MAINT: pin ruff rule set, lint whole repo, fix sum_spectra NameError

.github/workflows/ci.yml

@@ -18,6 +18,6 @@ jobs:
 
       - run: pip install -e ".[dev]"
 
-      - run: ruff check src/
+      - run: ruff check .
 
       - run: pytest -v tests/

pyproject.toml

@@ -39,3 +39,9 @@ spectroplot = "spectroplot:main"
 
 [tool.setuptools.packages.find]
 where = ["src"]
+
+[tool.ruff]
+line-length = 80
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I"]

src/spectroplot/_patterns.py

@@ -5,6 +5,7 @@
 """
 
 import re
+
 from spectroplot.global_constants import RE_SPECTRUM_ROOT_PATTERN
 
 RE_SPECTRUM_ROOT = re.compile(RE_SPECTRUM_ROOT_PATTERN)

src/spectroplot/data_reader.py

@@ -5,16 +5,18 @@
 """
 
 import logging
-import re                           #regex
-
-from pathlib import Path            #path processing (replace os)
+import re  #regex
+from pathlib import Path  #path processing (replace os)
 from typing import Iterator, Optional, Tuple
 
+from spectroplot._patterns import RE_SPECTRUM_ROOT
 from spectroplot.global_constants import (
-    SPECSTRING_START, SPECSTRING_END, IR_STRING, VPT2_STRING,
+    IR_STRING,
     RAMAN_STRING,
+    SPECSTRING_END,
+    SPECSTRING_START,
+    VPT2_STRING,
 )
-from spectroplot._patterns import RE_SPECTRUM_ROOT
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())

src/spectroplot/functions.py

@@ -5,10 +5,13 @@
 """
 
 from typing import Optional
-import numpy as np                      #element-wise tensor processing
-import pandas as pd                     #dataframe processing
-from spectroplot.global_constants import npt_nm, npt_wn, npt_ev, CONV_WNTOEV
+
+import numpy as np  #element-wise tensor processing
+import pandas as pd  #dataframe processing
+
 from spectroplot._patterns import RE_SPECTRUM_ROOT
+from spectroplot.global_constants import CONV_WNTOEV, npt_ev, npt_nm, npt_wn
+
 
 def show_plots(ext: str, s: list[bool]) -> bool:
     """Check if the file type matches any requested plot type.

src/spectroplot/spectroplot.py

@@ -4,37 +4,77 @@
 @author: Emmanuel Bourret
 """
 
-import sys                              #sys files processing
+import argparse  #argument parser
+import sys  #sys files processing
+from pathlib import Path  #path processing
 from typing import Optional
-from pathlib import Path                #path processing
-import argparse                         #argument parser
-import numpy as np                      #element-wise tensor processing
-import pandas as pd                     #dataframes processing
-import matplotlib.pyplot as plt         #plots
-import seaborn as sns                   #color palettes
-from scipy.signal import find_peaks     #peak detection
 
-from spectroplot.global_constants import (
-    th_fac, esd_fac, ex_fac, color_palette,
-    label_tddft, label_sticks, label_expt, label_roots,
-    label_ir, label_raman, label_vpt2, label_vpt2_overt,
-    label_sticks_vib,
-    show_single_lineshape, show_single_lineshape_area,
-    show_conv_spectrum, show_sticks, show_exp_spectrum,
-    show_esd_spectrum, show_single_root_area,
-    show_label_peaks, show_label_roots,
-    show_minor_ticks, show_grid, show_legend, linear_locator,
-    y_label, y_label_PL, x_label_wn, x_label_ev, x_label_nm,
-    label_rotation_angle, figure_dpi, acs_w, acs_h, output_name,
-    CONV_WNTOEV, w_nm, w_wn, w_ev, w_ir, w_raman,
-)
+import matplotlib.pyplot as plt  #plots
+import numpy as np  #element-wise tensor processing
+import pandas as pd  #dataframes processing
+import seaborn as sns  #color palettes
+from scipy.signal import find_peaks  #peak detection
+
 from spectroplot._patterns import RE_SPECTRUM_ROOT
+from spectroplot.data_reader import SpectrumData  #spectrum data parser
 from spectroplot.functions import (
-    atLeastTwo, plotType, show_plots, rootSum,
-    xdataPrep, xdatamin, xdatamax, plotxrange,
-    lineshape, normalization, rounddown, roundup,
+    atLeastTwo,
+    lineshape,
+    normalization,
+    plotType,
+    plotxrange,
+    rootSum,
+    rounddown,
+    roundup,
+    show_plots,
+    xdatamax,
+    xdatamin,
+    xdataPrep,
+)
+from spectroplot.global_constants import (
+    CONV_WNTOEV,
+    acs_h,
+    acs_w,
+    color_palette,
+    esd_fac,
+    ex_fac,
+    figure_dpi,
+    label_expt,
+    label_ir,
+    label_raman,
+    label_roots,
+    label_rotation_angle,
+    label_sticks,
+    label_sticks_vib,
+    label_tddft,
+    label_vpt2,
+    label_vpt2_overt,
+    linear_locator,
+    output_name,
+    show_conv_spectrum,
+    show_esd_spectrum,
+    show_exp_spectrum,
+    show_grid,
+    show_label_peaks,
+    show_label_roots,
+    show_legend,
+    show_minor_ticks,
+    show_single_lineshape,
+    show_single_lineshape_area,
+    show_single_root_area,
+    show_sticks,
+    th_fac,
+    w_ev,
+    w_ir,
+    w_nm,
+    w_raman,
+    w_wn,
+    x_label_ev,
+    x_label_nm,
+    x_label_wn,
+    y_label,
+    y_label_PL,
 )
-from spectroplot.data_reader import SpectrumData    #spectrum data parser
 
