rectanglepy 0.0.39__tar.gz

rectanglepy-0.0.39/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.0.39
+tag = True
+commit = True
+
+[bumpversion:file:./pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

rectanglepy-0.0.39/.cruft.json

@@ -0,0 +1,23 @@
+{
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
+    "checkout": null,
+    "context": {
+        "cookiecutter": {
+            "project_name": "Rectangle",
+            "package_name": "rectanglepy",
+            "project_description": "A very interesting piece of code",
+            "author_full_name": "Bernhard Eder",
+            "author_email": "yourname@example.com",
+            "github_user": "bernheder",
+            "project_repo": "https://github.com/bernheder/Rectangle",
+            "license": "MIT License",
+            "_copy_without_render": [
+                ".github/workflows/**.yaml",
+                "docs/_templates/autosummary/**.rst"
+            ],
+            "_template": "https://github.com/scverse/cookiecutter-scverse"
+        }
+    },
+    "directory": null
+}

rectanglepy-0.0.39/.editorconfig

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+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[Makefile]
+indent_style = tab

rectanglepy-0.0.39/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+    - type: markdown
+      attributes:
+          value: |
+              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+              detailing how to provide the necessary information for us to reproduce your bug. In brief:
+                * Please provide exact steps how to reproduce the bug in a clean Python environment.
+                * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+                * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+                  available datasets or to share a subset of your data.
+
+    - type: textarea
+      id: report
+      attributes:
+          label: Report
+          description: A clear and concise description of what the bug is.
+      validations:
+          required: true
+
+    - type: textarea
+      id: versions
+      attributes:
+          label: Version information
+          description: |
+              Please paste below the output of
+
+              ```python
+              import session_info
+              session_info.show(html=False, dependencies=True)
+              ```
+          placeholder: |
+              -----
+              anndata             0.8.0rc2.dev27+ge524389
+              session_info        1.0.0
+              -----
+              asttokens           NA
+              awkward             1.8.0
+              backcall            0.2.0
+              cython_runtime      NA
+              dateutil            2.8.2
+              debugpy             1.6.0
+              decorator           5.1.1
+              entrypoints         0.4
+              executing           0.8.3
+              h5py                3.7.0
+              ipykernel           6.15.0
+              jedi                0.18.1
+              mpl_toolkits        NA
+              natsort             8.1.0
+              numpy               1.22.4
+              packaging           21.3
+              pandas              1.4.2
+              parso               0.8.3
+              pexpect             4.8.0
+              pickleshare         0.7.5
+              pkg_resources       NA
+              prompt_toolkit      3.0.29
+              psutil              5.9.1
+              ptyprocess          0.7.0
+              pure_eval           0.2.2
+              pydev_ipython       NA
+              pydevconsole        NA
+              pydevd              2.8.0
+              pydevd_file_utils   NA
+              pydevd_plugins      NA
+              pydevd_tracing      NA
+              pygments            2.12.0
+              pytz                2022.1
+              scipy               1.8.1
+              setuptools          62.5.0
+              setuptools_scm      NA
+              six                 1.16.0
+              stack_data          0.3.0
+              tornado             6.1
+              traitlets           5.3.0
+              wcwidth             0.2.5
+              zmq                 23.1.0
+              -----
+              IPython             8.4.0
+              jupyter_client      7.3.4
+              jupyter_core        4.10.0
+              -----
+              Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+              Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+              -----
+              Session information updated at 2022-07-07 17:55

rectanglepy-0.0.39/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+    - name: Scverse Community Forum
+      url: https://discourse.scverse.org/
+      about: If you have questions about “How to do X”, please ask them here.

rectanglepy-0.0.39/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for Rectangle
+labels: enhancement
+body:
+    - type: textarea
+      id: description
+      attributes:
+          label: Description of feature
+          description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      validations:
+          required: true

rectanglepy-0.0.39/.github/PULL_REQUEST_TEMPLATE.md

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+### Description
+
+Please explain the changes you made here.
+
+### Associated Task
+
+Please list closed, fixed, or resolved issues here with a # and the number.
+
+### Checklist
+
+-   [ ] Code builds correctly
+-   [ ] Added tests that fail without the change (if possible)
+-   [ ] All tests passing
+-   [ ] Extended the documentation

rectanglepy-0.0.39/.github/workflows/build.yaml

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+name: CI Checks
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: ubuntu-latest
+                      python: "3.10"
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python }}
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
+
+            - name: Install test dependencies
+              run: |
+                  python -m pip install --upgrade pip wheel
+            - name: Install dependencies
+              run: |
+                  pip install ${{ matrix.pip-flags }} ".[dev,test]"
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest -v --color=yes
+
+    package:
+        runs-on: ubuntu-latest
+        needs: test
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.10"
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl

rectanglepy-0.0.39/.github/workflows/release.yaml

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+name: Release
+
+on:
+    push:
+        tags:
+            - "*.*.*"
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: ubuntu-latest
+                      python: "3.10"
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python }}
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
+
+            - name: Install test dependencies
+              run: |
+                  python -m pip install --upgrade pip wheel
+            - name: Install dependencies
+              run: |
+                  pip install ${{ matrix.pip-flags }} ".[dev,test]"
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest -v --color=yes
+    package:
+        runs-on: ubuntu-latest
+        needs: test
+        steps:
+            - uses: actions/checkout@v2
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.10"
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl
+
+    release:
+        name: Release
+        needs: test
+        runs-on: ubuntu-latest
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v3
+
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+
+            - name: Install hatch
+              run: pip install hatch
+
+            - name: Build project for distribution
+              run: hatch build
+
+            - name: Publish a Python distribution to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1
+              with:
+                  password: ${{ secrets.PYPI_API_TOKEN }}

