imperandi 0.1.0__tar.gz

imperandi-0.1.0/.gitattributes

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+.githooks/* text eol=lf

imperandi-0.1.0/.githooks/pre-push

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+#!/usr/bin/env sh
+set -eu
+
+zero_sha="0000000000000000000000000000000000000000"
+repo_root="$(git rev-parse --show-toplevel)"
+cd "$repo_root"
+
+if command -v py >/dev/null 2>&1 && py -3 -c "import sys" >/dev/null 2>&1; then
+  python_launcher="py"
+elif command -v python >/dev/null 2>&1 && python -c "import sys" >/dev/null 2>&1; then
+  python_launcher="python"
+elif command -v python3 >/dev/null 2>&1 && python3 -c "import sys" >/dev/null 2>&1; then
+  python_launcher="python3"
+elif command -v py >/dev/null 2>&1; then
+  python_launcher="py"
+else
+  echo "No Python interpreter was found. Cannot clean notebook outputs." >&2
+  exit 1
+fi
+
+tmp_refs="$(mktemp 2>/dev/null || mktemp -t imperandi_nbpush_refs)"
+tmp_files="$(mktemp 2>/dev/null || mktemp -t imperandi_nbpush_files)"
+cleanup() {
+  rm -f "$tmp_refs" "$tmp_files"
+}
+trap cleanup EXIT INT TERM
+
+cat > "$tmp_refs"
+
+while IFS=' ' read -r local_ref local_sha remote_ref remote_sha; do
+  local_ref="$(printf '%s' "${local_ref:-}" | tr -d '\r')"
+  local_sha="$(printf '%s' "${local_sha:-}" | tr -d '\r')"
+  remote_ref="$(printf '%s' "${remote_ref:-}" | tr -d '\r')"
+  remote_sha="$(printf '%s' "${remote_sha:-}" | tr -d '\r')"
+
+  [ -n "${local_ref:-}" ] || continue
+  [ "$local_sha" = "$zero_sha" ] && continue
+
+  if [ "$remote_sha" = "$zero_sha" ]; then
+    revs="$(git rev-list "$local_sha" --not --remotes)"
+  else
+    revs="$(git rev-list "$remote_sha..$local_sha")"
+  fi
+
+  [ -n "$revs" ] || continue
+  printf '%s\n' "$revs" | git diff-tree --stdin --no-commit-id --name-only -r --diff-filter=ACMRT -- '*.ipynb' >> "$tmp_files"
+done < "$tmp_refs"
+
+if [ ! -s "$tmp_files" ]; then
+  exit 0
+fi
+
+sort -u "$tmp_files" > "${tmp_files}.sorted"
+mv "${tmp_files}.sorted" "$tmp_files"
+
+changed=0
+while IFS= read -r notebook_path; do
+  [ -n "$notebook_path" ] || continue
+  [ -f "$notebook_path" ] || continue
+
+  status=0
+  if [ "$python_launcher" = "py" ]; then
+    py -3 ".githooks/strip_notebook_outputs.py" "$notebook_path" || status=$?
+  else
+    "$python_launcher" ".githooks/strip_notebook_outputs.py" "$notebook_path" || status=$?
+  fi
+
+  if [ "$status" -eq 2 ]; then
+    git add "$notebook_path"
+    changed=1
+  elif [ "$status" -ne 0 ]; then
+    echo "Failed to strip outputs from $notebook_path." >&2
+    exit "$status"
+  fi
+done < "$tmp_files"
+
+if [ "$changed" -eq 1 ]; then
+  echo "Notebook outputs were stripped and staged."
+  echo "Create a commit for the cleaned notebook(s), then push again."
+  exit 1
+fi
+
+exit 0

imperandi-0.1.0/.githooks/strip_notebook_outputs.py

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+#!/usr/bin/env python3
+"""Strip execution outputs from Jupyter notebooks."""
+
+from __future__ import annotations
+
+import json
+import sys
+from pathlib import Path
+
+
+def strip_notebook(path: Path) -> bool:
+    notebook = json.loads(path.read_text(encoding="utf-8-sig"))
+    changed = False
+
+    cells = notebook.get("cells", [])
+    if isinstance(cells, list):
+        for cell in cells:
+            if not isinstance(cell, dict) or cell.get("cell_type") != "code":
+                continue
+
+            outputs = cell.get("outputs")
+            if outputs:
+                cell["outputs"] = []
+                changed = True
+
+            if cell.get("execution_count") is not None:
+                cell["execution_count"] = None
+                changed = True
+
+    metadata = notebook.get("metadata")
+    if isinstance(metadata, dict) and "widgets" in metadata:
+        metadata.pop("widgets", None)
+        changed = True
+
+    if changed:
+        rendered = json.dumps(notebook, ensure_ascii=False, indent=1)
+        path.write_text(rendered + "\n", encoding="utf-8")
+
+    return changed
+
+
+def main(argv: list[str]) -> int:
+    if len(argv) < 2:
+        print(
+            "Usage: strip_notebook_outputs.py <notebook.ipynb> [...]", file=sys.stderr
+        )
+        return 1
+
+    any_changed = False
+    for raw_path in argv[1:]:
+        path = Path(raw_path)
+        try:
+            if strip_notebook(path):
+                any_changed = True
+        except Exception as exc:  # pragma: no cover - defensive for hook execution
+            print(f"{path}: {exc}", file=sys.stderr)
+            return 1
+
+    return 2 if any_changed else 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main(sys.argv))

