mantispy 0.1.0a1__tar.gz

mantispy-0.1.0a1/.codecov.yaml

@@ -0,0 +1,17 @@
+# 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

mantispy-0.1.0a1/.cruft.json

@@ -0,0 +1,44 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "e6f473c32cd4bda50015ac236697ee3223c70bde",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "mantispy",
+      "package_name": "mantispy",
+      "project_description": "Image-based profiling on AnnData",
+      "author_full_name": "Tim Treis",
+      "author_email": "tim.treis@outlook.de",
+      "github_user": "scverse",
+      "github_repo": "mantispy",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "issue_categorization": "issue types",
+      "_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": "e6f473c32cd4bda50015ac236697ee3223c70bde"
+    }
+  },
+  "directory": null
+}

mantispy-0.1.0a1/.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

mantispy-0.1.0a1/.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

mantispy-0.1.0a1/.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.

mantispy-0.1.0a1/.github/ISSUE_TEMPLATE/feature_request.yml

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

mantispy-0.1.0a1/.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:
+          - "*"

mantispy-0.1.0a1/.github/workflows/autofix.yaml

@@ -0,0 +1,29 @@
+# The workflow name is mandated by autofix.ci.
+# It needs to be a dedicated workflow, as autofix.ci times out on long runs.
+name: autofix.ci
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+          filter: blob:none
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          enable-cache: true
+      - run: uv tool install hatch
+      - name: Run pre-commit hooks
+        run: uvx prek run --all-files --show-diff-on-failure --color=always
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
+        if: '!cancelled()'

mantispy-0.1.0a1/.github/workflows/build.yaml

@@ -0,0 +1,30 @@
+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@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

mantispy-0.1.0a1/.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/mantispy
+    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@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          enable-cache: false
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

mantispy-0.1.0a1/.github/workflows/test.yaml

@@ -0,0 +1,163 @@
+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: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - &clone
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - &setup-uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(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/page/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@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
+        with:
+          fail_ci_if_error: true
+          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
+      - tutorials
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
+          with:
+            jobs: ${{ toJSON(needs) }}
+
+  ensure-data-is-cached:
+    runs-on: ubuntu-latest
+    steps:
+      - *clone
+      - *setup-uv
+      - &restore-data
+        name: Restore data cache
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: ~/.cache/mantispy # IMPORTANT: this will fail if mantispy.settings.cache_dir default changes
+          key: data-${{ hashFiles('**/download_data.py') }}
+          restore-keys: |
+            data-
+          enableCrossOsArchive: true
+      - name: Download datasets
+        # Always run to ensure any missing files are downloaded
+        # (restore-keys may provide partial cache)
+        run: uvx hatch run data:download
+
+  tutorials:
+    name: Tutorials run
+    needs: ensure-data-is-cached
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+      - *setup-uv
+      - name: Restore the notebook execution cache
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: docs/_build/.jupyter_cache
+          key: jupyter-cache-${{ hashFiles('docs/tutorials/**/*.ipynb', 'src/mantispy/**/*.py') }}
+      - *restore-data
+      - name: Execute every notebook
+        run: uvx hatch run tutorials:run
+
+  # Non-blocking, main and schedule only (never on a pull request): rebuilds every staged variant from the
+  # current pipeline and compares against the shipped artifacts. The registry sha256 is the hard gate on
+  # downloads; this only has to notice on main if the pipeline diverges from the uploaded bytes. A rebuild
+  # pulls the raw inputs, sometimes multiple gigabytes, so it is too heavy to gate a pull request on. On
+  # drift: regenerate, re-upload, and re-pin the sha256 in registry.yaml.
+  data-drift-check:
+    name: Staged variants match the pipeline
+    if: github.event_name != 'pull_request'
+    needs: ensure-data-is-cached
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - *clone
+      - *setup-uv
+      - *restore-data
+      - name: Rebuild every variant and compare against the shipped artifacts
+        run: uvx hatch run data:drift-check --include-heavy

