Remove all large files and stop using git-lfs (#289)

.gitattributes

-*.h5 filter=lfs diff=lfs merge=lfs -text
-tests/test_data/ANI1_subset/* filter=lfs diff=lfs merge=lfs -text
-tests/test_data/NIST/* filter=lfs diff=lfs merge=lfs -text
-tests/test_data/NeuroChemOptimized/* filter=lfs diff=lfs merge=lfs -text
-tests/test_data/benzene-md/* filter=lfs diff=lfs merge=lfs -text
-tests/test_data/tripeptide-md/* filter=lfs diff=lfs merge=lfs -text
-tools/generate-unit-test-expect/nist-dataset/result.json filter=lfs diff=lfs merge=lfs -text
-

.gitignore

@@ -28,3 +28,5 @@ dist
 # No vim swap files
 *.swp
 *.swo
+/download
+/download.tar.xz

README.md

@@ -46,6 +46,12 @@ See also [PyTorch's official site](https://pytorch.org/get-started/locally/) for
 
 Please install nightly PyTorch through `pip install` instead of `conda install`. If your PyTorch is installed through `conda install`, then `pip` would mistakenly recognize the package name as `torch` instead of `torch-nightly`, which would cause dependency issue when installing TorchANI.
 
+To run the tests and examples, you must manually download a data package
+
+```bash
+./download.sh
+```
+
 # Paper
 
 The original ANI-1 paper is:
@@ -72,6 +78,8 @@ install dependencies:
 pip install sphinx sphinx-gallery pillow matplotlib sphinx_rtd_theme
 ```
 
+To manually run unit tests, do `python setup.py nosetests`
+
 # Note to TorchANI developers
 
 Never commit to the master branch directly. If you need to change something, create a new branch, submit a PR on GitHub.
@@ -79,5 +87,3 @@ Never commit to the master branch directly. If you need to change something, cre
 You must pass all the tests on GitHub before your PR can be merged.
 
 Code review is required before merging pull request.
-
-To manually run unit tests, do `python setup.py test`

azure/deploy-docs.yml

@@ -26,6 +26,9 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install h5py pytorch-ignite-nightly tb-nightly sphinx sphinx_rtd_theme matplotlib pillow sphinx-gallery && pip install .'
   displayName: 'Install dependencies'
 
+- script: './download.sh'
+  displayName: 'Download data files'
+
 - script: 'sphinx-build docs build'
   displayName: Build documents
 

azure/deploy-pypi.yml

@@ -26,6 +26,9 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install nose coverage twine wheel'
   displayName: 'Install dependencies'
 
+- script: './download.sh'
+  displayName: 'Download data files'
+
 - script: 'python setup.py nosetests'
   displayName: Unit tests
 

azure/docs.yml

@@ -21,5 +21,8 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install h5py pytorch-ignite-nightly tb-nightly sphinx sphinx_rtd_theme matplotlib pillow sphinx-gallery && pip install .'
   displayName: 'Install dependencies'
 
+- script: './download.sh'
+  displayName: 'Download data files'
+
 - script: 'sphinx-build docs build'
   displayName: Documents

azure/runnable_submodules.yml

@@ -21,6 +21,9 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install h5py .'
   displayName: 'Install dependencies'
 
+- script: './download.sh'
+  displayName: 'Download data files'
+
 - script: 'python -m torchani.data.cache_aev tmp dataset/ani1-up_to_gdb4/ani_gdb_s01.h5 256'
   displayName: Cache AEV
 

azure/tests.yml

@@ -24,6 +24,9 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install nose coverage codecov'
   displayName: 'Install dependencies'
 
+- script: './download.sh'
+  displayName: 'Download data files'
+
 - script: 'python setup.py nosetests'
   displayName: Unit tests
 

azure/tools.yml

@@ -25,20 +25,23 @@ steps:
 - script: 'azure/install_dependencies.sh && pip install .'
   displayName: 'Install dependencies'
 
-- script: 'python tools/inference-benchmark.py --tqdm ./dataset/xyz_files/CH4-5.xyz'
+- script: './download.sh'
+  displayName: 'Download data files'
+
+- script: 'python tools/inference-benchmark.py --tqdm dataset/xyz_files/CH4-5.xyz'
   displayName: Inference Benchmark
 
 - script: 'pip install h5py'
   displayName: 'Install more dependencies'
 
-- script: 'python tools/comp6.py ./dataset/COMP6/COMP6v1/s66x8'
+- script: 'python tools/comp6.py dataset/COMP6/COMP6v1/s66x8'
   displayName: COMP6 Benchmark
 
 - script: 'pip install pytorch-ignite-nightly'
   displayName: 'Install more dependencies'
 
-- script: 'python tools/training-benchmark.py ./dataset/ani1-up_to_gdb4/ani_gdb_s01.h5'
+- script: 'python tools/training-benchmark.py dataset/ani1-up_to_gdb4/ani_gdb_s01.h5'
   displayName: Training Benchmark
 
-- script: 'python tools/neurochem-test.py ./dataset/ani1-up_to_gdb4/ani_gdb_s01.h5'
+- script: 'python tools/neurochem-test.py dataset/ani1-up_to_gdb4/ani_gdb_s01.h5'
   displayName: NeuroChem Test

dataset/ani-1x

+../download/dataset/ani-1x/
\ No newline at end of file

dataset/ani1-up_to_gdb4

+../download/dataset/ani1-up_to_gdb4/
\ No newline at end of file

download.sh

+#!/bin/sh
+
+wget http://atl.ipv6.ai/download.tar.xz
+tar xvf download.tar.xz

tests/test_data/ANI1_subset

+../../download/test_data/ANI1_subset/
\ No newline at end of file