nlesc-nano/CAT issues and pull requests

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

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

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

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

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

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

#265 - Bump actions/checkout from 3 to 4

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

#264 - MAINT: Get rid `pkg_resources`

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

#263 - ENH: Add the option to disable ligand canonicalization

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

#262 - Ligand order in CAT

Issue - State: closed - Opened by RobertaPascazio almost 2 years ago - 1 comment
Labels: enhancement

#261 - Failed to employ polyatomic core anchors

Issue - State: open - Opened by juliette1996 about 2 years ago - 4 comments
Labels: question

#260 - BLD: Bump the minimum QMFlows version to 0.12.0

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

#259 - ENH: Add support for polyatomic core anchors

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

#258 - BUG: Investigate potential PLAMS-related failures

Issue - State: open - Opened by BvB93 over 2 years ago
Labels: bug

#257 - REL: Bump CAT to 1.0.0

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

#256 - ENH: Lay the groundwork fork for the Nano-CAT ligand branching workflow

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

#255 - Changing only ligand chain

Issue - State: closed - Opened by juliette1996 over 2 years ago - 1 comment
Labels: enhancement

#254 - REL: Prepare for CAT 0.11.0 release

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

#253 - TST: Update the `test_multi_ligand` coordinates

Issue - State: open - Opened by BvB93 over 2 years ago
Labels: Tests

#252 - BUG: Fix the `anchor.kind = "mean"` keyword being broken

Pull Request - State: closed - Opened by BvB93 over 2 years ago - 3 comments
Labels: bug

#251 - optional.ligand.anchor.mean

Issue - State: closed - Opened by juliette1996 over 2 years ago

#250 - BUG: Only disable the rdkit `SANITIZE_ADJUSTHS` when strictly required

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

#249 - BUG: Fix the ligand conformation optimizer failing for certain cyclic systems

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

#248 - ENH: Set the default Indium (formal) charge to 3+

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

#247 - BUG: Fix the CAT logger failing to write to stdout

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

#246 - ENH: Improve the ligand conformation search

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

#245 - ENH: Improve the ligand conformation search

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

#244 - TST: Let `assert_mol_allclose` check for both bonds and lattices as well as atomic coordinates

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

#243 - TST,ENH: Add a function for checking if the coordinates of two molecules are equal within a given tolerance

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

#242 - TST: Re-enable windows tests

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

#241 - ENH: Minor improvements to computing the ligand conformer optimization cost function

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

#240 - ENH: Add the `remove_anchor_hydrogens` option to the cone-angle workflow

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

#239 - ENH: Add a new workflow for computing ligand cone angles

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

#238 - ENH: Improve the optimized geometries of linear ligands

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

#237 - ENH: When optimizing ligand conformations, fully relax the geometry before computing the cost function

Pull Request - State: closed - Opened by BvB93 about 3 years ago - 2 comments
Labels: enhancement

#236 - Name too long

Issue - State: open - Opened by juliette1996 about 3 years ago

#235 - BUG: Ensure that the ligand is properly aligned after PLAMS optimizations

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

#234 - BUG: FIx an issue wherein optimized geometries were not correctly written to the .hdf5 file

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

#233 - ENH: Allow multiple values for the bulkiness latice spacing

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

#232 - ENH: Add the `anchor.multi_anchor_filter` option

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

#231 - BUG: Fixed an issue where certain properties could not be extracted from CP2K frequency jobs

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

#230 - ENH: Add the ``qd.dissociate.qd_opt`` keyword

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

#229 - BUG: Fix thermochemical properties not properly being set to `nan` for crashed jobs

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

#228 - REL: Update `master` branch after CAT 0.10.3 release

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

#227 - ENH: Expose a keyword for the BDE XYn-preoptimization

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

#226 - BUG: Fix the BDE `core_atom` and `lig_count` keys not being optional

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

#225 - ENH: Allow the BDE workflow to parse qmflows-style generic keywords

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

#224 - ENH: Allow `core.allignment: "surface"` for cores with <4 anchor atoms

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

#223 - REL: Update `master` branch after 0.10.2 release

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

#222 - REL: Prepare for CAT 0.10.2

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

#221 - BLD: Allow installing `CAT` without the use of conda

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

#220 - BLD: Add minimum versions to more packages

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

#219 - BUG: Fix an issue wherein anchor-group-parsing could fail for mono-atomic anchors

