Move to src layout

pyproject.toml

@@ -6,8 +6,9 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
+where = ["src"]
 include = ["lobsterpy*"]
-exclude = ["docs*", "tests*", "paper*"]
+#exclude = ["docs*", "tests*", "paper*"]
 
 [project]
 name = "lobsterpy"
@@ -165,7 +166,7 @@ exclude_lines = [
 ]
 
 [tool.coverage.run]
-include = ["lobsterpy/*"]
+include = ["src/"]
 omit = [
     # omit anything in test directory anywhere
     "tests/*",

lobsterpy/plotting/layout_dicts.py → src/lobsterpy/plotting/layout_dicts.py

@@ -1,141 +1,141 @@
-"""
-Dictionaries for plotly figure layouts.
-
-Layout inspired by
-https://github.com/materialsproject/crystaltoolkit/blob/main/crystal_toolkit/components/bandstructure.py
-
-Contains dicts for
-    1. general figure layout
-    2. axes ((I)COHP / energy)
-    3. traces (Spin.up / Spin.down)
-    4. legend
-
-"""
-
-layout_dict = {
-    "titlefont": {"size": 18},
-    "showlegend": True,
-    "title_x": 0.1,
-    "title_y": 0.9,
-    "hovermode": "closest",
-    "paper_bgcolor": "rgba(0,0,0,0)",
-    "plot_bgcolor": "rgba(0,0,0,0)",
-}
-
-"""
-    General layout of Plotly figure.
-
-    :param dict titlefont: Line style dictionary.
-    :param bool showlegend: Legend hide or show.
-    :param float title_x: x axis title size.
-    :param float title_y: y axis title size.
-    :param str hovermode: hover behaviour.
-    :param str paper_bgcolor: background color.
-    :param str plot_bgcolor: plot background color.
-"""
-
-cohp_axis_style_dict = {
-    "titlefont": {"size": 20},
-    "tickfont": {"size": 16},
-    "ticks": "inside",
-    "tickwidth": 2,
-    "showgrid": False,
-    "showline": True,
-    "zeroline": True,
-    "zerolinecolor": "black",
-    "zerolinewidth": 3,
-    "mirror": True,
-    "linewidth": 2,
-    "linecolor": "black",
-}
-
-"""
-    COXX axis style.
-
-    :param dict titlefont: axis title font style.
-    :param dict tickfont: axis tick font style.
-    :param str ticks: ticks style.
-    :param float tickwidth: width of ticks.
-    :param bool showgrid: show or hide axis grid.
-    :param bool showline: show or hide axis.
-    :param bool zeroline: show or hide zero line.
-    :param str zerolinecolor: color of zero line.
-    :param float zerolinewidth: width of zero line.
-    :param bool mirror: mirror axis.
-    :param float linewidth: width of axis line.
-    :param str linecolor: color of axis line.
-"""
-
-energy_axis_style_dict = {
-    "titlefont": {"size": 20},
-    "tickfont": {"size": 16},
-    "ticks": "inside",
-    "tickwidth": 2,
-    "showgrid": False,
-    "showline": True,
-    "zeroline": True,
-    "zerolinecolor": "rgba(0,0,0,0.5)",
-    "zerolinewidth": 3,
-    "mirror": True,
-    "linewidth": 2,
-    "linecolor": "black",
-}
-
-"""
-    Energy axis style.
-
-    :param dict titlefont: axis title font style.
-    :param dict tickfont: axis tick font style.
-    :param str ticks: ticks style.
-    :param float tickwidth: width of ticks.
-    :param bool showgrid: show or hide axis grid.
-    :param bool showline: show or hide axis.
-    :param bool zeroline: show or hide zero line.
-    :param str zerolinecolor: color of zero line.
-    :param float zerolinewidth: width of zero line.
-    :param bool mirror: mirror axis.
-    :param float linewidth: width of axis line.
-    :param str linecolor: color of axis line.
-"""
-
-spin_up_trace_style_dict = {
-    "line": {"width": 3},
-    "mode": "lines",
-    "visible": "legendonly",
-}
-
-"""
-    Line style for Spin.up traces.
-
-    :param dict line: Line style dictionary.
-    :param str mode: Plotly mode.
-    :param str visible: Trace visibility.
-"""
-
-spin_down_trace_style_dict = {
-    "line": {"width": 3, "dash": "dash"},
-    "mode": "lines",
-    "visible": "legendonly",
-}
-
-"""
-    Line style for Spin.down traces.
-
-    :param dict line: Line style dictionary.
-    :param str mode: Plotly mode.
-    :param str visible: Trace visibility.
-"""
-
-legend_style_dict = {
-    "bordercolor": "black",
-    "borderwidth": 2,
-    "traceorder": "normal",
-}
-
-"""
-    Legend style.
-
-    :param str bordercolor: border color of legend.
-    :param int borderwidth: width of border.
-    :param str traceorder: order of trace.
-"""
+"""
+Dictionaries for plotly figure layouts.
+
+Layout inspired by
+https://github.com/materialsproject/crystaltoolkit/blob/main/crystal_toolkit/components/bandstructure.py
+
+Contains dicts for
+    1. general figure layout
+    2. axes ((I)COHP / energy)
+    3. traces (Spin.up / Spin.down)
+    4. legend
+
+"""
+
+layout_dict = {
+    "titlefont": {"size": 18},
+    "showlegend": True,
+    "title_x": 0.1,
+    "title_y": 0.9,
+    "hovermode": "closest",
+    "paper_bgcolor": "rgba(0,0,0,0)",
+    "plot_bgcolor": "rgba(0,0,0,0)",
+}
+
+"""
+    General layout of Plotly figure.
+
+    :param dict titlefont: Line style dictionary.
+    :param bool showlegend: Legend hide or show.
+    :param float title_x: x axis title size.
+    :param float title_y: y axis title size.
+    :param str hovermode: hover behaviour.
+    :param str paper_bgcolor: background color.
+    :param str plot_bgcolor: plot background color.
+"""
+
+cohp_axis_style_dict = {
+    "titlefont": {"size": 20},
+    "tickfont": {"size": 16},
+    "ticks": "inside",
+    "tickwidth": 2,
+    "showgrid": False,
+    "showline": True,
+    "zeroline": True,
+    "zerolinecolor": "black",
+    "zerolinewidth": 3,
+    "mirror": True,
+    "linewidth": 2,
+    "linecolor": "black",
+}
+
+"""
+    COXX axis style.
+
+    :param dict titlefont: axis title font style.
+    :param dict tickfont: axis tick font style.
+    :param str ticks: ticks style.
+    :param float tickwidth: width of ticks.
+    :param bool showgrid: show or hide axis grid.
+    :param bool showline: show or hide axis.
+    :param bool zeroline: show or hide zero line.
+    :param str zerolinecolor: color of zero line.
+    :param float zerolinewidth: width of zero line.
+    :param bool mirror: mirror axis.
+    :param float linewidth: width of axis line.
+    :param str linecolor: color of axis line.
+"""
+
+energy_axis_style_dict = {
+    "titlefont": {"size": 20},
+    "tickfont": {"size": 16},
+    "ticks": "inside",
+    "tickwidth": 2,
+    "showgrid": False,
+    "showline": True,
+    "zeroline": True,
+    "zerolinecolor": "rgba(0,0,0,0.5)",
+    "zerolinewidth": 3,
+    "mirror": True,
+    "linewidth": 2,
+    "linecolor": "black",
+}
+
+"""
+    Energy axis style.
+
+    :param dict titlefont: axis title font style.
+    :param dict tickfont: axis tick font style.
+    :param str ticks: ticks style.
+    :param float tickwidth: width of ticks.
+    :param bool showgrid: show or hide axis grid.
+    :param bool showline: show or hide axis.
+    :param bool zeroline: show or hide zero line.
+    :param str zerolinecolor: color of zero line.
+    :param float zerolinewidth: width of zero line.
+    :param bool mirror: mirror axis.
+    :param float linewidth: width of axis line.
+    :param str linecolor: color of axis line.
+"""
+
+spin_up_trace_style_dict = {
+    "line": {"width": 3},
+    "mode": "lines",
+    "visible": "legendonly",
+}
+
+"""
+    Line style for Spin.up traces.
+
+    :param dict line: Line style dictionary.
+    :param str mode: Plotly mode.
+    :param str visible: Trace visibility.
+"""
+
+spin_down_trace_style_dict = {
+    "line": {"width": 3, "dash": "dash"},
+    "mode": "lines",
+    "visible": "legendonly",
+}
+
+"""
+    Line style for Spin.down traces.
+
+    :param dict line: Line style dictionary.
+    :param str mode: Plotly mode.
+    :param str visible: Trace visibility.
+"""
+
+legend_style_dict = {
+    "bordercolor": "black",
+    "borderwidth": 2,
+    "traceorder": "normal",
+}
+
+"""
+    Legend style.
+
+    :param str bordercolor: border color of legend.
+    :param int borderwidth: width of border.
+    :param str traceorder: order of trace.
+"""

