bump ruff pre-commit to 0.3.0 + auto-fixes

janosh · janosh · commit 71a5edc666a5 · 2024-03-06T19:29:26.000+01:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,14 +7,14 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.0
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
 
   - repo: https://github.com/janosh/format-ipy-cells
-    rev: v0.1.10
+    rev: v0.1.11
     hooks:
       - id: format-ipy-cells
 
@@ -80,7 +80,7 @@ repos:
       - id: check-github-actions
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.351
+    rev: v1.1.352
     hooks:
       - id: pyright
         args: [--level, error]
diff --git a/data/mp/build_phase_diagram.py b/data/mp/build_phase_diagram.py
@@ -2,7 +2,6 @@
 DFT-ground truth convex hull energies.
 """
 
-
 # %%
 import gzip
 import json
diff --git a/data/mp/eda_mp_trj.py b/data/mp/eda_mp_trj.py
@@ -1,6 +1,5 @@
 """MPtrj exploratory data analysis (EDA)."""
 
-
 # %%
 import io
 import os
diff --git a/data/mp/get_mp_traj.py b/data/mp/get_mp_traj.py
@@ -5,7 +5,6 @@
 all 1.6M task docs.
 """
 
-
 # %%
 import os
 import subprocess
diff --git a/data/wbm/compile_wbm_test_set.py b/data/wbm/compile_wbm_test_set.py
@@ -39,7 +39,6 @@
 https://nature.com/articles/s41524-020-00481-6
 """
 
-
 # %% links to google drive files received via email from 1st author Hai-Chen Wang
 # on 2021-06-15 containing initial and relaxed structures
 google_drive_ids = {
diff --git a/models/chgnet/analyze_chgnet.py b/models/chgnet/analyze_chgnet.py
@@ -1,6 +1,5 @@
 """Compare CHGNet long vs short relaxations."""
 
-
 # %%
 import os
 
diff --git a/models/chgnet/join_chgnet_results.py b/models/chgnet/join_chgnet_results.py
@@ -2,7 +2,6 @@
 into single file.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/chgnet/test_chgnet.py b/models/chgnet/test_chgnet.py
@@ -5,7 +5,6 @@
 pip install -e ./chgnet.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/m3gnet/join_m3gnet_results.py b/models/m3gnet/join_m3gnet_results.py
@@ -2,7 +2,6 @@
 into single file.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/m3gnet/pre_vs_post_m3gnet_relaxation.py b/models/m3gnet/pre_vs_post_m3gnet_relaxation.py
@@ -1,6 +1,5 @@
 """Compare M3GNet-relaxed vs DFT-relaxed WBM lattice volumes and angles."""
 
-
 # %%
 import os
 
diff --git a/models/m3gnet/test_m3gnet.py b/models/m3gnet/test_m3gnet.py
@@ -4,7 +4,6 @@
 https://github.com/materialsvirtuallab/m3gnet.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/mace/analyze_mace.py b/models/mace/analyze_mace.py
@@ -1,6 +1,5 @@
 """Investigate MACE energy underpredictions."""
 
-
 # %%
 import os
 
diff --git a/models/mace/join_mace_results.py b/models/mace/join_mace_results.py
@@ -2,7 +2,6 @@
 into single file.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/megnet/test_megnet.py b/models/megnet/test_megnet.py
@@ -4,7 +4,6 @@
 See https://github.com/materialsvirtuallab/megnet.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/voronoi_rf/join_voronoi_features.py b/models/voronoi_rf/join_voronoi_features.py
@@ -2,7 +2,6 @@
 into single file.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/voronoi_rf/train_test_voronoi_rf.py b/models/voronoi_rf/train_test_voronoi_rf.py
@@ -1,6 +1,5 @@
 """Train and test a Voronoi RandomForestRegressor model."""
 
-
 # %%
 import os
 import sys
diff --git a/models/voronoi_rf/voronoi_featurize_dataset.py b/models/voronoi_rf/voronoi_featurize_dataset.py
@@ -2,7 +2,6 @@
 Voronoi tessellation structure-based features.
 """
 
-
 # %%
 import os
 import sys
diff --git a/models/wrenformer/analyze_wrenformer.py b/models/wrenformer/analyze_wrenformer.py
@@ -1,6 +1,5 @@
 """Compare CHGNet long vs short relaxations."""
 
-
 # %%
 import numpy as np
 import pandas as pd
diff --git a/models/wrenformer/test_wrenformer.py b/models/wrenformer/test_wrenformer.py
@@ -3,7 +3,6 @@
 saves predictions to CSV.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/models/wrenformer/train_wrenformer.py b/models/wrenformer/train_wrenformer.py
@@ -1,6 +1,5 @@
 """Train a Wrenformer ensemble on target_col of data_path."""
 
-
 # %%
 import os
 from importlib.metadata import version
diff --git a/scripts/analyze_model_failure_cases.py b/scripts/analyze_model_failure_cases.py
@@ -3,7 +3,6 @@
 Might point to deficiencies in the data or models architecture.
 """
 
-
 # %%
 import itertools
 
diff --git a/scripts/compute_struct_fingerprints.py b/scripts/compute_struct_fingerprints.py
@@ -3,7 +3,6 @@
 Might point to deficiencies in the data or models architecture.
 """
 
-
 # %%
 import os
 from glob import glob
diff --git a/scripts/hist_classified_stable_vs_hull_dist.py b/scripts/hist_classified_stable_vs_hull_dist.py
@@ -4,7 +4,6 @@
 See fig. S1 in https://science.org/doi/10.1126/sciadv.abn4117.
 """
 
