nlesc-nano/auto-FOX issues and pull requests

#304 - angular distribution function - periodic boundary conditions

Issue - State: open - Opened by bananenpampe 3 months ago

#303 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#302 - Bump actions/setup-python from 4 to 5

Pull Request - State: open - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#301 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: open - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#300 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#299 - ENH: Add support for the `pairs_nb` directive

Pull Request - State: closed - Opened by BvB93 11 months ago - 1 comment
Labels: enhancement

#298 - ENH: Add the ability to specify custom .top atomtypes

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: enhancement

#297 - ENH: Add the `TOPContainer.generate_pairs` method for generation 1,4-pairs

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: enhancement

#296 - ENH: Add the TOPContainer class for managing .top files

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: enhancement

#295 - BUG: Multiple fixes to the xyz_to_gro recipe

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: bug

#294 - ENH: Add a new recipe for interconverting between .gro and .xyz

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: enhancement

#293 - ENH: Add a dedicated class for managing .top files

Issue - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: enhancement

#292 - ENH: Add a script for converting .xyz to .gro

Issue - State: closed - Opened by BvB93 12 months ago
Labels: enhancement

#291 - DOC: Fix the .top recipe automodule directive

Pull Request - State: closed - Opened by BvB93 12 months ago - 1 comment
Labels: documentation

#290 - ENH: Add a dedicated class for reading CHARMM .rtf files and use it in the GROMACS .top recipe

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: enhancement

#289 - ENH: Add the option the specify additional weights for system- & descriptor-specific ARMC sub-errors

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: enhancement

#288 - ENH: Add basic support for writing .top file molecule and system directives

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: enhancement

#287 - ENH: Add a workflow for converting CHARMM .rtf & .prm files into GROMACS .top files

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: enhancement

#286 - BUG: Fix potential index mismatches in the psf/molecule validation

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: bug

#285 - ENH: Add a workflow for convert CHARM .prm & .rtf files into GROMACS .top files

Issue - State: closed - Opened by BvB93 about 1 year ago
Labels: enhancement

#284 - ENH: Validate whether a psf and molecule actually match

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: enhancement

#283 - MAINT: General maintenance in preperation for Auto-FOX 1.0.0

Pull Request - State: closed - Opened by BvB93 about 1 year ago - 1 comment
Labels: Maintenance

#282 - BUG: Fix an issue with parsing multiple ligands in `generate_psf2`

Pull Request - State: closed - Opened by BvB93 over 1 year ago - 1 comment
Labels: bug

#281 - ENH: Issue a warning in the psf recipe if the qd or ligands don't have any bonds

Pull Request - State: closed - Opened by BvB93 over 1 year ago - 1 comment
Labels: enhancement

#280 - DEP: Bump qmflows and deal with deprecations

Pull Request - State: closed - Opened by BvB93 almost 2 years ago - 1 comment

#279 - BUG: Do not directly rely on PLAMS for obtaining the Boost `ArgumentError` type

Pull Request - State: closed - Opened by BvB93 almost 2 years ago - 1 comment
Labels: bug

#278 - ENH: Add special casing for zero-division in the ARMC error func

Pull Request - State: closed - Opened by BvB93 about 2 years ago - 1 comment
Labels: enhancement

#277 - ENH: Allow the .xyz parser to handle empty lines

Pull Request - State: closed - Opened by BvB93 about 2 years ago - 1 comment
Labels: enhancement

#276 - XYZ

Issue - State: closed - Opened by maxsw2 about 2 years ago - 2 comments
Labels: question

#275 - BUG: Fix improper dihedral-indices being incorrectly sorted

Pull Request - State: closed - Opened by BvB93 over 2 years ago
Labels: bug

#274 - TST: Enable windows tests

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: Tests

#273 - BUG: Fix only settings not being properly updated for PES-averaged ARMC

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#272 - BUG: Fix `DataFrame.loc` indexing failing when passed a 2-tuple

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#271 - ENH: Export warnings to the logger when running ARMC

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement, Tests

#270 - BUG: Fix the ARMC constraints solver falsely rejecting moves due to 0 division

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#269 - ENH: Print the offending atoms whenever the ARMC constraint-resolver fails