mantispy-0.1.0a1/.gitignore

@@ -0,0 +1,28 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+uv.lock
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+# written by scripts/build_dataset.py
+/build/
+
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
+
+# docs
+/docs/api/generated/
+/docs/_build/
+
+# planning docs kept out of the repo
+mantispy_release_plan.md
+/tasks/

mantispy-0.1.0a1/.pre-commit-config.yaml

@@ -0,0 +1,65 @@
+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: v2.5.15
+    hooks:
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+        groups: [format]
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.30.3
+    hooks:
+      - id: pyproject-fmt
+        groups: [format]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.17.0
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        groups: [format]
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: hatch check types
+        language: system
+        types: [python]
+        files: ^(src|tests)/
+        require_serial: true
+        pass_filenames: false
+        groups: [typecheck]
+      - id: scrub-notebook-outputs
+        name: scrub-notebook-outputs
+        entry: python .scripts/ci/scrub_notebook_outputs.py
+        language: system
+        files: ^docs/.*\.ipynb$
+        groups: [format]
+  - 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
+        groups: [format]
+      - id: mixed-line-ending
+        args: [--fix=lf]
+        groups: [format]
+      - id: trailing-whitespace
+        groups: [format]
+      - 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: v1.30.1
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]

mantispy-0.1.0a1/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/page/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.14"
+    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

mantispy-0.1.0a1/.scripts/ci/download_data.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+"""Download datasets to populate CI cache.
+
+This script downloads every dataset the tutorials need.
+The loaders cache to mantispy.settings.cache_dir.
+"""
+
+from __future__ import annotations
+
+import argparse
+
+_CNT = 2  # increment this when you want to rebuild the CI cache
+
+# The plates docs/tutorials/multisite/cross_laboratory.ipynb loads by name for its cross-source hierarchy.
+_TARGET2_HIERARCHY = [
+    "JCPQC051", "JCPQC052", "JCPQC053", "JCPQC054",
+    "BR00121438", "BR00121439", "BR00126113", "BR00126114",
+    "110000294936", "110000296682", "110000296339", "110000296356",
+]  # fmt: skip
+
+
+def main(args: argparse.Namespace) -> None:
+    """Call each loader once, so its files and anything it assembles from them land in the cache."""
+    import mantispy as mt
+
+    def jump_lite_all() -> None:
+        """Every feature set, because tutorial 12 compares them and each is a separate file."""
+        for model in mt.ds.JUMP_LITE_MODELS:
+            mt.ds.jump_lite(model=model)
+        mt.ds.jump_lite_targets()
+
+    loaders = {
+        "bbbc021": mt.ds.bbbc021,
+        "rohban": mt.ds.rohban,
+        # The staged rohban variants, so tutorials and tests that load them hit the cache (<7 MB each).
+        "rohban_selected": lambda: mt.ds.rohban(feature_selected=True),
+        "rohban_gene": lambda: mt.ds.rohban(aggregated=True),
+        "rohban_gene_selected": lambda: mt.ds.rohban(aggregated=True, feature_selected=True),
+        "pki": mt.ds.pki,
+        # These two come to ~1.2 GB; all 141 plates would be 9.4 GB, over GitHub's 10 GB cache.
+        "jump_target2": mt.ds.jump_target2,
+        "jump_target2_hierarchy": lambda: mt.ds.jump_target2(plates=_TARGET2_HIERARCHY),
+        "jump_cells": mt.ds.jump_cells,
+        "jump_plate": mt.ds.jump_plate,
+        "jump_export": mt.ds.jump_export,
+        "jump_lite": jump_lite_all,
+        "oasis_pilot": mt.ds.oasis_pilot,
+        "jump_crispr": mt.ds.jump_crispr,
+        "corum": mt.ds.corum,
+    }
+    if args.dry_run:
+        print(f"Cache: {mt.settings.cache_dir}\nWould download: {', '.join(loaders)}")
+        return
+
+    for load in loaders.values():
+        load()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Download datasets to populate CI cache.")
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Do not download, just print what would be downloaded.",
+    )
+
+    main(parser.parse_args())