First commit into master (#38)

* initial upload

* dev branch workflow

* Update README.md

* starting to setup coverage

* flake err cleanup

* deleted more unused code

* can't find a good githubactions coverage

* can't find a good githubactions coverage

* bug fixes

* consolidating tests

* XGB Regressor is failing

* commiting lgbm regressor tests

* using params

* fixing lgbm max_depth bug

* better test output. TODO: fix the max_depth for lgbm and xgb to not fall through to None, need to compute

* adding failure case test. TODO: why does RF  not have extra_config in  regressor

* pinning to xgboost .90 for now

* refactoring tree's extra_config for xgb and lgbm

* fixing reversed param

* adding gbdt test file

* refactoring beam params functions

* making  all beam params  as numpy

* increasing coverege by shifting label starts  and by deleting unused model.infer_initial_types()

* extra config for rf reg

* flake8

* more error testing

* using onnxconverter types instead of copypaste

* more consolidation

* more test coverage

* first step in refactor

* cleaning up batch params

* adding beam++ to node size 1 test

* there is a bug, documenting

* renaming trees to match paper

* test

* adding precommit hooks

* README.md

* readme update

* commit hooks

* Fixing badge link to be relative

* notebook for demo

* notebook for demo

* notebook params change

* reveriting 2c95f48 and reopening issue #9; this solution is too clunky

* bumping pyt req

* Fix pytorch requirements

* Fix to brackets for alpha in xgboost

* Few minor fixes to comments in tests

* Removed unecessary regression tests

* Add binary classification tests for gemm, tree_trav and perf_tree_trav

* Fixes to whitespaces

* updating readme

* filling out contrib section

* expanding readme example so that (1) it actually runs (2) it actually does a thing

* cleaning notebook example

* Fix to typo and update to the requirements

* Fix to flake8 errors

* readme changes from this morning

* changes based on feedback

* Few edits to contributing

* Few edits in the README file

* fixing mailto: syntax

* Remove initial_types from the converter API

* Rename Skl2PyTorch container into HBPyTorch

* Add convert_xgboost and convert_lightgbm API

* Fix to spacing

* remove pandas check (for the moment)

* fix import

* Fix readme to use the new API

* removed common directory

* add some documentation

* renamed few things

* code refactoring for trees

* refactor lightgbm and xgboost by moving stuff into gbdt_commons

* done with a pass on gbdt after moving everything to _gbdt_common

* final refactoring of gbdt classes

* rename random forest stuff into decision tree

* major refactoring for tree implementations

* some renaming here and there

* minor fix

* Add test to validate that issue #7 is closed.

* import container stuff from onnx-common

* fix the parser to use the topology in onnx-common

* remove unnecessary files

* address first chunk of Karla's comments

* fix typo in calibration

* Another round of comments addressed

* fix typo

* these two lines seem unnecessary

* moving notebooks from broken branch

* adding notebooks with new API changes

* removing comment

* removed few unnecessary code and edited some documentation

* Update CONTRIBUTING.md

* remove . from git clone

* Final pass over non-converters files documentation / API

* add constants for converters

* simplify a bit the API by using extra_config for optional parameters

* Update CONTRIBUTING.md

* done with documentation over public classes , methods

* add contants and extra config management

* addressing Karla's comments

* pip install pdoc; pdoc --html hummingbird

* pdoc3, using overrides to get extra doc if we want it

* add few tests to check that we actually pick the correct implementation

* Update README.md

* Reformat doc

* add HB logo to readme file

* Add HB logo in doc

* add assertion on model being not None

Co-authored-by: Karla Saur <karla.saur@microsoft.com>
Co-authored-by: Matteo Interlandi <mainterl@microsoft.com>

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+branch = True
+source = hummingbird
+omit =
+  *tests*

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401, C901
+max-line-length = 127
+max-complexity = 10
+select = B,C,E,F,W,T4,B9

