rectanglepy 1.2.1__tar.gz → 1.4.0__tar.gz

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.1
+current_version = 1.4.0
 tag = True
 commit = True
 

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/.github/PULL_REQUEST_TEMPLATE.md

@@ -8,6 +8,7 @@ Please list closed, fixed, or resolved issues here with a # and the number.
 
 ### Checklist
 
+-   [ ] I have read and agree to the [Contributor License Agreement (CLA)](https://github.com/ComputationalBiomedicineGroup/Rectangle/blob/main/CLA.md)
 -   [ ] Code builds correctly
 -   [ ] Added tests that fail without the change (if possible)
 -   [ ] All tests passing

rectanglepy-1.4.0/LICENCE_COM

@@ -0,0 +1,203 @@
+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

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rectanglepy
-Version: 1.2.1
+Version: 1.4.0
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -681,6 +681,7 @@ License:                     GNU GENERAL PUBLIC LICENSE
         the library.  If this is what you want to do, use the GNU Lesser General
         Public License instead of this License.  But first, please read
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
+License-File: LICENCE_COM
 License-File: LICENSE
 Requires-Python: >=3.10
 Requires-Dist: anndata<0.10.9,>=0.8.0
@@ -690,7 +691,6 @@ 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: setuptools>=80.0.0
 Requires-Dist: statsmodels>=0.14.1
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'
@@ -745,6 +745,17 @@ Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/
 pip install rectanglepy
 ```
 
+## Licence
+
+Rectangle is available under a **dual licence**:
+
+-   **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.
+
+-   **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.
+
+For commercial licensing enquiries, please contact: **innovation-psb@uibk.ac.at**
+
 ## Release notes
 
 See the [changelog][changelog].
@@ -753,6 +764,8 @@ See the [changelog][changelog].
 
 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)

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/README.md

@@ -33,6 +33,17 @@ Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/
 pip install rectanglepy
 ```
 
+## Licence
+
+Rectangle is available under a **dual licence**:
+
+-   **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.
+
+-   **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.
+
+For commercial licensing enquiries, please contact: **innovation-psb@uibk.ac.at**
+
 ## Release notes
 
 See the [changelog][changelog].
@@ -41,6 +52,8 @@ See the [changelog][changelog].
 
 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)

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/docs/contributing.md

@@ -2,6 +2,10 @@
 
 We welcome contributions! The best way to contribute is by opening a pull request on GitHub.
 
+## 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.
+
 ## How to Contribute
 
 1. Fork the repository and create a new branch for your changes.

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "1.2.1"
+version = "1.4.0"
 description = "Hierarchical deconvolution of bulk  transcriptomics"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -27,7 +27,6 @@ dependencies = [
     "numpy>=1.0.0,<2.0.0",
     "anndata>=0.8.0,<0.10.9",
     "statsmodels>=0.14.1",
-    "setuptools>=80.0.0",
 
 ]
 

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/src/rectanglepy/rectangle.py

@@ -1,8 +1,9 @@
+from importlib.resources import files
+
 import pandas as pd
 from anndata import AnnData
 from loguru import logger
 from pandas import DataFrame
-from pkg_resources import resource_stream
 
 from .pp import RectangleSignatureResult, build_rectangle_signatures
 from .tl import deconvolution
@@ -93,13 +94,15 @@ def load_tutorial_data() -> tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame]:
     -------
     The single-cell count data, annotations, and bulk data.
     """
-    with resource_stream(__name__, "data/hao1_annotations_small.zip") as annotations_file:
+    data_dir = files(__package__) / "data"
+
+    with (data_dir / "hao1_annotations_small.zip").open("rb") as annotations_file:
         annotations = pd.read_csv(annotations_file, index_col=0, compression="zip")["0"]
 
-    with resource_stream(__name__, "data/hao1_counts_small.zip") as counts_file:
+    with (data_dir / "hao1_counts_small.zip").open("rb") as counts_file:
         sc_counts = pd.read_csv(counts_file, index_col=0, compression="zip").astype("int")
 
-    with resource_stream(__name__, "data/small_fino_bulks.zip") as bulks_file:
+    with (data_dir / "small_fino_bulks.zip").open("rb") as bulks_file:
         bulks = pd.read_csv(bulks_file, index_col=0, compression="zip")
 
     return sc_counts.T, annotations, bulks.T

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/src/rectanglepy/tl/deconvolution.py

@@ -121,13 +121,18 @@ def solve_qp(
         P = P / scale
         q = q / scale
 
+    # OSQP can return noticeably different solutions from active-set QP when P is singular/ill-conditioned.
+    # Add tiny ridge to make the problem strictly convex and closer to quadprog behavior.
+    ridge = 1e-8
+    P = ((P + P.T) / 2.0) + ridge * np.eye(n_vars, dtype=np.float64)
+
     # OSQP uses l <= A x <= u
     A = C.T  # (n_constraints, n_vars)
     l = b
     u = np.full_like(l, np.inf, dtype=np.float64)
 
