pyjuno 0.1.0__tar.gz

pyjuno-0.1.0/.clang-format

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pyjuno-0.1.0/.github/release.yml

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+changelog:
+  categories:
+    - title: New Features
+      labels:
+        - feature
+    - title: Bug Fixes and Performance Improvements
+      labels:
+        - bug fix
+        - performance
+    - title: Other Changes
+      labels:
+        - '*'

pyjuno-0.1.0/.github/workflows/build-wheels.yml

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+name: Build wheels
+
+on:
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  run-tests:
+    uses: ./.github/workflows/run-tests.yml
+
+  build-wheels:
+    needs: run-tests
+    runs-on: ${{ matrix.os }}
+    name: Build wheels on ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+
+      - name: Install cibuildwheel
+        run: pip install "cibuildwheel~=3.4"
+
+      - name: Build wheels
+        run: cibuildwheel --output-dir ./wheelhouse
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v7
+        with:
+          name: ci-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build-sdist:
+    needs: run-tests
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: ci-sdist
+          path: dist/*.tar.gz

pyjuno-0.1.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build-wheels:
+    uses: ./.github/workflows/build-wheels.yml
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - build-wheels
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      url: https://pypi.org/project/pyjuno
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v8
+        with:
+          path: dist/
+          pattern: ci-*
+          merge-multiple: true
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

pyjuno-0.1.0/.github/workflows/run-tests.yml

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+name: Run tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  run-pytest:
+    name: Test for ${{ matrix.os }}-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: true
+
+      - name: Install dependencies
+        run: |
+          uv sync --only-group dev
+
+      - name: Run tests
+        run: |
+          uv run pytest -v tests/

pyjuno-0.1.0/.github/workflows/semantic-pr-titles.yml

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+name: Lint PR
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - reopened
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: read
+    steps:
+      - uses: amannn/action-semantic-pull-request@v6
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

pyjuno-0.1.0/.gitignore

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+# VS Code
+.vscode/
+
+# scikit-build-core
+_version.py
+
+# cibuildwheel
+wheelhouse/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.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/
+
+# PyPI configuration file
+.pypirc

pyjuno-0.1.0/.pre-commit-config.yaml

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+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  autoupdate_schedule: monthly
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+        exclude: |
+          (?x)^(
+            mkdocs\.yml|
+            \.clang-format
+          )
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.4
+    hooks:
+      - id: ruff-check
+        args: [--fix, --show-fixes]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v22.1.0
+    hooks:
+      - id: clang-format
+        types_or: [c++, c]

pyjuno-0.1.0/CONTRIBUTION.md

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+## Development environment setup
+
+### Step 1: Install uv
+
+For macOS and Linux, run:
+
+```shell
+curl -LsSf https://astral.sh/uv/install.sh | sh
+```
+
+For Windows, run:
+
+```shell
+powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+```
+
+> [!TIP]
+> You can refer [this link](https://docs.astral.sh/uv/getting-started/installation/) to install `uv`.
+
+### Step 2: Create and setup virtual environment
+
+```shell
+python3 -m venv .venv
+source .venv/bin/activate
+uv sync
+```
+
+> [!TIP]
+> If the synchronization is too slow, you can run `export UV_DEFAULT_INDEX="https://pypi.tuna.tsinghua.edu.cn/simple"` to change the download mirror.
+
+### Step 3: Setup pre-commit
+
+```shell
+pre-commit install
+```
+
+This may take several minutes. It downloads hooks from github repositories.
+
+## Rebuild pyjuno when C++ files are modified
+
+Every time you modify the C++ files, run following commands to rebuild the project:
+
+```shell
+uv pip install -e .
+```

pyjuno-0.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Mingrun Li
+
+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.

