rectanglepy 1.4.1__tar.gz → 1.5.0__tar.gz

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1
+current_version = 1.5.0
 tag = True
 commit = True
 

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/.readthedocs.yaml

@@ -1,7 +1,7 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
+    os: ubuntu-24.04
     tools:
         python: "3.10"
 sphinx:

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/CHANGELOG.md

@@ -10,6 +10,12 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+## [1.4.2] - 2026-05-24
+
+### Changed
+
+-   Changed the open-source license from GPLv3 to BSD-3-Clause while retaining the commercial licensing option.
+
 ## [1.4.1] - 2026-04-23
 
 ### Changed
@@ -20,10 +26,10 @@ and this project adheres to [Semantic Versioning][].
 
 ### Changed
 
--   **Licensing: Rectangle is now available under a dual licence.**
-    -   Non-commercial use: GNU General Public Licence v3 (GPLv3).
-    -   Commercial use: A proprietary licence is available for companies wishing to use Rectangle in closed-source or proprietary applications. For enquiries, contact innovation-psb@uibk.ac.at.
-    -   See [LICENCE_COM](LICENCE_COM) for full commercial licence terms.
+-   **Licensing: Rectangle is available under a dual license.**
+    -   Non-commercial use: GNU General Public License v3 (GPLv3).
+    -   Commercial use: A proprietary license is available for companies wishing to use Rectangle in closed-source or proprietary applications. For enquiries, contact innovation-psb@uibk.ac.at.
+    -   See the commercial license terms for details.
 -   Added Contributor License Agreement (CLA) for external contributions.
 
 ## [1.2.0] - 2026-01-31

rectanglepy-1.5.0/CLA.md

@@ -0,0 +1,38 @@
+# Rectangle Contributor License Agreement (CLA)
+
+## Purpose
+
+Rectangle is dual-licensed: BSD-3-Clause open source OR a proprietary Commercial license. This CLA ensures Contributions can be used under the BSD-3-Clause license and also re-licensed under the Commercial license.
+
+## Definitions
+
+-   **Contribution**: Any work submitted for inclusion, including code, documentation, tests, examples, or other materials.
+-   **Contributor**: The individual or entity submitting a Contribution.
+-   **Project Owners**: Francesca Finotello and Bernhard Eder.
+
+## Grant of rights
+
+The Contributor grants the Project Owners a perpetual, worldwide, irrevocable, non-exclusive, transferable license to use, reproduce, modify, create derivative works of, publicly display, perform, sublicense, and distribute the Contribution:
+
+-   under the BSD-3-Clause license; and
+-   under one or more proprietary licenses at the Project Owners’ discretion.
+
+## Copyright
+
+The Contributor retains copyright in their Contribution.
+
+## Disclaimer
+
+Contributions are provided “AS IS,” without warranties or conditions of any kind.
+
+## Compensation
+
+No compensation is owed for Contributions unless separately agreed in writing.
+
+## Governing law
+
+This CLA is governed by the laws of Austria, excluding conflict of law rules.
+
+## Acceptance
+
+By submitting a Contribution, for example via pull request, you agree to this CLA.

rectanglepy-1.5.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Francesca Finotello and Bernhard Eder
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the names of the copyright holders nor the names of contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES, INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT, INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF
+THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

rectanglepy-1.5.0/LICENSE-Commercial.md

@@ -0,0 +1,61 @@
+# Rectangle – Commercial License Terms
+
+Copyright (c) 2026 Francesca Finotello and Bernhard Eder
+Contact: innovation-psb@uibk.ac.at
+
+These Commercial License Terms apply only if the Licensors and Licensee have entered into a written commercial license agreement, order form, or other written agreement that expressly incorporates these terms. Otherwise, Rectangle is available under the BSD-3-Clause license in the `LICENSE` file.
+
+## Dual licensing
+
+-   Rectangle is dual-licensed: BSD-3-Clause OR Commercial.
+-   If you use Rectangle under the BSD-3-Clause license, the terms in `LICENSE` apply.
+-   If you require different terms, such as warranties, indemnities, dedicated support, or redistribution without BSD notices, you must obtain a commercial license from the copyright holders.
+
+## Grant of rights Commercial
+
+Subject to full payment of the agreed license fee, the applicable written agreement or order form, and compliance with these terms, the Licensee is granted a non-exclusive, non-transferable, worldwide license to:
+
+-   use Rectangle internally and in products/services;
+-   modify and create derivative works; and
+-   distribute Rectangle, in source or binary form, as part of proprietary applications, without any obligation to disclose source code and without attribution requirements beyond what is agreed here.
+
+## Term and scope
+
+-   Perpetual term unless otherwise stated in the order form.
+-   License is limited to the legal entity named in the order form.
+-   Sub-licensing, assignment, or transfer requires prior written consent of the Licensors.
+
+## Attribution and notices
+
+-   No attribution is required unless otherwise agreed in the order form.
+-   The Licensee may not use the Licensors’ or contributors’ names or trademarks to endorse or promote products without prior written permission.
+
+## Support and updates
+
+-   Support, maintenance, and updates are not included unless purchased separately under a support agreement.
+
+## Compliance
+
+-   The Licensee is responsible for ensuring that distribution and use comply with applicable laws and third-party licenses.
+-   Anyone who has not entered into a separate commercial license agreement may use Rectangle only under the BSD-3-Clause license.
+
+## Liability and warranty
+
+-   Rectangle is provided “AS IS.” The Licensors disclaim all warranties unless explicitly provided in a separate support agreement or SLA.
+-   To the extent permitted by law, Licensors’ aggregate liability is limited to the amount paid by the Licensee for the commercial license during the 12 months preceding the claim.
+-   Licensors are not liable for indirect, incidental, special, or consequential damages.
+
+## Termination
+
+-   Licensors may terminate this license for material breach if not cured within 30 days of written notice.
+-   Upon termination, Licensee shall cease use and destroy copies within a reasonable time.
+
+## Governing law and venue
+
+-   This Agreement is governed by the laws of Austria, excluding conflict of law rules.
+-   Exclusive jurisdiction and venue are the competent courts at the Licensors’ registered seat, to the extent legally permissible.
+
+## Entire agreement and amendments
+
+-   This constitutes the entire agreement for commercial use.
+-   Amendments must be in writing and signed by both parties.

