Merge pull request #195 from softboiler/194-migrate-stabilized-morph-…

…functionality-to-boilercv

Migrate stabilized `Morph` functionality to `boilercv`

changelog/194.change.md

@@ -0,0 +1 @@
+Migrate stabilized `Morph` functionality to `boilercv`

docs/conf.py

@@ -4,6 +4,9 @@
 from hashlib import sha256
 from pathlib import Path
 
+from ruamel.yaml import YAML
+from sphinx.application import Sphinx
+
 from boilercv_docs import DOCS, PYPROJECT, chdir_docs
 from boilercv_docs.intersphinx import get_ispx, get_rtd, get_url
 from boilercv_docs.nbs import init_nb_env
@@ -12,8 +15,6 @@
 from boilercv_pipeline.correlations.dimensionless_bubble_diameter.morphs import (
     EQUATIONS,
 )
-from ruamel.yaml import YAML
-from sphinx.application import Sphinx
 
 # ! Initialization
 patch_nbs()
@@ -45,17 +46,17 @@
 """Package version."""
 # ! Intersphinx and related
 ISPX_MAPPING: dict[str, IspxMappingValue] = {
-    **{pkg: get_rtd(pkg) for pkg in ["myst_parser", "nbformat", "numpydoc"]},
+    **{pkg: get_rtd(pkg) for pkg in ["myst_parser", "nbformat", "numpydoc", "tomlkit"]},
     **{pkg: get_rtd(pkg, latest=True) for pkg in ["pyqtgraph"]},
     "jupyterbook": get_url("jupyterbook.org/en"),
     "numpy": get_url("numpy.org/doc"),
     "matplotlib": get_url("matplotlib.org"),
     "pytest": get_url("docs.pytest.org/en"),
     "sympy": get_url("docs.sympy.org", latest=True),
+    "colorcet": get_ispx("https://colorcet.holoviz.org/"),
     "cv2": get_ispx("docs.opencv.org/2.4"),
-    "python": get_ispx("docs.python.org/3"),
     "pandas": get_ispx("pandas.pydata.org/docs"),
-    "colorcet": get_ispx("https://colorcet.holoviz.org/"),
+    "python": get_ispx("docs.python.org/3"),
 }
 """Intersphinx mapping."""
 TIPPY_RTD_URLS = [
@@ -142,7 +143,7 @@ def dpath(path: Path, rel: Path = DOCS) -> str:
     "sphinxcontrib.towncrier",
 ]
 suppress_warnings = [
-    "autodoc2.dup_item"  # "Duplicate items in boilercv_tests.test_morph
+    "autodoc2.dup_item"  # "Duplicate items in boilercv_tests.test_morphs
 ]
 # ! Theme
 html_title = PACKAGE
@@ -250,15 +251,15 @@ def dpath(path: Path, rel: Path = DOCS) -> str:
     (r"py:.*", r"_pytest\..+"),
     (r"py:.*", r"boilercore\..+"),
     (r"py:.*", r"numpy\.typing\..+"),
+    (r"py:.*", r"tomlkit\.container\..+"),
     # ? sympy: https://github.com/sympy/sympy/issues/17619#issuecomment-536781620
     (r"py:.*", r"sympy\..+"),
     (r"py:.*", r"pydantic\..+"),  # ? https://github.com/pydantic/pydantic/issues/1339
     (r"py:.*", r"PySide6\..+"),  # ? https://bugreports.qt.io/browse/PYSIDE-2215
     # ? TypeAlias: https://github.com/sphinx-doc/sphinx/issues/10785
     (r"py:class", rf"{PACKAGE}.*\.types\..+"),
     (r"py:class", rf"{PACKAGE}_pipeline\.captivate\.previews\..+"),
-    (r"py:class", rf"{PACKAGE}_pipeline\.equations\..+"),
-    (r"py:class", rf"{PACKAGE}_tests\.test_morph\..+"),
+    (r"py:.*", rf"{PACKAGE}_tests\.test_morphs\..+"),
     # ? Until done with Pydantic v1
     (r"py:.*", r"pydantic\.v1\..+"),
 ]