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

#218 - BUG: Disable the `PNG` and `PNG_FILE` anchor format options for RDKit <2020.09.01

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

#217 - TST: Add a mypy run to the linting checks

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

#216 - ENH: Allow specifying the format type of the anchor `group`

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

#215 - ENH: Allow specifying dummy atoms as anchor group

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

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

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

#213 - DOC: Do not use conda when building RTD docs

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

#212 - MAINT: Backport the PLAMS <= 1.5.1 `Molecule.get_formula` method

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

#211 - ENH: Bring the core anchoring options up to par with its ligand-based counterpart

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

#210 - ENH: Bring the core anchor options up to par with its ligand anchor counterpart

Issue - State: closed - Opened by BvB93 about 3 years ago - 2 comments
Labels: enhancement

#209 - TST: Add a dedicated CI job for pre-releases

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

#208 - ENH,WIP: Add an option for inverting the core vectors

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

#207 - MAINT: Do not modify global logging settings when configuring the CAT logger

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

#206 - TST: Update coordinates for RDKit 2021.03.4

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

#205 - TST: Improve the test coverage for the anchor input parsing

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

#204 - ENH: Allow specification of a fixed ligand-vector dihedral angle

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

#203 - TST: Debugging

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

#202 - ENH: Add the `angle_offset` option for manually rotating ligand vectors

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

#201 - TST: Move test dependencies to pypi

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

#200 - REL: Release CAT 0.10.0

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

#199 - ENH: Add basic support for (pseudo-)multi-dentate ligands

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

#198 - BLD: Reintroduce support for Python 3.6

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

#197 - TST: Fix the macos python 3.9 CI failure

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

#196 - ENH: Lay the groundwork for improved ligand `anchor` parsing

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

#195 - TST: CI maintenance

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

#194 - MAINT: Fix AMS 2021 related problems

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

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

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

#192 - BUG: Fixed an issue wherein loading previous jobs could fail

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

#191 - MAINT: Add a safeguard against too long files when creating .xyz/.pdb files

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

#190 - BUG: Fixed an issue wherein `substructure_split` could fail

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

#189 - MAINT: Fixed an issue wherein `split_mol` could iterate through atoms in a pseudo-random manner

Pull Request - State: closed - Opened by BvB93 over 3 years ago

#188 - BUG: Use all rdkit sanitize flags when importing input compounds

Pull Request - State: closed - Opened by BvB93 over 3 years ago - 1 comment
Labels: bug, Work in Progress

#187 - BUG: Fixed an issue wherein small cores would fail with the `cKDTree`

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#186 - MAINT: Raise a `NotImplementedError` if a core has an insufficient number of anchors

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: Maintenance

#185 - BUG: FIxed an issue wherein bondorders would be ignored by `AMSJob`

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#184 - BUG: Fixed an issue where truth testing could fail for `str`-based arrays

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: bug

#183 - ENH: Allow `qd.optimize.job2` to be `None`

Pull Request - State: closed - Opened by BvB93 almost 4 years ago - 1 comment
Labels: enhancement

#182 - Issue with ADF environmental variables

Issue - State: closed - Opened by felipeZ about 4 years ago - 5 comments

#181 - ENH: Expose the `distribution` module to the main CAT namespace

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#180 - TST: Freeze the pip version

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: Tests

#179 - HDF5 error running CAT

Issue - State: closed - Opened by felipeZ about 4 years ago

#178 - Error Running when there is a network file system

Issue - State: open - Opened by felipeZ about 4 years ago

#177 - MAINT: Do not call `os.path.abspath()` when loading jobs

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: Maintenance

#176 - ENH: Dump all local variables in the logger whenever an exception is encountered

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#175 - ENH: Added the new `bulkiness.h_lim` and `bulkiness.d` options

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#174 - DOC: Mock rdkit when building the documentation

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 2 comments
Labels: documentation

#173 - DOC: Added documentation for the new entropy recipe

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: documentation

#172 - MAINT: Relax the PLAMS version

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: Maintenance

#171 - Error specifying custom job type

Issue - State: closed - Opened by felipeZ about 4 years ago - 4 comments

#170 - ENH: Added the `validate_only` keyword to `validate_input()`

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 1 comment
Labels: enhancement

#169 - ENH: Ensure that CAT settings can be validated multiply times without raising exceptions

Pull Request - State: closed - Opened by BvB93 about 4 years ago - 2 comments
Labels: enhancement

GitHub / nlesc-nano/CAT issues and pull requests