pertpy 1.0.0__tar.gz → 1.0.1__tar.gz

{pertpy-1.0.0 → pertpy-1.0.1}/.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "1.0.0 🌈"
-tag-template: 1.0.0
+name-template: "1.0.1 🌈"
+tag-template: 1.0.1
 exclude-labels:
     - "skip-changelog"
 

pertpy-1.0.1/.github/workflows/test_tutorials.yml

@@ -0,0 +1,94 @@
+name: Test tutorials
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        defaults:
+            run:
+              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+              shell: bash -euo pipefail {0}
+
+        env:
+            NOTEBOOK_PATH: docs/tutorials/notebooks
+
+        strategy:
+            fail-fast: false
+            matrix:
+                notebook: [
+                        "augur.ipynb",
+                        "cinemaot.ipynb",
+                        "differential_gene_expression.ipynb",
+                        "distances.ipynb",
+                        "distance_tests.ipynb",
+                        "enrichment.ipynb",
+                        "guide_rna_assignment.ipynb",
+                        "milo.ipynb",
+                        "mixscape.ipynb",
+                        "perturbation_space.ipynb",
+                        "sccoda.ipynb",
+                        # "dialogue.ipynb", takes too long
+                        # "tasccoda.ipynb", a pain to get running because of the required QT dependency. The QT action leads to a dead kernel
+                        # also no use cases yet
+                    ]
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                filter: blob:none
+                fetch-depth: 0
+                submodules: "true"
+
+            - name: Cache .pertpy_cache
+              uses: actions/cache@v4
+              with:
+                path: cache
+                key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('pertpy/metadata/**') }}
+                restore-keys: |
+                  ${{ runner.os }}-pertpy-cache
+
+            - name: Set up Python
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.13"
+            - name: Install R
+              uses: r-lib/actions/setup-r@v2
+              with:
+                  r-version: "4.4.3"
+
+            - name: Cache R packages
+              id: r-cache
+              uses: actions/cache@v3
+              with:
+                path: ${{ env.R_LIBS_USER }}
+                key: ${{ runner.os }}-r-${{ hashFiles('**/pertpy/tools/_milo.py') }}
+                restore-keys: ${{ runner.os }}-r-
+
+            - name: Install R dependencies
+              if: steps.r-cache.outputs.cache-hit != 'true'
+              run: |
+                mkdir -p ${{ env.R_LIBS_USER }}
+                Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); BiocManager::install('edgeR', lib='${{ env.R_LIBS_USER }}')"
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+              with:
+                enable-cache: true
+                cache-dependency-glob: pyproject.toml
+            - name: Install dependencies
+              run: |
+                  uv pip install --system rpy2 decoupler muon
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
+                  uv pip install --system nbconvert ipykernel
+
+            - name: Run ${{ matrix.notebook }} Notebook
+              run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}

{pertpy-1.0.0 → pertpy-1.0.1}/.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/biomejs/pre-commit
-      rev: v1.9.4
+      rev: v2.1.1
       hooks:
           - id: biome-format
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.9
+      rev: v0.12.3
       hooks:
-          - id: ruff
+          - id: ruff-check
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -33,7 +33,7 @@ repos:
           - id: no-commit-to-branch
             args: ["--branch=main"]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.15.0
+      rev: v1.16.1
       hooks:
           - id: mypy
             args: [--no-strict-optional, --ignore-missing-imports]

{pertpy-1.0.0 → pertpy-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pertpy
-Version: 1.0.0
+Version: 1.0.1
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -49,7 +49,7 @@ Requires-Python: <3.14,>=3.11
 Requires-Dist: adjusttext
 Requires-Dist: arviz
 Requires-Dist: blitzgsea
-Requires-Dist: fast-array-utils
+Requires-Dist: fast-array-utils[accel,sparse]
 Requires-Dist: lamin-utils
 Requires-Dist: mudata
 Requires-Dist: openpyxl
@@ -93,7 +93,7 @@ Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Provides-Extra: tcoda
 Requires-Dist: ete4; extra == 'tcoda'
 Requires-Dist: pyqt6; extra == 'tcoda'
-Requires-Dist: toytree; extra == 'tcoda'
+Requires-Dist: toytree>=3.0; extra == 'tcoda'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
 Requires-Dist: leidenalg; extra == 'test'

