phylogenie 1.0.8__tar.gz → 2.0.0__tar.gz

{phylogenie-1.0.8 → phylogenie-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 1.0.8
+Version: 2.0.0
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com
@@ -23,9 +23,9 @@ Description-Content-Type: text/markdown
 
 ---
 
-[![TreeSimulator](https://img.shields.io/badge/Powered%20by-TreeSimulator-green?style=flat-square)](https://github.com/evolbioinfo/treesimulator)
-[![Remaster](https://img.shields.io/badge/Powered%20by-Remaster-blue?style=flat-square)](https://tgvaughan.github.io/remaster/)
 [![AliSim](https://img.shields.io/badge/Powered%20by-AliSim-orange?style=flat-square)](https://iqtree.github.io/doc/AliSim)
+[![PyPI package](https://badge.fury.io/py/phylogenie.svg)](https://pypi.org/project/phylogenie/)
+[![PyPI downloads](https://shields.io/pypi/dm/phylogenie)](https://pypi.org/project/phylogenie/)
 
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 
@@ -46,7 +46,7 @@ Phylogenie comes packed with useful features, including:
   Simply specify the number of cores to use, and Phylogenie handles multiprocessing automatically.
 
 - **Pre-implemented parameterizations** 🎯  
-  Include canonical, fossilized birth-death, epidemiological, birth-death with exposed-infectious (BDEI), birth-death with superspreading (BDSS), contact-tracing (CT), and more.
+  Include canonical, fossilized birth-death, epidemiological, birth-death with exposed-infectious (BDEI), birth-death with superspreading (BDSS), and more.
 
 - **Skyline parameter support** 🪜  
   Support for piece-wise constant parameters.
@@ -54,9 +54,6 @@ Phylogenie comes packed with useful features, including:
 - **Arithmetic operations on parameters** 🧮  
   Perform flexible arithmetic operations between parameters directly within the config file.
 
-- **Support for common phylogenetic simulation tools** 🛠️  
-  Compatible backends include ReMASTER, TreeSimulator, and AliSim.
-
 - **Modular and extendible architecture** 🧩  
   Easily add new simulation backends as needed.
 
@@ -76,18 +73,9 @@ cd phylogenie
 pip install .
 ```
 
-## 🛠 Backend dependencies
-
-Phylogenie works with the following simulation backends:
-
-- **[TreeSimulator](https://github.com/evolbioinfo/treesimulator)**  
-  A [Python](https://www.python.org/) package for simulating phylogenetic trees. It is automatically installed with Phylogenie, so you can use it right away.
-
-- **[ReMASTER](https://tgvaughan.github.io/remaster/)**  
-  A [BEAST2](https://www.beast2.org/) package designed for tree simulation. To use ReMASTER as a backend, you need to install it separately.
+## 🛠 Backend dependency
 
-- **[AliSim](https://iqtree.github.io/doc/AliSim)**  
-  A tool for simulating multiple sequence alignments (MSAs). It is distributed with [IQ-TREE](https://iqtree.github.io/) and also requires separate installation if you wish to use it as a backend.
+Phylogenie relies on [AliSim](https://iqtree.github.io/doc/AliSim) for simulating multiple sequence alignments (MSAs). AliSim is a powerful MSAs simulation tool distributed with [IQ-TREE](https://iqtree.github.io/), and requires separate installation to use it as a simulation backend.
 
 ## 🚀 Quick Start
 

{phylogenie-1.0.8 → phylogenie-2.0.0}/README.md

@@ -4,9 +4,9 @@
 
 ---
 
-[![TreeSimulator](https://img.shields.io/badge/Powered%20by-TreeSimulator-green?style=flat-square)](https://github.com/evolbioinfo/treesimulator)
-[![Remaster](https://img.shields.io/badge/Powered%20by-Remaster-blue?style=flat-square)](https://tgvaughan.github.io/remaster/)
 [![AliSim](https://img.shields.io/badge/Powered%20by-AliSim-orange?style=flat-square)](https://iqtree.github.io/doc/AliSim)
+[![PyPI package](https://badge.fury.io/py/phylogenie.svg)](https://pypi.org/project/phylogenie/)
+[![PyPI downloads](https://shields.io/pypi/dm/phylogenie)](https://pypi.org/project/phylogenie/)
 
 Phylogenie is a [Python](https://www.python.org/) package designed to easily simulate phylogenetic datasets—such as trees and multiple sequence alignments (MSAs)—with minimal setup effort. Simply specify the distributions from which your parameters should be sampled, and Phylogenie will handle the rest!
 
@@ -27,7 +27,7 @@ Phylogenie comes packed with useful features, including:
   Simply specify the number of cores to use, and Phylogenie handles multiprocessing automatically.
 
 - **Pre-implemented parameterizations** 🎯  
-  Include canonical, fossilized birth-death, epidemiological, birth-death with exposed-infectious (BDEI), birth-death with superspreading (BDSS), contact-tracing (CT), and more.
+  Include canonical, fossilized birth-death, epidemiological, birth-death with exposed-infectious (BDEI), birth-death with superspreading (BDSS), and more.
 
 - **Skyline parameter support** 🪜  
   Support for piece-wise constant parameters.
@@ -35,9 +35,6 @@ Phylogenie comes packed with useful features, including:
 - **Arithmetic operations on parameters** 🧮  
   Perform flexible arithmetic operations between parameters directly within the config file.
 
-- **Support for common phylogenetic simulation tools** 🛠️  
-  Compatible backends include ReMASTER, TreeSimulator, and AliSim.
-
 - **Modular and extendible architecture** 🧩  
   Easily add new simulation backends as needed.
 
@@ -57,18 +54,9 @@ cd phylogenie
 pip install .
 ```
 
