diff --git a/CHANGES.md b/CHANGES.md index 5f765f5bb3e..f24e67ddd03 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -121,34 +121,34 @@ nav_order: 4 ## v2023.5.31 -- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" `#3022 `_ -- Unignore ruff PD011 `#3020 `_ -- Tweak variable names `#3019 `_ -- MaterialsProjectCompatibility issue silencable deprecation warning `#3017 `_ -- Optimize cython find_points_in _spheres `#3015 `_ -- Cp2k 2.0 `#2672 `_ -- Added methods to compute and compare DOS fingerprints `#2772 `_ -- Breaking: Overhaul class PymatgenTest `#3014 `_ -- Fix ValueError when structure.selective_dynamics has type np.array `#3012 `_ -- Clean up `#3010 `_ -- Update .pytest-split-durations `#3005 `_ -- Lookup MPRester API key in settings if None provided as arg `#3004 `_ -- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) `#3003 `_ -- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None `#3002 `_ -- Species parse oxi state from symbol str `#2998 `_ -- Re-export SiteCollection + DummySpecies from pymatgen.core `#2995 `_ -- Orbital-resolved icohplist `#2993 `_ -- Hide all type-hint-only imports behind if TYPE_CHECKING `#2992 `_ -- Add type hints for pymatgen.io.ase module `#2991 `_ -- Enable ruff doc rules in CI `#2990 `_ -- Suspected Typo Fix in pymatgen.io.vasp.optics `#2989 `_ -- Doc strings `#2987 `_ -- Fix average error `#2986 `_ -- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports `#2981 `_ -- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) `#3022 `_ -- fix unwanted x margins in get_elt_projected_plots_color (closes #562) `#562 `_ -- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) `#2756 `_ -- add doc str explaining need for class ElementBase (closes #2999) `#2999 `_ +- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" [#3022](https://github.com/materialsproject/pymatgen/pull/3022) +- Unignore ruff PD011 [#3020](https://github.com/materialsproject/pymatgen/pull/3020) +- Tweak variable names [#3019](https://github.com/materialsproject/pymatgen/pull/3019) +- MaterialsProjectCompatibility issue silencable deprecation warning [#3017](https://github.com/materialsproject/pymatgen/pull/3017) +- Optimize cython find_points_in _spheres [#3015](https://github.com/materialsproject/pymatgen/pull/3015) +- Cp2k 2.0 [#2672](https://github.com/materialsproject/pymatgen/pull/2672) +- Added methods to compute and compare DOS fingerprints [#2772](https://github.com/materialsproject/pymatgen/pull/2772) +- Breaking: Overhaul class PymatgenTest [#3014](https://github.com/materialsproject/pymatgen/pull/3014) +- Fix ValueError when structure.selective_dynamics has type np.array [#3012](https://github.com/materialsproject/pymatgen/pull/3012) +- Clean up [#3010](https://github.com/materialsproject/pymatgen/pull/3010) +- Update .pytest-split-durations [#3005](https://github.com/materialsproject/pymatgen/pull/3005) +- Lookup MPRester API key in settings if None provided as arg [#3004](https://github.com/materialsproject/pymatgen/pull/3004) +- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) [#3003](https://github.com/materialsproject/pymatgen/pull/3003) +- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None [#3002](https://github.com/materialsproject/pymatgen/pull/3002) +- Species parse oxi state from symbol str [#2998](https://github.com/materialsproject/pymatgen/pull/2998) +- Re-export SiteCollection + DummySpecies from pymatgen.core [#2995](https://github.com/materialsproject/pymatgen/pull/2995) +- Orbital-resolved icohplist [#2993](https://github.com/materialsproject/pymatgen/pull/2993) +- Hide all type-hint-only imports behind if TYPE_CHECKING [#2992](https://github.com/materialsproject/pymatgen/pull/2992) +- Add type hints for pymatgen.io.ase module [#2991](https://github.com/materialsproject/pymatgen/pull/2991) +- Enable ruff doc rules in CI [#2990](https://github.com/materialsproject/pymatgen/pull/2990) +- Suspected Typo Fix in pymatgen.io.vasp.optics [#2989](https://github.com/materialsproject/pymatgen/pull/2989) +- Doc strings [#2987](https://github.com/materialsproject/pymatgen/pull/2987) +- Fix average error [#2986](https://github.com/materialsproject/pymatgen/pull/2986) +- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports [#2981](https://github.com/materialsproject/pymatgen/pull/2981) +- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) [#3022](https://github.com/materialsproject/pymatgen/pull/3022) +- fix unwanted x margins in get_elt_projected_plots_color (closes #562) [#562](https://github.com/materialsproject/pymatgen/issues/562) +- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) [#2756](https://github.com/materialsproject/pymatgen/issues/2756) +- add