pertpy-1.0.1/biome.jsonc

@@ -0,0 +1,34 @@
+{
+    "$schema": "https://biomejs.dev/schemas/2.0.5/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "includes": [".vscode/**/*.json", "**/*.jsonc", "**/asv.conf.json"],
+            "json": {
+                "formatter": {
+                    "trailingCommas": "all",
+                },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+    "linter": {
+        "rules": {
+            "style": {
+                "noParameterAssign": "error",
+                "useAsConstAssertion": "error",
+                "useDefaultParameterLast": "error",
+                "useEnumInitializers": "error",
+                "useSelfClosingElements": "error",
+                "useSingleVarDeclarator": "error",
+                "noUnusedTemplateLiteral": "error",
+                "useNumberNamespace": "error",
+                "noInferrableTypes": "error",
+                "noUselessElse": "error",
+            },
+        },
+    },
+}

{pertpy-1.0.0 → pertpy-1.0.1}/docs/api/tools_index.md

@@ -423,8 +423,6 @@ ps_adata = ps.compute(
     target_col="gene_target",
     groups_col="gene_target",
     mode="mean",
-    min_cells=0,
-    min_counts=0,
 )
 ```
 

{pertpy-1.0.0 → pertpy-1.0.1}/docs/changelog.md

@@ -5,6 +5,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1
+
+
+### 🚀 Features
+
+* Add support for gamma parameter in MMD distance ([#825](https://github.com/scverse/pertpy/pull/825)) @Zethson
+* Run notebooks in CI ([#815](https://github.com/scverse/pertpy/pull/815)) @Zethson
+
+## 🐛 Bug Fixes
+
+* Fix milo output writing ([#821](https://github.com/scverse/pertpy/pull/821)) @Zethson
+
 ## v1.0.0
 
 ### 🚀 Features

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Lukas Heumos"
 __email__ = "lukas.heumos@posteo.net"
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 import warnings
 

pertpy-1.0.1/pertpy/data/_dataloader.py

@@ -0,0 +1,117 @@
+import shutil
+import tempfile
+import time
+from pathlib import Path
+from random import choice
+from string import ascii_lowercase
+from zipfile import ZipFile
+
+import requests
+from filelock import FileLock
+from lamin_utils import logger
+from requests.exceptions import RequestException
+from rich.progress import Progress
+
+
+def _download(  # pragma: no cover
+    url: str,
+    output_file_name: str | None = None,
+    output_path: str | Path | None = None,
+    block_size: int = 1024,
+    overwrite: bool = False,
+    is_zip: bool = False,
+    timeout: int = 30,
+    max_retries: int = 3,
+    retry_delay: int = 5,
+) -> Path:
+    """Downloads a dataset irrespective of the format.
+
+    Args:
+        url: URL to download
+        output_file_name: Name of the downloaded file
+        output_path: Path to download/extract the files to.
+        block_size: Block size for downloads in bytes.
+        overwrite: Whether to overwrite existing files.
+        is_zip: Whether the downloaded file needs to be unzipped.
+        timeout: Request timeout in seconds.
+        max_retries: Maximum number of retry attempts.
+        retry_delay: Delay between retries in seconds.
+    """
+    if output_file_name is None:
+        letters = ascii_lowercase
+        output_file_name = f"pertpy_tmp_{''.join(choice(letters) for _ in range(10))}"
+
+    if output_path is None:
+        output_path = tempfile.gettempdir()
+
+    download_to_path = Path(output_path) / output_file_name
+
+    Path(output_path).mkdir(parents=True, exist_ok=True)
+    lock_path = Path(output_path) / f"{output_file_name}.lock"
+
+    try:
+        with FileLock(lock_path, timeout=300):
+            if Path(download_to_path).exists() and not overwrite:
+                logger.warning(f"File {download_to_path} already exists!")
+                return download_to_path
+
+            temp_file_name = Path(f"{download_to_path}.part")
+
+            retry_count = 0
+            while retry_count <= max_retries:
+                try:
+                    head_response = requests.head(url, timeout=timeout)
+                    head_response.raise_for_status()
+                    content_length = int(head_response.headers.get("content-length", 0))
+
+                    free_space = shutil.disk_usage(output_path).free
+                    if content_length > free_space:
+                        raise OSError(
+                            f"Insufficient disk space. Need {content_length} bytes, but only {free_space} available."
+                        )
+
+                    response = requests.get(url, stream=True)
