initial commit v0

.github/workflows/hypertrack-install-test.yml

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+# Github actions CI (continuous integration) setup.
+#
+# m.mieskolainen@imperial.ac.uk, 2023
+
+name: hypertrack-install-test
+
+on: [push]
+
+jobs:
+  icenet-install-test:
+    runs-on: ubuntu-22.04
+
+    # Needed for Conda
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v1
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10.11'
+
+      # Conda environment
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: hypertrack
+          environment-file: environment.yml
+          auto-activate-base: false
+      - run: |
+          conda info
+          conda list
+      
+      # Pip packages
+      - name: Install requirements
+        run: |
+          pip install -r requirements.txt
+          pip install -r requirements-aux.txt
+          pip install -r requirements-docs.txt
+        
+      ## Docs building
+      - name: Build docs
+        run: |
+          if [ -e yarn.lock ]; then
+          yarn install --frozen-lockfile
+          elif [ -e package-lock.json ]; then
+          npm ci
+          else
+          npm i
+          fi
+          npm run build
+          make -C docs/ clean
+          make -C docs/ html
+          touch docs/build/html/.nojekyll
+      
+      ## Release to gh-pages
+      - name: Release docs to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html/

.gitignore

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+*.pk
+*.pkl
+*.pt
+*.pdf
+*.png
+*.log
+dev_*
+.fuse*
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+.pytest_cache
+
+/trash
+/tmp
+/dev

LICENSE

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+MIT License
+
+Copyright (c) 2023 Mikael Mieskolainen
+
+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.

README.md

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+# *hypertrack*
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Build Status](https://github.com/mieskolainen/hypertrack/actions/workflows/hypertrack-install-test.yml/badge.svg)](https://github.com/mieskolainen/hypertrack/actions)
+
+https://arxiv.org/abs/2309.14113 <br>
+
+## *HyperTrack*: Neural Combinatorics for High Energy Physics
+Presented in CHEP 2023<br>
+https://indico.jlab.org/event/459/contributions/11748
+<br>
+<br>
+Mikael Mieskolainen<br>
+m.mieskolainen@imperial.ac.uk <br>
+<br>
+
+## Overview
+
+_HyperTrack_ is a new hybrid algorithm for deep learned clustering based on a learned graph constructor called Voxel-Dynamics, Graph Neural Networks and Transformers. For more details, see the paper and the conference talk.
+</br>
+
+This repository together with pre-trained torch models downloaded from Hugging Face can be used to reproduce the paper results on the charged particle track reconstruction problem.
+</br>
+
+The technical API and instructions at:
+
+https://mieskolainen.github.io/hypertrack
+
+</br>
+
+
+## Hugging Face Quick Start
+
+Install the framework, process TrackML dataset files, download the pre-trained models from Hugging Face https://huggingface.co/mieskolainen and follow the documentation for inference.
+
+</br>
+
+
+## Citation
+
+If you use this in your work or find ideas interesting, please cite:
+
+```
+@Conference{citekey,
+  author    = "Mikael Mieskolainen",
+  title     = "HyperTrack: Neural Combinatorics for High Energy Physics",
+  booktitle = "CHEP 2023, 26th International Conference on Computing in High Energy & Nuclear Physics",
+  year      = "2023"
+}
+```

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/notes/DEVELOPER.md

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+# Python Developer Mini Guide
+m.mieskolainen@imperial.ac.uk, 2023
+
+
+## Google Python Style Guide
+```
+http://google.github.io/styleguide/pyguide.html
+```
+
+## Git
+
+
+### Branching
+
+Show branches
+```
+git branch
+```
+
+Create a new branch
+```
+git checkout -b <new-branch>
+```
+
+Change to another branch
+```
+git checkout <another-branch>
+```
+
+Create a branch from commit hash
+```
+git branch <branch-name> <hash>
+```
+
+### Commits
+
+Add all files
+```
+git add -A
+```
+
+Undo latest local commit (not yet pushed)
+```
+git reset HEAD~
+```
+
+Commit message (add " [no ci]" to the message to skip github actions)
+```
+git commit -m "commit message"
+```
+
+Push to (github)
+```
+git push origin <branch-name>
+```
+
+Pull from (github)
+```
+git pull origin <branch-name>
+```
+
+### Status
+
+Show log
+```
+git log --pretty=oneline
+```
+
+Show status
+```
+git status
+```
+
+### Risky
+
+[Dangerous] hard undo latest commit (removes updates physically)
+```
+git reset --hard HEAD~
+```
+
+
+## Profiler in Python
+```
+python -m cProfile -o out.profile "main.py" --config $CONFIG
+snakeviz out.profile # visualize
+```

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+
+import datetime
+import sphinx_rtd_theme
+import doctest
+import hypertrack
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+autosummary_generate = True
+templates_path = ['_templates']
+
+source_suffix  = '.rst'
+master_doc     = 'index'
+
+add_module_names = False
+
+
+### Author
+
+author    = 'Mikael Mieskolainen, I-X and Blackett Laboratory, Imperial College London'
+project   = 'hypertrack'
+copyright = '{}, {}'.format(datetime.datetime.now().year, author)
+
+version = hypertrack.__version__
+release = hypertrack.__release__
+
+
+### HTML setup
+
+doctest_default_flags = doctest.NORMALIZE_WHITESPACE
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}
+
+
+### https://sphinx-themes.org/
+
+## "Alabaster" scheme
+#html_theme       = 'alabaster'
+
+## "RTD" scheme 
+html_theme      = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme_options = {
+    'collapse_navigation': False,
+    'display_version': True,
+    'logo_only': True,
+    'navigation_depth': 3,
+}
+
+#html_logo = '_static/img/logo.svg'
+html_static_path = ['_static']
+#html_static_path = []
+
+#html_context = {'css_files': ['_static/css/custom.css']}
+
+
+def setup(app):
+    def skip(app, what, name, obj, skip, options):
+        members = [
+            '__init__',
+            '__repr__',
+            '__weakref__',
+            '__dict__',
+            '__module__',
+        ]
+        return True if name in members else skip
+
+    app.connect('autodoc-skip-member', skip)