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3abb306
Move tests to their own folder.
Aug 2, 2023
f2fc326
Fix tests.
Aug 2, 2023
4d93656
Switch out of using Pymatgen.assert_all_close.
Aug 3, 2023
a3484b9
Ensure all tests follow pytest naming convention.
Aug 3, 2023
6c5fbf9
Move `PymatgenTest.TEST_FILES_DIR` attribute into module scope (#3227)
janosh Aug 6, 2023
45d324c
f-string path construction everywhere, no need for `os.path.join(...)…
janosh Aug 7, 2023
1f2dd81
Breaking: Have plot methods return `plt.Axes` object, not `matplotlib…
janosh Aug 17, 2023
bb3007d
Use `numpy.testing.assert_allclose` over `assert np.allclose` (#3253)
janosh Aug 18, 2023
6df80a6
Don't let tests pollute the `pymatgen` repo (#3255)
janosh Aug 19, 2023
c25c3ec
Google-style doc string return types (#3258)
janosh Aug 21, 2023
ea13884
Add `PotcarSingle.__repr__` (#3273)
janosh Aug 25, 2023
dba02a5
Snake case test method names (#3339)
janosh Sep 17, 2023
6d0a688
Breaking: New method of POTCAR validation (#3351)
esoteric-ephemera Sep 30, 2023
069e940
remove single-arg os.path.join('path') calls
janosh Oct 2, 2023
050ee3a
New class to handle `NcICOBILIST.lobster` files (#2878)
QuantumChemist Oct 4, 2023
e130da0
Fix `ruff` `N806` (#3394)
janosh Oct 10, 2023
7087fd4
Add LobsterMatrices parser to lobster.io.outputs (#3361)
naik-aakash Oct 14, 2023
e94d6c1
Fix `LobsterMatrices` calculated incorrectly (#3407)
naik-aakash Oct 15, 2023
4858384
Fix lobsterin dict inheritance and treat \t in lobsterins correctly (…
JaGeo Nov 2, 2023
1199600
write test-created files to temporary directory (#3454)
janosh Nov 3, 2023
d52324a
rename single-letter vars like m->mol, a->pg_analyzer
janosh Nov 13, 2023
3fc779e
replace tests 'str(x) is not None' with actual expected value (#3472)
janosh Nov 14, 2023
17884c9
Improve handling of Vasprun POTCAR search, expanded fake POTCAR libra…
esoteric-ephemera Jan 17, 2024
8fbf898
CONSTANT_CASE module-scoped TEST_DIR
janosh Jan 23, 2024
09d4a39
rename single-letter variables f->file
janosh Jan 23, 2024
800b0f5
Lobster io improvements (#3627)
naik-aakash Feb 15, 2024
989ee57
[WIP] Lobsterenv improvements (#3624)
naik-aakash Feb 18, 2024
e7d3223
Fix Lobsterenv Bug (#3637)
naik-aakash Feb 21, 2024
2e53589
LOBSTER IO improvements (#3649)
naik-aakash Feb 24, 2024
5836759
ruff pre-commit to 0.3.1 + auto-fixes, e.g. metaclass=abc.ABCMeta to …
janosh Mar 7, 2024
0cd0fa5
Clean up test files: VASP outputs (#3653)
DanielYang59 Mar 7, 2024
ad110ee
Clean up test files: VASP inputs (#3674)
DanielYang59 Mar 8, 2024
b473c11
Generalize fatband plots from Lobster (#3688)
JaGeo Mar 14, 2024
5519ab4
Improve Bandoverlaps parser (#3689)
naik-aakash Mar 15, 2024
a27be30
use f-strings for test file paths
janosh Mar 15, 2024
cee7804
replace assert hasattr(...) with more sensitive asserts
janosh Mar 15, 2024
3ab4b80
Plotting of Multicenter COBIs (#2926)
JaGeo Mar 16, 2024
eb9b693
Clean up tests (#3713)
janosh Mar 26, 2024
804a217
Remove unnecessary `unittest.TestCase` subclassing (#3718)
janosh Mar 27, 2024
c886188
`pyright` fixes for `ext/io/phonon/symmetry/transformations/util/vis/…
DanielYang59 Apr 15, 2024
3467791
Separate test files by modules and collect test files `csv/cif` into …
DanielYang59 Apr 19, 2024
b5a76a3
Officially support Python 3.12 and test in CI (#3685)
janosh May 1, 2024
37613e5
Simplify case handling in `lobster.inputs` (#3848)
DanielYang59 Jun 8, 2024
5a03974
Enable more ruff rules including `A`, `DTZ`, `PGH` and more (#3871)
DanielYang59 Jun 21, 2024
4c9cf5a
Move to src layout.
