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Merged
DomFijan merged 3 commits into from
Apr 9, 2026
Merged

chore: pre-commit autoupdate #118

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6528f39
chore: pre-commit autoupdate
github-actions[bot] Apr 1, 2026
2b7ad86
Merge branch 'main' into pre-commit-autoupdate-20260401
DomFijan Apr 8, 2026
78feffe
appease ruff
DomFijan Apr 8, 2026
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6 changes: 3 additions & 3 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ ci:

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: 'v4.5.0'
rev: 'v6.0.0'
hooks:
- id: end-of-file-fixer
- id: trailing-whitespace
Expand All @@ -18,10 +18,10 @@ repos:
- id: requirements-txt-fixer
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.4.10
rev: v0.15.8
hooks:
# Run the linter.
- id: ruff
- id: ruff-check
types_or: [ python, pyi, jupyter ]
args: [ --fix ]
# Run the formatter.
Expand Down
79 changes: 40 additions & 39 deletions ConservedWaterSearch/hydrogen_orientation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,11 @@

from typing import TYPE_CHECKING

try:
import matplotlib.pyplot as plt
except ImportError:
plt = None

if TYPE_CHECKING:
try:
from matplotlib.axes import Axes
Expand Down Expand Up @@ -360,7 +365,7 @@ def find_fully_conserved_orientations(
sk = (
f"Conserved - kmeans analysis:\n"
f"angle - mean: {ang:.2f}(calced)<{kmeans_ang_cutoff:.2f};"
f" inertia per H: {kmeans.inertia_/len(orientations):.2f}"
f" inertia per H: {kmeans.inertia_ / len(orientations):.2f}"
f"(calced)<{kmeans_inertia_cutoff:.2f}\n"
)
if debugH == 2 or (debugH == 1 and len(fully_conserved) > 0):
Expand All @@ -372,11 +377,11 @@ def find_fully_conserved_orientations(
f" buffer:{pct_size_buffer:.2f}\n"
f"cluster sizes: {counts}; clust labels:{values};biggest: {biggest}"
f"; secondbiggest: {secondbiggest}\n"
f"clusters size: {neioc*pct_size_buffer:.2f}<"
f"clusters size: {neioc * pct_size_buffer:.2f}<"
f"{len(orientations[labels == biggest])},"
f"{len(orientations[labels == secondbiggest])}"
f"(calced)<{neioc*(2-pct_size_buffer):.2f}\n"
f"angle mean: {np.abs(np.mean(angs21)-np.mean(angs12)):.2f}(calced)"
f"(calced)<{neioc * (2 - pct_size_buffer):.2f}\n"
f"angle mean: {np.abs(np.mean(angs21) - np.mean(angs12)):.2f}(calced)"
f"<{angdiff_cutoff:.2f}); 12 std : {np.std(angs12):.2f};21 std: "
f"{np.std(angs21):.2f} (both <{angstd_cutoff:.2f})\n"
)
Expand All @@ -391,7 +396,7 @@ def find_fully_conserved_orientations(
ss,
(
f"Reachability of optics plot\n"
f"minsamples={int(neioc*pct_size_buffer)}; xi={xi}"
f"minsamples={int(neioc * pct_size_buffer)}; xi={xi}"
),
len(fully_conserved) > 0,
debugH,
Expand Down Expand Up @@ -480,8 +485,8 @@ def find_half_conserved_orientations(
N_elems = len(orientations[labels == bestcand])
# Debug
if verbose > 0:
sk += f"Cluster {bestcand} has {neioc*pct_size_buffer:.2f}<"
sk += f"{N_elems}<{neioc*(2-pct_size_buffer):.2f} elements\n"
sk += f"Cluster {bestcand} has {neioc * pct_size_buffer:.2f}<"
sk += f"{N_elems}<{neioc * (2 - pct_size_buffer):.2f} elements\n"
# check if number of elements in hydrogen orientation cluster is
# between 0.80 and 1.20 elements of Oxygen cluster
if (
Expand All @@ -499,7 +504,7 @@ def find_half_conserved_orientations(
# Debug
if verbose > 0 or debugH > 0:
sk += "result angles: mean= "
sk += f"{np.abs(np.mean(angs1all)-104.5):.2f}(Calced)<"
sk += f"{np.abs(np.mean(angs1all) - 104.5):.2f}(Calced)<"
sk += f"{angdiff_cutoff:.2f}; std dev={np.std(angs1all):.2f}"
sk += f"(Calced)<{angstd_cutoff:.2f}\n"
# check if angle and its std deviation is satisfactory
Expand All @@ -522,10 +527,10 @@ def find_half_conserved_orientations(
ss = (
f"Half Conserved - OPTICS analysis;xi={xi}"
f"best: {bestcand}; N_hyd_cls (w/o -1): "
f"{len(np.unique(labels[labels!=-1]))};\n N elem in biggest:"
f"{neioc*(2-pct_size_buffer):.2f}>"
f"{len(orientations[labels==bestcand])}>"
f"{neioc*pct_size_buffer:.2f}\n"
f"{len(np.unique(labels[labels != -1]))};\n N elem in biggest:"
f"{neioc * (2 - pct_size_buffer):.2f}>"