-## 🛠 Backend dependencies
-
-Phylogenie works with the following simulation backends:
-
-- **[TreeSimulator](https://github.com/evolbioinfo/treesimulator)**  
-  A [Python](https://www.python.org/) package for simulating phylogenetic trees. It is automatically installed with Phylogenie, so you can use it right away.
-
-- **[ReMASTER](https://tgvaughan.github.io/remaster/)**  
-  A [BEAST2](https://www.beast2.org/) package designed for tree simulation. To use ReMASTER as a backend, you need to install it separately.
+## 🛠 Backend dependency
 
-- **[AliSim](https://iqtree.github.io/doc/AliSim)**  
-  A tool for simulating multiple sequence alignments (MSAs). It is distributed with [IQ-TREE](https://iqtree.github.io/) and also requires separate installation if you wish to use it as a backend.
+Phylogenie relies on [AliSim](https://iqtree.github.io/doc/AliSim) for simulating multiple sequence alignments (MSAs). AliSim is a powerful MSAs simulation tool distributed with [IQ-TREE](https://iqtree.github.io/), and requires separate installation to use it as a simulation backend.
 
 ## 🚀 Quick Start
 

phylogenie-2.0.0/phylogenie/generators/__init__.py

@@ -0,0 +1,14 @@
+from typing import Annotated
+
+from pydantic import Field
+
+from phylogenie.generators.alisim import AliSimDatasetGenerator
+from phylogenie.generators.dataset import DatasetGenerator
+from phylogenie.generators.trees import TreeDatasetGeneratorConfig
+
+DatasetGeneratorConfig = Annotated[
+    TreeDatasetGeneratorConfig | AliSimDatasetGenerator,
+    Field(discriminator="data_type"),
+]
+
+__all__ = ["DatasetGeneratorConfig", "DatasetGenerator"]