shyuep Jun 26, 2024
6dfae03
Move to src layout.
shyuep Jun 26, 2024
3354aa2
Linting fixes.
shyuep Jun 26, 2024
e92108a
SpaceGroup changes (#3859)
kaueltzen Jul 14, 2024
2607a18
Fix import sorting (#3968)
janosh Aug 2, 2024
e75b16c
Fix import sorting (#3968)
janosh Aug 2, 2024
d35a432
Fix import sorting (#3968)
janosh Aug 2, 2024
fc8c76c
Improve types for `electronic_structure.{bandstructure/cohp}` (#3873)
DanielYang59 Aug 3, 2024
a80b9a7
Improve types for `electronic_structure.{bandstructure/cohp}` (#3873)
DanielYang59 Aug 3, 2024
8923d14
Improve types for `electronic_structure.{bandstructure/cohp}` (#3873)
DanielYang59 Aug 3, 2024
4dc68e7
standardize doc strings
janosh Aug 3, 2024
e8248e1
standardize doc strings
janosh Aug 3, 2024
63a626a
refactor dict.update() to use |= operator
janosh Aug 3, 2024
3b60be0
fix double spaces in doc strings
janosh Aug 4, 2024
0be5f86
Fix mypy errors for `io.cp2k` (#3984)
DanielYang59 Aug 9, 2024
ee904ff
Docstring tweaks for `io.vasp.inputs` and format tweaks for some othe…
DanielYang59 Aug 14, 2024
454feb3
Ruff fixes.
shyuep Aug 15, 2024
054df4e
Ruff fixes.
shyuep Aug 15, 2024
2c8dee9
Drop Python 3.9 support (#4009)
DanielYang59 Aug 21, 2024
ab61803
Drop Python 3.9 support (#4009)
DanielYang59 Aug 21, 2024
f1cff7e
Drop Python 3.9 support (#4009)
DanielYang59 Aug 21, 2024
293b430
Use `strict=True` with `zip` to ensure length equality (#4011)
DanielYang59 Aug 22, 2024
561c573
Use `strict=True` with `zip` to ensure length equality (#4011)
DanielYang59 Aug 22, 2024
366e880
Fix ruff PD901 and prefer `sum` over `len`+`if` (#4012)
janosh Aug 22, 2024
ebcab67
Improve type annotations for `io.lobster.{lobsterenv/outputs}` (#3887)
DanielYang59 Aug 30, 2024
f775324
Improve type annotations for `io.lobster.{lobsterenv/outputs}` (#3887)
DanielYang59 Aug 30, 2024
1624cef
Update `FermiDos.get_doping()` to be more robust (#3879)
kavanase Aug 31, 2024
750e423
Fix `S101`, replace all `assert` in code base (except for tests) (#4017)
DanielYang59 Aug 31, 2024
a0e4ea3
Fix `S101`, replace all `assert` in code base (except for tests) (#4017)
DanielYang59 Aug 31, 2024
e7053e0
Recover commented out code in tests and mark with `pytest.mark.skip` …
DanielYang59 Sep 2, 2024
a4117cd
fix typo in docstring (#4039)
DanielYang59 Sep 6, 2024
5c7e2c4
Fix `ruff` PLC0206 and PLR6104 (#4035)
janosh Sep 8, 2024
f8d52b3
Fix `ruff` PLC0206 and PLR6104 (#4035)
janosh Sep 8, 2024
db596f6
Fix typo in `Cp2kOutput.parse_hirshfeld` `add_site_property("hirshf[i…
janosh Sep 8, 2024
386d947
Fix typo in `Cp2kOutput.parse_hirshfeld` `add_site_property("hirshf[i…
janosh Sep 8, 2024
77f4514
Add support to LOBSTER >=5.0 (#4065)
naik-aakash Oct 17, 2024
4cfa660
Add support to LOBSTER >=5.0 (#4065)
naik-aakash Oct 17, 2024
50321d6
Remove all `no_type_check` mark, fix new `mypy` error in `1.12.0` (#4…
DanielYang59 Oct 21, 2024
83257e3
Ruff format.