f"{len(orientations[labels == bestcand])}>"
f"{neioc * pct_size_buffer:.2f}\n"
)
# Printing
if verbose == 2 or (verbose == 1 and len(half_conserved) > 0):
Expand All @@ -538,7 +543,7 @@ def find_half_conserved_orientations(
ss + sk,
(
f"Reachability of optics plot\n minsamples="
f"{int(neioc*min_samp_data_size_pct)}; xi={xi}"
f"{int(neioc * min_samp_data_size_pct)}; xi={xi}"
),
len(half_conserved) > 0,
debugH,
Expand Down Expand Up @@ -645,8 +650,8 @@ def find_weakly_conserved_orientations(
N_elems = len(orientations[labels == ii])
# Debug
if verbose > 0 or debugH > 0:
sk += f"Cluster {ii} has {neioc*lower_bound_pct_buffer:.2f}<"
sk += f"{N_elems}<{neioc*(2-pct_size_buffer):.2f} elements\n"
sk += f"Cluster {ii} has {neioc * lower_bound_pct_buffer:.2f}<"
sk += f"{N_elems}<{neioc * (2 - pct_size_buffer):.2f} elements\n"
# check if size of hydorgen orientation cluster is between 1.20
# and lower_bound_pct_buffer times number of elements in oxygen cluster
if (
Expand Down Expand Up @@ -675,11 +680,11 @@ def find_weakly_conserved_orientations(
maxcomp = np.max([N_elems, N_elems_jj])
calcedcomp = (1 - pct_size_buffer) * maxcomp
sk += f"cluster combo:{ii} & {jj}size:{N_elems},"
sk += f"{neioc*lower_bound_pct_buffer:.2f}<{N_elems_jj}<"
sk += f"{neioc*(2-pct_size_buffer):.2f}\n"
sk += f"size comparison {np.abs(N_elems -N_elems_jj)}"
sk += f"{neioc * lower_bound_pct_buffer:.2f}<{N_elems_jj}<"
sk += f"{neioc * (2 - pct_size_buffer):.2f}\n"
sk += f"size comparison {np.abs(N_elems - N_elems_jj)}"
sk += f"(calced) < {calcedcomp} \n"
sk += f"ang diff={np.abs(np.mean(angs1j)-104.5):.2f}"
sk += f"ang diff={np.abs(np.mean(angs1j) - 104.5):.2f}"
sk += f"(calced)<{angdiff_cutoff:.2f},std dev:"
sk += f"{angstd_cutoff:.2f}>{np.std(angs1j):.2f}(calced)\n"
# check if size of new cluster and check if size of clusters
Expand Down Expand Up @@ -796,20 +801,20 @@ def find_weakly_conserved_orientations(
sk += "size check "
sk += f"{np.abs(N_elems - (N_elems_jj + N_elems_kk))}"
sk += f"(calced)< {sizeingprint}\n"
sk += f"ang diff={np.abs(np.mean(angs1jk)-104.5):.2f}"
sk += f"ang diff={np.abs(np.mean(angs1jk) - 104.5):.2f}"
sk += f"(calced)<{angdiff_cutoff:.2f},std dev:"
sk += f"{angstd_cutoff:.2f}>{np.std(angs1jk):.2f}"
sk += "(calced)\n"
sk += f"ij {ii},{jj}, {np.abs(np.mean(angs1j)-104.5)},"
sk += f"ij {ii},{jj}, {np.abs(np.mean(angs1j) - 104.5)},"
sk += f"<,angdiff_cutoff,and std {np.std(angs1j)}<"
sk += f"{angstd_cutoff} \n"
sk += f"ik {ii},{kk}, {np.abs(np.mean(angs1k)-104.5)},"
sk += f"ik {ii},{kk}, {np.abs(np.mean(angs1k) - 104.5)},"
sk += f"<,angdiff_cutoff,and std {np.std(angs1k)}<"
sk += f"{angstd_cutoff} \n"
sk += f"kj {kk},{jj}, {np.abs(np.mean(angskj)-104.5)},"
sk += f"kj {kk},{jj}, {np.abs(np.mean(angskj) - 104.5)},"
sk += f"<,angdiff_cutoff,and std {np.std(angskj)}<"
sk += f"{angstd_cutoff} \n"
sk += f"jk {jj},{kk}, {np.abs(np.mean(angsjk)-104.5)},"
sk += f"jk {jj},{kk}, {np.abs(np.mean(angsjk) - 104.5)},"
sk += f"<,angdiff_cutoff,and std {np.std(angsjk)}<"
sk += f"{angstd_cutoff} \n"
# check if size of clusters is about equal ii==jj+kk
Expand Down Expand Up @@ -981,8 +986,8 @@ def find_weakly_conserved_orientations(
f"weakly Conserved - OPTICS analysis;xi={xi}\n"
f"Number of hydrogen clusters : {len(np.unique(labels))};\n"
f"number of elements : {counts}; range needed for best cluster:"
f"(depends on numbpct) {neioc*(2-pct_size_buffer):.2f},"
f"{neioc*lower_bound_pct_buffer:.2f}\n"
f"(depends on numbpct) {neioc * (2 - pct_size_buffer):.2f},"
f"{neioc * lower_bound_pct_buffer:.2f}\n"
)
# Debug Printing
if verbose == 2 or (verbose == 1 and len(weakly_conserved) > 0):
Expand All @@ -995,7 +1000,7 @@ def find_weakly_conserved_orientations(
ss,
(
f"Reachability of optics plot\n"
f"minsamples={int(neioc*min_samp_data_size_pct)}; xi={xi}"
f"minsamples={int(neioc * min_samp_data_size_pct)}; xi={xi}"
),
len(weakly_conserved) > 0,
debugH,
Expand Down Expand Up @@ -1026,11 +1031,9 @@ def __plot3Dorients(subplot, labels: int, orientations: np.ndarray, tip: str) ->
For debuging only.