docs/experiments/e230920_subcool/find_centers.ipynb

@@ -33,10 +33,6 @@
     "\n",
     "paths = init()\n",
     "\n",
-    "from boilercv_docs.nbs import HIDE, nowarn, style_df\n",
-    "from boilercv_pipeline.experiments.e230920_subcool import GBC, bounded_ax\n",
-    "from boilercv_pipeline.experiments.e240215_plotting import cool, warm\n",
-    "from boilercv_pipeline.sets import get_contours_df, get_dataset\n",
     "from geopandas import GeoDataFrame, points_from_xy\n",
     "from matplotlib.pyplot import subplots\n",
     "from myst_nb import glue\n",
@@ -45,6 +41,10 @@
     "from shapely import LinearRing\n",
     "\n",
     "from boilercv.images import scale_bool\n",
+    "from boilercv_docs.nbs import HIDE, nowarn, style_df\n",
+    "from boilercv_pipeline.experiments.e230920_subcool import GBC, bounded_ax\n",
+    "from boilercv_pipeline.experiments.e240215_plotting import cool, warm\n",
+    "from boilercv_pipeline.sets import get_contours_df, get_dataset\n",
     "\n",
     "COMPARE_WITH_TRACKPY = True\n",
     "\"\"\"Whether to get centers using the Trackpy approach.\"\"\"\n",

docs/experiments/e230920_subcool/find_objects.ipynb

@@ -33,17 +33,17 @@
     "\n",
     "paths = init()\n",
     "\n",
-    "from boilercv_docs.nbs import HIDE, nowarn, style_df\n",
-    "from boilercv_pipeline.experiments.e230920_subcool import GBC, bounded_ax\n",
-    "from boilercv_pipeline.experiments.e240215_plotting import cool, warm\n",
-    "from boilercv_pipeline.sets import get_contours_df, get_dataset\n",
     "from geopandas import GeoDataFrame, points_from_xy\n",
     "from numpy import pi, sqrt\n",
     "from pandas import DataFrame, IndexSlice, NamedAgg\n",
     "from seaborn import scatterplot\n",
     "from shapely import LinearRing, Polygon\n",
     "\n",
     "from boilercv.images import scale_bool\n",
+    "from boilercv_docs.nbs import HIDE, nowarn, style_df\n",
+    "from boilercv_pipeline.experiments.e230920_subcool import GBC, bounded_ax\n",
+    "from boilercv_pipeline.experiments.e240215_plotting import cool, warm\n",
+    "from boilercv_pipeline.sets import get_contours_df, get_dataset\n",
     "\n",
     "COMPARE_WITH_TRACKPY = True\n",
     "\"\"\"Whether to get objects using the Trackpy approach.\"\"\"\n",

docs/experiments/e230920_subcool/find_tracks.ipynb

@@ -33,6 +33,9 @@
     "\n",
     "paths = init()\n",
     "\n",
+    "from numpy import diff, linalg\n",
+    "from pandas import DataFrame, read_hdf\n",
+    "\n",
     "from boilercv_docs.nbs import HIDE, display_dataframe_with_math, nowarn, style_df\n",
     "from boilercv_pipeline.experiments.e230920_subcool import (\n",
     "    GBC,\n",
@@ -43,8 +46,6 @@
     "    transform_cols,\n",
     ")\n",
     "from boilercv_pipeline.sets import get_dataset\n",
-    "from numpy import diff, linalg\n",
-    "from pandas import DataFrame, read_hdf\n",
     "\n",
     "with nowarn(capture=True):\n",
     "    from trackpy import link, quiet\n",

docs/experiments/e230920_subcool/find_tracks_trackpy.ipynb

@@ -27,6 +27,23 @@
     "\n",
     "paths = init()\n",
     "\n",
+    "from matplotlib.figure import Figure\n",
+    "from matplotlib.pyplot import subplot_mosaic, subplots\n",
+    "from numpy import diff, linalg, logspace\n",
+    "from pandas import CategoricalDtype, DataFrame, read_hdf\n",
+    "from seaborn import lineplot, move_legend, scatterplot\n",
+    "\n",
+    "from boilercv.data import apply_to_img_da\n",
+    "from boilercv.dimensionless_params import (\n",
+    "    fourier,\n",
+    "    jakob,\n",
+    "    kinematic_viscosity,\n",
+    "    prandtl,\n",
+    "    reynolds,\n",
+    "    thermal_diffusivity,\n",
+    ")\n",
+    "from boilercv.images import scale_bool\n",
+    "from boilercv.images.cv import Op, Transform, transform\n",
     "from boilercv_docs.nbs import HIDE, nowarn, style_df\n",
     "from boilercv_pipeline.correlations.dimensionless_bubble_diameter import (\n",
     "    florschuetz_chao_1965,\n",
@@ -47,23 +64,6 @@
     "from boilercv_pipeline.experiments.e240215_plotting import cool, warm\n",
     "from boilercv_pipeline.models.params import PARAMS\n",
     "from boilercv_pipeline.sets import get_dataset\n",
-    "from matplotlib.figure import Figure\n",
-    "from matplotlib.pyplot import subplot_mosaic, subplots\n",
-    "from numpy import diff, linalg, logspace\n",
-    "from pandas import CategoricalDtype, DataFrame, read_hdf\n",
-    "from seaborn import lineplot, move_legend, scatterplot\n",
-    "\n",
-    "from boilercv.data import apply_to_img_da\n",
-    "from boilercv.dimensionless_params import (\n",
-    "    fourier,\n",
-    "    jakob,\n",
-    "    kinematic_viscosity,\n",
-    "    prandtl,\n",
-    "    reynolds,\n",
-    "    thermal_diffusivity,\n",
-    ")\n",
-    "from boilercv.images import scale_bool\n",
-    "from boilercv.images.cv import Op, Transform, transform\n",
     "\n",
     "with nowarn(capture=True):\n",
     "    from trackpy import batch, link, locate, quiet\n",

