spatial-aim 1.0.0__tar.gz

spatial_aim-1.0.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0 # setuptools-scm needs history for the version
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+        with:
+          python-version: "3.13"
+      - name: Install lint tools
+        run: pip install black mypy types-PyYAML
+      - name: Install package without deps so `aim` is importable for mypy
+        run: pip install -e . --no-deps
+      - name: black
+        run: black --check .
+      - name: mypy
+        run: mypy src
+
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+        with:
+          python-version: "3.13"
+      - name: Install package + dev deps
+        run: pip install -e .[dev]
+      - name: Run fast tests
+        run: pytest -m "not slow"
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+        with:
+          python-version: "3.13"
+      - name: Build sdist + wheel
+        run: |
+          pip install build twine
+          python -m build
+          twine check dist/*
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: dist
+          path: dist/*
+
+  integration-aim:
+    # End-to-end AIM sweep on the sample dataset in aim_env.
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+        with:
+          activate-environment: aim_env
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniforge-version: latest
+          cache-environment: true
+      - name: Install package (no deps; env already has them)
+        run: pip install -e . --no-deps
+      - name: aim run — single pair (nearest_centroid)
+        run: |
+          aim run \
+            --scdata     sample_dataset/scRNA/sample_sc.h5ad \
+            --stdata     sample_dataset/ST/sample_st.h5ad \
+            --output_dir sample_output/novel/nearest_centroid \
+            --mapping    nearest_centroid --leiden_resolution 3.0
+      - name: aim run — single pair (wann)
+        run: |
+          aim run \
+            --scdata     sample_dataset/scRNA/sample_sc.h5ad \
+            --stdata     sample_dataset/ST/sample_st.h5ad \
+            --output_dir sample_output/novel/wann \
+            --mapping    wann --leiden_resolution 3.0
+      - name: aim run — batch (all pairs)
+        run: |
+          aim run \
+            --pairs_csv  sample_dataset/pairs.csv \
+            --sc_dir     sample_dataset/scRNA \
+            --st_dir     sample_dataset/ST \
+            --output_dir sample_output/novel/sample_batch \
+            --mapping    nearest_centroid --leiden_resolution 3.0
+      - name: Slow / integration tests (sample data)
+        run: pytest -m slow
+
+  integration-reference:
+    # Reference-aligner path: aim_env orchestrates the sweep (single + batch) with
+    # `--mapping tangram`, so ReferenceMapper drives an AlignerWorker and
+    # tangram_env runs the aligner via `conda run`, once per K.
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+        with:
+          activate-environment: aim_env
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniforge-version: latest
+          cache-environment: true
+      - name: Create tangram_env
+        run: conda env create -f src/aim/reference_aligners/environment_tangram.yml
+      - name: Install package into both envs (no deps)
+        run: |
+          pip install -e . --no-deps
+          conda run -n tangram_env pip install -e . --no-deps
+      - name: aim run — single pair (tangram)
+        run: |
+          aim run --mapping tangram \
+            --scdata     sample_dataset/scRNA/sample_sc.h5ad \
+            --stdata     sample_dataset/ST/sample_st.h5ad \
+            --output_dir sample_output/tangram/sample
+      - name: aim run — batch (tangram)
+        run: |
+          aim run --mapping tangram \
+            --pairs_csv  sample_dataset/pairs.csv \
+            --sc_dir     sample_dataset/scRNA \
+            --st_dir     sample_dataset/ST \
+            --output_dir sample_output/tangram/sample_batch

spatial_aim-1.0.0/.github/workflows/release.yml

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+name: Release
+
+# A vX.Y.Z tag publishes to TestPyPI. A published GitHub Release publishes to
+# PyPI. Both use PyPI trusted publishing (OIDC); configure the trusted publisher
+# for this repo and workflow on (Test)PyPI before use.
+
+on:
+  push:
+    tags: ["v*"]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          fetch-depth: 0 # setuptools-scm derives the version from the tag
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+        with:
+          python-version: "3.13"
+      - name: Build sdist + wheel
+        run: |
+          pip install build twine
+          python -m build
+          twine check dist/*
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: dist
+          path: dist/*
+
+  publish-testpypi:
+    # On a tag push.
+    if: github.event_name == 'push'
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write # OIDC — required for trusted publishing
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    # On a published GitHub Release.
+    if: github.event_name == 'release'
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # release/v1

spatial_aim-1.0.0/.gitignore

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+
+# Playground
+00_Playground/
+**/.DS_Store
+CLAUDE.md
+.claude/
+sample_output/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+# Covers JetBrains IDEs: IntelliJ, GoLand, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+.idea/sonarlint.xml # see https://community.sonarsource.com/t/is-the-file-idea-idea-idea-sonarlint-xml-intended-to-be-under-source-control/121119
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based HTTP Client
+.idea/httpRequests
+http-client.private.env.json
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+# Apifox Helper cache
+.idea/.cache/.Apifox_Helper
+.idea/ApifoxUploaderProjectSetting.xml
+
+# Github Copilot persisted session migrations, see: https://github.com/microsoft/copilot-intellij-feedback/issues/712#issuecomment-3322062215
+.idea/**/copilot.data.migration.*.xml
+
+
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

spatial_aim-1.0.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        entry: black
+        language: system
+        types: [python]
+
+      - id: mypy
+        name: mypy
+        entry: mypy
+        language: system
+        types: [python]
+        pass_filenames: false
+        args: [src]