phylogenie-2.0.0/phylogenie/generators/alisim.py

@@ -0,0 +1,71 @@
+import os
+import subprocess
+from pathlib import Path
+from typing import Any, Literal
+
+from numpy.random import Generator
+
+from phylogenie.generators.dataset import DatasetGenerator, DataType
+from phylogenie.generators.trees import TreeDatasetGeneratorConfig
+from phylogenie.io import dump_newick
+
+MSAS_DIRNAME = "MSAs"
+TREES_DIRNAME = "trees"
+
+
+class AliSimDatasetGenerator(DatasetGenerator):
+    data_type: Literal[DataType.MSAS] = DataType.MSAS
+    trees: TreeDatasetGeneratorConfig
+    keep_trees: bool = False
+    iqtree_path: str = "iqtree2"
+    args: dict[str, str | int | float]
+
+    def _generate_one_from_tree(
+        self, filename: str, tree_file: str, rng: Generator, data: dict[str, Any]
+    ) -> None:
+        command = [
+            self.iqtree_path,
+            "--alisim",
+            filename,
+            "--tree",
+            tree_file,
+            "--seed",
+            str(rng.integers(2**32)),
+        ]
+
+        for key, value in self.args.items():
+            command.extend(
+                [key, value.format(**data) if isinstance(value, str) else str(value)]
+            )
+
+        command.extend(["-af", "fasta"])
+        subprocess.run(command, check=True, stdout=subprocess.DEVNULL)
+        subprocess.run(["rm", f"{tree_file}.log"], check=True)
+
+    def _generate_one(
+        self, filename: str, rng: Generator, data: dict[str, Any]
+    ) -> None:
+        if self.keep_trees:
+            base_dir = Path(filename).parent
+            file_id = Path(filename).stem
+            tree_filename = os.path.join(base_dir, TREES_DIRNAME, file_id)
+            msas_dir = os.path.join(base_dir, MSAS_DIRNAME)
+            os.makedirs(msas_dir, exist_ok=True)
+            msa_filename = os.path.join(msas_dir, file_id)
+        else:
+            tree_filename = f"{filename}.temp-tree"
+            msa_filename = filename
+
+        tree = self.trees.simulate_one(rng, data)
+        if tree is None:
+            return
+
+        for leaf in tree.get_leaves():
+            leaf.id += f"|{leaf.get_time()}"
+        dump_newick(tree, f"{tree_filename}.nwk")
+
+        self._generate_one_from_tree(
+            filename=msa_filename, tree_file=f"{tree_filename}.nwk", rng=rng, data=data
+        )
+        if not self.keep_trees:
+            os.remove(f"{tree_filename}.nwk")

phylogenie-2.0.0/phylogenie/generators/configs.py

@@ -0,0 +1,41 @@
+from pydantic import BaseModel, ConfigDict
+
+import phylogenie.typings as pgt
+
+
+class DistributionConfig(BaseModel):
+    type: str
+    model_config = ConfigDict(extra="allow")
+
+
+IntegerConfig = str | int
+ScalarConfig = str | pgt.Scalar
+ManyScalarsConfig = str | list[ScalarConfig]
+OneOrManyScalarsConfig = ScalarConfig | list[ScalarConfig]
+OneOrMany2DScalarsConfig = ScalarConfig | list[list[ScalarConfig]]
+
+
+class StrictBaseModel(BaseModel):
+    model_config = ConfigDict(extra="forbid")
+
+
+class SkylineParameterModel(StrictBaseModel):
+    value: ManyScalarsConfig
+    change_times: ManyScalarsConfig
+
+
+class SkylineVectorModel(StrictBaseModel):
+    value: str | list[OneOrManyScalarsConfig]
+    change_times: ManyScalarsConfig
+
+
+class SkylineMatrixModel(StrictBaseModel):
+    value: str | list[OneOrMany2DScalarsConfig]
+    change_times: ManyScalarsConfig
+
+
+SkylineParameterConfig = ScalarConfig | SkylineParameterModel
+SkylineVectorConfig = (
+    str | pgt.Scalar | list[SkylineParameterConfig] | SkylineVectorModel
+)
+SkylineMatrixConfig = str | pgt.Scalar | list[SkylineVectorConfig] | SkylineMatrixModel

{phylogenie-1.0.8/phylogenie/core → phylogenie-2.0.0/phylogenie/generators}/dataset.py

@@ -1,15 +1,16 @@
 import os
 from abc import ABC, abstractmethod
 from enum import Enum
+from itertools import product
+from typing import Any
 
 import joblib
+import numpy as np
 import pandas as pd
 from numpy.random import Generator, default_rng
 from tqdm import tqdm
 
-import phylogenie.typings as pgt
-from phylogenie.configs import StrictBaseModel
-from phylogenie.core.context import ContextConfig, context_factory
+from phylogenie.generators.configs import DistributionConfig, StrictBaseModel
 
 
 class DataType(str, Enum):
@@ -17,51 +18,52 @@ class DataType(str, Enum):
     MSAS = "msas"
 
