Code

Release 2023.4.0#184

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Merged

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

+5,661-892

Commits

Commits on Jun 29, 2023

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

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  7fe12f5

Commits on Jun 30, 2023

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

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  4dc3969

Commits on Jul 3, 2023

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

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  a0c7df7

• Update Python variants for development builds.

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  84a4882

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

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  bddd28d

• Merge pull request #125 from OpenBioSim/fix_124

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  5eb871f

Commits on Jul 7, 2023

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

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  committed
  39b3b82

• Update search.

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  009bb8f

• Blacken.

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  0eb2c7b

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

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  46de830

• Pass work_dir to Plumed constructor as a string.

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  committed
  8aee0e8

• Merge pull request #128 from OpenBioSim/fix_tutorials

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  authored
  637c462

Commits on Jul 10, 2023

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

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  ee5cad7

• Increase distance tolerance in test.

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  5dae34c

Commits on Jul 11, 2023

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

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  committed
  6000c22

• Merge pull request #133 from OpenBioSim/fix_132

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  authored
  6eb3ce2

• Merge pull request #135 from OpenBioSim/fix_134

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  authored
  cdfbbbf

Commits on Jul 13, 2023

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

  mb2055

  committed
  d25022e

• Fix the extract in the gmx.process

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  xiki-tempula

  committed
  d9c37e6

Commits on Jul 14, 2023

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

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  xiki-tempula

  authored
  0c7601f

• Merge pull request #138 from OpenBioSim/fix_137

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  mb2055

  authored
  d7f3c5c

Commits on Jul 25, 2023

• Update issue template. [ci skip]

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  376966d

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

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  committed
  89bf399

Commits on Jul 26, 2023

• Merge pull request #143 from OpenBioSim/feature_139

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  authored
  10d39ec

Commits on Jul 31, 2023

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

  

  msuruzhon

  authored and

  Miroslav Suruzhon

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  64183f8

Commits on Aug 1, 2023

• Fix use of totalSteps in OpenMM StateDataReporter.

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  lohedges

  committed
  86244be

• Fix totalSteps for minimisation protocol.

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  committed
  ff55b2a

• Need to use totalSteps=1.

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  committed
  5df899e

• Merge pull request #146 from OpenBioSim/fix_145

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  authored
  d36e73c

• Add support for trajectory RMSD calculations with Sire.

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  committed
  9aeebb3

• Modify test so that it passes for debugging purposes.

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  committed
  d89be54

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

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  430467d

Commits on Aug 2, 2023

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

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  committed
  3a18893

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

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  committed
  92a815c

• Optimise by avoiding duplication of water topology check.

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  committed
  a702a6b

• Make sure property map is passed using keyword formatting.

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  committed
  f470d23

• Further optimisations by avoiding duplicate water topology checks.

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  67531fc

Commits on Aug 3, 2023

• Use new Sire trajectory RMSD API.

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  committed
  0e353be

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

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  committed
  c773e29

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

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  committed
  8c4f38c

• Merge branch 'fix_148' into feature_crystal_water

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  committed
  e5ae912

Commits on Aug 4, 2023

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

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  committed
  a5e326d

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

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  committed
  8f6c2fb

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

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  c36b04b

Commits on Aug 7, 2023

• Remove debug statement.

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  committed
  28f97d7

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

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  committed
  837937a

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

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  committed
  01b1924

• Merge pull request #151 from OpenBioSim/fix_150

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  authored
  686141c

• Merge branch 'devel' into feature_crystal_water

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  committed
  96f96b0

• Allow user to choose topology compatibility during parameterisation.

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  committed
  0c3cac0

Commits on Aug 8, 2023

• Merge branch 'devel' into feature_sire_trajectory_rmsd

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  committed
  55cd074

• Only return incompatible molecule if makeCompatibleWith fails.

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  committed
  da215b0

• Merge pull request #152 from OpenBioSim/feature_sire_trajectory_rmsd

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  lohedges

  authored
  40db118

• Merge branch 'devel' into feature_crystal_water

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  committed
  0f00eeb

Commits on Aug 9, 2023

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

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  committed
  8d11aec

• Merge branch 'devel' into feature_crystal_water

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  committed
  bfa5360

• Add tutorial section for crystal waters.

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  committed
  8cd856d

• Pass property map as a keyword argument.

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  committed
  ff36bb4

Commits on Aug 10, 2023

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

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  committed
  850fb06

• Assert alchemlyb is imported when used as analysis method.

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  committed
  8d98b6a

• Use internal command_split utility function.

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  committed
  6f84111

• Expose threshold to instance checkOverlap method.

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  committed
  a623f59

• Remove debug pickle file.

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  committed
  aaf4f63

• Fix indentation of conditional block.

