Manual Sync of Trunk Branches #134
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Manual sync from SCM git trunk to GitHub master
David Ormrod Morley: Merge pull request 'Add github ci workflow for PLAMS SCMSUITE-9942 SO107' (!27) from DavidOrmrodMorley/SCMSUITE-9942.plams_github_ci_workflow into trunk SO-- David Ormrod Morley: Add python test versions 3.9 and 3.10 and trigger for new version tags for plams ci workflow SCMSUITE-9942 SO107 David Ormrod Morley: Fix PLAMS logger to avoid creating workdir SCMSUITE-8687 SO107 Matti Hellström: fix plams Molecule docstring SO-- Matti Hellström: rearrange/tidy plams docs, move examples and AMS to more prominent positions SO-- Matti Hellström: fix parameter interface not being used for singlepoint, allow None to 'unset' option in plams SCMJob (similar to AMSJob) SO103 David Ormrod Morley: Fix ci workflow too avoid continuing on black error SCMSUITE-9942 SO107 David Ormrod Morley: Merge pull request 'Update PLAMS examples and tests SCMSUITE-9919 SO--' (!24) from DavidOrmrodMorley/SCMSUITE-9919.plams_examples_and_tests into trunk SO-- Robert Rüger: fix the obvious noqa TODOs SCMSUITE-9942 SO-- David Ormrod Morley: Add github ci workflow for PLAMS SCMSUITE-9942 SO107 David Ormrod Morley: Add review todos for flake8 issues in PLAMS SCMSUITE-9942 SO-- David Ormrod Morley: Fix trivial flake8 issues in PLAMS SCMSUITE-9942 SO-- David Ormrod Morley: Fix cross-project links in PLAMS docs SCMSUITE-9919 SO-- David Ormrod Morley: Minor fixes for PLAMS test examples SCMSUITE-9919 SO-- David Ormrod Morley: Remove a couple more init/finish from PLAMS examples SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS examples with small fixes SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example IRSpectrumFromMD SCMSUITE-9919 SO-- David Ormrod Morley: Convert PLAMS ipynb examples subsection headings to subsubsection SCMSUITE-9919 SO-- David Ormrod Morley: Format PLAMS examples with black SCMSUITE-9919 SO-- David Ormrod Morley: Run black formatter for PLAMS generate_example script SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example numgrad SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example ADFNBO SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example ReorganizationEnergy SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example ADFFrag SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example XRD SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS misc examples SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example AMSPlumedMD SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example BandStructure SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS misc examples SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS examples AMSCalculator SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example PropertyPrediction SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example ReactionsDiscovery SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example ConformersMultipleMolecules SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example ConformersGeneration SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example TuningRangeSeparation SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example ChargeTransferIntegralsADF SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example AMSTSWorkflow SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example ExcitationsWorkflow SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example BasisSetBenchmark SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS examples for MD trajectory analysis SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example PlotCorrelation SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS example MoleculesTable SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example MoleculeSubstitution SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example ManyJobsInParallel SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example He2DissociationCurve SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example AMSSettingsSystem SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS test and example WaterOptimization SCMSUITE-9919 SO-- Paul Spiering: Merge pull request 'Allow for dipoleMoments to propagate in the hybrid engine. SO--' (!15) from hybrid_dipoles into trunk SO-- Matti Hellström: do not interpret imaxmo/MAXMOV as convergence.step reaxff-to-ams conversion SO-- David Ormrod Morley: Merge pull request 'Add template for PLAMS examples SCMSUITE-9919 SO--' (!19) from DavidOrmrodMorley/SCMSUITE-9919.plams_examples into trunk SO-- David Ormrod Morley: Run black formatter on PLAMS SCMSUITE-8687 SO107 David Ormrod Morley: Update PLAMS unit tests to skip when ams installation unavailable SCMSUITE-8687 SO107 David Ormrod Morley: Do not call clean for uninitialised jobmanager in PLAMS finish SCMSUITE-8687 SO107 Matti Hellström: use basename to extract example name in plams generate_examples (allows e.g. trailing slash in directory name) SO107 David Ormrod Morley: Update PLAMS example template readme SCMSUITE-9919 SO-- David Ormrod Morley: Update PLAMS water optimisation example SCMSUITE-9919 SO-- David Ormrod Morley: Update generate_example script to use PLAMS template files SCMSUTIE-9919 SO-- David Ormrod Morley: Add PLAMS example template files SCMSUTIE-9919 SO-- David Ormrod Morley: Convert generate_example script from bash to sh and update readme SCMSUTIE-9919 SO-- David Ormrod Morley: Add readme for PLAMS examples SCMSUTIE-9919 SO-- David Ormrod Morley: Update PLAMS test to use example water optimization notebook SCMSUITE-9919 SO-- David Ormrod Morley: Add script in PLAMS to generate doc examples from notebook and run for water optimization SCMSUITE-9919 SO-- David Ormrod Morley: Update build plams doc script SCMSUITE-9919 SO--- David Ormrod Morley: Add _explicit_init to config settings in PLAMS SCMSUITE-8687 SO107 Robert Rüger: add forgotten quotes around not yet imported JobManager class in finish() typehint SCMSUITE-8687 SO107 Robert Rüger: remove technical note from docs which is no longer true (was not true for a while already: plams importing is now just 'normal') SO-- Robert Rüger: add type hint for plams.finish() function SCMSUITE-8687 SO107 Robert Rüger: fix small type hinting issues SCMSUITE-8687 SO107 David Ormrod Morley: Update docs on PLAMS init and finish functions SCMSUITE-8687 SO-- David Ormrod Morley: Make PLAMS init and finish functions optional SCMSUITE-8687 SO-- David Ormrod Morley: Fix paths for windows in PLAMS function unit test #3 SCMSUITE-8687 SO-- David Ormrod Morley: Fix paths for windows in PLAMS function unit test #2 SCMSUITE-8687 SO-- David Ormrod Morley: Fix paths for windows in PLAMS function unit test SCMSUITE-8687 SO-- David Ormrod Morley: Reinstate support for PLAMS defaults file in code and add unit tests SCMSUITE-8687 SO107 David Ormrod Morley: Update PLAMS defaults docs SCMSUITE-8687 SO107 David Ormrod Morley: Remove usage of plams_defaults file in PLAMS SCMSUITE-8687 SO107 David Ormrod Morley: Remove plams_defaults file SCMSUITE-8687 SO107 Paul Spiering: Allow for dipoleMoments to propagate in the hybrid engine. SO-- David Ormrod Morley: Add unit tests for PLAMS kf tools SCMSUITE-8674 SO-- David Ormrod Morley: Add unit tests for PLAMS geometry tools SCMSUITE-8674 SO-- David Ormrod Morley: Add PLAMS test rkf file SCMSUITE-8674 SO-- David Ormrod Morley: Add unit tests for PLAMS Bond SCMSUITE-8674 SO-- David Ormrod Morley: Add unit tests for PLAMS Atom and minor property refactoring SCMSUITE-8674 SO--
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Description
This includes bringing in the CI pipeline for PRs
Manual sync of the commits:
David Ormrod Morley: Merge pull request 'Add github ci workflow for PLAMS SCMSUITE-9942 SO107' (!27) from DavidOrmrodMorley/SCMSUITE-9942.plams_github_ci_workflow into trunk SO--
David Ormrod Morley: Add python test versions 3.9 and 3.10 and trigger for new version tags for plams ci workflow SCMSUITE-9942 SO107
David Ormrod Morley: Fix PLAMS logger to avoid creating workdir SCMSUITE-8687 SO107
Matti Hellström: fix plams Molecule docstring SO--
Matti Hellström: rearrange/tidy plams docs, move examples and AMS to more prominent positions SO--
Matti Hellström: fix parameter interface not being used for singlepoint, allow None to 'unset' option in plams SCMJob (similar to AMSJob) SO103
David Ormrod Morley: Fix ci workflow too avoid continuing on black error SCMSUITE-9942 SO107
David Ormrod Morley: Merge pull request 'Update PLAMS examples and tests SCMSUITE-9919 SO--' (!24) from DavidOrmrodMorley/SCMSUITE-9919.plams_examples_and_tests into trunk SO--
Robert Rüger: fix the obvious noqa TODOs SCMSUITE-9942 SO--
David Ormrod Morley: Add github ci workflow for PLAMS SCMSUITE-9942 SO107
David Ormrod Morley: Add review todos for flake8 issues in PLAMS SCMSUITE-9942 SO--
David Ormrod Morley: Fix trivial flake8 issues in PLAMS SCMSUITE-9942 SO--
David Ormrod Morley: Fix cross-project links in PLAMS docs SCMSUITE-9919 SO--
David Ormrod Morley: Minor fixes for PLAMS test examples SCMSUITE-9919 SO--
David Ormrod Morley: Remove a couple more init/finish from PLAMS examples SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS examples with small fixes SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example IRSpectrumFromMD SCMSUITE-9919 SO--
David Ormrod Morley: Convert PLAMS ipynb examples subsection headings to subsubsection SCMSUITE-9919 SO--
David Ormrod Morley: Format PLAMS examples with black SCMSUITE-9919 SO--