 
+DATA_DIRNAME = "data"
+METADATA_FILENAME = "metadata.csv"
+
+
 class DatasetGenerator(ABC, StrictBaseModel):
-    output_dir: str = "phylogenie-out"
-    data_dir: str = "data"
-    metadata_filename: str = "metadata.csv"
+    output_dir: str = "phylogenie-outputs"
     n_samples: int | dict[str, int] = 1
     n_jobs: int = -1
     seed: int | None = None
-    context: ContextConfig | None = None
+    context: dict[str, DistributionConfig] | None = None
 
     @abstractmethod
-    def _generate_one(self, filename: str, rng: Generator, data: pgt.Data) -> None: ...
+    def _generate_one(
+        self, filename: str, rng: Generator, data: dict[str, Any]
+    ) -> None: ...
 
     def generate_one(
-        self, filename: str, data: pgt.Data | None = None, seed: int | None = None
+        self, filename: str, data: dict[str, Any] | None = None, seed: int | None = None
     ) -> None:
         data = {} if data is None else data
         self._generate_one(filename=filename, rng=default_rng(seed), data=data)
 
     def _generate(self, rng: Generator, n_samples: int, output_dir: str) -> None:
-        data_dir = os.path.join(output_dir, self.data_dir)
-        metadata_file = os.path.join(output_dir, self.metadata_filename)
+        data_dir = os.path.join(output_dir, DATA_DIRNAME)
         if os.path.exists(data_dir):
             print(f"Output directory {data_dir} already exists. Skipping.")
             return
         os.makedirs(data_dir)
 
-        data = [
-            {} if self.context is None else context_factory(self.context, rng)
-            for _ in range(n_samples)
-        ]
+        data: list[dict[str, Any]] = [{}] * n_samples
+        if self.context is not None:
+            for d, (k, v) in product(data, self.context.items()):
+                args = v.model_extra if v.model_extra is not None else {}
+                d[k] = np.array(getattr(rng, v.type)(**args)).tolist()
+            df = pd.DataFrame([{"file_id": str(i), **d} for i, d in enumerate(data)])
+            df.to_csv(os.path.join(output_dir, METADATA_FILENAME), index=False)
 
         joblib.Parallel(n_jobs=self.n_jobs)(
             joblib.delayed(self.generate_one)(
                 filename=os.path.join(data_dir, str(i)),
-                data=d,
-                seed=int(rng.integers(0, 2**32)),
-            )
-            for i, d in tqdm(
-                enumerate(data), total=n_samples, desc=f"Generating {data_dir}..."
+                data=data[i],
+                seed=int(rng.integers(2**32)),
             )
+            for i in tqdm(range(n_samples), desc=f"Generating {data_dir}...")
         )
 
-        df = pd.DataFrame([{"file_id": str(i), **d} for i, d in enumerate(data)])
-        df.to_csv(metadata_file, index=False)
-
     def generate(self) -> None:
         rng = default_rng(self.seed)
         if isinstance(self.n_samples, dict):

{phylogenie-1.0.8/phylogenie/core → phylogenie-2.0.0/phylogenie/generators}/factories.py

@@ -2,8 +2,8 @@ from typing import Any
 
 import numpy as np
 
-import phylogenie.core.configs as cfg
-import phylogenie.core.typeguards as ctg
+import phylogenie.generators.configs as cfg
+import phylogenie.generators.typeguards as ctg
 import phylogenie.typeguards as tg
 import phylogenie.typings as pgt
 from phylogenie.skyline import (
@@ -16,7 +16,7 @@ from phylogenie.skyline import (
 )
 
 
-def _eval_expression(expression: str, data: pgt.Data) -> Any:
+def _eval_expression(expression: str, data: dict[str, Any]) -> Any:
     return np.array(
         eval(
             expression,
@@ -29,7 +29,7 @@ def _eval_expression(expression: str, data: pgt.Data) -> Any:
     ).tolist()
 
 
-def int_factory(x: cfg.IntConfig, data: pgt.Data) -> int:
+def integer(x: cfg.IntegerConfig, data: dict[str, Any]) -> int:
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if isinstance(e, int):
@@ -40,7 +40,7 @@ def int_factory(x: cfg.IntConfig, data: pgt.Data) -> int:
     return x
 
 
-def scalar_factory(x: cfg.ScalarConfig, data: pgt.Data) -> pgt.Scalar:
+def scalar(x: cfg.ScalarConfig, data: dict[str, Any]) -> pgt.Scalar:
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if isinstance(e, pgt.Scalar):
@@ -51,18 +51,7 @@ def scalar_factory(x: cfg.ScalarConfig, data: pgt.Data) -> pgt.Scalar:
     return x
 
 
-def many_ints_factory(x: cfg.ManyIntsConfig, data: pgt.Data) -> pgt.Many[int]:
-    if isinstance(x, str):
-        e = _eval_expression(x, data)
-        if tg.is_many_ints(e):
-            return e
-        raise ValueError(
-            f"Expression '{x}' evaluated to {e} of type {type(e)}, expected a sequence of integers."
-        )
-    return [int_factory(v, data) for v in x]
-
-
-def many_scalars_factory(x: cfg.ManyScalarsConfig, data: pgt.Data) -> pgt.ManyScalars:
+def many_scalars(x: cfg.ManyScalarsConfig, data: dict[str, Any]) -> pgt.ManyScalars:
     if isinstance(x, str):
         e = _eval_expression(x, data)
         if tg.is_many_scalars(e):
@@ -70,11 +59,11 @@ def many_scalars_factory(x: cfg.ManyScalarsConfig, data: pgt.Data) -> pgt.ManySc
         raise ValueError(
             f"Expression '{x}' evaluated to {e} of type {type(e)}, expected a sequence of scalars."
         )
-    return [scalar_factory(v, data) for v in x]
+    return [scalar(v, data) for v in x]
 
 
-def one_or_many_scalars_factory(
-    x: cfg.OneOrManyScalarsConfig, data: pgt.Data
+def one_or_many_scalars(
+    x: cfg.OneOrManyScalarsConfig, data: dict[str, Any]
 ) -> pgt.OneOrManyScalars:
     if isinstance(x, str):
         e = _eval_expression(x, data)
@@ -85,22 +74,22 @@ def one_or_many_scalars_factory(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    return many_scalars_factory(x, data)
+    return many_scalars(x, data)
 
 
-def skyline_parameter_like_factory(
-    x: cfg.SkylineParameterLikeConfig, data: pgt.Data
+def skyline_parameter(
+    x: cfg.SkylineParameterConfig, data: dict[str, Any]
 ) -> SkylineParameterLike:
     if isinstance(x, cfg.ScalarConfig):
-        return scalar_factory(x, data)
+        return scalar(x, data)
     return SkylineParameter(
-        value=many_scalars_factory(x.value, data),
-        change_times=many_scalars_factory(x.change_times, data),
+        value=many_scalars(x.value, data),
+        change_times=many_scalars(x.change_times, data),
     )
 
 
-def skyline_vector_coercible_factory(
-    x: cfg.SkylineVectorCoercibleConfig, data: pgt.Data
+def skyline_vector(
+    x: cfg.SkylineVectorConfig, data: dict[str, Any]
 ) -> SkylineVectorCoercible:
     if isinstance(x, str):
         e = _eval_expression(x, data)
@@ -111,12 +100,12 @@ def skyline_vector_coercible_factory(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    if ctg.is_list_of_skyline_parameter_like_configs(x):
-        return [skyline_parameter_like_factory(p, data) for p in x]
+    if ctg.is_list_of_skyline_parameter_configs(x):
+        return [skyline_parameter(p, data) for p in x]
 
-    assert isinstance(x, cfg.SkylineVectorValueModel)
+    assert isinstance(x, cfg.SkylineVectorModel)
 
-    change_times = many_scalars_factory(x.change_times, data)
+    change_times = many_scalars(x.change_times, data)
     if isinstance(x.value, str):
         e = _eval_expression(x.value, data)
         if tg.is_many_one_or_many_scalars(e):
@@ -126,7 +115,7 @@ def skyline_vector_coercible_factory(
                 f"Expression '{x.value}' evaluated to {e} of type {type(e)}, which cannot be coerced to a valid value for a SkylineVector (expected a sequence composed of scalars and/or sequences of scalars)."
             )
     else:
-        value = [one_or_many_scalars_factory(v, data) for v in x.value]
+        value = [one_or_many_scalars(v, data) for v in x.value]
 
     if tg.is_many_scalars(value):
         return SkylineParameter(value=value, change_times=change_times)
@@ -142,8 +131,8 @@ def skyline_vector_coercible_factory(
     return SkylineVector(value=value, change_times=change_times)
 
