rectanglepy 0.4.7__tar.gz → 0.5.1__tar.gz

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.7
+current_version = 0.5.1
 tag = True
 commit = True
 

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: rectanglepy
-Version: 0.4.7
+Version: 0.5.1
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -28,26 +28,29 @@ License: MIT License
         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
+License-File: LICENSE
 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: pydeseq2==0.4.11
 Requires-Dist: quadprog==0.1.12
+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>=1.0.0; extra == 'doc'
+Requires-Dist: sphinx-book-theme; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
-Requires-Dist: sphinx>=4; extra == 'doc'
-Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'doc'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
@@ -61,10 +64,13 @@ Description-Content-Type: text/markdown
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
-methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
-To establish a precise deconvolution method, we employ a hierarchical analysis approach, incorporate mRNA bias
-correction, and provide an estimation of unknown cellular content.
+Rectangle is an open-source Python package developed for computational deconvolution.
+
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
+an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+
+Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
+improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
 
 ## Getting started
 
@@ -74,12 +80,12 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system. If you don't have
+You need to have Python 3.10 or higher installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 How to install Rectangle:
 
-Install the latest release of `Rectangle` from `PyPI <https://pypi.org/project/rectanglepy/>`:
+Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/rectanglepy/>:
 
 ```bash
 pip install rectanglepy

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/README.md

@@ -7,10 +7,13 @@
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
-methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
-To establish a precise deconvolution method, we employ a hierarchical analysis approach, incorporate mRNA bias
-correction, and provide an estimation of unknown cellular content.
+Rectangle is an open-source Python package developed for computational deconvolution.
+
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
+an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+
+Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
+improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
 
 ## Getting started
 
@@ -20,12 +23,12 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system. If you don't have
+You need to have Python 3.10 or higher installed on your system. If you don't have
 Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 How to install Rectangle:
 
-Install the latest release of `Rectangle` from `PyPI <https://pypi.org/project/rectanglepy/>`:
+Install the latest release of `Rectangle` from `PyPI` <https://pypi.org/project/rectanglepy/>:
 
 ```bash
 pip install rectanglepy

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/docs/Makefile

@@ -18,3 +18,6 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+html:
+	@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

rectanglepy-0.5.1/docs/api.md

@@ -0,0 +1,15 @@
+# API
+
+## Rectangle
+
+```{eval-rst}
+.. currentmodule:: rectanglepy
+
+.. autosummary::
+    :toctree: generated
+
+    rectangle
+    pp.build_rectangle_signatures
+    tl.deconvolution
+    pp.RectangleSignatureResult
+```

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/docs/conf.py

@@ -37,6 +37,8 @@ html_context = {
     "github_repo": "Rectangle",  # Repo name
     "github_version": "main",  # Version
     "conf_py_path": "/docs/",  # Path in the checkout to the docs root
+    "repository_url": repository_url,
+    "use_repository_button": True,
 }
 
 # -- General configuration ---------------------------------------------------
@@ -103,27 +105,31 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-html_theme = "sphinx_book_theme"
+
+html_theme = "furo"
 html_static_path = ["_static"]
 html_title = "rectangle"
 
+
+html_logo = "_static/rec_logo.001.png"
+
 html_theme_options = {
-    "repository_url": repository_url,
-    "use_repository_button": True,
     "path_to_docs": "docs/",
+    "sidebar_hide_name": True,  # Hide the project name in the sidebar
+    "footer_icons": [
+        {
+            "name": "GitHub",
+            "url": repository_url,
+            "html": """
+                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+                </svg>
+            """,
+            "class": "",
+        },
+    ],
 }
 
-pygments_style = "emacs"
-
-nitpick_ignore = [
-    # If building the documentation fails because of a missing link that is outside your control,
-    # you can add an exception to this list.
-    #     ("py:class", "igraph.Graph"),
-]
-
-print("Pygments style:", pygments_style)
-
 
 def setup(app):
     """App setup hook."""

{rectanglepy-0.4.7 → rectanglepy-0.5.1}/docs/contributing.md

@@ -7,48 +7,6 @@ information to get you started on contributing.
 We assume that you are already familiar with git and with making pull requests on GitHub. If not, please refer
 to the [scanpy developer guide][].
 
-## Installing dev dependencies
-
-In addition to the packages needed to _use_ this package, you need additional python packages to _run tests_ and _build
-the documentation_. It's easy to install them using `pip`:
-
-```bash
-cd Rectangle
-pip install -e ".[dev,test,doc]"
-```
-
-## Code-style
-
-This template uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either
-automatically fix issues with the code, or raise an error message. See [pre-commit checks](template_usage.md#pre-commit-checks) for
-a full list of checks enabled for this repository.
-
-To enable pre-commit locally, simply run
-
-```bash
-pre-commit install
-```
-
-in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
-
-Alternatively, you can rely on the [pre-commit.ci][] service enabled on GitHub. If you didn't run `pre-commit` before
-pushing changes to GitHub it will automatically commit fixes to your pull request, or show an error message.
-
-If pre-commit.ci added a commit on a branch you still have been working on locally, simply use
-
-```bash
-git pull --rebase
-```
-
-to integrate the changes into yours.
-While the [pre-commit.ci][] is useful, we strongly encourage installing and running pre-commit locally first to understand its usage.
-
-Finally, most editors have an _autoformat on save_ feature. Consider enabling this option for [black][black-editors]
-and [prettier][prettier-editors].
-
-[black-editors]: https://black.readthedocs.io/en/stable/integrations/editors.html
-[prettier-editors]: https://prettier.io/docs/en/editors.html
-
 ## Writing tests
 
 ```{note}
@@ -102,38 +60,6 @@ to publish the created tag on GitHub.
 
 [bump2version]: https://github.com/c4urself/bump2version
 
-### Building and publishing the package on PyPI
-
-Python packages are not distributed as source code, but as _distributions_. The most common distribution format is the so-called _wheel_. To build a _wheel_, run
-
-```bash
-python -m build
-```
-
-This command creates a _source archive_ and a _wheel_, which are required for publishing your package to [PyPI][]. These files are created directly in the root of the repository.
-
-Before uploading them to [PyPI][] you can check that your _distribution_ is valid by running:
-
-```bash
-twine check dist/*
-```
-
-and finally publishing it with:
-
-```bash
-twine upload dist/*
-```
-
-Provide your username and password when requested and then go check out your package on [PyPI][]!
-
-For more information, follow the [Python packaging tutorial][].
-
-It is possible to automate this with GitHub actions, see also [this feature request][pypi-feature-request]
-in the cookiecutter-scverse template.
-
-[python packaging tutorial]: https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
-[pypi-feature-request]: https://github.com/scverse/cookiecutter-scverse/issues/88
-
 ## Writing documentation
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features: