mantpy 0.2.0__tar.gz

mantpy-0.2.0/.codecov.yaml

@@ -0,0 +1,19 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+    patch:
+      default:
+        target: 80%
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

mantpy-0.2.0/.cruft.json

@@ -0,0 +1,20 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "e2ed7b27425642fa3eb759f0457a2d5d9bd961f2",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "mantpy",
+      "package_name": "mantpy",
+      "project_description": "scverse-aligned spatial omics and ECM analysis on multiplexed imaging and spatial transcriptomics",
+      "author_full_name": "Mohamed Ghafoor",
+      "author_email": "moeghaf@gmail.com",
+      "github_user": "moeghaf",
+      "github_repo": "Mantpy",
+      "license": "MIT License",
+      "ide_integration": "false",
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
+}

mantpy-0.2.0/.editorconfig

@@ -0,0 +1,15 @@
+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

mantpy-0.2.0/.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

mantpy-0.2.0/.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.

mantpy-0.2.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for mantpy
+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

mantpy-0.2.0/.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: pre-commit
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns: ["*"]
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"

mantpy-0.2.0/.github/workflows/build.yaml

@@ -0,0 +1,34 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*
+      - name: Build documentation strictly
+        run: >-
+          uv run --group doc --extra gnn --extra patch
+          sphinx-build -M html docs docs/_build -W --keep-going

mantpy-0.2.0/.github/workflows/release.yaml

@@ -0,0 +1,33 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/mantpy
+    permissions:
+      contents: read
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        with:
+          enable-cache: false
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0

mantpy-0.2.0/.github/workflows/test.yaml

@@ -0,0 +1,109 @@
+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
+
+permissions:
+  contents: read
+
+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-slim
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - &clone
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - &setup-uv
+        name: Install uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(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
+    permissions:
+       id-token: write  # for codecov OIDC
+       contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
+    env:
+      UV_PYTHON: ${{ matrix.env.python }}
+
+    steps:
+      - *clone
+      - *setup-uv
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
+      - 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@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        with:
+          # Test success must not depend on an external reporting integration.
+          fail_ci_if_error: false
+          use_oidc: true
+
+  # 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@05ac9388f0aebcb5727afa17fcccfecd6f8ec5fe # v1.2.2
+          with:
+            jobs: ${{ toJSON(needs) }}

mantpy-0.2.0/.gitignore

@@ -0,0 +1,35 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# IDEs
+/.idea/
+/.vscode/
+
+# Compiled files
+.venv*/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# Local-only tooling / editor workspaces
+.claude/
+.codex/
+
+# Stray test render artifact
+/tests/_bgfix_triptych.png
+
+# hatch-vcs auto-generated version file
+src/mantpy/_version.py

mantpy-0.2.0/.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+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: v2.5.4
+    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: v2.25.3
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.22
+    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]
+
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.27.0
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]

mantpy-0.2.0/.readthedocs.yaml

@@ -0,0 +1,28 @@
+# https://docs.readthedocs.io/page/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.14"
+    nodejs: latest
+  jobs:
+    # Read the Docs clones shallow and without tags. hatch-vcs derives the
+    # version from `git describe`, so without this the docs advertise
+    # `0.1.dev1+g<sha>` instead of the released version.
+    #
+    # Two commands on purpose. Published history is a single commit, so the
+    # `--depth 1` clone is already complete and `--unshallow` aborts with
+    # "does not make sense"; combined as one command that failure would take
+    # the tag fetch with it and the version would stay `0.1.dev1` even after
+    # the release is tagged.
+    post_checkout:
+      - git fetch --unshallow || true
+      - git fetch --tags --force || true
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uv run --group doc --extra gnn --extra patch sphinx-build -M html docs docs/_build -W
+        - mv docs/_build $READTHEDOCS_OUTPUT

mantpy-0.2.0/CHANGELOG.md

@@ -0,0 +1,25 @@
+# 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]
+
+## [0.2.0]
+
+### Added
+
+- AnnData-native ECM image patches, spatial graph construction, cell–ECM
+  integration, clustering, permutation analysis, and topology tools.
+- Optional patch encoders, GraphMAE representations, node classification, and
+  neighbour-composition baselines.
+- Reusable plotting, palette, and explicit publication-style helpers for Mantpy
+  analysis outputs.
+- Verified one-line loaders for the four public tutorial datasets, with safe
+  caching, integrity checks, progress reporting, and source citations.
+- Scanpy, Squidpy, PyTorch Geometric, SpatialData, and H5AD interoperability.

mantpy-0.2.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,16 @@
+# Code of Conduct
+
+The mantpy project is part of the [scverse](https://scverse.org) ecosystem and
+adopts the **Contributor Covenant**, version 2.1, as its Code of Conduct.
+
+The full text is available at:
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct/>
+
+All participants in mantpy project spaces — contributors, maintainers and users —
+are expected to follow it, and to uphold the wider
+[scverse community standards](https://scverse.org/about/).
+
+## Reporting
+
+To report an issue or a possible violation, contact the maintainer at
+**moeghaf@gmail.com**. Reports will be reviewed and handled confidentially.

mantpy-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026, Mohamed Ghafoor
+
+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.