tests/cli/test_cli.py

@@ -14,9 +14,8 @@
 import matplotlib.style
 import numpy as np
 import pytest
-from matplotlib.figure import Figure
-
 from lobsterpy.cli import get_parser, run
+from matplotlib.figure import Figure
 
 CurrentDir = Path(__file__).absolute().parent
 TestDir = CurrentDir / "../"

tests/cohp/test_analyze.py

@@ -5,12 +5,11 @@
 from pathlib import Path
 
 import pytest
+from lobsterpy.cohp.analyze import Analysis
 from pymatgen.core import Structure
 from pymatgen.io.lobster import Bandoverlaps, Charge, Doscar, Lobsterin, Lobsterout
 from pymatgen.io.vasp import Vasprun
 
-from lobsterpy.cohp.analyze import Analysis
-
 CurrentDir = Path(__file__).absolute().parent
 TestDir = CurrentDir / "../"
 

tests/conftest.py

@@ -5,11 +5,10 @@
 from pathlib import Path
 
 import pytest
-from pymatgen.electronic_structure.cohp import CompleteCohp
-from pymatgen.io.lobster import Charge, Doscar, Icohplist
-
 from lobsterpy.cohp.analyze import Analysis
 from lobsterpy.cohp.describe import Description
+from pymatgen.electronic_structure.cohp import CompleteCohp
+from pymatgen.io.lobster import Charge, Doscar, Icohplist
 
 TestDir = Path(__file__).absolute().parent
 

tests/featurize/test_batch.py

@@ -2,15 +2,14 @@
 
 import pandas as pd
 import pytest
-from pymatgen.analysis.graphs import StructureGraph
-
 from lobsterpy.featurize.batch import (
     BatchCoxxFingerprint,
     BatchDosFeaturizer,
     BatchStructureGraphs,
     BatchSummaryFeaturizer,
 )
 from lobsterpy.featurize.core import CoxxFingerprint, DosFingerprint
+from pymatgen.analysis.graphs import StructureGraph
 
 CurrentDir = Path(__file__).absolute().parent
 TestDir = CurrentDir / "../"

tests/featurize/test_core.py

@@ -3,7 +3,6 @@
 import numpy as np
 import pandas as pd
 import pytest
-
 from lobsterpy.featurize.core import (
     DosFingerprint,
     FeaturizeCharges,

tests/featurize/test_utils.py

@@ -2,9 +2,8 @@
 import shutil
 from pathlib import Path
 
-from pymatgen.core import Structure
-
 from lobsterpy.featurize import get_file_paths, get_structure_path
+from pymatgen.core import Structure
 
 CurrentDir = Path(__file__).absolute().parent
 TestDir = CurrentDir / "../"

tests/plotting/test_plotting.py

@@ -4,17 +4,16 @@
 
 import numpy as np
 import pytest
-from plotly.io import read_json
-from pymatgen.electronic_structure.cohp import Cohp
-from pymatgen.electronic_structure.core import Spin
-
 from lobsterpy.cohp.describe import Description
 from lobsterpy.plotting import (
     IcohpDistancePlotter,
     InteractiveCohpPlotter,
     PlainCohpPlotter,
     PlainDosPlotter,
 )
+from plotly.io import read_json
+from pymatgen.electronic_structure.cohp import Cohp
+from pymatgen.electronic_structure.core import Spin
 
 CurrentDir = Path(__file__).absolute().parent
 TestDir = CurrentDir / "../"