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Remove duplicate ruff rule in pyproject.toml (#3755)
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* Remove duplicate ruff rule in `pyproject.toml`

"TID" was listed twice.

Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>

* enable ruff PLR0402 PLR1714 PLR5501 in pyproject.toml and auto-fix

* unignore ruff PLW1514 open() without explicit encoding argument

---------

Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
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@Andrew-S-Rosen @janosh
Andrew-S-Rosen and janosh committed Apr 13, 2024
1 parent 9aacf65 commit a4e033a
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Showing 11 changed files with 144 additions and 155 deletions.
19 changes: 9 additions & 10 deletions pymatgen/analysis/chemenv/connectivity/connected_components.py
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Original file line number Diff line number Diff line change
Expand Up @@ -241,17 +241,16 @@ def __init__(
if links_data is None:
edge_data = None

elif (env_node1, env_node2, key) in links_data:
edge_data = links_data[(env_node1, env_node2, key)]
elif (env_node2, env_node1, key) in links_data:
edge_data = links_data[(env_node2, env_node1, key)]
elif (env_node1, env_node2) in links_data:
edge_data = links_data[(env_node1, env_node2)]
elif (env_node2, env_node1) in links_data:
edge_data = links_data[(env_node2, env_node1)]
else:
if (env_node1, env_node2, key) in links_data:
edge_data = links_data[(env_node1, env_node2, key)]
elif (env_node2, env_node1, key) in links_data:
edge_data = links_data[(env_node2, env_node1, key)]
elif (env_node1, env_node2) in links_data:
edge_data = links_data[(env_node1, env_node2)]
elif (env_node2, env_node1) in links_data:
edge_data = links_data[(env_node2, env_node1)]
else:
edge_data = None
edge_data = None

if edge_data:
self._connected_subgraph.add_edge(env_node1, env_node2, key, **edge_data)
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85 changes: 40 additions & 45 deletions pymatgen/electronic_structure/cohp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -772,57 +772,52 @@ def from_file(
# LMTO COHPs have 5 significant figures
avg_data[i].update({spin: np.array([round_to_sigfigs(a, 5) for a in avg], dtype=float)})
avg_cohp = Cohp(efermi, energies, avg_data["COHP"], icohp=avg_data["ICOHP"])
elif not are_multi_center_cobis:
avg_cohp = Cohp(
efermi,
energies,
cohp_data["average"]["COHP"],
icohp=cohp_data["average"]["ICOHP"],
are_coops=are_coops,
are_cobis=are_cobis,
are_multi_center_cobis=are_multi_center_cobis,
)
del cohp_data["average"]
else:
if not are_multi_center_cobis:
avg_cohp = Cohp(
efermi,
energies,
cohp_data["average"]["COHP"],
icohp=cohp_data["average"]["ICOHP"],
are_coops=are_coops,
are_cobis=are_cobis,
are_multi_center_cobis=are_multi_center_cobis,
)
del cohp_data["average"]
else:
# only include two-center cobis in average
# do this for both spin channels
cohp = {}
cohp[Spin.up] = np.array(
[np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
# only include two-center cobis in average
# do this for both spin channels
cohp = {}
cohp[Spin.up] = np.array(
[np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
).mean(axis=0)
try:
cohp[Spin.down] = np.array(
[np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
).mean(axis=0)
except KeyError:
pass
try:
icohp = {}
icohp[Spin.up] = np.array(
[np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
).mean(axis=0)
try:
cohp[Spin.down] = np.array(
[np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
icohp[Spin.down] = np.array(
[np.array(c["ICOHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
).mean(axis=0)
except KeyError:
pass
try:
icohp = {}
icohp[Spin.up] = np.array(
[np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
).mean(axis=0)
try:
icohp[Spin.down] = np.array(
[
np.array(c["ICOHP"][Spin.down])
for c in cohp_file.cohp_data.values()
if len(c["sites"]) <= 2
]
).mean(axis=0)
except KeyError:
pass
except KeyError:
icohp = None
avg_cohp = Cohp(
efermi,
energies,
cohp,
icohp=icohp,
are_coops=are_coops,
are_cobis=are_cobis,
are_multi_center_cobis=are_multi_center_cobis,
)
except KeyError:
icohp = None
avg_cohp = Cohp(
efermi,
energies,
cohp,
icohp=icohp,
are_coops=are_coops,
are_cobis=are_cobis,
are_multi_center_cobis=are_multi_center_cobis,
)

cohp_dict = {
key: Cohp(
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5 changes: 2 additions & 3 deletions pymatgen/io/aims/sets/bs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,8 @@ def prepare_band_input(structure: Structure, density: float = 20):
current_segment["length"] += 1
lines_and_labels.append(current_segment)
current_segment = None
else:
if current_segment is not None:
current_segment["length"] += 1
elif current_segment is not None:
current_segment["length"] += 1