David Ormrod Morley: Run black formatter for PLAMS generate_example script SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example numgrad SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example ADFNBO SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example ReorganizationEnergy SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example ADFFrag SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example XRD SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS misc examples SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example AMSPlumedMD SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example BandStructure SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS misc examples SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS examples AMSCalculator SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example PropertyPrediction SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example ReactionsDiscovery SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example ConformersMultipleMolecules SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example ConformersGeneration SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example TuningRangeSeparation SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example ChargeTransferIntegralsADF SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example AMSTSWorkflow SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example ExcitationsWorkflow SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example BasisSetBenchmark SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS examples for MD trajectory analysis SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example PlotCorrelation SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS example MoleculesTable SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example MoleculeSubstitution SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example ManyJobsInParallel SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example He2DissociationCurve SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example AMSSettingsSystem SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS test and example WaterOptimization SCMSUITE-9919 SO--
Paul Spiering: Merge pull request 'Allow for dipoleMoments to propagate in the hybrid engine. SO--' (!15) from hybrid_dipoles into trunk SO--
Matti Hellström: do not interpret imaxmo/MAXMOV as convergence.step reaxff-to-ams conversion SO--
David Ormrod Morley: Merge pull request 'Add template for PLAMS examples SCMSUITE-9919 SO--' (!19) from DavidOrmrodMorley/SCMSUITE-9919.plams_examples into trunk SO--
David Ormrod Morley: Run black formatter on PLAMS SCMSUITE-8687 SO107
David Ormrod Morley: Update PLAMS unit tests to skip when ams installation unavailable SCMSUITE-8687 SO107
David Ormrod Morley: Do not call clean for uninitialised jobmanager in PLAMS finish SCMSUITE-8687 SO107
Matti Hellström: use basename to extract example name in plams generate_examples (allows e.g. trailing slash in directory name) SO107
David Ormrod Morley: Update PLAMS example template readme SCMSUITE-9919 SO--
David Ormrod Morley: Update PLAMS water optimisation example SCMSUITE-9919 SO--
David Ormrod Morley: Update generate_example script to use PLAMS template files SCMSUTIE-9919 SO--
David Ormrod Morley: Add PLAMS example template files SCMSUTIE-9919 SO--
David Ormrod Morley: Convert generate_example script from bash to sh and update readme SCMSUTIE-9919 SO--
David Ormrod Morley: Add readme for PLAMS examples SCMSUTIE-9919 SO--
David Ormrod Morley: Update PLAMS test to use example water optimization notebook SCMSUITE-9919 SO--
David Ormrod Morley: Add script in PLAMS to generate doc examples from notebook and run for water optimization SCMSUITE-9919 SO--
David Ormrod Morley: Update build plams doc script SCMSUITE-9919 SO---
David Ormrod Morley: Add _explicit_init to config settings in PLAMS SCMSUITE-8687 SO107
Robert Rüger: add forgotten quotes around not yet imported JobManager class in finish() typehint SCMSUITE-8687 SO107
Robert Rüger: remove technical note from docs which is no longer true (was not true for a while already: plams importing is now just 'normal') SO--
Robert Rüger: add type hint for plams.finish() function SCMSUITE-8687 SO107
Robert Rüger: fix small type hinting issues SCMSUITE-8687 SO107
David Ormrod Morley: Update docs on PLAMS init and finish functions SCMSUITE-8687 SO--
David Ormrod Morley: Make PLAMS init and finish functions optional SCMSUITE-8687 SO--
David Ormrod Morley: Fix paths for windows in PLAMS function unit test #3 SCMSUITE-8687 SO--
David Ormrod Morley: Fix paths for windows in PLAMS function unit test #2 SCMSUITE-8687 SO--
David Ormrod Morley: Fix paths for windows in PLAMS function unit test SCMSUITE-8687 SO--
David Ormrod Morley: Reinstate support for PLAMS defaults file in code and add unit tests SCMSUITE-8687 SO107
David Ormrod Morley: Update PLAMS defaults docs SCMSUITE-8687 SO107
David Ormrod Morley: Remove usage of plams_defaults file in PLAMS SCMSUITE-8687 SO107
David Ormrod Morley: Remove plams_defaults file SCMSUITE-8687 SO107
Paul Spiering: Allow for dipoleMoments to propagate in the hybrid engine. SO--
David Ormrod Morley: Add unit tests for PLAMS kf tools SCMSUITE-8674 SO--
David Ormrod Morley: Add unit tests for PLAMS geometry tools SCMSUITE-8674 SO--
David Ormrod Morley: Add PLAMS test rkf file SCMSUITE-8674 SO--
David Ormrod Morley: Add unit tests for PLAMS Bond SCMSUITE-8674 SO--
David Ormrod Morley: Add unit tests for PLAMS Atom and minor property refactoring SCMSUITE-8674 SO--