imperandi-0.1.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v[0-9]*.[0-9]*.[0-9]*"
+  release:
+    types: [published]
+
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test on Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout tagged source
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package and test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[all-dev]"
+          python -m pip install "pyradiomics @ git+https://github.com/AIM-Harvard/pyradiomics.git@master"
+
+      - name: Run lint
+        run: python -m ruff check .
+
+      - name: Run unit tests
+        run: >-
+          python -m pytest -m "not slow"
+          --cov=imperandi
+          --cov-report=term-missing
+          --cov-fail-under=70
+
+  build:
+    name: Build and verify distributions
+    needs: test
+    runs-on: ubuntu-latest
+    outputs:
+      prerelease: ${{ steps.validate-tag.outputs.prerelease }}
+
+    steps:
+      - name: Checkout tagged source
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install release tooling
+        run: python -m pip install --upgrade build packaging twine
+
+      - name: Validate release tag
+        id: validate-tag
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python - <<'PY'
+          import os
+          from packaging.version import InvalidVersion, Version
+
+          tag = os.environ["RELEASE_TAG"]
+          if not tag.startswith("v"):
+              raise SystemExit(f"Release tag must start with 'v': {tag}")
+          try:
+              release = Version(tag[1:])
+          except InvalidVersion as exc:
+              raise SystemExit(f"Release tag is not a valid version: {tag}") from exc
+          if release.local is not None:
+              raise SystemExit("PyPI release tags cannot contain a local version segment")
+          with open(os.environ["GITHUB_OUTPUT"], "a", encoding="utf-8") as output:
+              is_prerelease = release.is_prerelease or release.is_devrelease
+              print(f"prerelease={str(is_prerelease).lower()}", file=output)
+          print(f"Validated release version {release}")
+          PY
+
+      - name: Build wheel and source distribution
+        run: python -m build
+
+      - name: Verify project-local configuration is excluded
+        run: |
+          python - <<'PY'
+          import tarfile
+          import zipfile
+          from pathlib import Path, PurePosixPath
+
+          artifacts = [
+              *Path("dist").glob("*.whl"),
+              *Path("dist").glob("*.tar.gz"),
+          ]
+          if len(artifacts) != 2:
+              raise SystemExit(f"Expected one wheel and one sdist, found: {artifacts}")
+          PY
+
+      - name: Check distribution metadata
+        run: python -m twine check --strict dist/*
+
+      - name: Verify built version matches tag
+        env:
+          RELEASE_TAG: ${{ github.ref_name }}
+        run: |
+          python -m pip install --force-reinstall --no-deps dist/*.whl
+          python - <<'PY'
+          import os
+          from importlib.metadata import version
+          from packaging.version import Version
+
+          expected = Version(os.environ["RELEASE_TAG"][1:])
+          built = Version(version("imperandi"))
+          if built != expected:
+              raise SystemExit(
+                  f"Built distribution version {built} does not match tag {expected}"
+              )
+          print(f"Verified imperandi {built}")
+          PY
+
+      - name: Store distributions
+        uses: actions/upload-artifact@v7
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+          retention-days: 30
+          overwrite: true
+
+  publish-github:
+    name: Publish GitHub Release assets
+    if: github.repository == 'dmandache/IMPERANDI'
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v8
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Create or update release assets
+        env:
+          EVENT_NAME: ${{ github.event_name }}
+          GH_TOKEN: ${{ github.token }}
+          GH_REPO: ${{ github.repository }}
+          PRERELEASE: ${{ needs.build.outputs.prerelease }}
+        run: |
+          if [[ "${EVENT_NAME}" == "release" ]]; then
+            gh release upload "${GITHUB_REF_NAME}" dist/* --clobber
+            exit 0
+          fi
+
+          release_flags=()
+          if [[ "${PRERELEASE}" == "true" ]]; then
+            release_flags+=(--prerelease)
+          fi
+          gh release create "${GITHUB_REF_NAME}" \
+            dist/* \
+            --verify-tag \
+            --generate-notes \
+            --title "${GITHUB_REF_NAME}" \
+            "${release_flags[@]}"
+
+  publish-pypi:
+    name: Publish to PyPI
+    if: github.repository == 'dmandache/IMPERANDI'
+    needs: [build, publish-github]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/imperandi
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v8
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distributions
+        uses: pypa/gh-action-pypi-publish@release/v1

imperandi-0.1.0/.github/workflows/tests.yml

@@ -0,0 +1,39 @@
+name: tests
+
+on:
+  push:
+    branches: ["main", "master"]
+  pull_request:
+    branches: ["main", "master"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install -e ".[all-dev]"
+          python -m pip install "pyradiomics @ git+https://github.com/AIM-Harvard/pyradiomics.git@master"
+      - name: Run lint
+        run: |
+          python -m ruff check .
+      - name: Run tests
+        run: |
+          python -m pytest -m "not slow" --cov=imperandi --cov-report=xml --cov-fail-under=70
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

imperandi-0.1.0/.gitignore

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+.codex
+
+# Generic temp directories
+.tmp/
+.temp/
+tmp/
+temp/
+
+# Generic temp files
+*.tmp
+*.temp
+*.bak
+*.swp
+*.swo
+*.orig
+*~
+
+# Big test data
+tests/data/
+tests/slow/*/data/input/
+tests/slow/*/data/work/
+
+# 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
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+.conda
+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/
+
+# 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
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

imperandi-0.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.10"
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .