rectanglepy 1.4.1__tar.gz → 1.4.2__tar.gz

{rectanglepy-1.4.1 → rectanglepy-1.4.2}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1
+current_version = 1.4.2
 tag = True
 commit = True
 

{rectanglepy-1.4.1 → rectanglepy-1.4.2}/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-1.4.2/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-1.4.2/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-1.4.2/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-1.4.2/PKG-INFO

@@ -0,0 +1,110 @@
+Metadata-Version: 2.4
+Name: rectanglepy
+Version: 1.4.2
+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-1.4.2}/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-1.4.2}/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-1.4.2}/pyproject.toml

@@ -4,11 +4,12 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "1.4.1"
+version = "1.4.2"
 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-1.4.2}/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

{rectanglepy-1.4.1 → rectanglepy-1.4.2}/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-1.4.2}/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

{rectanglepy-1.4.1 → rectanglepy-1.4.2}/src/rectanglepy/tl/deconvolution.py

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

rectanglepy-1.4.1/LICENCE_COM

@@ -1,203 +0,0 @@
-Rectangle - Open Source Version
-
-Copyright (C) 2026 Francesca Finotello, Bernhard Eder
-
-This programme is released under proprietary licence for commercial use
-(for proprietary licences, contact: innovation-psb@uibk.ac.at), but can
-be used for non commercial use under the following conditions:
-
-For non commercial use open source licence GNU General Public Licence v3 (GPLv3)
-
-
-Rectangle
-
-Rectangle is an open-source Python package for single-cell-informed cell-type
-deconvolution of bulk and spatial transcriptomic data.
-
-
-## Licence
-
-Rectangle is available under a **dual licence**:
-
-- **Open source licence:** GNU General Public Licence v3 (GPLv3)
-  → Free to use as long as modifications and redistributions are also under GPLv3.
-
-- **Commercial licence:** For companies that want to use Rectangle in proprietary
-  or closed applications the following applies:
-
-Rectangle - Commercial Licence Terms
-
-Copyright (C) 2026 Francesca Finotello, Bernhard Eder
-
-
-For all users who use Rectangle under GPL v3 the following shall apply:
-
-
-Contributor License Agreement (CLA)
-
-Purpose of this Agreement
-
-The project is distributed under a dual-licensing model, consisting of:
-an open source license (GNU General Public License, GPL), and
-a proprietary license offered by the project owner.
-The purpose of this Agreement is to ensure that contributions initially
-submitted under the GPL can be lawfully reused, integrated, and distributed
-under the proprietary license.
-
-
-Definitions
-
-"Contribution" means any source code, documentation, bug fix, enhancement,
-or other work intentionally submitted by the Contributor for inclusion in
-the project.
-"Contributor" means the individual or legal entity submitting a Contribution.
-"Project Owner" means Francesca Finotello and Bernhard Eder, who maintain
-and license the project.
-
-
-Authorship and Authority
-
-The Contributor represents and warrants that:
-they are the sole author of the Contribution or have all necessary rights
-to submit it;
-the Contribution does not infringe any third-party rights;
-the Contribution is free of patents, licenses, or other restrictions that
-would conflict with the rights granted under this Agreement.
-
-
-Grant of Rights (Dual Licensing Grant)
-
-The Contributor hereby grants the Project Owner a perpetual, worldwide,
-irrevocable, non-exclusive, transferable license to:
-use,
-reproduce,
-modify,
-combine with other works,
-publish,
-sublicense,
-and distribute
-the Contribution, including but not limited to the right to license and
-distribute the Contribution:
-under the GNU General Public License (GPL), and
-under one or more proprietary licenses, as determined at the sole discretion
-of the Project Owner.
-This grant explicitly includes the right to incorporate Contributions
-originally submitted under the GPL version of the project into proprietary
-versions of the project.
-
-
-No Obligation to Disclose Proprietary Versions
-
-The Contributor acknowledges that Contributions submitted under this
-Agreement are not required to be disclosed, published, or distributed
-under an open source license in the proprietary version of the project.
-
-
-Retention of Copyright
-
-The Contributor retains all copyrights in their Contribution. This Agreement
-does not constitute a transfer of ownership, but rather a comprehensive
-grant of rights.
-
-
-Attribution
-
-Unless otherwise agreed, the Project Owner may list the Contributor's name
-in a list of contributors. There is no obligation to provide attribution.
-
-
-No Compensation
-
-Contributions are made voluntarily and without compensation. The Contributor
-is not entitled to fees, royalties, or other remuneration.
-
-
-Disclaimer of Warranty
-
-The Contribution is provided "AS IS", without warranty of any kind, express
-or implied, including but not limited to warranties of merchantability or
-fitness for a particular purpose.
-
-
-Governing Law
-
-This Agreement shall be governed by the laws of Austria, excluding its
-conflict of law provisions.
-
-
-Entire Agreement
-
-This Agreement constitutes the entire agreement between the Contributor
-and the Project Owner regarding Contributions and supersedes all prior
-agreements or understandings.
-
-
-Acceptance
-
-By submitting a Contribution, the Contributor confirms that they have read,
-understood, and agreed to the terms of this Agreement.
-
-
-
-This licence permits the use of Rectangle in proprietary or non-open projects
-under the following conditions:
-
-1. The licensee may use and distribute Rectangle in closed applications
-   without publishing the source code.
-2. The licence is non-transferable and applies only to the licensed company.
-3. Use is unlimited in time, provided that the licence fee has been paid in full.
-4. Support and updates are optional and must be agreed separately.
-5. Any use without a valid commercial licence is automatically subject to GPLv3.
-
-For offers and pricing models: innovation-psb@uibk.ac.at
-→ Please contact us at innovation-psb@uibk.ac.at to obtain a commercial licence.
-
-
-For all users of rectangle the following applies:
-
-
-Updates & Support
-
-1. The copyright holder offers optional paid updates, maintenance and
-   technical support.
-2. Without a support contract, there is no entitlement to future versions
-   or bug fixes.
-
-
-Liability & Warranty
-
-1. Rectangle is provided 'as is' without any express or implied warranty.
-2. The rights holder is not liable for any damage, loss of data or
-   consequential damage resulting from use.
-3. Liability is limited to a maximum of the licence fee paid.
-
-
-Copyright & Ownership
-
-1. Rectangle remains the intellectual property of the rights holder at
-   all times.
-2. This licence does not transfer ownership, only rights of use.
-3. Modifications or derivative works by the licensee remain the property
-   of the licensee, unless they are derived directly from Rectangle code.
-
-
-Termination
-
-1. This licence shall automatically expire if the licensee violates any
-   material terms of the agreement.
-2. Upon termination, the licensee must delete all copies of the Rectangle
-   software and may no longer use it.
-
-
-Miscellaneous
-
-1. This licence is subject to the laws of Austria.
-2. The place of jurisdiction is the registered office of the rights holder.
-3. Amendments or additions must be made in writing.
-4. Should any provision be invalid, the remaining provisions shall remain valid.
-
-
-## Contact
-
-**Authors:** Francesca Finotello, Bernhard Eder
-**Email:** innovation-psb@uibk.ac.at