Migrate common model and notebook functionality in from boilerdata

.tools/requirements/requirements.txt

@@ -1,8 +1,12 @@
 # Latest working requirements of your package, should be ahead of pyproject.toml.
+IPython[notebook]==8.14.0
+pandas[hdf5,performance]==2.0.2
+pandas-stubs~=2.0.2
 ploomber-engine==0.0.30
 pydantic==1.10.12
 ruamel.yaml==0.17.32
 scipy==1.11.1
+sympy==1.12
 # Numba only supports numpy<1.25 https://github.com/numba/numba/issues/8698
 # ! Unpin numba once it supports numpy>=1.25
 numba==0.57.1

pyproject.toml

@@ -17,10 +17,13 @@ license = { file = "LICENSE" }
 requires-python = ">=3.11"
 classifiers = ["License :: OSI Approved :: MIT License"]
 dependencies = [
+    "IPython[notebook]>=8.14.0",
+    "pandas[hdf5,performance]>=2.0.2",
     "ploomber-engine>=0.0.30",
     "pydantic>=1.10.12,<2",
     "ruamel.yaml>=0.17.32",
     "scipy>=1.11.1",
+    "sympy>=1.12",
     # Numba only supports numpy<1.25 https://github.com/numba/numba/issues/8698
     # ! Unpin numba once it supports numpy>=1.25
     "numba>=0.57.1",

src/boilercore/fits.py

@@ -1,3 +1,5 @@
+"""Model fits."""
+
 import warnings
 from collections.abc import Mapping, Sequence
 from functools import partial

src/boilercore/models.py

@@ -1,4 +1,4 @@
-"""Basic models for this project."""
+"""Basic models."""
 
 from collections.abc import Mapping, Sequence
 from pathlib import Path

src/boilercore/notebooks.py

@@ -0,0 +1,41 @@
+"""Notebook helpers."""
+
+from typing import Any
+
+import pandas as pd
+from IPython.core.display import Markdown, Math
+from IPython.display import display
+from sympy import FiniteSet
+from sympy.printing.latex import latex
+
+
+def set_format():
+    """Set up formatting for interactive notebook sessions.
+    The triple curly braces in the f-string allows the format function to be dynamically
+    specified by a given float specification. The intent is clearer this way, and may be
+    extended in the future by making `float_spec` a parameter.
+    """
+    float_spec = ":#.4g"
+    pd.options.display.min_rows = pd.options.display.max_rows = 50
+    pd.options.display.float_format = f"{{{float_spec}}}".format
+
+
+def disp_named(*args: tuple[Any, str]):
+    """Display objects with names above them."""
+    for elem, name in args:
+        display(Markdown(f"##### {name}"))
+        display(elem)
+
+
+def disp_free(title, eqn, **kwargs):
+    disp(title, eqn, **kwargs)
+    disp("Free symbols", FiniteSet(*eqn.rhs.free_symbols), **kwargs)
+
+
+def disp(title, *exprs, **kwargs):
+    print(f"{title}:")
+    display(*(math_mod(expr, **kwargs) for expr in exprs))
+
+
+def math_mod(expr, long_frac_ratio=3, **kwargs):
+    return Math(latex(expr, long_frac_ratio=long_frac_ratio, **kwargs))

src/boilercore/paths.py

@@ -0,0 +1,54 @@
+"""Paths and modules."""
+
+from collections.abc import Iterable
+from pathlib import Path
+from re import compile
+from types import ModuleType
+
+
+def get_package_dir(package: ModuleType) -> Path:
+    return Path(next(iter(package.__path__)))
+
+
+def map_stages(stages_dir: Path, package_dir: Path) -> dict[str, Path]:
+    """Map stage module names to their paths."""
+    stages: dict[str, Path] = {}
+    for path in walk_module_paths(stages_dir, package_dir, glob="[!__]*.[py ipynb]*"):
+        module = get_module_rel(get_module(path, package_dir), stages_dir.name)
+        stages[module.replace(".", "_")] = path
+    return stages
+
+
+def walk_module_paths(
+    package: Path, top: Path, suffix: str = ".py", glob: str | None = None
+) -> Iterable[Path]:
+    """Walk modules from a given submodule path and the top level library directory."""
+    for directory in (
+        package,
+        *[
+            path
+            for path in package.iterdir()
+            if path.is_dir() and "__" not in str(path.relative_to(top.parent))
+        ],
+    ):
+        yield from sorted(directory.glob(glob or f"[!__]*{suffix}"))
+
+
+def get_module(module: Path, package: Path) -> str:
+    """Get module name given the submodule path and the top level library directory."""
+    return (
+        str(module.relative_to(package.parent).with_suffix(""))
+        .replace("\\", ".")
+        .replace("/", ".")
+    )
+
+
+def walk_modules(package: Path, top: Path, suffix: str = ".py") -> Iterable[str]:
+    """Walk modules from a given submodule path and the top level library directory."""
+    for module in walk_module_paths(package, top, suffix):
+        yield get_module(module, top)
+
+
+def get_module_rel(module: str, relative: str) -> str:
+    """Get module name relative to another module."""
+    return compile(rf".*{relative}\.").sub(repl="", string=module)

src/boilercore/testing.py

@@ -1,9 +1,7 @@
-"""Helper functions for testing boiler code."""
+"""Test helpers."""
 
-from collections.abc import Iterable
 from contextlib import contextmanager
 from pathlib import Path
-from re import compile
 from shutil import copy, copytree
 
 import pytest
@@ -32,36 +30,3 @@ def before_tmp_workdir(tmp_path: Path, monkeypatch: pytest.MonkeyPatch):
         yield
     finally:
         monkeypatch.chdir(tmp_path)
-
-
-def walk_modules(package: Path, top: Path, suffix: str = ".py") -> Iterable[str]:
-    """Walk modules from a given submodule path and the top level library directory."""
-    for module in walk_module_paths(package, top, suffix):
-        yield get_module(module, top)
-
-
-def walk_module_paths(package: Path, top: Path, suffix: str = ".py") -> Iterable[Path]:
-    """Walk modules from a given submodule path and the top level library directory."""
-    for directory in (
-        package,
-        *[
-            path
-            for path in package.iterdir()
-            if path.is_dir() and "__" not in str(path.relative_to(top.parent))
-        ],
-    ):
-        yield from sorted(directory.glob(f"[!__]*{suffix}"))
-
-
-def get_module(submodule: Path, library: Path) -> str:
-    """Get module name given the submodule path and the top level library directory."""
-    return (
-        str(submodule.relative_to(library.parent).with_suffix(""))
-        .replace("\\", ".")
-        .replace("/", ".")
-    )
-
-
-def get_module_rel(module: str, relative: str) -> str:
-    """Get module name relative to another module."""
-    return compile(rf".*{relative}\.").sub(repl="", string=module)

src/boilercore/types.py

@@ -1,4 +1,4 @@
-"""Types used throughout this package."""
+"""Types."""
 
 from typing import Literal, TypeVar