rectanglepy-1.5.0/PKG-INFO

@@ -0,0 +1,110 @@
+Metadata-Version: 2.4
+Name: rectanglepy
+Version: 1.5.0
+Summary: Hierarchical deconvolution of bulk  transcriptomics
+Project-URL: Documentation, https://rectanglepy.readthedocs.io/
+Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
+Project-URL: Home-page, https://github.com/ComputationalBiomedicineGroup/Rectangle
+Author: Bernhard Eder
+Maintainer-email: Bernhard Eder <Bernhard.Eder@student.uibk.ac.at>
+License-Expression: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+License-File: LICENSE
+License-File: LICENSE-Commercial.md
+Requires-Python: >=3.10
+Requires-Dist: anndata<0.10.9,>=0.8.0
+Requires-Dist: loguru
+Requires-Dist: numpy<2.0.0,>=1.0.0
+Requires-Dist: osqp>=1.0.5
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: pydeseq2==0.4.11
+Requires-Dist: scipy==1.13.0
+Requires-Dist: statsmodels>=0.14.1
+Provides-Extra: dev
+Requires-Dist: bump2version; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: furo; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
+Requires-Dist: sphinx; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-book-theme; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'doc'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Rectangle
+
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/ComputationalBiomedicineGroup/Rectangle/build.yaml?branch=main
+[link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
+[badge-docs]: https://img.shields.io/readthedocs/rectanglepy
+
+Rectangle is an open-source Python package for single-cell-informed cell-type deconvolution of bulk and spatial transcriptomic data, which is part of the [scverse ecosystem](https://scverse.org/packages/).
+
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical signature building for fine-grained cell-type deconvolution, estimation and correction of unknown cellular content, and efficient handling of large-scale single-cell data during signature matrix computation.
+
+Rectangle was developed to overcome the current challenges in cell-type deconvolution, providing a robust and accurate methodology while ensuring a low computational profile.
+
+## Getting started
+
+Please refer to the [documentation][link-docs]. In particular, the
+
+-   [Tutorials][link-docs/tutorials] for a step-by-step guide on how to use Rectangle, and the
+
+-   [API documentation][link-api].
+
+## Installation
+
+You need Python 3.10–3.12 installed on your system.
+
+How to install Rectangle:
+
+Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/rectanglepy/>:
+
+```bash
+pip install rectanglepy
+```
+
+## License
+
+Rectangle is dual-licensed: BSD-3-Clause OR Commercial.
+
+### Open-source option: BSD-3-Clause
+
+You may use, modify, and redistribute Rectangle, including in proprietary products, if you keep the copyright and license notices and do not use the authors’ names for endorsement.
+
+See [LICENSE](LICENSE).
+
+### Commercial option
+
+For alternative terms, such as warranties, indemnities, dedicated support, SLAs, or redistribution without BSD notice requirements, contact innovation-psb@uibk.ac.at.
+
+See [LICENSE-Commercial.md](LICENSE-Commercial.md).
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+For commercial licensing: **innovation-psb@uibk.ac.at**
+
+## Citation
+
+> If you use Rectangle in your project, please cite: (TBA)
+
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/ComputationalBiomedicineGroup/Rectangle/issues
+[changelog]: https://rectanglepy.readthedocs.io/changelog.html
+[link-docs]: https://Rectanglepy.readthedocs.io
+[link-api]: https://rectanglepy.readthedocs.io/api.html
+[link-docs/tutorials]: https://rectanglepy.readthedocs.io/notebooks/example.html

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/README.md

@@ -33,16 +33,21 @@ Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/
 pip install rectanglepy
 ```
 
-## Licence
+## License
 
-Rectangle is available under a **dual licence**:
+Rectangle is dual-licensed: BSD-3-Clause OR Commercial.
 
--   **Open-source licence:** [GNU General Public License v3.0 (GPLv3)](LICENSE)
-    → Free to use, modify, and redistribute as long as modifications and redistributions are also under GPLv3.
+### Open-source option: BSD-3-Clause
 
--   **Commercial licence:** For companies and individuals who wish to use Rectangle in proprietary or closed-source applications, a separate commercial licence is available. See [LICENCE_COM](LICENCE_COM) for details.
+You may use, modify, and redistribute Rectangle, including in proprietary products, if you keep the copyright and license notices and do not use the authors’ names for endorsement.
 
-For commercial licensing enquiries, please contact: **innovation-psb@uibk.ac.at**
+See [LICENSE](LICENSE).
+
+### Commercial option
+
+For alternative terms, such as warranties, indemnities, dedicated support, SLAs, or redistribution without BSD notice requirements, contact innovation-psb@uibk.ac.at.
+
+See [LICENSE-Commercial.md](LICENSE-Commercial.md).
 
 ## Release notes
 

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/docs/contributing.md

@@ -4,7 +4,7 @@ We welcome contributions! The best way to contribute is by opening a pull reques
 
 ## Contributor License Agreement (CLA)
 
-Rectangle uses a dual-licensing model (GPLv3 + commercial). By submitting a contribution (e.g., via pull request), you agree to the terms of our [Contributor License Agreement (CLA)](https://github.com/ComputationalBiomedicineGroup/Rectangle/blob/main/CLA.md). This ensures that contributions can be included in both the open-source and commercial versions of Rectangle.
+Rectangle uses a dual-licensing model (BSD-3-Clause OR Commercial). By submitting a contribution (e.g., via pull request), you agree to the terms of our [Contributor License Agreement (CLA)](https://github.com/ComputationalBiomedicineGroup/Rectangle/blob/main/CLA.md). This ensures that contributions can be included in both the open-source and commercial versions of Rectangle.
 
 ## How to Contribute
 

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/pyproject.toml

@@ -4,11 +4,12 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "1.4.1"
+version = "1.5.0"
 description = "Hierarchical deconvolution of bulk  transcriptomics"
 readme = "README.md"
 requires-python = ">=3.10"
-license = {file = "LICENSE"}
+license = "BSD-3-Clause OR LicenseRef-Rectangle-Commercial"
+license-files = ["LICENSE", "LICENSE-Commercial.md"]
 authors = [
     {name = "Bernhard Eder"},
 ]

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/src/rectanglepy/__init__.py

@@ -1,8 +1,9 @@
 from importlib.metadata import version
 
 from . import pp, tl
+from .parameters import RectangleAdvancedParameters
 from .rectangle import load_tutorial_data, rectangle
 
-__all__ = ["pp", "tl", "load_tutorial_data", "rectangle"]
+__all__ = ["pp", "tl", "RectangleAdvancedParameters", "load_tutorial_data", "rectangle"]
 
 __version__ = version("rectanglepy")

rectanglepy-1.5.0/src/rectanglepy/parameters.py

@@ -0,0 +1,11 @@
+# SPDX-License-Identifier: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class RectangleAdvancedParameters:
+    """Advanced parameters for Rectangle internals."""
+
+    number_of_bootstraps: int = 7
+    grid_search_split_size: int = 50

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/src/rectanglepy/pp/create_signature.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+
 import numpy as np
 import pandas as pd
 import scipy.sparse
@@ -11,6 +13,7 @@ from scipy.cluster.hierarchy import fcluster, linkage
 from scipy.stats import pearsonr
 from sklearn.metrics import silhouette_score
 
+from rectanglepy.parameters import RectangleAdvancedParameters
 from rectanglepy.tl.deconvolution import solve_qp
 
 from .rectangle_signature import RectangleSignatureResult
@@ -127,11 +130,16 @@ def _filter_de_analysis_results(de_analysis_result, p, logfc):
 
 
 def _run_deseq2(
-    countsig: pd.DataFrame, sc_data, annotations: pd.Series, n_cpus: int = None, gene_expression_threshold=0.5