bands = []
for segment in lines_and_labels:
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93 changes: 46 additions & 47 deletions pymatgen/io/vasp/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -355,7 +355,7 @@ def _parse(self, stream, parse_dos, parse_eigen, parse_projected_eigen):
# The start event tells us when we have entered blocks
if tag == "calculation":
parsed_header = True
elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
in_kpoints_opt = True
else: # event == "end":
# The end event happens when we have read a block, so have
Expand Down Expand Up @@ -411,7 +411,7 @@ def _parse(self, stream, parse_dos, parse_eigen, parse_projected_eigen):
self.eigenvalues = self._parse_eigen(elem)
elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
in_kpoints_opt = False
if self.kpoints_opt_props is None:
self.kpoints_opt_props = KpointOptProps()
Expand Down Expand Up @@ -1615,54 +1615,53 @@ def __init__(
or (tag == "dos" and elem.attrib.get("comment") == "kpoints_opt")
):
in_kpoints_opt = True
else: # if event == "end":
if not parsed_header:
if tag == "generator":
self.generator = self._parse_params(elem)
elif tag == "incar":
self.incar = self._parse_params(elem)
elif tag == "kpoints":
self.kpoints, self.actual_kpoints, self.actual_kpoints_weights = self._parse_kpoints(elem)
elif tag == "parameters":
self.parameters = self._parse_params(elem)
elif tag == "atominfo":
self.atomic_symbols, self.potcar_symbols = self._parse_atominfo(elem)
self.potcar_spec = [
{"titel": p, "hash": None, "summary_stats": {}} for p in self.potcar_symbols
]
parsed_header = True
elif tag == "i" and elem.attrib.get("name") == "efermi":
if in_kpoints_opt:
if self.kpoints_opt_props is None:
self.kpoints_opt_props = KpointOptProps()
self.kpoints_opt_props.efermi = float(elem.text)
in_kpoints_opt = False
else:
self.efermi = float(elem.text)
elif tag == "eigenvalues" and not in_kpoints_opt:
self.eigenvalues = self._parse_eigen(elem)
elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt":
elif not parsed_header:
if tag == "generator":
self.generator = self._parse_params(elem)
elif tag == "incar":
self.incar = self._parse_params(elem)
elif tag == "kpoints":
self.kpoints, self.actual_kpoints, self.actual_kpoints_weights = self._parse_kpoints(elem)
elif tag == "parameters":
self.parameters = self._parse_params(elem)
elif tag == "atominfo":
self.atomic_symbols, self.potcar_symbols = self._parse_atominfo(elem)
self.potcar_spec = [
{"titel": p, "hash": None, "summary_stats": {}} for p in self.potcar_symbols
]
parsed_header = True
elif tag == "i" and elem.attrib.get("name") == "efermi":
if in_kpoints_opt:
if self.kpoints_opt_props is None:
self.kpoints_opt_props = KpointOptProps()
self.kpoints_opt_props.efermi = float(elem.text)
in_kpoints_opt = False
# projected_kpoints_opt includes occupation information whereas
# eigenvalues_kpoints_opt doesn't.
self.kpoints_opt_props.eigenvalues = self._parse_eigen(elem.find("eigenvalues"))
if tag == "eigenvalues_kpoints_opt":
(
self.kpoints_opt_props.kpoints,
self.kpoints_opt_props.actual_kpoints,
self.kpoints_opt_props.actual_kpoints_weights,
) = self._parse_kpoints(elem.find("kpoints"))
elif parse_projected_eigen: # and tag == "projected_kpoints_opt": (implied)
(
self.kpoints_opt_props.projected_eigenvalues,
self.kpoints_opt_props.projected_magnetisation,
) = self._parse_projected_eigen(elem)
elif tag == "structure" and elem.attrib.get("name") == "finalpos":
self.final_structure = self._parse_structure(elem)
else:
self.efermi = float(elem.text)
elif tag == "eigenvalues" and not in_kpoints_opt:
self.eigenvalues = self._parse_eigen(elem)
elif parse_projected_eigen and tag == "projected" and not in_kpoints_opt:
self.projected_eigenvalues, self.projected_magnetisation = self._parse_projected_eigen(elem)
elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"):
if self.kpoints_opt_props is None:
self.kpoints_opt_props = KpointOptProps()
in_kpoints_opt = False
# projected_kpoints_opt includes occupation information whereas
# eigenvalues_kpoints_opt doesn't.
self.kpoints_opt_props.eigenvalues = self._parse_eigen(elem.find("eigenvalues"))
if tag == "eigenvalues_kpoints_opt":
(
self.kpoints_opt_props.kpoints,
self.kpoints_opt_props.actual_kpoints,
self.kpoints_opt_props.actual_kpoints_weights,
) = self._parse_kpoints(elem.find("kpoints"))
elif parse_projected_eigen: # and tag == "projected_kpoints_opt": (implied)
(
self.kpoints_opt_props.projected_eigenvalues,
self.kpoints_opt_props.projected_magnetisation,
) = self._parse_projected_eigen(elem)
elif tag == "structure" and elem.attrib.get("name") == "finalpos":
self.final_structure = self._parse_structure(elem)
self.vasp_version = self.generator["version"]
if parse_potcar_file:
self.update_potcar_spec(parse_potcar_file)
Expand Down
7 changes: 3 additions & 4 deletions pymatgen/io/vasp/sets.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1114,11 +1114,10 @@ def calculate_ng(

if custom_encut is not None:
encut = custom_encut
elif self.incar.get("ENCUT", 0) > 0:
encut = self.incar["ENCUT"] # get the ENCUT val
else:
if self.incar.get("ENCUT", 0) > 0:
encut = self.incar["ENCUT"] # get the ENCUT val
else:
encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])
encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])