.github/workflows/pythonapp.yml

@@ -0,0 +1,49 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+  pull_request:
+    branches:
+      - master
+      - develop
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # The GitHub editor is 127 chars wide
+        flake8 . --count  --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pip install -r requirements.txt && pip install -e . && pip install pytest
+        pytest
+    - name: Coverage
+      run: |
+        pip install -r requirements.txt && pip install -e . && pip install coverage
+        coverage run -m pytest tests
+        MINIMUM=70
+        SCORE=$(coverage report -m | tail -n 1 | awk '{print $NF}' | rev | cut -c2- | rev)
+        if [ $SCORE -ge $MINIMUM ]; then echo "COVERAGE ($SCORE) OK"; else echo "WARNING: Coverage is $SCORE but should be at least $MINIMUM"; fi

.gitignore

@@ -0,0 +1,80 @@
+# 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/
+pip-wheel-metadata/
+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
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Environments
+.env
+.venv
+env
+env/
+venv
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+
+# project specific
+.vscode/*
+configs/db/*.config
+configs/github/*.token
+

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.6
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+    - id: flake8
+    - id: check-added-large-files
+    - id: check-ast
+    - id: check-byte-order-marker
+    - id: check-merge-conflict
+    - id: detect-private-key
+    - id: trailing-whitespace
+    - id: no-commit-to-branch

CONTRIBUTING.md

@@ -0,0 +1,80 @@
+# Contributing
+
+## Welcome
+
+If you are here, it means you are interested in helping us out. A hearty welcome and thank you! There are many ways you can contribute to Hummingbird:
+
+* Offer PR's to fix bugs or implement new features;
+* Give us feedback and bug reports regarding the software or the documentation;
+* Improve our examples, and documentation.
+This project welcomes contributions and suggestions.  
+
+## Getting Started
+
+Please join the community on Gitter *gitter badge*. Also please make sure to take a look at the project [roadmap](wiki/Roadmap-for-Upcoming-Features-and-Support).
+
+
+### Pull requests
+If you are new to GitHub [here](https://help.github.com/categories/collaborating-with-issues-and-pull-requests/) is a detailed help source on getting involved with development on GitHub.
+
+As a first time contributor, you will be invited to sign the Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us
+the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com. You will only need to do this once across all repos using our CLA.
+
+Your pull request needs to reference a filed issue. Please fill in the template that is populated for the pull request. Only pull requests addressing small typos can have no issues associated with them.
+
+All commits in a pull request will be [squashed](https://github.blog/2016-04-01-squash-your-commits/) to a single commit with the original creator as author.
+
+### Code of Conduct
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+For more information see the [Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/) or
+contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with any additional questions or comments.
+
+## Developing
+The simplest setup is:
+```
+mkdir hummingbird
+cd hummingbird
+git clone https://github.com/microsoft/hummingbird.git .
+pip install -e .
+```
+
+#### Pre-commit
+This project uses [pre-commit](https://pre-commit.com/) hooks. Run  `pip install pre-commit` if you don't already have this in your machine. Afterward, run `pre-commit install` to install pre-commit into your git hooks.
+
+And before you commit, you can run it like this `pre-commit run --all-files` and should see output such as:
+
+```
+black............................Passed
+Flake8...........................Passed
+...
+Don't commit to branch...........Passed
+```
+
+If you have installed your pre-commit hooks successfully, you should see something like this if you try to commit something non-conformant:
+```
+$ git commit -m "testing"
+black............................Failed
+- hook id: black
+- files were modified by this hook
+
+reformatted hummingbird/convert.py
+All done!
+1 file reformatted.
+```
+
+#### Formatting
+We generally use all pep8 checks, with the exception of line length 127.
+
+To do a quick check-up before commit, try:
+```
+flake8 . --count  --max-complexity=10 --max-line-length=127 --statistics
+```
+
+#### Coverage
+
+For coverage, we use [coverage.py](https://coverage.readthedocs.io/en/coverage-5.0.4/) in our Github Actions.  Run  `pip install coverage` if you don't already have this, and any code you commit should generally not significantly impact coverage.
+
+We strive to keep our test coverage about 70%.  To run all unit tests:
+```
+coverage run -m pytest tests
+```

