Remove cumulative.py and associated tests + assets (#257)

* remove cumulative.py and associated tests and assets

contained cumulative_error() and cumulative_residual() plotting functions

* move spacegroup_bar() assets into their own "Bar Plots" readme section

* add test_readme_function_names that checks functions listed in readme table match the names in source files

* remove local hook no-missing-readme-images

* include *.yml in pyproject.toml tool.setuptools.package-data (to have keys.yml in PyPI package)

.pre-commit-config.yaml

@@ -53,14 +53,6 @@ repos:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
 
-  - repo: local
-    hooks:
-      - id: no-missing-readme-images
-        name: No missing readme images
-        entry: python -c 'from tests.test_readme import test_no_missing_images; test_no_missing_images()'
-        language: system
-        files: readme.md
-
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:

assets/scripts/coordination/coordination_hist.py

@@ -57,9 +57,8 @@
 for strategy in (CrystalNN(), VoronoiNN()):
     cls_name = type(strategy).__name__
     fig = pmv.coordination_hist(structures[key1], strategy=strategy)
-    fig.layout.title = dict(
-        text=f"Coordination Histogram ({cls_name}): {key1}", x=0.5, y=0.98
-    )
+    title = f"Coordination Histogram ({cls_name}): {key1}"
+    fig.layout.title = dict(text=title, x=0.5, y=0.98)
     fig.layout.margin.t = 50
     fig.show()
     pmv.io.save_and_compress_svg(fig, f"coordination-hist-{cls_name.lower()}")
@@ -68,29 +67,26 @@
 # %% Custom analyzer example
 fig = pmv.coordination_hist(structures[key1], strategy=VoronoiNN())
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text=f"Coordination Histogram (VoronoiNN): {key1}", x=0.5, y=0.98
-)
+title = f"Coordination Histogram (VoronoiNN): {key1}"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-voronoi")
 
 
 # %% Multiple structures example
 fig = pmv.coordination_hist({key1: structures[key1], key2: structures[key2]})
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text="Coordination Histogram: Multiple Structures", x=0.5, y=0.98
-)
+title = "Coordination Histogram: Multiple Structures"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-multiple")
 
 
 # %% By element example (now default, but explicitly specified for clarity)
 fig = pmv.coordination_hist(structures[key1], split_mode=CnSplitMode.by_element)
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text=f"Coordination Histogram by Element: {key1}", x=0.5, y=0.98
-)
+title = f"Coordination Histogram by Element: {key1}"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-by-element")
 
@@ -100,9 +96,8 @@
     {key1: structures[key1], key2: structures[key2], key3: structures[key3]},
 )
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text="Coordination Histogram by Element: Multiple Structures", x=0.5, y=0.98
-)
+title = "Coordination Histogram by Element: Multiple Structures"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-multiple-by-element")
 
@@ -113,7 +108,8 @@
     split_mode=CnSplitMode.by_structure,
 )
 fig.layout.margin.t = 50
-fig.layout.title = dict(text="Coordination Histogram by Structure", x=0.5, y=0.98)
+title = "Coordination Histogram by Structure"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-by-structure")
 
@@ -124,9 +120,8 @@
     split_mode=CnSplitMode.by_structure_and_element,
 )
 fig.layout.margin.t = 60
-fig.layout.title = dict(
-    text="Coordination Histogram by Structure and Element", x=0.5, y=0.98
-)
+title = "Coordination Histogram by Structure and Element"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-by-structure-and-element")
 
@@ -137,11 +132,8 @@
     hover_data=("oxidation_state", "wyckoff"),
 )
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text="Coordination Histogram by Element: Multiple Structures (with custom hover)",
-    x=0.5,
-    y=0.98,
-)
+title = "Coordination Histogram by Element: Multiple Structures (with custom hover)"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-multiple-by-element-custom-hover")
 
@@ -154,11 +146,8 @@
     element_color_scheme=custom_colors,
 )
 fig.layout.margin.t = 60
-fig.layout.title = dict(
-    text="Coordination Histogram by Element: Multiple Structures (with custom colors)",
-    x=0.5,
-    y=0.99,
-)
+title = "Coordination Histogram by Element: Multiple Structures (with custom colors)"
+fig.layout.title = dict(text=title, x=0.5, y=0.99)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-multiple-by-element-custom-colors")
 
@@ -169,9 +158,8 @@
     split_mode=CnSplitMode.none,
 )
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text="Coordination Histogram: All Structures Combined", x=0.5, y=0.98
-)
+title = "Coordination Histogram: All Structures Combined"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-all-combined")
 
@@ -184,8 +172,7 @@
     bar_kwargs=dict(width=0.2),
 )
 fig.layout.margin.t = 50
-fig.layout.title = dict(
-    text="Coordination Histogram: All Structures Combined (Side-by-side)", x=0.5, y=0.98
-)
+title = "Coordination Histogram: All Structures Combined (Side-by-side)"
+fig.layout.title = dict(text=title, x=0.5, y=0.98)
 fig.show()
 pmv.io.save_and_compress_svg(fig, "coordination-hist-all-combined-side-by-side")

pymatviz/__init__.py

@@ -22,7 +22,6 @@
     classify,
     colors,
     coordination,
-    cumulative,
     data,
     enums,
     io,
@@ -45,7 +44,6 @@
 from pymatviz.classify import precision_recall_curve_plotly, roc_curve_plotly
 from pymatviz.classify.confusion_matrix import confusion_matrix
 from pymatviz.coordination import coordination_hist, coordination_vs_cutoff_line
-from pymatviz.cumulative import cumulative_error, cumulative_residual
 from pymatviz.enums import Key, angstrom_per_atom, cubic_angstrom, eV
 from pymatviz.histogram import elements_hist, histogram, spacegroup_bar
 from pymatviz.io import df_to_html, df_to_pdf, df_to_svg, save_fig

pymatviz/coordination/plotly.py

@@ -316,15 +316,8 @@ def coordination_hist(
     fig.update_layout(barmode=bar_mode, bargap=0.15, bargroupgap=0.1)
 
     # start x-axis just below the smallest observed CN
-    fig.update_xaxes(
-        tick0=int(min_cn),
-        dtick=1,
-        range=[min_cn - 0.5, max_cn + 0.5],
-    )
-    dev_fig = fig.full_figure_for_development(warn=False)
-    y_max = dev_fig.layout.yaxis.range[1]
-    # Ensure y-axis starts at 0
-    fig.update_yaxes(title="Count", range=[0, y_max])
+    fig.update_xaxes(tick0=int(min_cn), dtick=1, range=[min_cn - 0.5, max_cn + 0.5])
+    fig.update_yaxes(title="Count", rangemode="tozero")  # Ensure y_min=0, not <0
 
     # Add title "Coordination Number" to x axes of the last n_cols subplots
     for idx in range(n_subplots - n_cols + 1, n_subplots + 1):

pymatviz/enums.py

@@ -235,9 +235,6 @@ def __reduce_ex__(self, proto: object) -> tuple[type, tuple[str]]:
     # Structure Prototyping
     protostructure = "protostructure"
     prototype = "prototype"
-    aflow_prototype = "aflow_prototype"
-    canonical_proto = "canonical_proto"
-    uniq_proto = "uniq_proto"
 
     # Composition
     arity = "arity"
@@ -612,7 +609,7 @@ def __reduce_ex__(self, proto: object) -> tuple[type, tuple[str]]:
     id = "id"
     db_id = "db_id"
     uuid = "uuid"
-    mat_id = "mat_id"
+    mat_id = "material_id"
     frame_id = "frame_id"
     task = "task"
     job_id = "job_id"