rectanglepy-0.0.39/.github/workflows/test.yaml

@@ -0,0 +1,50 @@
+name: CI Checks
+
+on:
+    push:
+        branches-ignore:
+            - main
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: ubuntu-latest
+                      python: "3.10"
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python }}
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
+
+            - name: Install test dependencies
+              run: |
+                  python -m pip install --upgrade pip wheel
+            - name: Install dependencies
+              run: |
+                  pip install ${{ matrix.pip-flags }} ".[dev,test]"
+            - name: Test
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: |
+                  pytest -v --color=yes

rectanglepy-0.0.39/.gitignore

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+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/

rectanglepy-0.0.39/.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/psf/black
+      rev: "23.1.0"
+      hooks:
+          - id: black
+    - repo: https://github.com/asottile/blacken-docs
+      rev: 1.13.0
+      hooks:
+          - id: blacken-docs
+    - repo: https://github.com/pre-commit/mirrors-prettier
+      rev: v3.0.0-alpha.6
+      hooks:
+          - id: prettier
+            # Newer versions of node don't work on systems that have an older version of GLIBC
+            # (in particular Ubuntu 18.04 and Centos 7)
+            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+            # https://github.com/jupyterlab/jupyterlab/issues/12675
+            language_version: "17.9.1"
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.256
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: detect-private-key
+          - id: check-ast
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: trailing-whitespace
+          - id: check-case-conflict
+    - repo: local
+      hooks:
+          - id: forbid-to-commit
+            name: Don't commit rej files
+            entry: |
+                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+                Fix the merge conflicts manually and remove the .rej files.
+            language: fail
+            files: '.*\.rej$'

rectanglepy-0.0.39/.readthedocs.yaml

@@ -0,0 +1,17 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+    os: ubuntu-20.04
+    apt_packages:
+        - r-base
+    tools:
+        python: "3.10"
+sphinx:
+    configuration: docs/conf.py
+    fail_on_warning: false
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - doc

rectanglepy-0.0.39/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [Unreleased]
+
+### Added
+
+-   Basic tool, preprocessing and plotting functions

rectanglepy-0.0.39/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023, Bernhard Eder
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+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.

rectanglepy-0.0.39/PKG-INFO

@@ -0,0 +1,104 @@
+Metadata-Version: 2.1
+Name: rectanglepy
+Version: 0.0.39
+Summary: A very interesting piece of code
+Project-URL: Documentation, https://rectanglepy.readthedocs.io/
+Project-URL: Source, https://github.com/bernheder/Rectangle
+Project-URL: Home-page, https://github.com/bernheder/Rectangle
+Author: Bernhard Eder
+Maintainer-email: Bernhard Eder <Bernhard.Eder@student.uibk.ac.at>
+License: MIT License
+        
+        Copyright (c) 2023, Bernhard Eder
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        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: loguru
+Requires-Dist: pydeseq2==0.4.1
+Requires-Dist: quadprog==0.1.11
+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: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=1.0.0; 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/bernheder/Rectangle/test.yaml?branch=main
+[link-tests]: https://github.com/bernheder/Rectangle/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/Rectangle
+
+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.
+
+## Getting started
+
+Please refer to the [documentation][link-docs]. In particular, the
+
+-   [API documentation][link-api].
+
+## Installation
+
+You need to have Python 3.10 or newer 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:
+
+<!--
+1) Install the latest release of `Rectangle` from `PyPI <https://pypi.org/project/rectanglepy/>`_:
+
+```bash
+pip install rectanglepy
+```
+-->
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> t.b.a
+
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/bernheder/Rectangle/issues
+[changelog]: https://Rectanglepy.readthedocs.io/latest/changelog.html
+[link-docs]: https://Rectanglepy.readthedocs.io
+[link-api]: https://Rectanglepy.readthedocs.io/latest/api.html

rectanglepy-0.0.39/README.md

@@ -0,0 +1,52 @@
+# Rectangle
+
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/bernheder/Rectangle/test.yaml?branch=main
+[link-tests]: https://github.com/bernheder/Rectangle/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/Rectangle
+
+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.
+
+## Getting started
+
+Please refer to the [documentation][link-docs]. In particular, the
+
+-   [API documentation][link-api].
+
+## Installation
+
+You need to have Python 3.10 or newer 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:
+
+<!--
+1) Install the latest release of `Rectangle` from `PyPI <https://pypi.org/project/rectanglepy/>`_:
+
+```bash
+pip install rectanglepy
+```
+-->
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> t.b.a
+
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/bernheder/Rectangle/issues
+[changelog]: https://Rectanglepy.readthedocs.io/latest/changelog.html
+[link-docs]: https://Rectanglepy.readthedocs.io
+[link-api]: https://Rectanglepy.readthedocs.io/latest/api.html