origin for rotation of vector properties.

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• Add unit test for triclinic box vector rotation.

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• Add comment regarding unchanged angles.

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Commits on Sep 14, 2023

• Decouple custom parameters and additional LEaP commands.

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• Allow user to compute delta G between single leg end states. [ci skip]

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• Fix use of wrong error variable. [ci skip]

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Commits on Sep 15, 2023

• Don't generate velocities when performing a continuation. [closes #168]

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• Update expected box angles in test.

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Commits on Sep 18, 2023

• Added some fixes to the solvation (#25)

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• Fixed PBC fixing when unsquashing for dummy atoms (#20)

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• Have amber process write binary RST file instead of text rst7 file (#22)

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• Merge pull request #169 from OpenBioSim/fix_168

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• remove skip

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• fix import

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• Merge pull request #26 from Exscientia/feat_merge_0.9.2

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• Simplify expresssion. [ci skip]

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• Fix gradient unit for SOMD TI analysis.

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• Remove redundant code and fix gradient units for SOMD2 TI analysis.

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• Update expected TI result in test.

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• Merge branch 'devel' into feature_analysis

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• Merge branch 'devel' into feature_167

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Commits on Sep 19, 2023

• Merge pull request #154 from OpenBioSim/feature_crystal_water

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• Merge branch 'devel' into feature_analysis [ci skip]

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• Merge branch 'devel' into feature_reduce

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• Fix test in devel (#27)

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• Fix the tests such that it no longer require the working directory to be the root directory (#28)

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• Add a function for marking the alchemical ion (#30)

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Commits on Sep 20, 2023

• Don't replace original space if loaded system has Cartesian space.

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• Make sure space isn't replaced when parsing trajectory frames too.

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• Try to get the space information from the trajectory file.

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• Merge pull request #173 from OpenBioSim/fix_172

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Commits on Sep 22, 2023

• Merge pull request #170 from OpenBioSim/feature_167

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• Merge branch 'devel' into feature_analysis. [ci skip]

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• Merge branch 'devel' into feature_reduce

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• Operate on a copy of the system to avoid breaking later test.

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• Merge pull request #175 from OpenBioSim/feature_reduce

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• Merge branch 'devel' into feature_analysis [ci skip]

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Commits on Sep 26, 2023

• Simplify SOMD2 analysis following to_alchemlyb Pandas conversion.

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• Simplify TI gradient calculation. [ci skip]

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Commits on Sep 27, 2023

• Sire DataFrames now correctly use floats for fep-lamda and columns.

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Commits on Sep 29, 2023

• Remove redundant imports. [ci skip]

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Commits on Oct 2, 2023

• Add equality operators.

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• Fix docstring formatting.

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Commits on Oct 3, 2023

• Protocol options can be passed as floats and add equality operators.

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• Allow delta in equality due to rounding on unit conversion.

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• Fixed conditional block.

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• Standardise exception message.

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• Fix Copilot error.

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• Add missing equality operators and attribute comparisons.

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• Add tests for protocol instantiation equivalence.

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Commits on Oct 6, 2023

• Always set gpu = 0, since it is an index into CUDA_VISIBLE_DEVICES.

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Commits on Oct 11, 2023

• Merge pull request #179 from OpenBioSim/feature_string_protocol

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• Merge pull request #181 from OpenBioSim/fix_180

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• Merge branch 'devel' into feature_analysis [ci skip]

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• review small fixes

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• Merge pull request #182 from annamherz/feature_analysis

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• Formatting tweak. [ci skip]

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Commits on Oct 12, 2023

• Skip Sire MCS fallback on Windows since currently unsupported.

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• Merge pull request #155 from OpenBioSim/feature_analysis

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• Merge remote-tracking branch 'exscientia/devel' into sync_exscientia

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• Increase distance tolerance.

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• Guard tests against missing packages.

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Commits on Oct 13, 2023

• Merge pull request #183 from OpenBioSim/sync_exscientia

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• Merge branch 'main' into release_2023.4.0

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• Update Sire version.

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• Update Python variants.

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• Update CHANGELOG for the 2023.4.0 release.

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