docs/experiments/e230920_subcool/get_thermal_data.ipynb

@@ -30,11 +30,12 @@
     "\n",
     "paths = init()\n",
     "\n",
-    "from boilercv_docs.nbs import HIDE\n",
-    "from boilercv_pipeline.experiments.e230920_subcool import ALL_THERMAL_DATA\n",
     "from pandas import DataFrame, read_csv\n",
     "from seaborn import scatterplot\n",
     "\n",
+    "from boilercv_docs.nbs import HIDE\n",
+    "from boilercv_pipeline.experiments.e230920_subcool import ALL_THERMAL_DATA\n",
+    "\n",
     "BOILING = 97.33  # (C) inferred from mean pressure over the time span\n",
     "TIME = \"time\"\n",
     "BASE_TEMP = \"T0cal (C)\"\n",

docs/experiments/e230920_subcool/plot_tracks.ipynb

@@ -32,6 +32,21 @@
     "from boilercv_docs.nbs import init\n",
     "\n",
     "paths = init()\n",
+    "from matplotlib.figure import Figure\n",
+    "from matplotlib.pyplot import subplot_mosaic, subplots\n",
+    "from numpy import diff, log10, logspace\n",
+    "from pandas import DataFrame, Series, read_hdf\n",
+    "from seaborn import lineplot, move_legend, scatterplot\n",
+    "\n",
+    "from boilercv.dimensionless_params import (\n",
+    "    fourier,\n",
+    "    jakob,\n",
+    "    kinematic_viscosity,\n",
+    "    prandtl,\n",
+    "    reynolds,\n",
+    "    thermal_diffusivity,\n",
+    ")\n",
+    "from boilercv.images import scale_bool\n",
     "from boilercv_docs.nbs import HIDE\n",
     "from boilercv_pipeline.correlations.dimensionless_bubble_diameter import (\n",
     "    akiyama_1973,\n",
@@ -57,21 +72,6 @@
     ")\n",
     "from boilercv_pipeline.experiments.e240215_plotting import cool, warm12\n",
     "from boilercv_pipeline.sets import get_dataset\n",
-    "from matplotlib.figure import Figure\n",
-    "from matplotlib.pyplot import subplot_mosaic, subplots\n",
-    "from numpy import diff, log10, logspace\n",
-    "from pandas import DataFrame, Series, read_hdf\n",
-    "from seaborn import lineplot, move_legend, scatterplot\n",
-    "\n",
-    "from boilercv.dimensionless_params import (\n",
-    "    fourier,\n",
-    "    jakob,\n",
-    "    kinematic_viscosity,\n",
-    "    prandtl,\n",
-    "    reynolds,\n",
-    "    thermal_diffusivity,\n",
-    ")\n",
-    "from boilercv.images import scale_bool\n",
     "\n",
     "S = Series\n",
     "\n",

pipeline/boilercv_pipeline/correlations/dimensionless_bubble_diameter/morphs.py

@@ -4,34 +4,34 @@
 from pathlib import Path
 from re import sub
 from string import whitespace
-from typing import Annotated, Any, ClassVar, Generic, Self, TypeAlias, overload
+from typing import Any, ClassVar, Generic, Self, overload
 
 from numpy import linspace, pi
-from pydantic import BaseModel, Field, PlainValidator, model_validator
+from pydantic import BaseModel, Field, model_validator
 from pydantic_core import PydanticUndefinedType
-from sympy import Basic, symbols, sympify
 from tomlkit import parse
 from tomlkit.container import Container
 from tomlkit.items import Item
 