+                    response.raise_for_status()
+                    total = int(response.headers.get("content-length", 0))
+
+                    with Progress(refresh_per_second=5) as progress:
+                        task = progress.add_task("[red]Downloading...", total=total)
+                        with Path(temp_file_name).open("wb") as file:
+                            for data in response.iter_content(block_size):
+                                file.write(data)
+                                progress.update(task, advance=len(data))
+                            progress.update(task, completed=total, refresh=True)
+
+                    Path(temp_file_name).replace(download_to_path)
+
+                    if is_zip:
+                        with ZipFile(download_to_path, "r") as zip_obj:
+                            zip_obj.extractall(path=output_path)
+                        return Path(output_path)
+
+                    return download_to_path
+                except (OSError, RequestException) as e:
+                    retry_count += 1
+                    if retry_count <= max_retries:
+                        logger.warning(
+                            f"Download attempt {retry_count}/{max_retries} failed: {str(e)}. Retrying in {retry_delay} seconds..."
+                        )
+                        time.sleep(retry_delay)
+                    else:
+                        logger.error(f"Download failed after {max_retries} attempts: {str(e)}")
+                        if Path(temp_file_name).exists():
+                            Path(temp_file_name).unlink(missing_ok=True)
+                        raise
+
+                except Exception as e:
+                    logger.error(f"Download failed: {str(e)}")
+                    if Path(temp_file_name).exists():
+                        Path(temp_file_name).unlink(missing_ok=True)
+                    raise
+                finally:
+                    if Path(temp_file_name).exists():
+                        Path(temp_file_name).unlink(missing_ok=True)
+    finally:
+        lock_path.unlink(missing_ok=True)
+
+    return Path(download_to_path)

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/tools/__init__.py

@@ -1,24 +1,5 @@
 from importlib import import_module
 
-
-def lazy_import(module_path: str, class_name: str, extras: list[str]):
-    try:
-        for extra in extras:
-            import_module(extra)
-        module = import_module(module_path)
-        return getattr(module, class_name)
-    except ImportError:
-
-        class Placeholder:
-            def __init__(self, *args, **kwargs):
-                raise ImportError(
-                    f"Extra dependencies required: {', '.join(extras)}. "
-                    f"Please install with: pip install {' '.join(extras)}"
-                )
-
-        return Placeholder
-
-
 from pertpy.tools._augur import Augur
 from pertpy.tools._cinemaot import Cinemaot
 from pertpy.tools._coda._sccoda import Sccoda
@@ -42,15 +23,25 @@ from pertpy.tools._perturbation_space._simple import (
 )
 from pertpy.tools._scgen import Scgen
 
-CODA_EXTRAS = ["toytree", "ete4"]  # also "pyqt6" but it cannot be imported
-Tasccoda = lazy_import("pertpy.tools._coda._tasccoda", "Tasccoda", CODA_EXTRAS)
 
-DE_EXTRAS = ["formulaic", "pydeseq2"]
-EdgeR = lazy_import("pertpy.tools._differential_gene_expression", "EdgeR", DE_EXTRAS)  # edgeR will be imported via rpy2
-PyDESeq2 = lazy_import("pertpy.tools._differential_gene_expression", "PyDESeq2", DE_EXTRAS)
-Statsmodels = lazy_import("pertpy.tools._differential_gene_expression", "Statsmodels", DE_EXTRAS + ["statsmodels"])
-TTest = lazy_import("pertpy.tools._differential_gene_expression", "TTest", DE_EXTRAS)
-WilcoxonTest = lazy_import("pertpy.tools._differential_gene_expression", "WilcoxonTest", DE_EXTRAS)
+def __getattr__(name: str):
+    if name == "Tasccoda":
+        try:
+            for extra in ["toytree", "ete4"]:
+                import_module(extra)
+            module = import_module("pertpy.tools._coda._tasccoda")
+            return module.Tasccoda
+        except ImportError:
+            raise ImportError(
+                "Extra dependencies required: toytree, ete4. Please install with: pip install toytree ete4"
+            ) from None
+
+    elif name in ["EdgeR", "PyDESeq2", "Statsmodels", "TTest", "WilcoxonTest"]:
+        module = import_module("pertpy.tools._differential_gene_expression")
+        return getattr(module, name)
+
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
 
 __all__ = [
     "Augur",