doc str explaining need for class ElementBase (closes #2999) [#2999](https://github.com/materialsproject/pymatgen/issues/2999) - Update docs. `3e3c31c `_ - ruff set isort.split-on-trailing-comma = false `c0ec534 `_ @@ -169,43 +169,43 @@ On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds. -For more details see `#2968 `_and `#2969 `_. +For more details see [#2968](https://github.com/materialsproject/pymatgen/pull/2968)and [#2969](https://github.com/materialsproject/pymatgen/pull/2969). What's Changed -- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in `#2907 `_ -- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in `#2908 `_ -- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in `#2909 `_ -- Update team.rst by @jmmshn in `#2912 `_ -- Faff by @janosh in `#2915 `_ -- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in `#2916 `_ -- Modified dosplotter by @kaueltzen in `#2844 `_ -- auto version by @jmmshn in `#2925 `_ -- bug fix for potcar parsing by @jmmshn in `#2910 `_ -- Fix breaking changes from pandas v2 by @janosh in `#2935 `_ -- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in `#2927 `_ -- fix on reading multiple route in Gaussian input file by @Ameyanagi in `#2939 `_ -- Fix CI errors by @janosh in `#2940 `_ -- Add ResParser support for reading files with spin values by @ScottNotFound in `#2941 `_ -- Ignore bad unicode characters in Structure.from_file() by @janosh in `#2948 `_ -- Minor modification for symmetrically distinct Miller index generation by @fyalcin in `#2949 `_ -- Fixed Wulff shape for new versions of matplotlib by @CifLord in `#2950 `_ -- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in `#2953 `_ -- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in `#2954 `_ -- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in `#2945 `_ -- self.assertArrayEqual->assert by @janosh in `#2955 `_ -- fix GaussianOutput bug with multiple route lines by @xjf729 in `#2937 `_ -- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in `#2951 `_ -- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in `#2962 `_ -- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in `#2959 `_ -- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in `#2960 `_ -- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in `#2963 `_ -- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in `#2961 `_ -- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in `#2964 `_ -- Link /addons from new subsection on /contributing page by @janosh in `#2967 `_ -- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in `#2969 `_ -- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in `#2973 `_ -- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in `#2972 +- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in [#2907](https://github.com/materialsproject/pymatgen/pull/2907) +- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in [#2908](https://github.com/materialsproject/pymatgen/pull/2908) +- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in [#2909](https://github.com/materialsproject/pymatgen/pull/2909) +- Update team.rst by @jmmshn in [#2912](https://github.com/materialsproject/pymatgen/pull/2912) +- Faff by @janosh in [#2915](https://github.com/materialsproject/pymatgen/pull/2915) +- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in [#2916](https://github.com/materialsproject/pymatgen/pull/2916) +- Modified dosplotter by @kaueltzen in [#2844](https://github.com/materialsproject/pymatgen/pull/2844) +- auto version by @jmmshn in [#2925](https://github.com/materialsproject/pymatgen/pull/2925) +- bug fix for potcar parsing by @jmmshn in [#2910](https://github.com/materialsproject/pymatgen/pull/2910) +- Fix breaking changes from pandas v2 by @janosh in [#2935](https://github.com/materialsproject/pymatgen/pull/2935) +- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in [#2927](https://github.com/materialsproject/pymatgen/pull/2927) +- fix on reading multiple route in Gaussian input file by @Ameyanagi in [#2939](https://github.com/materialsproject/pymatgen/pull/2939) +- Fix CI errors by @janosh in [#2940](https://github.com/materialsproject/pymatgen/pull/2940) +- Add ResParser support for reading files with spin values by @ScottNotFound in [#2941](https://github.com/materialsproject/pymatgen/pull/2941) +- Ignore bad unicode characters in Structure.from_file() by @janosh in [#2948](https://github.com/materialsproject/pymatgen/pull/2948) +- Minor modification for symmetrically distinct Miller index generation by @fyalcin in [#2949](https://github.com/materialsproject/pymatgen/pull/2949) +- Fixed Wulff shape for new versions