pyjuno-0.1.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: pyjuno
+Version: 0.1.0
+Summary: Standalone Python module for JUNO
+Author-Email: Mingrun Li <mrli@ihep.ac.cn>
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Requires-Python: <3.14,>=3.9
+Requires-Dist: uproot>=5.6.8
+Requires-Dist: awkward
+Requires-Dist: uproot-custom==2.3.*
+Requires-Dist: numba
+Description-Content-Type: text/markdown
+
+# pyjuno
+
+Pyjuno is a Python package that helps JUNO users analyzing data more easily. The core functionality of pyjuno is its JUNO-specific format data reading.
+
+> [!WARNING]
+> This package is still under developing.
+
+## Installation
+
+```bash
+pip install pyjuno
+```
+
+> [!TIP]
+> If you are working on IHEP computing nodes (lxlogin server), it is recommended to move `~/.local` and `~/.cache` to somewhere else, in case of the installation reaches your disk quota in `/afs` file system.
+
+## JUNO format data reading
+
+Basing on [Uproot](https://uproot.readthedocs.io/), [uproot-custom](https://mrzimu.github.io/uproot-custom/index.html) and [awkward-array](https://awkward-array.org/doc/main/user-guide/index.html), pyjuno can read most of JUNO-specific data format without ROOT or junosw environment.
+
+### Standalone subevent reading
+
+```python
+>>> import uproot
+>>> import pyjuno # automatically register JUNO format to uproot
+>>> f = uproot.open("rec.root")
+>>> calib_pmt = f["Event/CdLpmtCalib/CdLpmtCalibEvt/m_calibPMTCol"].array()
+>>> calib_pmt.show()
+[[{m_nPE: 0.842, m_pmtId: 269619712, m_firstHitTime: 386, ...}, ..., {...}],
+ [{m_nPE: 0.427, m_pmtId: 269500928, m_firstHitTime: 433, ...}, ..., {...}],
+ [{m_nPE: 0.751, m_pmtId: 269500928, m_firstHitTime: 385, ...}, ..., {...}],
+ [{m_nPE: 1.04, m_pmtId: 269558272, m_firstHitTime: 387, ...}, ..., {...}],
+ [{m_nPE: 2.41, m_pmtId: 269500928, m_firstHitTime: 979, ...}, ..., {...}],
+ [{m_nPE: 3.9, m_pmtId: 269586944, m_firstHitTime: 899, ...}, ..., {...}],
+ [{m_nPE: 1.33, m_pmtId: 269615616, m_firstHitTime: 673, ...}, ..., {...}],
+ [{m_nPE: 0.539, m_pmtId: 269496832, m_firstHitTime: 401, ...}, ..., {...}],
+ [{m_nPE: 0.478, m_pmtId: 269554176, m_firstHitTime: 377, ...}, ..., {...}],
+ [{m_nPE: 0.554, m_pmtId: 269496832, m_firstHitTime: 389, ...}, ..., {...}]]
+```
+
+### Assembling all subevents
+
+In JUNO, subevents are not always present in one event. To assemble different subevent tree, a method `pyjuno.assemble_event` is provided:
+
+```python
+>>> import uproot
+>>> import pyjuno # automatically register JUNO format to uproot
+>>> f = uproot.open("rec.root")
+>>> events = pyjuno.assemble_event(f)
+>>> events.show()
+[{SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...},
+ {SimEvt: [{m_tracks: [{...}], ...}], CdLpmtElecTruthEvt: [[...]], ...}]
+```
+
+Reading all data from file at once could consume much memory. You can either read less events by specifying `entry_start` and `entry_stop` arguments, or only read necesarry subevents by passing `filter_path` argument:
+
+```python
+# Read a small batch of events
+batch_events = pyjuno.assemble_event(f, entry_start=0, entry_stop=10)
+
+# Read CdLpmtTruth and CdSpmtTruth
+spec_events = pyjuno.assemble_event(f, filter_path=["/Event/CdLpmtTruth", "/Event/CdSpmtTruth"])
+# or
+spec_events = pyjuno.assemble_event(f, filter_path="*pmtTruth")
+```
+
+---
+
+> [!NOTE]
+> At present, `GenEvent` is not supported to be read in Python, since it contains recursive data that awkward-array cannot handle.
+
+> [!TIP]
+> For frequently used data, it is more efficient to read it with pyjuno once, then use `ak.to_parquet` to save it in `parquet` format and use `ak.from_parquet` to read it back.