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/tools/_coda/_base_coda.py

@@ -1181,7 +1181,7 @@ class CompositionalModel2(ABC):
                 r,
                 bars,
                 bottom=cum_bars,
-                color=palette(n % palette.N),
+                color=palette(n % palette.N),  # type: ignore
                 width=barwidth,
                 label=type_names[n],
                 linewidth=0,
@@ -1377,6 +1377,7 @@ class CompositionalModel2(ABC):
         plot_df.columns = covariate_names
         plot_df = pd.melt(plot_df, ignore_index=False, var_name="Covariate")
 
+        plot_df.index.name = "Cell Type"
         plot_df = plot_df.reset_index()
 
         if len(covariate_names_zero) != 0 and plot_facets and plot_zero_covariate and not plot_zero_cell_type:
@@ -1472,6 +1473,7 @@ class CompositionalModel2(ABC):
         if return_fig and not plot_facets:
             return plt.gcf()
         plt.show()
+
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
@@ -1823,6 +1825,7 @@ class CompositionalModel2(ABC):
         if return_fig:
             return plt.gcf()
         plt.show()
+
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
@@ -1881,7 +1884,7 @@ class CompositionalModel2(ABC):
             from ete4.treeview import CircleFace, NodeStyle, TextFace, TreeStyle, faces
         except ImportError:
             raise ImportError(
-                "To use tasccoda please install additional dependencies with `pip install pertpy[coda]`"
+                "To use tasccoda please install additional dependencies: `pip install pertpy[coda]`"
             ) from None
 
         if isinstance(data, MuData):
@@ -1902,8 +1905,8 @@ class CompositionalModel2(ABC):
             tree.render(save, tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
         if return_fig:
             return tree, tree_style
+
         return tree.render("%%inline", tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
-        return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
     def plot_draw_effects(  # pragma: no cover # noqa: D417
@@ -1969,7 +1972,7 @@ class CompositionalModel2(ABC):
             from ete4.treeview import CircleFace, NodeStyle, TextFace, TreeStyle, faces
         except ImportError:
             raise ImportError(
-                "To use tasccoda please install additional dependencies as `pip install pertpy[coda]`"
+                "To use tasccoda please install additional dependencies: `pip install pertpy[coda]`"
             ) from None
 
         if isinstance(data, MuData):
@@ -2207,6 +2210,7 @@ class CompositionalModel2(ABC):
         if return_fig:
             return fig
         plt.show()
+
         return None
 
 
@@ -2325,6 +2329,7 @@ def df2newick(df: pd.DataFrame, levels: list[str], inner_label: bool = True) ->
     strs = [traverse(df_tax, a, 0, inner_label) for a in alevel]
 
     newick = f"({','.join(strs)});"
+
     return newick
 
 
@@ -2562,6 +2567,7 @@ def from_scanpy(
     covariate_obs = list(set(covariate_obs or []) | set(sample_identifier))
 
     if isinstance(sample_identifier, list):
+        adata.obs = adata.obs.copy()
         adata.obs["scCODA_sample_id"] = adata.obs[sample_identifier].agg("-".join, axis=1)
         sample_identifier = "scCODA_sample_id"
 

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/tools/_coda/_sccoda.py

@@ -409,6 +409,48 @@ class Sccoda(CompositionalModel2):
         import arviz as az
 
         # Create arviz object
+        if use_posterior_predictive:
+            posterior_predictive = Predictive(self.model, self.mcmc.get_samples())(
+                rng_key,
+                counts=None,
+                covariates=numpyro_covariates,
+                n_total=numpyro_n_total,
+                ref_index=ref_index,
+                sample_adata=sample_adata,
+            )
+            # Remove problematic posterior predictive arrays with wrong dimensions
+            if posterior_predictive and "counts" in posterior_predictive:
+                counts_shape = posterior_predictive["counts"].shape
+                expected_dims = 2  # ['sample', 'cell_type']
+                if len(counts_shape) != expected_dims:
+                    posterior_predictive = {k: v for k, v in posterior_predictive.items() if k != "counts"}
+                    logger.warning(
+                        f"Removed 'counts' from posterior_predictive due to dimension mismatch: got {len(counts_shape)}D, expected {expected_dims}D"
+                    )
+        else:
+            posterior_predictive = None