 
 def _plot_tddft(ax, row, i, plt_range_x, w, ls_gauss, palette, lw,

tests/test_data_reader.py

@@ -5,11 +5,11 @@
 """
 
 import sys
+
 sys.path.insert(0, "src")
 
 from spectroplot.data_reader import SpectrumData
-from spectroplot.global_constants import SPECSTRING_START, SPECSTRING_END
-
+from spectroplot.global_constants import SPECSTRING_END, SPECSTRING_START
 
 DATA_DIR = "data"
 
@@ -296,7 +296,9 @@ def test_read_ir_lines(self):
         assert abs(x[2] - 300.0) < 1e-6
 
     def test_read_ir_early_exit(self):
-        x, y = self.sd.read_ir(lines=IR_LINES + ["extra\n", "    4:   400.00      0.200000\n"])
+        x, y = self.sd.read_ir(
+            lines=IR_LINES + ["extra\n", "    4:   400.00      0.200000\n"]
+        )
         assert len(x) == 3, "should stop at blank line, not read extra"
 
 
@@ -311,7 +313,10 @@ def test_read_raman_lines(self):
         assert abs(y[0] - 0.5) < 1e-6
 
     def test_read_raman_early_exit(self):
-        x, y = self.sd.read_raman(lines=RAMAN_LINES + ["extra\n", "    4:   400.00      0.200000      0.500000\n"])
+        x, y = self.sd.read_raman(
+            lines=RAMAN_LINES
+            + ["extra\n", "    4:   400.00      0.200000      0.500000\n"]
+        )
         assert len(x) == 3, "should stop at blank line, not read extra"
 
 

tests/test_functions.py

@@ -4,27 +4,43 @@
 @author: Emmanuel Bourret
 """
 
+import sys
+
 import numpy as np
 import pandas as pd
-import sys
+
 sys.path.insert(0, "src")
 
-from hypothesis import given, strategies as st, settings
+from hypothesis import given, settings
+from hypothesis import strategies as st
 
 from spectroplot.functions import (
-    wntonm, wntoev, nmtown, nmtoev,
-    lineshape, normalization, atLeastTwo,
-    plotType, roundup, rounddown, unitConverter,
-    show_plots, is_unique, rootSum,
-    xdataPrep, xdatamin, xdatamax, plotxrange,
+    atLeastTwo,
+    is_unique,
+    lineshape,
+    nmtoev,
+    nmtown,
+    normalization,
+    plotType,
+    plotxrange,
+    rootSum,
+    rounddown,
+    roundup,
+    show_plots,
+    unitConverter,
+    wntoev,
+    wntonm,
+    xdatamax,
+    xdatamin,
+    xdataPrep,
 )
-from spectroplot.global_constants import CONV_WNTOEV
 
 # Strategies for property-based converter tests
 positive_floats = st.floats(min_value=1, max_value=1e6, allow_infinity=False,
                             allow_nan=False)
 positive_nparrays = st.lists(
-    st.floats(min_value=1, max_value=1e6, allow_infinity=False, allow_nan=False),
+    st.floats(min_value=1, max_value=1e6, allow_infinity=False,
+              allow_nan=False),
     min_size=1, max_size=10,
 ).map(np.array)
 