     # Sparse matrices (required/expected)
-    P_sp = sp.csc_matrix((P + P.T) / 2.0)  # enforce symmetry
+    P_sp = sp.csc_matrix(P)
     A_sp = sp.csc_matrix(A)
 
     solver = osqp.OSQP()
@@ -138,9 +143,12 @@ def solve_qp(
         l=l,
         u=u,
         verbose=False,
-        eps_abs=1e-5,
-        eps_rel=1e-5,
-        max_iter=10000,
+        eps_abs=1e-8,
+        eps_rel=1e-8,
+        max_iter=50000,
+        polish=True,
+        warm_start=False,
+        scaled_termination=False,
     )
 
     res = solver.solve()
@@ -151,7 +159,7 @@ def solve_qp(
     return res.x
 
 
-def _find_dampening_constant(signature: pd.DataFrame, bulk: pd.Series, qp_gld: np.ndarray) -> int:
+def _calculate_dampening_constant(signature: pd.DataFrame, bulk: pd.Series, qp_gld: np.ndarray) -> int:
     solutions_std = []
     np.random.seed(1)
     weights = np.square(1 / (np.dot(signature, qp_gld)))
@@ -182,7 +190,7 @@ def _find_dampening_constant(signature: pd.DataFrame, bulk: pd.Series, qp_gld: n
     return best_dampening_constant
 
 
-def _calculate_dwls(
+def _calculate_ls(
     signature: pd.DataFrame,
     bulk: pd.Series,
     prev_assignments: list[int or str] = None,
@@ -193,7 +201,7 @@ def _calculate_dwls(
     bulk = bulk.loc[genes].sort_index().astype("double")
 
     approximate_solution = solve_qp(signature, bulk, prev_assignments, prev_weights)
-    dampening_constant = _find_dampening_constant(signature, bulk, approximate_solution)
+    dampening_constant = _calculate_dampening_constant(signature, bulk, approximate_solution)
     multiplier = 2**dampening_constant
 
     max_iterations = 1000
@@ -296,7 +304,7 @@ def _deconvolute(
         bias_factors = bias_factors * 0 + 1  # set all bias factors to 1
 
     signature = pseudobulk_sig_cpm.loc[signature_genes_direct_reduced] * bias_factors
-    start_fractions = _calculate_dwls(signature, bulk)
+    start_fractions = _calculate_ls(signature, bulk)
 
     if clustered_pseudobulk_sig_cpm is None:
         start_fractions, bulk_err = correct_for_unknown_cell_content(
@@ -315,8 +323,8 @@ def _deconvolute(
     clustered_signature = clustered_pseudobulk_sig_cpm.loc[clustered_signature_genes] * cluster_bias_factors
 
     try:
-        clustered_fractions = _calculate_dwls(clustered_signature, bulk)
-        recursive_fractions = _calculate_dwls(signature, bulk, signatures.assignments, clustered_fractions)
+        clustered_fractions = _calculate_ls(clustered_signature, bulk)
+        recursive_fractions = _calculate_ls(signature, bulk, signatures.assignments, clustered_fractions)
     except Exception as e:
         logger.warning(f"Recursive deconvolution failed with error: {e}")
         start_fractions, bulk_err = correct_for_unknown_cell_content(

{rectanglepy-1.2.1 → rectanglepy-1.4.0}/tests/test_tl.py

@@ -9,7 +9,7 @@ from rectanglepy.pp.create_signature import (
     build_rectangle_signatures,
 )
 from rectanglepy.tl.deconvolution import (
-    _calculate_dwls,
+    _calculate_ls,
     _scale_weights,
     correct_for_unknown_cell_content,
     deconvolution,
@@ -58,7 +58,7 @@ def test_simple_weighted_dampened_deconvolution(quantiseq_data):
     bulk = bulk.iloc[:, j]
     expected = real_fractions.T.iloc[:, j]
 
-    result = _calculate_dwls(signature, bulk)
+    result = _calculate_ls(signature, bulk)
     corr = np.corrcoef(result, expected)[0, 1]
     rsme = np.sqrt(np.mean((result - expected) ** 2))
 
@@ -74,7 +74,7 @@ def test_correct_for_unknown_cell_content(small_data, quantiseq_data):
     bulk = bulk.iloc[:, 5]
     pseudo_signature = signature.pseudobulk_sig_cpm
     sig = pseudo_signature.loc[signature.signature_genes]
-    fractions = _calculate_dwls(sig, bulk)
+    fractions = _calculate_ls(sig, bulk)
     biasfact = (pseudo_signature > 0).sum(axis=0)
     biasfact = biasfact / biasfact.min()
     result, bulk_err = correct_for_unknown_cell_content(bulk, pseudo_signature, fractions, biasfact)