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  committed
  5742d67

• Fix case in string comparison.

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  committed
  06b3964

• Fix extraction of SOMD TI data.

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  committed
  8a23197

• Handle different data type for alchemlyb 2+.

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  committed
  70c10bc

• Fix use of alchemlyb extract functions following refactor.

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  committed
  b906f70

• Grammar tweak.

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  53d8fe2

Commits on Aug 11, 2023

• Reorder member functions.

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  committed
  e757cad

• Silence excessive pymbar warnings on startup.

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  2787f90

• Add FEP analysis unit test.

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  79856c1

• Unpin alchemlyb requirement.

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  813dfba

• Add alchemlyb requirement.

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  cbc244d

• Change dictionary name.

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  22be4e1

• Formatting tweak.

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  committed
  68a13d4

• Remove GROMACS version check since meaningless in a staticmethod.

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  committed
  9f69f2a

• Check GROMACS is installed when performing native analysis.

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  committed
  b05f707

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

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  committed
  1849ee4

• Use pathlib for OS agnostic file globbing.

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  committed
  8872354

• No need to wrap partial in a staticmethod.

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  d6068b5

• Blacken.

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  2da1660

Commits on Aug 14, 2023

• Refactor to provide separate u_nk and dhdl extraction functions.

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  committed
  c835706

Commits on Aug 15, 2023

• Fix comments. [ci skip]

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  committed
  0ab909c

Commits on Aug 16, 2023

• Make the saveMetric method more robust (#19)

  Show description for 1f1802a
  xiki-tempula

  authored
  1f1802a

Commits on Aug 21, 2023

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

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  f3a6d82

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

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  committed
  19343e4

• Handle different connectivity in either end state.

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  committed
  fb42edb

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

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  committed
  7cc2d8a

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

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  committed
  594210f

Commits on Aug 22, 2023

• Allow support for different engines for analysis only.

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  committed
  e6c2ee9

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

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  committed
  0b97a4a

• Use try/except on NumPy array conversion.

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  committed
  42ebe5a

Commits on Aug 23, 2023

• Merge pull request #157 from OpenBioSim/fix_merge_connectivity

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  lohedges

  authored
  a13c1e2

• Use a shared property for file format.

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  committed
  5e5bb53

• Handle shared properties on read.

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  committed
  fe5e17c

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

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  committed
  a614ac9

• No need to set and add property.

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  committed
  616a7eb

Commits on Aug 24, 2023

• Merge pull request #160 from OpenBioSim/fix_159

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  lohedges

  authored
  6fdda73

Commits on Sep 1, 2023

• Ensure that SOMD pert files are always correct for ABFE

  Show description for c37f9e2
  

  Finlay Clark

  committed
  c37f9e2

• Merge some recent bugfixes (#24)

  msuruzhon

  authored
  f328386

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

  lohedges

  committed
  9f522d7

• Merge pull request #164 from fjclark/bugfix_somd_pert_files

  Show description for e26d2d0
  lohedges

  authored
  e26d2d0

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

  lohedges

  committed
  3c3129c

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

  Show description for a5c5e1e
  lohedges

  committed
  a5c5e1e

Commits on Sep 2, 2023

• Fix reduced potential calculation. [ci skip]

  lohedges

  committed
  6358a4b

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

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  committed
  eba8da2

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

  lohedges

  committed
  bd4a680

Commits on Sep 4, 2023

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

  Show description for 24bbaa0
  

  Miroslav Suruzhon

  committed
  24bbaa0

Commits on Sep 7, 2023

• Remove note regarding reduction rounding bias.

  lohedges

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  bd77d4e

• Update expected box angles in test.

  lohedges

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  0930573

• Add methods to rotate and reduce box vectors.

  lohedges

  committed
  7e79b8b

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

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  d01d82f

• Use correct property name to avoid confusion.

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  a04ec64

• Update space property in system following rotation.

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  committed
  e3dced0

• Grammar tweak.

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  1abdc4e

Commits on Sep 12, 2023

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

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  f70ee55

• Add unit test for triclinic box vector rotation.

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  38a88e0

• Add comment regarding unchanged angles.

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  b392af9

Commits on Sep 14, 2023

• Decouple custom parameters and additional LEaP commands.

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  lohedges

  committed
  fe7ab04

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

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  committed
  db24da9

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

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  committed
  41a132a

Commits on Sep 15, 2023

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

  lohedges

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  b7c6627

• Update expected box angles in test.

