Package TrajectoryNet

.github/workflows/pre-commit.yml

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+name: pre-commit
+on:
+  push:
+    branches-ignore:
+      - 'master'
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+          architecture: "x64"
+
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}-
+
+      - uses: pre-commit/[email protected]
+        continue-on-error: true
+
+      - name: Commit files
+        run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git commit -m "pre-commit" -a
+          fi
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#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: Publish Python 🐍 distributions 📦 to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish distribution 📦 to Test PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        skip_existing: true
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

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-*__pycache__*
-*.pyc
 results/tmp/
 *.jpg
-.snakemake
 
-.ipynb_checkpoints
+#Vim
+*.sw?
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# DotEnv configuration
+.env
+
+# Database
+*.db
+*.rdb
+
+# Pycharm
+.idea
+
+# VS Code
+.vscode/
+
+# Spyder
+.spyproject/
+
+# Jupyter NB Checkpoints
+.ipynb_checkpoints/
+
+# exclude data from source control by default
+/data/
+
+# exclude old folder by default
+/old/
+
+# Mac OS-specific storage files
+.DS_Store
+
+# vim
+*.swp
+*.swo
+
+# Mypy cache
+.mypy_cache/
+
+# Snakemake cache
+.snakemake/

README.rst

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+Pytorch Implementation of TrajectoryNet
+=======================================
+
+This library runs code associated with the TrajectoryNet paper [1].
+
+
+Installation
+------------
+
+TrajectoryNet is available in `pypi`. Install by running the following
+
+.. code-block:: bash
+
+    pip install TrajectoryNet
+
+This code was tested with python 3.7 and 3.8.
+
+Example
+-------
+
+.. image:: figures/eb_high_quality.png
+    :alt: EB PHATE Scatterplot
+    :height: 300
+
+.. image:: figures/EB-Trajectory.gif
+    :alt: Trajectory of density over time
+    :height: 300
+
+
+Basic Usage
+-----------
+
+Run with
+
+.. code-block:: bash
+
+    python -m TrajectoryNet.main --dataset EB
+
+To use a custom dataset expose the coordinates and timepoint information according to the example jupyter notebooks in the `/notebooks/` folder.
+
+TrajectoryNet requires the following:
+
+1. An embedding matrix titled `[embedding_name]` (Cells x Dimensions)
+2. A sample labels array titled `sample_labels` (Cells)
+3. (Optionally) a delta embedding representing RNA velocity titled `delta_[embedding_name]` (Cells x Dimensions)
+
+
+
+To run TrajectoryNet with a custom dataset use:
+
+.. code-block:: bash
+
+    python -m TrajectoryNet.main --dataset [PATH_TO_NPZ_FILE] --embedding_name [EMBEDDING_NAME]
+    python -m TrajectoryNet.eval --dataset [PATH_TO_NPZ_FILE] --embedding_name [EMBEDDING_NAME]
+
+
+See `notebooks/EB-Eval.ipynb` for an example on how to use TrajectoryNet on a PCA embedding to get trajectories in the gene space.
+
+
+References
+----------
+[1] Tong, A., Huang, J., Wolf, G., van Dijk, D., and Krishnaswamy, S. TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. In International Conference on Machine Learning, 2020. `arxiv <http://arxiv.org/abs/2002.04461>`_ `ICML <https://proceedings.icml.cc/paper/2020/hash/9d740bd0f36aaa312c8d504e28c42163>`_
+
+---
+
+If you found this library useful, please consider citing::
+
+    @inproceedings{tong2020trajectorynet,
+      title = {TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics},
+      shorttitle = {{{TrajectoryNet}}},
+      booktitle = {Proceedings of the 37th International Conference on Machine Learning},
+      author = {Tong, Alexander and Huang, Jessie and Wolf, Guy and {van Dijk}, David and Krishnaswamy, Smita},
+      year = {2020}
+    }