mxlpy 0.10.0__py3-none-any.whl → 0.11.0__py3-none-any.whl

mxlpy/__init__.py

@@ -49,6 +49,7 @@ from . import (
     mc,
     mca,
     plot,
+    report,
     sbml,
     surrogates,
 )
@@ -95,6 +96,7 @@ __all__ = [
     "mc",
     "mca",
     "plot",
+    "report",
     "sbml",
     "steady_state",
     "surrogates",

mxlpy/report.py

@@ -0,0 +1,209 @@
+"""Generate a report comparing two models."""
+
+from collections.abc import Callable
+from datetime import UTC, datetime
+from pathlib import Path
+from typing import cast
+
+import sympy
+
+from mxlpy.meta.source_tools import fn_to_sympy
+from mxlpy.model import Model
+
+__all__ = ["AnalysisFn", "markdown"]
+
+type AnalysisFn = Callable[[Model, Model, Path], tuple[str, Path]]
+
+
+def _list_of_symbols(args: list[str]) -> list[sympy.Symbol | sympy.Expr]:
+    return [sympy.Symbol(arg) for arg in args]
+
+
+def _new_removed_changed[T](
+    d1: dict[str, T], d2: dict[str, T]
+) -> tuple[dict[str, T], list[str], dict[str, tuple[T, T]]]:
+    s1 = set(d1)
+    s2 = set(d2)
+
+    removed = sorted(s1 - s2)
+    new = {k: d2[k] for k in s2 - s1}
+    changed = {k: (v1, v2) for k in s1 - set(removed) if (v1 := d1[k]) != (v2 := d2[k])}
+    return new, removed, changed
+
+
+def markdown(
+    m1: Model,
+    m2: Model,
+    analyses: list[AnalysisFn] | None = None,
+    rel_change: float = 1e-2,
+    img_path: Path = Path(),
+) -> str:
+    """Generate a markdown report comparing two models.
+
+    Args:
+        m1: The first model to compare.
+        m2: The second model to compare.
+        analyses: A list of functions that take a Path and return a tuple of a string and a Path. Defaults to None.
+        rel_change: The relative change threshold for numerical differences. Defaults to 1e-2.
+        img_path: The path to save images. Defaults to Path().
+
+    """
+    content: list[str] = [
+        f"# Report:  {datetime.now(UTC).strftime('%Y-%m-%d')}",
+    ]
+
+    # Variables
+    new_variables, removed_variables, changed_variables = _new_removed_changed(
+        m1.variables, m2.variables
+    )
+    variables = []
+    variables.extend(
+        f"| <span style='color:green'>{k}<span> | - | {v} |"
+        for k, v in new_variables.items()
+    )
+    variables.extend(
+        f"| <span style='color: orange'>{k}</span> | {v1} | {v2} |"
+        for k, (v1, v2) in changed_variables.items()
+    )
+    variables.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_variables
+    )
+    if len(variables) >= 1:
+        content.extend(
+            (
+                "## Variables\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(variables))
+
+    # Parameters
+    new_parameters, removed_parameters, changed_parameters = _new_removed_changed(
+        m1.parameters, m2.parameters
+    )
+    pars = []
+    pars.extend(
+        f"| <span style='color:green'>{k}<span> | - | {v} |"
+        for k, v in new_parameters.items()
+    )
+    pars.extend(
+        f"| <span style='color: orange'>{k}</span> | {v1} | {v2} |"
+        for k, (v1, v2) in changed_parameters.items()
+    )
+    pars.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_parameters
+    )
+    if len(pars) >= 1:
+        content.extend(
+            (
+                "## Parameters\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(pars))
+
+    # Derived
+    new_derived, removed_derived, changed_derived = _new_removed_changed(
+        m1.derived, m2.derived
+    )
+    derived = []
+    for k, v in new_derived.items():
+        expr = sympy.latex(fn_to_sympy(v.fn, _list_of_symbols(v.args)))
+        derived.append(f"| <span style='color:green'>{k}<span> | - | ${expr}$ |")
+    for k, (v1, v2) in changed_derived.items():
+        expr1 = sympy.latex(fn_to_sympy(v1.fn, _list_of_symbols(v1.args)))
+        expr2 = sympy.latex(fn_to_sympy(v2.fn, _list_of_symbols(v2.args)))
+        derived.append(
+            f"| <span style='color: orange'>{k}</span> | ${expr1}$ | ${expr2}$ |"
+        )
+    derived.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_derived
+    )
+    if len(derived) >= 1:
+        content.extend(
+            (
+                "## Derived\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(derived))
+
+    # Reactions
+    new_reactions, removed_reactions, changed_reactions = _new_removed_changed(
+        m1.reactions, m2.reactions
+    )
+    reactions = []
+    for k, v in new_reactions.items():
+        expr = sympy.latex(fn_to_sympy(v.fn, _list_of_symbols(v.args)))
+        reactions.append(f"| <span style='color:green'>{k}<span> | - | ${expr}$ |")
+    for k, (v1, v2) in changed_reactions.items():
+        expr1 = sympy.latex(fn_to_sympy(v1.fn, _list_of_symbols(v1.args)))
+        expr2 = sympy.latex(fn_to_sympy(v2.fn, _list_of_symbols(v2.args)))
+        reactions.append(
+            f"| <span style='color: orange'>{k}</span> | ${expr1}$ | ${expr2}$ |"
+        )
+    reactions.extend(
+        f"| <span style='color:red'>{k}</span> | - | - |" for k in removed_reactions
+    )
+
+    if len(reactions) >= 1:
+        content.extend(
+            (
+                "## Reactions\n",
+                "| Name | Old Value | New Value |",
+                "| ---- | --------- | --------- |",
+            )
+        )
+        content.append("\n".join(reactions))
+
+    # Now check for any numerical differences
+    dependent = []
+    d1 = m1.get_dependent()
+    d2 = m2.get_dependent()
+    rel_diff = ((d1 - d2) / d1).dropna()
+    for k, v in rel_diff.loc[rel_diff.abs() >= rel_change].items():
+        k = cast(str, k)
+        dependent.append(
+            f"| <span style='color:orange'>{k}</span> | {d1[k]:.2f} | {d2[k]:.2f} |  {v:.1%} "
+        )
+    if len(dependent) >= 1:
+        content.extend(
+            (
+                "## Numerical differences of dependent values\n",
+                "| Name | Old Value | New Value | Relative Change | ",
+                "| ---- | --------- | --------- | --------------- | ",
+            )
+        )
+        content.append("\n".join(dependent))
+
+    rhs = []
+    r1 = m1.get_right_hand_side()
+    r2 = m2.get_right_hand_side()
+    rel_diff = ((r1 - r2) / r1).dropna()
+    for k, v in rel_diff.loc[rel_diff.abs() >= rel_change].items():
+        k = cast(str, k)
+        rhs.append(
+            f"| <span style='color:orange'>{k}</span> | {r1[k]:.2f} | {r2[k]:.2f} |  {v:.1%} "
+        )
+    if len(rhs) >= 1:
+        content.extend(
+            (
+                "## Numerical differences of right hand side values\n",
+                "| Name | Old Value | New Value | Relative Change | ",
+                "| ---- | --------- | --------- | --------------- | ",
+            )
+        )
+        content.append("\n".join(rhs))
+
+    # Comparison functions
+    if analyses is not None:
+        for f in analyses:
+            name, img_path = f(m1, m2, img_path)
+            content.append(name)
+            # content.append(f"![{name}]({img_path})")
+            content.append(f"<img src='{img_path}' alt='{name}' width='500'/>")
+
+    return "\n".join(content)