of matplotlib by @CifLord in [#2950](https://github.com/materialsproject/pymatgen/pull/2950) +- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in [#2953](https://github.com/materialsproject/pymatgen/pull/2953) +- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in [#2954](https://github.com/materialsproject/pymatgen/pull/2954) +- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in [#2945](https://github.com/materialsproject/pymatgen/pull/2945) +- self.assertArrayEqual->assert by @janosh in [#2955](https://github.com/materialsproject/pymatgen/pull/2955) +- fix GaussianOutput bug with multiple route lines by @xjf729 in [#2937](https://github.com/materialsproject/pymatgen/pull/2937) +- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in [#2951](https://github.com/materialsproject/pymatgen/pull/2951) +- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in [#2962](https://github.com/materialsproject/pymatgen/pull/2962) +- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in [#2959](https://github.com/materialsproject/pymatgen/pull/2959) +- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in [#2960](https://github.com/materialsproject/pymatgen/pull/2960) +- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in [#2963](https://github.com/materialsproject/pymatgen/pull/2963) +- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in [#2961](https://github.com/materialsproject/pymatgen/pull/2961) +- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in [#2964](https://github.com/materialsproject/pymatgen/pull/2964) +- Link /addons from new subsection on /contributing page by @janosh in [#2967](https://github.com/materialsproject/pymatgen/pull/2967) +- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in [#2969](https://github.com/materialsproject/pymatgen/pull/2969) +- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in [#2973](https://github.com/materialsproject/pymatgen/pull/2973) +- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in [#2972](https://github.com/materialsproject/pymatgen/pull/2972) ## v2023.3.23 diff --git a/docs/CHANGES.md b/docs/CHANGES.md index fbe2b17a820..270229ba774 100644 --- a/docs/CHANGES.md +++ b/docs/CHANGES.md @@ -121,34 +121,34 @@ nav_order: 4 ## v2023.5.31 -- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" `#3022 `_ -- Unignore ruff PD011 `#3020 `_ -- Tweak variable names `#3019 `_ -- MaterialsProjectCompatibility issue silencable deprecation warning `#3017 `_ -- Optimize cython find_points_in _spheres `#3015 `_ -- Cp2k 2.0 `#2672 `_ -- Added methods to compute and compare DOS fingerprints `#2772 `_ -- Breaking: Overhaul class PymatgenTest `#3014 `_ -- Fix ValueError when structure.selective_dynamics has type np.array `#3012 `_ -- Clean up `#3010 `_ -- Update .pytest-split-durations `#3005 `_ -- Lookup MPRester API key in settings if None provided as arg `#3004 `_ -- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) `#3003 `_ -- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None `#3002 `_ -- Species parse oxi state from symbol str `#2998 `_ -- Re-export SiteCollection + DummySpecies from pymatgen.core `#2995 `_ -- Orbital-resolved icohplist `#2993 `_ -- Hide all type-hint-only imports behind if TYPE_CHECKING `#2992 `_ -- Add type hints for pymatgen.io.ase module `#2991 `_ -- Enable ruff doc rules in CI `#2990 `_ -- Suspected Typo Fix in pymatgen.io.vasp.optics `#2989 `_ -- Doc strings `#2987 `_ -- Fix average error `#2986 `_ -- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports `#2981 `_ -- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) `#3022 `_ -- fix unwanted x margins in get_elt_projected_plots_color (closes #562) `#562 `_ -- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) `#2756 `_ -- add doc str explaining need for class ElementBase (closes #2999) `#2999 `_ +- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" [#3022](https://github.com/materialsproject/pymatgen/pull/3022) +- Unignore ruff PD011 [#3020](https://github.com/materialsproject/pymatgen/pull/3020) +- Tweak variable names [#3019](https://github.com/materialsproject/pymatgen/pull/3019) +- MaterialsProjectCompatibility issue silencable deprecation warning [#3017](https://github.com/materialsproject/pymatgen/pull/3017) +- Optimize cython find_points_in _spheres [#3015](https://github.com/materialsproject/pymatgen/pull/3015) +- Cp2k 2.0 [#2672](https://github.com/materialsproject/pymatgen/pull/2672) +- Added methods to compute and compare DOS fingerprints [#2772](https://github.com/materialsproject/pymatgen/pull/2772) +- Breaking: Overhaul class PymatgenTest [#3014](https://github.com/materialsproject/pymatgen/pull/3014) +- Fix