@@ -221,32 +237,56 @@ def test_rounddown_nm(self):
 
 class TestShowPlots:
     def test_out_any_true(self):
-        assert show_plots(".out", [True, False, False, False, False, False, False]) is True
-        assert show_plots(".out", [False, True, False, False, False, False, False]) is True
-        assert show_plots(".out", [False, False, True, False, False, False, False]) is True
-        assert show_plots(".out", [False, False, False, True, False, False, False]) is True
+        assert show_plots(
+            ".out", [True, False, False, False, False, False, False]
+        ) is True
+        assert show_plots(
+            ".out", [False, True, False, False, False, False, False]
+        ) is True
+        assert show_plots(
+            ".out", [False, False, True, False, False, False, False]
+        ) is True
+        assert show_plots(
+            ".out", [False, False, False, True, False, False, False]
+        ) is True
 
     def test_out_all_false(self):
-        assert show_plots(".out", [False, False, False, False, False, False, False]) is False
+        assert show_plots(
+            ".out", [False, False, False, False, False, False, False]
+        ) is False
 
     def test_asc_true(self):
-        assert show_plots(".asc", [False, False, False, False, True, False, False]) is True
+        assert show_plots(
+            ".asc", [False, False, False, False, True, False, False]
+        ) is True
 
     def test_asc_false(self):
-        assert show_plots(".asc", [False, False, False, False, False, False, False]) is False
+        assert show_plots(
+            ".asc", [False, False, False, False, False, False, False]
+        ) is False
 
     def test_spectrum_true(self):
-        assert show_plots(".spectrum", [False, False, False, False, False, True, False]) is True
-        assert show_plots(".spectrum", [False, False, False, False, False, False, True]) is True
+        assert show_plots(
+            ".spectrum", [False, False, False, False, False, True, False]
+        ) is True
+        assert show_plots(
+            ".spectrum", [False, False, False, False, False, False, True]
+        ) is True
 
     def test_spectrum_false(self):
-        assert show_plots(".spectrum", [False, False, False, False, False, False, False]) is False
+        assert show_plots(
+            ".spectrum", [False, False, False, False, False, False, False]
+        ) is False
 
     def test_root_ext_true(self):
-        assert show_plots(".spectrum.root1", [False, False, False, False, False, True, False]) is True
+        assert show_plots(
+            ".spectrum.root1", [False, False, False, False, False, True, False]
+        ) is True
 
     def test_unknown_ext(self):
-        assert show_plots(".xyz", [True, True, True, True, True, True, True]) is False
+        assert show_plots(
+            ".xyz", [True, True, True, True, True, True, True]
+        ) is False
 
 
 class TestIsUnique:
@@ -275,7 +315,9 @@ def test_basic_sum(self):
         result = rootSum(df)
         assert len(result) == 1
         np.testing.assert_array_equal(result.iloc[0]["xdata"], xdata)
-        np.testing.assert_array_equal(result.iloc[0]["ydata"], np.array([5.0, 7.0, 9.0]))
+        np.testing.assert_array_equal(
+            result.iloc[0]["ydata"], np.array([5.0, 7.0, 9.0])
+        )
 
     def test_different_names_raises(self):
         df = pd.DataFrame([
@@ -351,7 +393,9 @@ def test_asc(self):
         assert xdatamin(row, 10.0) == 400.0 - 30.0
 
     def test_out(self):
-        row = pd.Series({"ext": ".out", "xdata_plot": np.array([1000.0, 2000.0])})
+        row = pd.Series(
+            {"ext": ".out", "xdata_plot": np.array([1000.0, 2000.0])}
+        )
         assert xdatamin(row, 10.0) == 1000.0
 
 
@@ -361,5 +405,7 @@ def test_asc(self):
         assert xdatamax(row, 10.0) == 500.0 + 30.0
 
     def test_out(self):
-        row = pd.Series({"ext": ".out", "xdata_plot": np.array([1000.0, 2000.0])})
+        row = pd.Series(
+            {"ext": ".out", "xdata_plot": np.array([1000.0, 2000.0])}
+        )
         assert xdatamax(row, 10.0) == 2000.0

tests/test_integration.py

@@ -5,7 +5,6 @@
 """
 
 import sys
-from pathlib import Path
 from unittest.mock import MagicMock, patch
 
 import pytest
@@ -95,7 +94,9 @@ def test_nonexistent_file_skipped(self):
             assert exc_info.value.code == 1
 
     def test_mixed_types(self):
-        mock_ax = self._run_main([TEST_FILES["tddft"], TEST_FILES["experimental"]])
+        mock_ax = self._run_main(
+            [TEST_FILES["tddft"], TEST_FILES["experimental"]]
+        )
         assert mock_ax.plot.called
 
     def test_multiple_esd_roots(self):