shyuep Oct 23, 2024
b7b825a
Ruff format.
shyuep Oct 23, 2024
de13adf
Ruff format.
shyuep Oct 23, 2024
a955591
partially test translations in lobsterenv
JaGeo Oct 30, 2024
4034ca1
partially test translations in lobsterenv
JaGeo Oct 30, 2024
3fdb3ec
pre-commit auto-fixes
pre-commit-ci[bot] Oct 30, 2024
5643523
pre-commit auto-fixes
pre-commit-ci[bot] Oct 30, 2024
5a490ac
Show `FutureWarning` and `DeprecationWarning` for `pytest` (#4138)
DanielYang59 Nov 12, 2024
7c62138
Show `FutureWarning` and `DeprecationWarning` for `pytest` (#4138)
DanielYang59 Nov 12, 2024
71872bc
Replace hard-coded `np.allclose/isclose` and `math.isclose` (for comp…
DanielYang59 Nov 13, 2024
f5e4992
Cleanup `codespell` ignore patterns (#4175)
DanielYang59 Nov 16, 2024
c5696f4
Fix incorrect comparison logic and update tests (#4181)
naik-aakash Nov 18, 2024
9bf3701
Fix incorrect comparison logic and update tests (#4181)
naik-aakash Nov 18, 2024
aee27a4
Merge branch 'materialsproject:master' into fix_icohp
naik-aakash Dec 3, 2024
2e913c7
`zopen`: explicit binary/text `mode` , and explicit `encoding` as UTF…
DanielYang59 Dec 11, 2024
537746e
pre-commit autoupdate (#4213)
pre-commit-ci[bot] Dec 11, 2024
856bf57
pre-commit autoupdate (#4213)
pre-commit-ci[bot] Dec 11, 2024
bda120c
Increase warnings `stacklevel` to 2, un-ignore RUFF `B028` (#4217)
DanielYang59 Dec 11, 2024
429a02b
Increase warnings `stacklevel` to 2, un-ignore RUFF `B028` (#4217)
DanielYang59 Dec 11, 2024
b5f8940
Revert "`zopen`: explicit binary/text `mode` , and explicit `encoding…
shyuep Dec 11, 2024
8b2de58
Reapply `zopen` explicit UTF-8 encoding, enable optional `EncodingWar…
DanielYang59 Jan 9, 2025
94fd612
Explicit UTF-8 encoding for VASP input files with `zopen`, and `open`…
DanielYang59 Jan 9, 2025
02e0db4
Merge branch 'master' into fix_icohp
JaGeo Jan 14, 2025
a0c708e
Merge branch 'master' into fix_icohp
JaGeo Jan 14, 2025
acee191
Avoid using full equality (`==`) to compare float, avoid `assert_arra…
DanielYang59 Jan 24, 2025
73ac3b4
merge current mastr
JaGeo Jan 24, 2025
27edee9
merge current mastr
JaGeo Jan 24, 2025
b30a4c8
pre-commit auto-fixes
pre-commit-ci[bot] Jan 24, 2025
79c6ef7
add new test data
JaGeo Feb 6, 2025
3b58fb7
add new test data
JaGeo Feb 6, 2025
78555ad
merge conflict
JaGeo Feb 6, 2025
5fa32b2
merge conflict
JaGeo Feb 6, 2025
93978da
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
40b2b28
fix some more
JaGeo Feb 6, 2025
96fb06d
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
ce92b65
fix nearly everything except for two inter neighbor things
JaGeo Feb 6, 2025
268f92d
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
ea884be
add more fixes
JaGeo Feb 7, 2025
638ba85
add more fixes
JaGeo Feb 7, 2025
c9568b0
add more fixes
JaGeo Feb 7, 2025
615bfe4
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
ca2b8fe
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
d66c4f9
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
baf8b55
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
02fd93e
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
11a0095
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
f0e126f
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
0c46992
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
4263230
fix next test by adapting cutoff
JaGeo Feb 7, 2025
08542eb
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 7, 2025
04f3220
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
9c9dbf2
fix some bugs
JaGeo Feb 7, 2025
6f7ffbb
fix some bugs
JaGeo Feb 7, 2025
7373b39
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 7, 2025
cc2d5a3
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
9f67623
remove translation correction
JaGeo Feb 7, 2025
fcf279f
Fix new `ruff` error in linting pipeline (#4327)
DanielYang59 Mar 17, 2025
59e10bc
Fix new `ruff` error in linting pipeline (#4327)
DanielYang59 Mar 17, 2025
a7a5a76
Deprecate `PymatgenTest`, migrate tests to `pytest` from `unittest` (…
DanielYang59 Apr 17, 2025
968ea43
Cleanup all unnecessary type definitions. There really isn't a need to
shyuep Apr 26, 2025
bfa8eef
Cleanup all unnecessary type definitions. There really isn't a need to
shyuep Apr 26, 2025
0e756fd
More typing fixes.