+
+        if num_prior_samples > 0:
+            prior = Predictive(self.model, num_samples=num_prior_samples)(
+                rng_key,
+                counts=None,
+                covariates=numpyro_covariates,
+                n_total=numpyro_n_total,
+                ref_index=ref_index,
+                sample_adata=sample_adata,
+            )
+            # Remove problematic prior arrays with wrong dimensions
+            if prior and "counts" in prior:
+                counts_shape = prior["counts"].shape
+                expected_dims = 2  # ['sample', 'cell_type']
+                if len(counts_shape) != expected_dims:
+                    prior = {k: v for k, v in prior.items() if k != "counts"}
+                    logger.warning(
+                        f"Removed 'counts' from prior due to dimension mismatch: got {len(counts_shape)}D, expected {expected_dims}D"
+                    )
+        else:
+            prior = None
+
         arviz_data = az.from_numpyro(
             self.mcmc, prior=prior, posterior_predictive=posterior_predictive, dims=dims, coords=coords
         )

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/tools/_dialogue.py

@@ -882,9 +882,9 @@ class Dialogue:
             if len(conditions_compare) != 2:
                 raise ValueError("Please specify conditions to compare or supply an object with only 2 conditions")
 
-        pvals = pd.DataFrame(1, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
-        tstats = pd.DataFrame(1, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
-        pvals_adj = pd.DataFrame(1, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
+        pvals = pd.DataFrame(1.0, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
+        tstats = pd.DataFrame(1.0, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
+        pvals_adj = pd.DataFrame(1.0, adata.obs[celltype_label].unique(), ["mcp_" + str(n) for n in range(n_mcps)])
 
         response = adata.obs.groupby(sample_label)[condition_label].agg(pd.Series.mode)
         for celltype in adata.obs[celltype_label].unique():

pertpy-1.0.1/pertpy/tools/_differential_gene_expression/__init__.py

@@ -0,0 +1,60 @@
+import contextlib
+from importlib import import_module
+from importlib.util import find_spec
+
+from ._base import LinearModelBase, MethodBase
+from ._dge_comparison import DGEEVAL
+from ._edger import EdgeR
+from ._simple_tests import SimpleComparisonBase, TTest, WilcoxonTest
+
+
+def __getattr__(name: str):
+    deps = {
+        "PyDESeq2": ["pydeseq2", "formulaic_contrasts", "formulaic"],
+        "EdgeR": ["rpy2", "formulaic_contrasts", "formulaic"],
+        "Statsmodels": ["formulaic_contrasts", "formulaic"],
+    }
+
+    if name in deps:
+        for dep in deps[name]:
+            if find_spec(dep) is None:
+                raise ImportError(f"{dep} is required but not installed")
+
+        module_map = {
+            "PyDESeq2": "pertpy.tools._differential_gene_expression._pydeseq2",
+            "EdgeR": "pertpy.tools._differential_gene_expression._edger",
+            "Statsmodels": "pertpy.tools._differential_gene_expression._statsmodels",
+        }
+
+        module = import_module(module_map[name])
+        return getattr(module, name)
+
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def _get_available_methods():
+    methods = [WilcoxonTest, TTest]
+    from importlib.util import find_spec
+
+    for name in ["Statsmodels", "PyDESeq2", "EdgeR"]:
+        with contextlib.suppress(ImportError):
+            methods.append(__getattr__(name))
+
+    return methods
+
+
+AVAILABLE_METHODS = _get_available_methods()
+
+
+AVAILABLE_METHODS = _get_available_methods()
+
+__all__ = [
+    "MethodBase",
+    "LinearModelBase",
+    "EdgeR",
+    "PyDESeq2",
+    "Statsmodels",
+    "SimpleComparisonBase",
+    "WilcoxonTest",
+    "TTest",
+]

{pertpy-1.0.0 → pertpy-1.0.1}/pertpy/tools/_differential_gene_expression/_base.py

@@ -12,7 +12,6 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import seaborn as sns
-from formulaic_contrasts import FormulaicContrasts
 from lamin_utils import logger
 from matplotlib.pyplot import Figure
 from matplotlib.ticker import MaxNLocator
@@ -881,6 +880,8 @@ class LinearModelBase(MethodBase):
         super().__init__(adata, mask=mask, layer=layer)
         self._check_counts()
 
+        from formulaic_contrasts import FormulaicContrasts
+
         self.formulaic_contrasts = None
         if isinstance(design, str):
             self.formulaic_contrasts = FormulaicContrasts(adata.obs, design)