 
-def one_or_many_2D_scalars_factory(
-    x: cfg.OneOrMany2DScalarsConfig, data: pgt.Data
+def one_or_many_2D_scalars(
+    x: cfg.OneOrMany2DScalarsConfig, data: dict[str, Any]
 ) -> pgt.OneOrMany2DScalars:
     if isinstance(x, str):
         e = _eval_expression(x, data)
@@ -154,11 +143,11 @@ def one_or_many_2D_scalars_factory(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    return [many_scalars_factory(v, data) for v in x]
+    return [many_scalars(v, data) for v in x]
 
 
-def skyline_matrix_coercible_factory(
-    x: cfg.SkylineMatrixCoercibleConfig, data: pgt.Data
+def skyline_matrix(
+    x: cfg.SkylineMatrixConfig, data: dict[str, Any]
 ) -> SkylineMatrixCoercible:
     if isinstance(x, str):
         e = _eval_expression(x, data)
@@ -169,12 +158,12 @@ def skyline_matrix_coercible_factory(
         )
     if isinstance(x, pgt.Scalar):
         return x
-    if ctg.is_list_of_skyline_vector_coercible_configs(x):
-        return [skyline_vector_coercible_factory(v, data) for v in x]
+    if ctg.is_list_of_skyline_vector_configs(x):
+        return [skyline_vector(v, data) for v in x]
 
-    assert isinstance(x, cfg.SkylineMatrixValueModel)
+    assert isinstance(x, cfg.SkylineMatrixModel)
 
-    change_times = many_scalars_factory(x.change_times, data)
+    change_times = many_scalars(x.change_times, data)
     if isinstance(x.value, str):
         e = _eval_expression(x.value, data)
         if tg.is_many_one_or_many_2D_scalars(e):
@@ -184,26 +173,27 @@ def skyline_matrix_coercible_factory(
                 f"Expression '{x.value}' evaluated to {e} of type {type(e)}, which cannot be coerced to a valid value for a SkylineMatrix (expected a sequence composed of scalars and/or nested (2D) sequences of scalars)."
             )
     else:
-        value = [one_or_many_2D_scalars_factory(v, data) for v in x.value]
+        value = [one_or_many_2D_scalars(v, data) for v in x.value]
 
     if tg.is_many_scalars(value):
         return SkylineParameter(value=value, change_times=change_times)
 
-    Ns: set[int] = set()
+    shapes: set[tuple[int, int]] = set()
     for elem in value:
         if tg.is_many_2D_scalars(elem):
-            n_rows = len(elem)
-            if any(len(row) != n_rows for row in elem):
+            Ms = len(elem)
+            Ns = {len(row) for row in elem}
+            if len(Ns) > 1:
                 raise ValueError(
-                    f"All elements in the value of a SkylineMatrix config must be scalars or square matrices (config {x.value} yeilded a non-square matrix: {elem})."
+                    f"The values of a SkylineMatrix config must be scalars or nested (2D) lists of them with a consistent row length (config {x.value} yielded element {elem} with row lengths {Ns})."
                 )
-            Ns.add(n_rows)
+            shapes.add((Ms, Ns.pop()))
 
-    if len(Ns) > 1:
+    if len(shapes) > 1:
         raise ValueError(
-            f"All elements in the value of a SkylineMatrix config must be scalars or have the same square shape (config {x.value} yielded value={value} with inconsistent lengths {Ns})."
+            f"All elements in the value of a SkylineMatrix config must be scalars or nested (2D) lists of them with the same shape (config {x.value} yielded value={value} with inconsistent shapes {shapes})."
         )
-    (N,) = Ns
-    value = [[[p] * N] * N if isinstance(p, pgt.Scalar) else p for p in value]
+    ((M, N),) = shapes
+    value = [[[e] * N] * M if isinstance(e, pgt.Scalar) else e for e in value]
 
     return SkylineMatrix(value=value, change_times=change_times)