shyuep Apr 26, 2025
a244348
More type fixes.
shyuep Apr 28, 2025
0e8d71e
fix(outputs.py): handle missing trailing newline in ICOHPLIST.lobster…
alibh95 May 1, 2025
4772c0f
fix(outputs.py): handle missing trailing newline in ICOHPLIST.lobster…
alibh95 May 1, 2025
8e939c8
Type fixes.
shyuep May 9, 2025
72463dc
Add `orjson` as required dependency as default JSON handler when cust…
DanielYang59 May 28, 2025
8000b82
Add custom as_dict/from_dict method for proper initialization of attr…
naik-aakash May 29, 2025
3d36592
pre-commit autoupdate (#4450)
pre-commit-ci[bot] Jul 29, 2025
859e5d0
Remove LOBSTER output file trailing line sensitivity (#4448)
DanielYang59 Jul 29, 2025
e5ded9d
Remove LOBSTER output file trailing line sensitivity (#4448)
DanielYang59 Jul 29, 2025
ebdf929
Fix `ruff` PERF401: manual-list-comprehension (#4449)
DanielYang59 Jul 30, 2025
a83e743
Fix `ruff` PERF401: manual-list-comprehension (#4449)
DanielYang59 Jul 30, 2025
76e4a82
Fix `has_cobicar` when NcICOBILIST is present (#4447)
tomdemeyere Aug 21, 2025
e855bb3
Added get_nn_info test case that fails without PR changes (correct or…
kaueltzen Jan 10, 2026
3ccca09
Merge branch 'master' into fix_icohp
kaueltzen Jan 14, 2026
e5cbcd3
Merge branch 'master' into fix_icohp
kaueltzen Jan 14, 2026
b3d9ac4
Merge branch 'master' into fix_icohp
kaueltzen Jan 14, 2026
f6eb0c1
Fix ruff codespell mypy
kaueltzen Jan 14, 2026
d737804
Fix ruff codespell mypy
kaueltzen Jan 14, 2026
62a9c94
check_ICOHPs skips those in same unit cell and uses int translations …
kaueltzen Jan 14, 2026
c7092bb
Switched translation in LOBSTER classes to tuple[int, int, int]
kaueltzen Jan 14, 2026
98ddf14
Switched translation in LOBSTER classes to tuple[int, int, int]
kaueltzen Jan 14, 2026
f88bdfb
removed mypy ignore
kaueltzen Jan 14, 2026
d74d20e
Added warning for case with backward_compatibility True
kaueltzen Jan 14, 2026
16d0176
check_ICOHPs float to int correction
kaueltzen Jan 14, 2026
6826835
Added test for backward_compatibility warning
kaueltzen Jan 14, 2026
5784075
Ruff fixes.
shyuep Feb 18, 2026
e8bb722
Ruff fixes.