{mxlpy-0.10.0.dist-info → mxlpy-0.11.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.10.0
+Version: 0.11.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>

{mxlpy-0.10.0.dist-info → mxlpy-0.11.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-mxlpy/__init__.py,sha256=HwV_l1PqCqWsn1TFwUMslbfuPjX6cUGzytyWPaUz4FM,4168
+mxlpy/__init__.py,sha256=XZYNFyDC5rWcKi6139mq04cROI7LwJvxB2_3ApKwcvY,4194
 mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
 mxlpy/fit.py,sha256=vJ0AWCvERxPkxgwuOmL9rsH4vXnlBSco4vG-5X98RK8,8085
 mxlpy/fns.py,sha256=ct_RFj9koW8vXHyr27GnbZUHUS_zfs4rDysybuFiOaU,4599
@@ -14,6 +14,7 @@ mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
 mxlpy/plot.py,sha256=z1JW7Si1JQyNMj_MMLkgbLkOkSjVcfAZJGjm_WqCgT4,24355
 mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mxlpy/report.py,sha256=TYG-cKo9u6izlnjB4vgu6I2hYrtS9e8wYc_A4MrHq-g,6982
 mxlpy/scan.py,sha256=3k4084d4eg-3Ok24cL8KWPF7P1L6fbEtiaOM9VC5Eko,19210
 mxlpy/simulator.py,sha256=T9t2jZ6U5NyK1ICF1UkST8M8v4EPV_H98kzZ4TvQK-w,20115
 mxlpy/types.py,sha256=ksdn76Sdw0XhQEpQepcETvuGqcJolfrmbIRBT0R_2Bg,13612
@@ -43,7 +44,7 @@ mxlpy/surrogates/_torch.py,sha256=E_1eDUlPSVFwROkdMDCqYwwHE-61pjNMJWotnhjzge0,58
 mxlpy/symbolic/__init__.py,sha256=3hQjCMw8-6iOxeUdfnCg8449fF_BRF2u6lCM1GPpkRY,222
 mxlpy/symbolic/strikepy.py,sha256=r6nRtckV1nxKq3i1bYYWZOkzwZ5XeKQuZM5ck44vUo0,20010
 mxlpy/symbolic/symbolic_model.py,sha256=YL9noEeP3_0DoKXwMPELtfmPuP6mgNcLIJgDRCkyB7A,2434
-mxlpy-0.10.0.dist-info/METADATA,sha256=wwkTfCscHZzrydDqVdVhVNI7isEc2YcwN4ZC5OAWA8M,4536
-mxlpy-0.10.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.10.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
-mxlpy-0.10.0.dist-info/RECORD,,
+mxlpy-0.11.0.dist-info/METADATA,sha256=N1-dMC1k0QUlSF2ZN_URFUyg119f9QUz7xcBS2Ia_PQ,4536
+mxlpy-0.11.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.11.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
+mxlpy-0.11.0.dist-info/RECORD,,