scbulkde 0.0.1__tar.gz

scbulkde-0.0.1/.codecov.yaml

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+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

scbulkde-0.0.1/.cruft.json

@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "e0b3a742ea5bb960dd2cb052ecd42e8b42f28ba0",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "scBulkDE",
+      "package_name": "scbulkde",
+      "project_description": "Performing differential testing on pseudobulked single-cell data",
+      "author_full_name": "Adnan Abouelela",
+      "author_email": "adnan.abouelela@bsse.ethz.ch",
+      "github_user": "AdnanAbouelela",
+      "github_repo": "scBulkDE",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "e0b3a742ea5bb960dd2cb052ecd42e8b42f28ba0"
+    }
+  },
+  "directory": null
+}

scbulkde-0.0.1/.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
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

scbulkde-0.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,93 @@
+name: Bug report
+description: Report something that is broken or incorrect
+type: 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.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+
+  - 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: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

scbulkde-0.0.1/.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.

scbulkde-0.0.1/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for scBulkDE
+type: 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

scbulkde-0.0.1/.github/workflows/build.yaml

@@ -0,0 +1,26 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

scbulkde-0.0.1/.github/workflows/release.yaml

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+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scbulkde
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

scbulkde-0.0.1/.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-latest
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.env.python }}
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
+      - name: generate coverage report
+        run: |
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}

scbulkde-0.0.1/.gitignore

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+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
+
+# docs
+/docs/generated/
+/docs/_build/

scbulkde-0.0.1/.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.3.8
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.11.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.9
+    hooks:
+      - id: ruff-check
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    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
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]

scbulkde-0.0.1/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+    nodejs: latest
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT

scbulkde-0.0.1/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}

scbulkde-0.0.1/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

scbulkde-0.0.1/.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

scbulkde-0.0.1/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

scbulkde-0.0.1/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Adnan Abouelela
+All rights reserved.
+
+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 name of the copyright holder nor the names of its
+   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 HOLDER 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.

scbulkde-0.0.1/PKG-INFO

@@ -0,0 +1,111 @@
+Metadata-Version: 2.4
+Name: scbulkde
+Version: 0.0.1
+Summary: Performing differential testing on pseudobulked single-cell data
+Project-URL: Documentation, https://scBulkDE.readthedocs.io/
+Project-URL: Homepage, https://github.com/AdnanAbouelela/scBulkDE
+Project-URL: Source, https://github.com/AdnanAbouelela/scBulkDE
+Author: Adnan Abouelela
+Maintainer-email: Adnan Abouelela <adnan.abouelela@bsse.ethz.ch>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2025, Adnan Abouelela
+        All rights reserved.
+        
+        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 name of the copyright holder nor the names of its
+           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 HOLDER 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.
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
+Requires-Dist: anndata
+Requires-Dist: formulaic
+Requires-Dist: pydeseq2
+Requires-Dist: rich
+Requires-Dist: session-info2
+Requires-Dist: statsmodels
+Requires-Dist: tqdm
+Description-Content-Type: text/markdown
+
+# scBulkDE
+
+[![Tests][badge-tests]][tests]
+[![Documentation][badge-docs]][documentation]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/AdnanAbouelela/scBulkDE/test.yaml?branch=main
+[badge-docs]: https://img.shields.io/readthedocs/scBulkDE
+
+Performing differential testing on pseudobulked single-cell data
+
+## Getting started
+
+Please refer to the [documentation][],
+in particular, the [API documentation][].
+
+## Installation
+
+You need to have Python 3.11 or newer installed on your system.
+If you don't have Python installed, we recommend installing [uv][].
+
+There are several alternative options to install scBulkDE:
+
+<!--
+1) Install the latest release of `scBulkDE` from [PyPI][]:
+
+```bash
+pip install scBulkDE
+```
+-->
+
+1. Install the latest development version:
+
+```bash
+pip install git+https://github.com/AdnanAbouelela/scBulkDE.git@main
+```
+
+## Release notes
+
+See the [changelog][].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse discourse][].
+If you found a bug, please use the [issue tracker][].
+
+## Citation
+
+> t.b.a
+
+[uv]: https://github.com/astral-sh/uv
+[scverse discourse]: https://discourse.scverse.org/
+[issue tracker]: https://github.com/AdnanAbouelela/scBulkDE/issues
+[tests]: https://github.com/AdnanAbouelela/scBulkDE/actions/workflows/test.yaml
+[documentation]: https://scBulkDE.readthedocs.io
+[changelog]: https://scBulkDE.readthedocs.io/en/latest/changelog.html
+[api documentation]: https://scBulkDE.readthedocs.io/en/latest/api.html
+[pypi]: https://pypi.org/project/scBulkDE