"""
try:
import matplotlib.pyplot as plt
except ModuleNotFoundError as err:
if plt is None:
msg = "install matplotlib"
raise Exception(msg) from err
raise Exception(msg)

fig = plt.figure()
if isinstance(labels, int):
Expand All @@ -1043,7 +1046,7 @@ def __plot3Dorients(subplot, labels: int, orientations: np.ndarray, tip: str) ->
jaba[:, 0],
jaba[:, 1],
jaba[:, 2],
label=f"{j} ({len(labels[labels==j])})",
label=f"{j} ({len(labels[labels == j])})",
)
if j > -1:
ax.quiver(
Expand Down Expand Up @@ -1075,15 +1078,13 @@ def __plotreachability(
For debuging purposes only.

"""
try:
import matplotlib.pyplot as plt
except ModuleNotFoundError as err:
if plt is None:
msg = "install matplotlib"
raise Exception(msg) from err
raise Exception(msg)

if fig is None:
fig: Figure = plt.figure()
if type(cc) != OPTICS:
if not isinstance(cc, OPTICS):
return fig
lblls = cc.labels_[cc.ordering_]
labels = cc.labels_
Expand All @@ -1100,15 +1101,15 @@ def __plotreachability(
ax2.plot(
space[lblls == clst],
reachability[lblls == clst],
label=f"{clst} ({len(space[lblls==clst])}), avg reach={label}",
label=f"{clst} ({len(space[lblls == clst])}), avg reach={label}",
color="blue",
)
else:
label = np.mean(np.ma.masked_invalid(cc.reachability_[labels == clst]))
ax2.plot(
space[lblls == clst],
reachability[lblls == clst],
label=f"{clst} ({len(space[lblls==clst])}), avg reach={label}",
label=f"{clst} ({len(space[lblls == clst])}), avg reach={label}",
)
ax2.legend()
return fig
Expand Down
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