README.md

@@ -1,14 +1,75 @@
-
-# Contributing
-
-This project welcomes contributions and suggestions.  Most contributions require you to agree to a
-Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us
-the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
-
-When you submit a pull request, a CLA bot will automatically determine whether you need to provide
-a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions
-provided by the bot. You will only need to do this once across all repos using our CLA.
-
-This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
-For more information see the [Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/) or
-contact [opencode@microsoft.com](mailto:opencode@microsoft.com) with any additional questions or comments.
+[![](https://i.imgur.com/0pp9lMS.png?1)](https://github.com/microsoft/hummingbird/)
+
+# Hummingbird
+
+![](https://github.com/microsoft/hummingbird/workflows/Python%20application/badge.svg?branch=develop)
+
+## Introduction
+*Hummingbird* converts trained traditional Machine Learning models into [PyTorch](https://pytorch.org/). Once in the PyTorch format, <!--you can further convert to [ONNX](https://github.com/onnx/onnx) or [TorchScript](https://pytorch.org/docs/stable/jit.html), and --> you can run the models on GPU for high performance native scoring. For full details, see [our paper](https://scnakandala.github.io/papers/TR_2020_Hummingbird.pdf).
+
+Currently we support [these](https://github.com/microsoft/hummingbird/blob/develop/hummingbird/_supported_operators.py#L26) tree-based classifiers and regressors.  These models include
+[scikit-learn](https://scikit-learn.org/stable/) models such as  Decision Trees and Random Forest, and also [LightGBM](https://github.com/Microsoft/LightGBM) and [XGBoost](https://github.com/dmlc/xgboost) Classifiers/Regressors.
+
+## Installation
+
+This was tested on Python 3.7 on a Linux machine.
+```
+mkdir hummingbird
+cd hummingbird
+git clone https://github.com/microsoft/hummingbird.git .
+python setup.py install
+```
+
+## Examples
+
+See the [notebooks](notebooks) section for examples that demonstrate use and speedups.
+
+In general, the syntax is very similar to [skl2onnx](https://github.com/onnx/sklearn-onnx), as hummingbird started as a fork of that project.
+
+```python
+import torch
+import numpy as np
+import lightgbm as lgb
+from hummingbird import convert_lightgbm
+
+# Create some random data for binary classification
+num_classes = 2
+X = np.array(np.random.rand(100000, 28), dtype=np.float32)
+y = np.random.randint(num_classes, size=100000)
+
+# Create and train a model (LightGBM in this case)
+model = lgb.LGBMClassifier()
+model.fit(X, y)
+
+# Use Hummingbird to convert the model to pytorch
+pytorch_model = convert_lightgbm(model)
+
+# Run Hummingbird on CPU
+pytorch_model.to('cpu')
+hb_cpu = pytorch_model(torch.from_numpy(X))
+
+# Run Hummingbird on GPU
+pytorch_model.to('cuda')
+hb_gpu = pytorch_model(torch.from_numpy(X).to('cuda'))
+```
+
+# Contributing
+
+We welcome contributions! Please see the guide on [Contributing](CONTRIBUTING.md).
+
+Also, see our [roadmap](wiki/Roadmap-for-Upcoming-Features-and-Support) of planned features.
+
+# Community
+
+Join our community! *gitter badge here*
+
+ For more formal enquiries, you can [contact us](mailto:hummingbird-dev@microsoft.com).
+
+# Authors
+
+* Supun Nakandala
+* Matteo Interlandi
+* Karla Saur
+
+# License
+[MIT License](LICENSE)