+    countsig: pd.DataFrame,
+    sc_data,
+    annotations: pd.Series,
+    n_cpus: int = None,
+    gene_expression_threshold=0.5,
+    number_of_bootstraps: int = 7,
 ) -> dict[str | int, pd.DataFrame]:
     results = {}
     inference = DefaultInference(n_cpus=n_cpus)
-    bootstrapped_signature = _create_bootstrap_signature(countsig, sc_data, annotations)
+    bootstrapped_signature = _create_bootstrap_signature(countsig, sc_data, annotations, number_of_bootstraps)
     np.random.seed(42)
     for _i, cell_type in enumerate(countsig.columns):
         bootstrapped_signature_copy = bootstrapped_signature.copy()
@@ -165,12 +173,11 @@ def _run_deseq2(
     return results
 
 
-def _create_bootstrap_signature(countsig, sc_data, annotations) -> pd.DataFrame:
+def _create_bootstrap_signature(countsig, sc_data, annotations, number_of_bootstraps: int = 7) -> pd.DataFrame:
     if scipy.sparse.issparse(sc_data):
         sc_data = sc_data.toarray()
     celltypes = countsig.columns
     bootstrapped_signature = pd.DataFrame()
-    number_of_bootstraps = 7
     samples_per_bootstrap = 500
     np.random.seed(42)
     for celltype in celltypes:
@@ -196,14 +203,30 @@ def _de_analysis(
     n_cpus: int = None,
     genes=None,
     gene_expression_threshold=0.5,
+    advanced_parameters: RectangleAdvancedParameters = None,
 ) -> tuple[Series, dict[str, [str]] :, DataFrame | None]:
     logger.info("Starting DE analysis")
-    deseq_results = _run_deseq2(pseudo_count_sig, sc_data, annotations, n_cpus, gene_expression_threshold)
+    advanced_parameters = advanced_parameters or RectangleAdvancedParameters()
+    deseq_results = _run_deseq2(
+        pseudo_count_sig,
+        sc_data,
+        annotations,
+        n_cpus,
+        gene_expression_threshold,
+        advanced_parameters.number_of_bootstraps,
+    )
     optimization_results = None
 
     if optimize_cutoffs:
         logger.info("Optimizing cutoff parameters p and lfc")
-        optimization_results = _optimize_parameters(sc_data, annotations, pseudo_count_sig, deseq_results, genes)
+        optimization_results = _optimize_parameters(
+            sc_data,
+            annotations,
+            pseudo_count_sig,
+            deseq_results,
+            genes,
+            advanced_parameters.grid_search_split_size,
+        )
         p, lfc = optimization_results.iloc[0, 0:2]
         logger.info(f"Optimization done\n Best cutoffs  p: {p} and lfc: {lfc}")
 
@@ -285,6 +308,7 @@ def build_rectangle_signatures(
     lfc=1.5,
     n_cpus: int = None,
     gene_expression_threshold=0.5,
+    advanced_parameters: RectangleAdvancedParameters = None,
 ) -> RectangleSignatureResult:
     r"""Builds rectangle signatures based on single-cell  count data and annotations.
 
@@ -301,7 +325,7 @@ def build_rectangle_signatures(
     raw
         A flag indicating whether to use the raw Anndata data. Defaults to False.
     optimize_cutoffs
-        Indicates whether to optimize the p-value and log fold change cutoffs using gridsearch. Defaults to True.
+        Indicates whether to optimize the log fold change cutoffs using gridsearch. Defaults to True.
     p
         The p-value threshold for the DE analysis (only used if optimize_cutoffs is False).
     lfc
@@ -310,11 +334,14 @@ def build_rectangle_signatures(
         The number of cpus to use for the DE analysis. Defaults to the number of cpus available.
     gene_expression_threshold
         The gene expression threshold for the DE analysis. How many cells need to express a gene to be considered in DGE
+    advanced_parameters
+        Optional advanced Rectangle parameters. Defaults are used when not provided.
 
     Returns
     -------
     The result of the rectangle signature analysis which is of type RectangleSignatureResult.
     """
+    advanced_parameters = advanced_parameters or RectangleAdvancedParameters()
     annotations = adata.obs[cell_type_col]
     adata = adata[:, adata.X.sum(axis=0) > len(annotations.value_counts())]
     assert adata.var_names.is_unique, "Duplicate gene found in adata"
@@ -342,7 +369,16 @@ def build_rectangle_signatures(
     m_rna_biasfactors = _create_bias_factors(pseudo_sig_counts, sc_counts, annotations)
 
     marker_genes, marker_genes_per_cell_type, optimization_result = _de_analysis(