# PREC=Normal is VASP default
PREC = self.incar.get("PREC", "Normal") if custom_prec is None else custom_prec
Expand Down
15 changes: 7 additions & 8 deletions pymatgen/phonon/plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,15 +205,14 @@ def get_plot(
ax.set_xlim(xlim)
if ylim:
ax.set_ylim(ylim)
elif invert_axes:
_ylim = ax.get_ylim()
relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim()
ax.set_xlim((min(relevant_x), max(relevant_x)))
else:
if invert_axes:
_ylim = ax.get_ylim()
relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim()
ax.set_xlim((min(relevant_x), max(relevant_x)))
else:
_xlim = ax.get_xlim()
relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim()
ax.set_ylim((min(relevant_y), max(relevant_y)))
_xlim = ax.get_xlim()
relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim()
ax.set_ylim((min(relevant_y), max(relevant_y)))

if invert_axes:
ax.axhline(0, linewidth=2, color="black", linestyle="--")
Expand Down
5 changes: 2 additions & 3 deletions pymatgen/util/provenance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -93,11 +93,10 @@ def parse_history_node(cls, h_node) -> Self:
"""Parses a History Node object from either a dict or a tuple.
Args:
h_node: A dict with name/url/description fields or a 3-element
tuple.
h_node: A dict with name/url/description fields or a 3-element tuple.
Returns:
History node.
HistoryNode
"""
if isinstance(h_node, dict):
return cls.from_dict(h_node)
Expand Down
2 changes: 1 addition & 1 deletion pymatgen/vis/structure_vtk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -988,7 +988,7 @@ def apply_tags(self):
tags = {}
for tag in self.tags:
istruct = tag.get("istruct", "all")
if istruct != "all" and istruct != self.istruct:
if istruct not in ("all", self.istruct):
continue
site_index = tag["site_index"]
color = tag.get("color", [0.5, 0.5, 0.5])
Expand Down
63 changes: 32 additions & 31 deletions pyproject.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,36 +23,38 @@ repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest
target-version = "py39"
line-length = 120
lint.select = [
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"D", # pydocstyle
"E", # pycodestyle error
"EXE", # flake8-executable
"F", # pyflakes
"FA", # flake8-future-annotations
"FBT003", # boolean-positional-value-in-call
"FLY", # flynt
"I", # isort
"ICN", # flake8-import-conventions
"ISC", # flake8-implicit-str-concat
"PD", # pandas-vet
"PERF", # perflint
"PIE", # flake8-pie
"PL", # pylint
"PT", # flake8-pytest-style
"PYI", # flakes8-pyi
"Q", # flake8-quotes
"RET", # flake8-return
"RSE", # flake8-raise
"RUF", # Ruff-specific rules
"SIM", # flake8-simplify
"SLOT", # flake8-slots
"TCH", # flake8-type-checking
"TID", # tidy imports
"TID", # flake8-tidy-imports
"UP", # pyupgrade
"W", # pycodestyle warning
"YTT", # flake8-2020
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"D", # pydocstyle
"E", # pycodestyle error
"EXE", # flake8-executable
"F", # pyflakes
"FA", # flake8-future-annotations
"FBT003", # boolean-positional-value-in-call
"FLY", # flynt
"I", # isort
"ICN", # flake8-import-conventions
"ISC", # flake8-implicit-str-concat
"PD", # pandas-vet
"PERF", # perflint
"PIE", # flake8-pie
"PL", # pylint
"PLR0402",
"PLR1714",
"PLR5501",
"PT", # flake8-pytest-style
"PYI", # flakes8-pyi
"Q", # flake8-quotes
"RET", # flake8-return
"RSE", # flake8-raise
"RUF", # Ruff-specific rules
"SIM", # flake8-simplify
"SLOT", # flake8-slots
"TCH", # flake8-type-checking
"TID", # flake8-tidy-imports
"UP", # pyupgrade
"W", # pycodestyle warning
"YTT", # flake8-2020
]
lint.ignore = [
"B023", # Function definition does not bind loop variable
Expand All @@ -70,7 +72,6 @@ lint.ignore = [
"PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
"PLC1901", # can be simplified to ... as empty is falsey
"PLR", # pylint refactor
"PLW1514", # open() without explicit encoding argument
"PLW2901", # Outer for loop variable overwritten by inner assignment target
"PT013", # pytest-incorrect-pytest-import
"PTH", # prefer pathlib to os.path
Expand Down

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