+from boilercv.morphs import BaseMorph, Morph
 from boilercv_pipeline.correlations.dimensionless_bubble_diameter.types import (
+    LOCALS,
     Eq,
     Expectation,
+    Expr,
     FormsRepl,
-    JsonStrPlainSerializer,
     K,
     Kind,
     Leaf,
+    Locals,
     Node,
     Param,
     Repl,
     Sym,
     V,
     kinds,
-    params,
-    syms,
+    solve_syms,
 )
-from boilercv_pipeline.equations import BaseMorph, Morph
 
 base = Path(__file__).with_suffix(".toml")
 EQUATIONS_TOML = base.with_stem("equations")
@@ -49,8 +49,6 @@
     for find, repl in {"{0}": r"\o", "{b0}": r"\b0"}.items()
 )
 """Replacements to make after parsing LaTeX from PNGs."""
-PARAMS = Morph[Param, Sym](dict(zip(params, syms, strict=True)))
-"""Parameters."""
 KWDS = Morph[Param, Expectation]({
     "bubble_fourier": linspace(start=0.0, stop=5.0e-3, num=10),
     "bubble_jakob": 1.0,
@@ -125,23 +123,6 @@ class Forms(DefaultMorph[Kind, str]):
 DefaultMorph.register(Forms)
 
 
-def validate_expr(v: Basic | str):
-    """Validate expression."""
-    return (
-        v
-        if isinstance(v, Basic)
-        else sympify(v, locals=LOCALS.model_dump(), evaluate=False)
-    )
-
-
-Expr: TypeAlias = Annotated[
-    Basic, PlainValidator(validate_expr), JsonStrPlainSerializer
-]
-"""Expression."""
-solve_syms: tuple[Sym, ...] = ("Fo_0", "beta")
-"""Symbols to solve for."""
-
-
 class Soln(BaseModel):
     """All solutions."""
 
@@ -159,20 +140,6 @@ class Solns(DefaultMorph[Sym, Soln]):
 DefaultMorph.register(Solns)
 
 
-Locals: TypeAlias = Morph[Sym, Expr]
-"""Locals."""
-LOCALS = Locals(
-    dict(
-        zip(
-            syms,
-            symbols(list(PARAMS.values()), nonnegative=True, real=True, finite=True),
-            strict=False,
-        )
-    )
-)
-"""Local variables."""
-
-
 def set_equation_forms(i: Forms, symbols: Locals) -> Forms:
     """Set equation forms."""
     return i.pipe(

pipeline/boilercv_pipeline/correlations/dimensionless_bubble_diameter/types.py

@@ -14,6 +14,9 @@
 from numpy import float64
 from numpy.typing import NDArray
 from pydantic import PlainSerializer, PlainValidator
+from sympy import Basic, symbols, sympify
+
+from boilercv.morphs import Morph
 
 T = TypeVar("T")
 K = TypeVar("K")
@@ -45,6 +48,8 @@ class Repl(NamedTuple, Generic[T]):
 """Symbol."""
 syms: tuple[Sym, ...] = get_args(Sym)
 """Symbols."""
+solve_syms: tuple[Sym, ...] = ("Fo_0", "beta")
+"""Symbols to solve for."""
 FormsRepl: TypeAlias = Repl[Kind]
 """Forms replacements."""
 Param: TypeAlias = Literal[
@@ -71,3 +76,33 @@ class Repl(NamedTuple, Generic[T]):
 """Leaf node."""
 Node: TypeAlias = dict[Any, "Node | Leaf"]
 """General node."""
+
+
+def validate_expr(v: Basic | str):
+    """Validate expression."""
+    return (
+        v
+        if isinstance(v, Basic)
+        else sympify(v, locals=LOCALS.model_dump(), evaluate=False)
+    )
+
+
+Expr: TypeAlias = Annotated[
+    Basic, PlainValidator(validate_expr), JsonStrPlainSerializer
+]
+"""Expression."""
+
+Locals: TypeAlias = Morph[Sym, Expr]
+"""Locals."""
+PARAMS = Morph[Param, Sym](dict(zip(params, syms, strict=True)))
+"""Parameters."""
+LOCALS = Locals(
+    dict(
+        zip(
+            syms,
+            symbols(list(PARAMS.values()), nonnegative=True, real=True, finite=True),
+            strict=False,
+        )
+    )
+)
+"""Local variables."""