-        pseudo_sig_counts, sc_counts, annotations, p, lfc, optimize_cutoffs, n_cpus, genes, gene_expression_threshold
+        pseudo_sig_counts,
+        sc_counts,
+        annotations,
+        p,
+        lfc,
+        optimize_cutoffs,
+        n_cpus,
+        genes,
+        gene_expression_threshold,
+        advanced_parameters,
     )
     pseudo_sig_cpm = _convert_to_cpm(pseudo_sig_counts)
     logger.info("Starting rectangle cluster analysis")
@@ -369,6 +405,7 @@ def build_rectangle_signatures(
         lfc,
         False,
         gene_expression_threshold=gene_expression_threshold,
+        advanced_parameters=advanced_parameters,
     )
     clustered_signature = _convert_to_cpm(clustered_signature)
     return RectangleSignatureResult(
@@ -398,7 +435,12 @@ def _create_pseudo_count_sig(sc_counts: np.ndarray, annotations: pd.Series, var_
 
 
 def _optimize_parameters(
-    sc_data: pd.DataFrame, annotations: pd.Series, pseudo_signature_counts: pd.DataFrame, de_results, genes=None
+    sc_data: pd.DataFrame,
+    annotations: pd.Series,
+    pseudo_signature_counts: pd.DataFrame,
+    de_results,
+    genes=None,
+    grid_search_split_size: int = 50,
 ) -> pd.DataFrame:
     # search space for p and lfc
     lfcs = [x / 100 for x in range(160, 230, 10)]
@@ -406,7 +448,7 @@ def _optimize_parameters(
 
     results = []
     logger.info("generating pseudo bulks")
-    bulks, real_fractions = _generate_pseudo_bulks(sc_data, annotations, genes)
+    bulks, real_fractions = _generate_pseudo_bulks(sc_data, annotations, genes, grid_search_split_size)
     for p in ps:
         for lfc in lfcs:
             try:
@@ -439,9 +481,8 @@ def _assess_parameter_fit(
     return rsme, pearson_r
 
 
-def _generate_pseudo_bulks(sc_data, annotations, genes=None):
+def _generate_pseudo_bulks(sc_data, annotations, genes=None, split_size: int = 50):
     number_of_bulks = 50
-    split_size = 50
     bulks = []
     real_fractions = []
     np.random.seed(42)

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/src/rectanglepy/pp/rectangle_signature.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+
 import pandas as pd
 
 

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/src/rectanglepy/rectangle.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+
 from importlib.resources import files
 
 import pandas as pd
@@ -5,6 +7,7 @@ from anndata import AnnData
 from loguru import logger
 from pandas import DataFrame
 
+from .parameters import RectangleAdvancedParameters
 from .pp import RectangleSignatureResult, build_rectangle_signatures
 from .tl import deconvolution
 
@@ -22,6 +25,7 @@ def rectangle(
     lfc=1.5,
     n_cpus: int = None,
     gene_expression_threshold=0.5,
+    advanced_parameters: RectangleAdvancedParameters = None,
 ) -> tuple[DataFrame, RectangleSignatureResult]:
     r"""All in one deconvolution method. Creates signatures and deconvolutes the bulk data. Has options for subsampling and consensus runs.
 
@@ -38,7 +42,7 @@ def rectangle(
     raw
         A flag indicating whether to use the raw Anndata data.
     optimize_cutoffs
-        Indicates whether to optimize the p-value and log fold change cutoffs using gridsearch.
+        Indicates whether to optimize the log fold change cutoffs using gridsearch.
     p
         The p-value threshold for the DE analysis (only used if optimize_cutoffs is False).
     lfc
@@ -49,6 +53,8 @@ def rectangle(
         A flag indicating whether to correct for mRNA bias. Defaults to True.
     gene_expression_threshold : float
         The threshold for gene expression. Genes with expression below this threshold are removed from the analysis.
+    advanced_parameters
+        Optional advanced Rectangle parameters. Defaults are used when not provided.
 
     Returns
     -------
@@ -69,6 +75,7 @@ def rectangle(
         lfc=lfc,
         n_cpus=n_cpus,
         gene_expression_threshold=gene_expression_threshold,
+        advanced_parameters=advanced_parameters,
     )
 
     estimations, bulk_err = deconvolution(signatures, bulks, correct_mrna_bias, n_cpus)

{rectanglepy-1.4.1 → rectanglepy-1.5.0}/src/rectanglepy/tl/deconvolution.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause OR LicenseRef-Rectangle-Commercial
+
 import math
 import multiprocessing