-
 # %%
 from typing import Final
 
diff --git a/scripts/hist_classified_stable_vs_hull_dist_batches.py b/scripts/hist_classified_stable_vs_hull_dist_batches.py
@@ -5,7 +5,6 @@
 See fig. S1 in https://science.org/doi/10.1126/sciadv.abn4117.
 """
 
-
 # %%
 from typing import Final
 
diff --git a/scripts/model_figs/analyze_model_disagreement.py b/scripts/model_figs/analyze_model_disagreement.py
@@ -2,7 +2,6 @@
 models can pinpoint DFT calculation gone wrong.
 """
 
-
 # %%
 import sys
 
diff --git a/scripts/model_figs/compile_model_stats.py b/scripts/model_figs/compile_model_stats.py
@@ -2,7 +2,6 @@
 pandas-styled HTML table and a plotly figure.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/scripts/model_figs/cumulative_metrics.py b/scripts/model_figs/cumulative_metrics.py
@@ -7,7 +7,6 @@
 will provide the best hit rate for the given budget.
 """
 
-
 # %%
 import pandas as pd
 from pymatviz.io import save_fig
diff --git a/scripts/model_figs/hist_classified_stable_vs_hull_dist_models.py b/scripts/model_figs/hist_classified_stable_vs_hull_dist_models.py
@@ -3,7 +3,6 @@
 histogram stacks true/false positives/negatives with different colors.
 """
 
-
 # %%
 import math
 from typing import Final
diff --git a/scripts/model_figs/metrics_tables.py b/scripts/model_figs/metrics_tables.py
@@ -2,7 +2,6 @@
 pandas-styled HTML table and a plotly figure.
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/scripts/model_figs/parity_energy_models.py b/scripts/model_figs/parity_energy_models.py
@@ -3,7 +3,6 @@
 Last plot is split into 2x3 subplots, one for each model.
 """
 
-
 # %%
 import math
 from typing import Literal
diff --git a/scripts/model_figs/per_element_errors.py b/scripts/model_figs/per_element_errors.py
@@ -3,7 +3,6 @@
 Might point to deficiencies in the data or models architecture.
 """
 
-
 # %%
 import pandas as pd
 import plotly.express as px
diff --git a/scripts/model_figs/roc_prc_curves_models.py b/scripts/model_figs/roc_prc_curves_models.py
@@ -1,6 +1,5 @@
 """Plot ROC and PR (precision-recall) curves for each model."""
 
-
 # %%
 import math
 
@@ -44,7 +43,7 @@
     fpr, tpr, thresholds = roc_curve(y_true, y_pred, pos_label=0)
     AUC = auc(fpr, tpr)
     title = f"{model} · {AUC=:.2f}"
-    thresholds = [f"{t:.3} eV/atom" for t in thresholds]
+    thresholds = [f"{thresh:.3} eV/atom" for thresh in thresholds]
     df_tmp = pd.DataFrame(
         {"FPR": fpr, "TPR": tpr, color_col: thresholds, "AUC": AUC, facet_col: title}
     ).round(3)
diff --git a/scripts/model_figs/rolling_mae_vs_hull_dist_models.py b/scripts/model_figs/rolling_mae_vs_hull_dist_models.py
@@ -1,6 +1,5 @@
 """Plot rolling MAE as a function of hull distance for all models."""
 
-
 # %%
 from typing import Final
 
diff --git a/scripts/model_figs/rolling_mae_vs_hull_dist_wbm_batches.py b/scripts/model_figs/rolling_mae_vs_hull_dist_wbm_batches.py
@@ -2,7 +2,6 @@
 batch in a single plot.
 """
 
-
 # %%
 from pymatviz.io import save_fig
 
diff --git a/scripts/model_figs/run_all.py b/scripts/model_figs/run_all.py
@@ -3,7 +3,6 @@
 model-comparison figure.
 """
 
-
 # %%
 import os
 import runpy
diff --git a/scripts/project_compositions.py b/scripts/project_compositions.py
@@ -1,6 +1,5 @@
 """Compute t-SNE or UMAP projections of WBM and MP compositions."""
 
-
 # %%
 import os
 from datetime import datetime
diff --git a/scripts/rolling_mae_vs_hull_dist.py b/scripts/rolling_mae_vs_hull_dist.py
@@ -1,6 +1,5 @@
 """Plot rolling MAE as a function of hull distance for a single model."""
 
-
 # %%
 from pymatviz.io import save_fig
 
diff --git a/scripts/update_wandb_runs.py b/scripts/update_wandb_runs.py
@@ -2,7 +2,6 @@
 https://wandb.ai/janosh/matbench-discovery.
 """
 
-
 # %%
 import pandas as pd
 import wandb
diff --git a/scripts/wbm_umap_projection.py b/scripts/wbm_umap_projection.py
@@ -9,7 +9,6 @@
 https://www.nature.com/articles/s41524-023-01012-9
 """
 
-
 # %%
 from __future__ import annotations
 
diff --git a/tests/test_slurm.py b/tests/test_slurm.py
@@ -41,9 +41,11 @@ def test_slurm_submit(
     assert stderr == stderr == ""
 
     # check slurm_submit() prints cmd and calls subprocess.run() in submit mode
-    with pytest.raises(SystemExit), patch("sys.argv", ["slurm-submit"]), patch(
-        "matbench_discovery.slurm.subprocess.run"
-    ) as mock_subprocess_run:
+    with (
+        pytest.raises(SystemExit),
+        patch("sys.argv", ["slurm-submit"]),
+        patch("matbench_discovery.slurm.subprocess.run") as mock_subprocess_run,
+    ):
         func_call()
 
     assert mock_subprocess_run.call_count == 1

-Original file line number
+Diff line change
@@ @@ -1,6 +1,5 @@ @@
 """Compare CHGNet long vs short relaxations."""
+-
 # %%
 import os