ValueError when structure.selective_dynamics has type np.array [#3012](https://github.com/materialsproject/pymatgen/pull/3012) +- Clean up [#3010](https://github.com/materialsproject/pymatgen/pull/3010) +- Update .pytest-split-durations [#3005](https://github.com/materialsproject/pymatgen/pull/3005) +- Lookup MPRester API key in settings if None provided as arg [#3004](https://github.com/materialsproject/pymatgen/pull/3004) +- Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma) [#3003](https://github.com/materialsproject/pymatgen/pull/3003) +- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None [#3002](https://github.com/materialsproject/pymatgen/pull/3002) +- Species parse oxi state from symbol str [#2998](https://github.com/materialsproject/pymatgen/pull/2998) +- Re-export SiteCollection + DummySpecies from pymatgen.core [#2995](https://github.com/materialsproject/pymatgen/pull/2995) +- Orbital-resolved icohplist [#2993](https://github.com/materialsproject/pymatgen/pull/2993) +- Hide all type-hint-only imports behind if TYPE_CHECKING [#2992](https://github.com/materialsproject/pymatgen/pull/2992) +- Add type hints for pymatgen.io.ase module [#2991](https://github.com/materialsproject/pymatgen/pull/2991) +- Enable ruff doc rules in CI [#2990](https://github.com/materialsproject/pymatgen/pull/2990) +- Suspected Typo Fix in pymatgen.io.vasp.optics [#2989](https://github.com/materialsproject/pymatgen/pull/2989) +- Doc strings [#2987](https://github.com/materialsproject/pymatgen/pull/2987) +- Fix average error [#2986](https://github.com/materialsproject/pymatgen/pull/2986) +- Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports [#2981](https://github.com/materialsproject/pymatgen/pull/2981) +- Breaking: Default user_potcar_settings to {"W": "W_sv"} in all input sets if user_potcar_functional == "PBE_54" (#3022) [#3022](https://github.com/materialsproject/pymatgen/pull/3022) +- fix unwanted x margins in get_elt_projected_plots_color (closes #562) [#562](https://github.com/materialsproject/pymatgen/issues/562) +- Add LightStructureEnvironments.from_structure_environments() fallback value if ce_and_neighbors is None (#3002) [#2756](https://github.com/materialsproject/pymatgen/issues/2756) +- add doc str explaining need for class ElementBase (closes #2999) [#2999](https://github.com/materialsproject/pymatgen/issues/2999) - Update docs. `3e3c31c `_ - ruff set isort.split-on-trailing-comma = false `c0ec534 `_ @@ -169,43 +169,43 @@ On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds. -For more details see `#2968 `_and `#2969 `_. +For more details see [#2968](https://github.com/materialsproject/pymatgen/pull/2968)and [#2969](https://github.com/materialsproject/pymatgen/pull/2969). What's Changed -- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in `#2907 `_ -- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in `#2908 `_ -- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in `#2909 `_ -- Update team.rst by @jmmshn in `#2912 `_ -- Faff by @janosh in `#2915 `_ -- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in `#2916 `_ -- Modified dosplotter by @kaueltzen in `#2844 `_ -- auto version by @jmmshn in `#2925 `_ -- bug fix for potcar parsing by @jmmshn in `#2910 `_ -- Fix breaking changes from pandas v2 by @janosh in `#2935 `_ -- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in `#2927 `_ -- fix on reading multiple route in Gaussian input file by @Ameyanagi in `#2939 `_ -- Fix CI errors by @janosh in `#2940 `_ -- Add ResParser support for reading files with spin values by @ScottNotFound in `#2941 `_ -- Ignore bad unicode characters in Structure.from_file() by @janosh in `#2948 `_ -- Minor modification for symmetrically distinct Miller index generation by @fyalcin in `#2949 `_ -- Fixed Wulff shape for new versions of matplotlib by @CifLord in `#2950 `_ -- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in `#2953 `_ -- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in `#2954 `_ -- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in `#2945 `_ -- self.assertArrayEqual->assert by @janosh in `#2955 `_ -- fix GaussianOutput bug with multiple route lines by @xjf729 in `#2937 `_ -- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in `#2951 `_ -- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in `#2962 `_ -- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in `#2959 `_ -- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in `#2960 `_ -- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in `#2963 `_ -- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in `#2961 `_ -- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in `#2964 `_ -- Link /addons from new subsection on /contributing page by @janosh in `#2967 `_ -- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in `#2969 `_ -- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in `#2973 `_ -- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in `#2972 +- Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in [#2907](https://github.com/materialsproject/pymatgen/pull/2907) +- Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in [#2908](https://github.com/materialsproject/pymatgen/pull/2908) +- Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in [#2909](https://github.com/materialsproject/pymatgen/pull/2909) +- Update team.rst by @jmmshn in [#2912](https://github.com/materialsproject/pymatgen/pull/2912) +- Faff by @janosh in [#2915](https://github.com/materialsproject/pymatgen/pull/2915) +- Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in [#2916](https://github.com/materialsproject/pymatgen/pull/2916) +- Modified dosplotter by @kaueltzen in [#2844](https://github.com/materialsproject/pymatgen/pull/2844) +- auto version by @jmmshn in [#2925](https://github.com/materialsproject/pymatgen/pull/2925) +- bug fix for potcar parsing by @jmmshn in [#2910](https://github.com/materialsproject/pymatgen/pull/2910) +- Fix breaking changes from pandas v2 by @janosh in [#2935](https://github.com/materialsproject/pymatgen/pull/2935) +- add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in [#2927](https://github.com/materialsproject/pymatgen/pull/2927) +- fix on reading multiple route in Gaussian input file by @Ameyanagi in [#2939](https://github.com/materialsproject/pymatgen/pull/2939) +- Fix CI errors by @janosh in [#2940](https://github.com/materialsproject/pymatgen/pull/2940) +- Add ResParser support for reading files with spin values by @ScottNotFound in [#2941](https://github.com/materialsproject/pymatgen/pull/2941) +- Ignore bad unicode characters in Structure.from_file() by @janosh in [#2948](https://github.com/materialsproject/pymatgen/pull/2948) +- Minor modification for symmetrically distinct Miller index generation by @fyalcin in [#2949](https://github.com/materialsproject/pymatgen/pull/2949) +- Fixed Wulff shape for new versions of matplotlib by @CifLord in [#2950](https://github.com/materialsproject/pymatgen/pull/2950) +- Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in [#2953](https://github.com/materialsproject/pymatgen/pull/2953) +- Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in [#2954](https://github.com/materialsproject/pymatgen/pull/2954) +- For MPcules: Molecule Trajectory and graph hashes by @espottesmith in [#2945](https://github.com/materialsproject/pymatgen/pull/2945) +- self.assertArrayEqual->assert by @janosh in [#2955](https://github.com/materialsproject/pymatgen/pull/2955) +- fix GaussianOutput bug with multiple route lines by @xjf729 in [#2937](https://github.com/materialsproject/pymatgen/pull/2937) +- Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in [#2951](https://github.com/materialsproject/pymatgen/pull/2951) +- Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in [#2962](https://github.com/materialsproject/pymatgen/pull/2962) +- Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in [#2959](https://github.com/materialsproject/pymatgen/pull/2959) +- Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in [#2960](https://github.com/materialsproject/pymatgen/pull/2960) +- Bump numpy from 1.23.2 to 1.24.3 by @dependabot in [#2963](https://github.com/materialsproject/pymatgen/pull/2963) +- Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in [#2961](https://github.com/materialsproject/pymatgen/pull/2961) +- Bump pandas from 1.4.4 to 2.0.1 by @dependabot in [#2964](https://github.com/materialsproject/pymatgen/pull/2964) +- Link /addons from new subsection on /contributing page by @janosh in [#2967](https://github.com/materialsproject/pymatgen/pull/2967) +- Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in [#2969](https://github.com/materialsproject/pymatgen/pull/2969) +- fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in [#2973](https://github.com/materialsproject/pymatgen/pull/2973) +- Revert to Yb_2 on pre-PBE_54 input sets by @janosh in [#2972](https://github.com/materialsproject/pymatgen/pull/2972) ## v2023.3.23 diff --git a/docs/index.md b/docs/index.md index ab7e1a7ae4a..1d470a2da91 100644 --- a/docs/index.md +++ b/docs/index.md @@ -419,9 +419,8 @@ If you use pymatgen in your research, please consider citing the following work: Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier, Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A. Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust, -Open-Source Python Library for Materials Analysis.* Computational -Materials Science, 2013, 68, 314–319. `doi:10.1016/j.commatsci.2012.10.028 -`_ +Open-Source Python Library for Materials Analysis.* Computational Materials +Science, 2013, 68, 314–319. https://doi.org/10.1016/j.commatsci.2012.10.028 ``` In addition, some of pymatgen's functionality is based on scientific advances / principles developed by various diff --git a/docs/installation.md b/docs/installation.md index 844f7bb9880..01bd24b1367 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -8,7 +8,7 @@ nav_order: 2 All required dependencies should be automatically taken care of if you install pymatgen using easy_install or pip. Otherwise, these packages should -be available on `PyPI `_. +be available on [PyPI](http://pypi.python.org). ## Optional dependencies @@ -41,9 +41,9 @@ Optional libraries that are required if you need certain features. Optional non-python libraries (because no good python alternative exists at the moment) required only for certain features: -1. ffmpeg: For generation of movies in structure_vtk.py. The executable ffmpeg +1. `ffmpeg`: For generation of movies in structure_vtk.py. The executable ffmpeg must be in the path. Get it at . -2. enum: For the use of +2. `enum`: For the use of `pymatgen.transformations.advanced_transformations.EnumerateStructureTransformation` and `pymatgen.command_line.enumlib_caller` module. This library by Gus Hart provides a robust way to enumerate derivative structures. It can be @@ -53,22 +53,22 @@ the moment) required only for certain features: EnumerateStructureTransformation. The enum.x and makestr.x executables must be in the path. Get it at and follow the instructions to compile enum.x and makestr.x. -3. bader: For use with :class:`pymatgen.command_line.bader_caller.BaderAnalysis`. +3. `bader`: For use with :class:`pymatgen.command_line.bader_caller.BaderAnalysis`. This library by Henkelmann et al. provides a robust way to calculate the Bader analysis from a CHGCAR. The bader executable must be in the path. Get it at . -4. gulp: For use with :mod:`pymatgen.command_line.gulp_caller`, +4. `gulp`: For use with :mod:`pymatgen.command_line.gulp_caller`, which is in turn used extensively by :mod:`pymatgen.analysis.defects` to compute empirical defect energies. -5. aconvasp: For use with the :mod:`pymatgen.command_line.aconvasp_caller`. -6. Zeo++ (): For defect structure +5. `aconvasp`: For use with the :mod:`pymatgen.command_line.aconvasp_caller`. +6. [Zeo++](https://zeoplusplus.org): For defect structure generation. This is required in addition to installing the zeo Python package. -7. critic2 (): For topological +7. [`critic2`](https://github.com/aoterodelaroza/critic2): For topological analysis of critical points from electronic charge density. Provides more detailed information compared to bader. For use with :class:`pymatgen.command_line.critic2_caller.Critic2Caller`. -8. graphviz (): For visualization of graphs generated +8. [`graphviz`](https://graphviz.org): For visualization of graphs generated using critic2. ## Conda-based install @@ -239,7 +239,7 @@ but it comes with some important caveats: however matplotlib is difficult to install. If trying PyPy, the current advice is to remove the matplotlib dependency, however this means any modules using matplotlib will not be importable. The easiest way to install dependencies is using the - `PyPy builds on conda-forge `_. For spglib, + [PyPy builds on conda-forge](https://conda-forge.org/blog/2020/03/10/pypy). For spglib, cloning the repository and running ``python setup.py install`` manually is advised. * Performance improvements are unpredictable. Since pymatgen makes heavy use of numpy and custom extensions where appropriate, many code hot spots have already been optimized. @@ -274,7 +274,7 @@ We welcome any developers interested in expanding our PyPy support. ### Step 2: Install pymatgen in developmental mode -1. Make sure you have git and `git-lfs `_ installed. +1. Make sure you have git and [git-lfs](https://git-lfs.github.com) installed. Clone the repo at . 2. Run `git lfs install` in the cloned repo first. diff --git a/pymatgen/io/babel.py b/pymatgen/io/babel.py index aa6270f4003..21fec9d0c6e 100644 --- a/pymatgen/io/babel.py +++ b/pymatgen/io/babel.py @@ -1,8 +1,7 @@ """ OpenBabel interface module, which opens up access to the hundreds of file formats supported by OpenBabel. Requires openbabel with python bindings to be -installed. Please consult the -`openbabel documentation `_. +installed. Please consult the openbabel docs https://openbabel.org. """ from __future__ import annotations