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  committed
  a181413

Commits on Sep 18, 2023

• Added some fixes to the solvation (#25)

  Show description for f9bed33
  

  msuruzhon

  and

  lohedges

  authored
  f9bed33

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

  xiki-tempula

  committed
  f1f5276

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

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  xiki-tempula

  committed
  55bb6fc

• Merge pull request #169 from OpenBioSim/fix_168

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  lohedges

  authored
  be48fe8

• remove skip

  xiki-tempula

  committed
  591a535

• fix import

  xiki-tempula

  committed
  e82f367

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

  Show description for 05667a2
  xiki-tempula

  authored
  05667a2

• Simplify expresssion. [ci skip]

  lohedges

  committed
  3357367

• Fix gradient unit for SOMD TI analysis.

  lohedges

  committed
  12c2806

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

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  3786be3

• Update expected TI result in test.

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  4a1f7ea

• Merge branch 'devel' into feature_analysis

  lohedges

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  2320fc7

• Merge branch 'devel' into feature_167

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  committed
  1d9bdf7

Commits on Sep 19, 2023

• Merge pull request #154 from OpenBioSim/feature_crystal_water

  Show description for 65045f0
  lohedges

  authored
  65045f0

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

  lohedges

  committed
  563f1ee

• Merge branch 'devel' into feature_reduce

  lohedges

  committed
  8dcc8bc

• Fix test in devel (#27)

  Show description for d5e28e8
  xiki-tempula

  authored
  d5e28e8

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

  Show description for 20da673
  xiki-tempula

  authored
  20da673

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

  Show description for 3c4a23d
  xiki-tempula

  authored
  3c4a23d

Commits on Sep 20, 2023

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

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  lohedges

  committed
  8f3f910

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

  Show description for 8aa7426
  lohedges

  committed
  8aa7426

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

  lohedges

  committed
  a2619d8

• Merge pull request #173 from OpenBioSim/fix_172

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  authored
  e3014dc

Commits on Sep 22, 2023

• Merge pull request #170 from OpenBioSim/feature_167

  Show description for 44def0b
  lohedges

  authored
  44def0b

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

  lohedges

  committed
  b321c13

• Merge branch 'devel' into feature_reduce

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  691ad64

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

  lohedges

  committed
  c74693a

• Merge pull request #175 from OpenBioSim/feature_reduce

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  lohedges

  authored
  3a4c5ca

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

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  committed
  5e61d49

Commits on Sep 26, 2023

• Simplify SOMD2 analysis following to_alchemlyb Pandas conversion.

  Show description for 110fd04
  lohedges

  committed
  110fd04

• Simplify TI gradient calculation. [ci skip]

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  f691d4c

Commits on Sep 27, 2023

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

  Show description for 8debf89
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  committed
  8debf89

Commits on Sep 29, 2023

• Remove redundant imports. [ci skip]

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  015c6ab

Commits on Oct 2, 2023

• Add equality operators.

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  b757035

• Fix docstring formatting.

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  62f28f0

Commits on Oct 3, 2023

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

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  3738ec9

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

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  dccb4fb

• Fixed conditional block.

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  b764f84

• Standardise exception message.

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  56a4480

• Fix Copilot error.

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  58ad468

• Add missing equality operators and attribute comparisons.

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  25ba5aa

• Add tests for protocol instantiation equivalence.

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  ff1fa23

Commits on Oct 6, 2023

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

  Show description for d29be4d
  lohedges

  committed
  d29be4d

Commits on Oct 11, 2023

• Merge pull request #179 from OpenBioSim/feature_string_protocol

  Show description for 85c71bc
  lohedges

  authored
  85c71bc

• Merge pull request #181 from OpenBioSim/fix_180

  Show description for 527b5f6
  lohedges

  authored
  527b5f6

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

  lohedges

  committed
  cd8095c

• review small fixes

  annamherz

  committed
  2782ab9

• Merge pull request #182 from annamherz/feature_analysis

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  lohedges

  authored
  607f0c4

• Formatting tweak. [ci skip]

  lohedges

  committed
  44cd871

Commits on Oct 12, 2023

• Skip Sire MCS fallback on Windows since currently unsupported.

  lohedges

  committed
  7dd1dae

• Merge pull request #155 from OpenBioSim/feature_analysis

  Show description for 60feb0d
  lohedges

  authored
  60feb0d

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

  lohedges

  committed
  2d4d01a

• Increase distance tolerance.

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  lohedges

  committed
  b9f1c84

• Guard tests against missing packages.

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  committed
  4cceb23

Commits on Oct 13, 2023

• Merge pull request #183 from OpenBioSim/sync_exscientia

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  lohedges

  authored
  a203510

• Merge branch 'main' into release_2023.4.0

  lohedges

  committed
  663ce2f

• Update Sire version.

  lohedges

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  95d81d6

• Update Python variants.

  lohedges

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  cc5556e

• Update CHANGELOG for the 2023.4.0 release.

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