Pull Request - State: closed - Opened by BvB93 over 2 years ago
Labels: enhancement

#268 - ENH: Store the git commit hash of auto-FOX in the ARMC .hdf5 file

Pull Request - State: closed - Opened by BvB93 over 2 years ago
Labels: enhancement

#267 - BUG: Transpose the axes when returning in `get_multi_lig_center`

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#266 - BUG: Fix the param columns being incorrectly written to the .hdf5 file

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#265 - BUG: Fix PA-ARMC not correctly reshaping the acceptance array

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#264 - BUG: Fix PES-averaged ARMC failing to create multiple `ParamMapping` columns

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#263 - ENH: Add a workflow for computing Debye scattering

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#262 - BUG: Fix atom-pairs not being sorted if certain parameters are guessed

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#261 - REL: Update `master` branch after release (0.10.1)

Pull Request - State: closed - Opened by BvB93 over 2 years ago

#260 - TST: Add tests for python 3.10

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 2 comments
Labels: Tests

#259 - REL: Release Auto-FOX 0.10.0

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: release

#258 - ENH: Round the net charge to the nearest integer

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#257 - ENH: Add the new `atom_pairs` keyword to `init_rdf` and `init_adf`

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#256 - ENH: Add error functions based on non-mse errors

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#255 - BUG: Fixed an issue wherein dataframes were summed along the wrong axis

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#254 - BUG: Fixed an issue wherein auto-FOX would not check the status of jobs

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: bug

#253 - MAINT,ENH: Rework the auto-FOX properties system

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement, Maintenance

#252 - ENH: Add two new error functions

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#251 - BLD: Make `rdkit` an optional dependency (again)

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment

#250 - ENH: Add a `max`-based error function

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#249 - ENH: Allow users to pass custom error functions

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement, Work in Progress

#248 - ENH: Allow users to provide custom error functions

Issue - State: closed - Opened by BvB93 over 2 years ago - 1 comment
Labels: enhancement

#247 - BLD: Bump the PLAMS minimum version to >= 1.5.1

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment

#246 - MAINT: Raise a `ValueError` if an atom type with multiple charges is found

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Maintenance

#245 - BUG: Fixed an issue wherein init_power_spectrum could raise when the atom subset is specified

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: bug, enhancement

#244 - ENH: Add a timestep parameter to `MultiMolecule.init_power_spectrum`

Issue - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: enhancement

#243 - TST: Refactor the `get_non_bonded` tests

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: Tests

#242 - ENH: Add a new `MultiMolecule` method for constructing supercells

Pull Request - State: closed - Opened by BvB93 almost 3 years ago - 1 comment
Labels: enhancement

#241 - REL: Auto-FOX 0.9.1

Pull Request - State: closed - Opened by BvB93 about 3 years ago
Labels: release

#240 - BUG: Fixed an issue wherein frozen atomic charges were ignored when not explicitly specified

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#239 - ENH: Added the new `segment_dict` parameter to the `PSFContainer.generate_x()` functions

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#238 - BUG: Fixed in issue wherein `PSFContainer.sort_values` did not not update the residue ID

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#237 - ENH: Add the new `PSFContainer.sort_values` method

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#236 - ENH: Use the bond length rather than the bond order in the `sparse_bond_matrix` output

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#235 - BUG: Fixed an issue wherein net charges weren't properly conserved in PES-averaged ARMC

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#234 - DOC,TST: Fix the CI failure for the new sphinx 4.0.0b1 pre-release

Issue - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: documentation, Tests

#233 - ENH: Store metadata and net charges for each individual system in PES-averaged ARMC and ARMCPT

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: enhancement

#232 - BUG: Fixed an issue wherein guessed parameters would overwrite ones that were explicitly specified

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#231 - MAINT: Write the super-/sub-iteration after updating all other datasets

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: Maintenance

#230 - BUG: FIxed an issue wherein frozen parameters weren't properly sorted

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#229 - BUG: Fixed an issue wherein the mean pair-density was computed using lattice vectors in non-periodic calculations

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 1 comment
Labels: bug

#228 - REL: Auto-FOX 0.9.0

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: release