shyuep Feb 18, 2026
fa480d1
Merge branch 'master' into fix_icohp
naik-aakash Feb 18, 2026
ab4b746
Merge branch 'master' into fix_icohp
naik-aakash Feb 18, 2026
f49afc3
Replace float compare with `==` with `math.isclose/approx` (#4591)
DanielYang59 Feb 18, 2026
eea8ea7
Merge branch 'master' into fix_icohp
naik-aakash Feb 19, 2026
833a44d
Simplify and clean up LobsterNeighbors (#4482)
naik-aakash Feb 20, 2026
c5b9ad8
Simplify and clean up LobsterNeighbors (#4482)
naik-aakash Feb 20, 2026
7950da7
Fix icohpcollection & add Missing keyword in Lobsterin (#4481)
naik-aakash Feb 20, 2026
e65cf00
Fix icohpcollection & add Missing keyword in Lobsterin (#4481)
naik-aakash Feb 20, 2026
d0fc6ff
Fix icohpcollection & add Missing keyword in Lobsterin (#4481)
naik-aakash Feb 20, 2026
ecac684
Merge branch 'master' into fix_icohp
naik-aakash Feb 20, 2026
d6c73c2
Merge branch 'master' into fix_icohp
naik-aakash Feb 20, 2026
77c1109
Merge branch 'master' into fix_icohp
naik-aakash Feb 20, 2026
91d2cb5
pre-commit auto-fixes
pre-commit-ci[bot] Feb 20, 2026
91ee32c
fix missing new attribute and failing test
naik-aakash Feb 20, 2026
9ea9f16
fix missing new attribute and failing test
naik-aakash Feb 20, 2026
74ef20d
Temporary fix for tests. Will be removed soon anyawy.
shyuep Feb 20, 2026
0f7f95e
resolve merge conflicts
naik-aakash Feb 23, 2026
cdaac3d
pre-commit auto-fixes
pre-commit-ci[bot] Feb 23, 2026
3ba2d2d
uncomment test
naik-aakash Feb 23, 2026
b53e58d
uncomment test
naik-aakash Feb 23, 2026
ce78a3b
refactor(lobster): Rewrite LOBSTER parsers with memory-efficient stre…
tomdemeyere Feb 24, 2026
676fa3b
refactor(lobster): Rewrite LOBSTER parsers with memory-efficient stre…
tomdemeyere Feb 24, 2026
0c88aa0
Merge branch 'master' into fix_icohp
naik-aakash Feb 24, 2026
4e0e1ee
Merge branch 'master' into fix_icohp
naik-aakash Feb 24, 2026
94df814
move lobsterenv module
naik-aakash Feb 25, 2026
5070414
move lobsterenv test
naik-aakash Feb 25, 2026
0709855
Major reorganization of pymatgen repo (#4595)
shyuep Mar 2, 2026
60bc568
Major reorganization of pymatgen repo (#4595)
shyuep Mar 2, 2026
ee2ae82
Merge branch 'master' into fix_icohp
naik-aakash Mar 3, 2026
011125d
Merge branch 'master' into fix_icohp
naik-aakash Mar 3, 2026
771042a
remove future module
naik-aakash Mar 9, 2026
1b4a124
Add 'src/pymatgen/io/lobster/' from commit 'ee2ae82842bef881faf4553c1…
naik-aakash Mar 9, 2026
4ddff52
Add cohp.py from pymatgen repo with full history
naik-aakash Mar 9, 2026
664fa30
remove exisiting tests
naik-aakash Mar 9, 2026
bf4e8c0
Add cohp.py tests from pymatgen repo with full history
naik-aakash Mar 9, 2026
1966ee3
Add lobster io tests from pymatgen with full history
naik-aakash Mar 9, 2026
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1,575 changes: 1,575 additions & 0 deletions src/pymatgen/electronic_structure/cohp.py

Large diffs are not rendered by default.

27 changes: 27 additions & 0 deletions src/pymatgen/io/lobster/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
"""
This package implements modules for input and output to and from LOBSTER. It
imports the key classes form both lobster.inputs and lobster.outputs to allow most
classes to be simply called as pymatgen.io.lobster.Lobsterin for example, to retain
backwards compatibility.
"""

from __future__ import annotations

from .inputs import Lobsterin
from .outputs import (
Bandoverlaps,
Bwdf,
Charge,
Cohpcar,
Doscar,
Fatband,
Grosspop,
Icohplist,
LobsterMatrices,
Lobsterout,
MadelungEnergies,
NciCobiList,
Polarization,
SitePotential,
Wavefunction,
)
1,521 changes: 5 additions & 1,516 deletions src/pymatgen/io/lobster/future/lobsterenv.py

Large diffs are not rendered by default.

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