GitLab

* Update install_cuda.sh

* Update install_cuda.sh

* Update install_cuda.sh

* update

* update

* update

* update

* update

* update

* update

* update

* Update docs.yml

* Update docs.yml

* Update docs.yml

* Update docs.yml

* Update docs.yml

* Update docs.yml

* Apply suggestions from code review
Co-authored-by: Richard Xue <yueyericardo@gmail.com>
Co-authored-by: Richard Xue <yueyericardo@gmail.com>

* Add convenience functions useful for active learning [WIP] (#10)

* Add convenience functions useful for active learning

* avoid training outputs

* modify gitignore

* Add convenience functions to directly get atomic energies

* fix bug

* fix mypy

* flake8

* fix bugs

* flake8

* mypy

* Add tests for functions

* add test to workflows and flake8

* empty to trigger tests

* trigger

* delete new test

* readd new test

* avoid training outputs

* trigger

* trigger tests again, they are all passing on my side

* fix isclose in tests

* save

* fix
Co-authored-by: Ignacio Pickering <ign.pickering@gmail.com>

* Rename pipelines so that they are better displayed

* Update unittest.yml

* Update clang-format.yml

* Update clang-format.yml

* Update README.md

* Update runnable_submodules.yml

* Update README.md

* Add dummy cuda extension build

* save

* run tests

* save

* fix

* pytorch cu110

* no vision

* save

* nl

* save

* save

* save

* save

* save

* save

* save

* autopep8

* more autopep8

* optional=True

* no todo

* fix

* refactor ci

* mypy

* save

* flake8

* os error

* Run cuaev test

* save

* clang format

* Delete delete-me.cu

* Search for cub in pytorch include paths

* nl

* instructions on test

* Add better handle cuaev install/not install

* test_cuaev.py

* clean

* fix
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Add clang-format ci

* format
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Disable Final for 3.6

* dont run mypy for 3.6

* Distribute source and weel

* trigger

* fix

* Remove test gradient from aev tests

* Add a dedicated test gradient for one model, and make it feasible

* add test_grad to unittests

* Add some comments and fix formatting

* flake8

* flake8

* remove unused var

Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Remove everything about chunking

* aev.py

* neurochem trainer

* training-benchmark-nsys-profile.py

* fix eval

* training-benchmark.py

* nnp_training.py

* flake8

* nnp_training_force.py

* fix dtype of species

* fix

* flake8

* requires_grad_

* git ignore

* fix

* original

* fix

* fix

* fix

* fix

* save

* save

* save

* save

* save

* save

* save

* save

* save

* collate

* fix

* save

* fix

* save

* save

* fix

* save

* fix

* fix

* no len

* float

* save

* save

* save

* save

* save

* save

* save

* save

* save

* fix

* save

* save

* save

* save

* fix

* fix

* fix

* fix mypy

* don't remove outliers

* save

* save

* save

* fix

* flake8

* save

* fix

* flake8

* docs

* more docs

* fix test_data

* remove test_data_new

* fix

* try

* try

* try

* fix

* fix

* Add Python 3.8 to CI

* only oldest + latest
Co-authored-by: Farhad Ramezanghorbani <farhadrgh@users.noreply.github.com>

* Add badge to display stable torch compatibility

* more

* more

* don't run on PR

* nl

* Support  periodic table Indexing in builtin models

* flake8

* more

* fix

* fix cuda

Add helper module to convert species from element id in periodic table to 0, 1, 2, 3, ... format (#396)

* Init

* fix test

* flake8

* try fix

* Fix stupidity of len(self)

This is copy-pasted from https://github.com/aiqm/torchani/blob/master/.github/workflows/deploy-test-pypi.yml but I forgot to update it...

We should use the tag created on GitHub, not add a new tag named after date

* add mypy

* update

* fix

* only core

* add badge

* try

* Fix race condition in test docs deploy

* try

* fix

* fix

* try

* fix

* Remove python2 step 1

* badge

* Delete _six.py

* Remove AEV cacher

* more

* more

* more

* flake8

* further cleanup

* Run tests on merge master, and everyday 0:00

* test

* try

* use array

* test

* test

* test

* fix all

* push only on master

* Remove ignite

* remove neurochem-test

* remove cache-aev

* deploy to aiqm/torchani-test-docs for testing

* Deploy to test PyPI on PR

* update

* fix tag version

* fix docs deploy format

* test

* fix

* deploy docs on release

* update

* deploy pypi

* update readme

* Add unit test for builtin models

* flake8

* Keep in-progress jobs once a test fails in Actions

By default, GitHub cancels all in-progress jobs if any `matrix` jobs fail in Actions. This PR will change the default to let all tests running in case one of them fails.

* Update unittest.yml

* Update unittest.yml

* Move unittest check to GitHub Actions

Tests are parallelized

* Delete tests.yml

* Update setup.py

* Create test_requirements.txt

* Update unittest.yml

* Update unittest.yml

* Update README.md

* Delete install_dependencies.sh

* Delete install_dependencies_python2.sh

* Update unittest.yml

* Move python2 check to GitHub Actions

* Delete python2.yml

* Rename azure/install_dependencies_python2.sh to ci/install_dependencies_python2.sh

* Create runnable_submodules.yml

* Delete runnable_submodules.yml

* Update runnable_submodules.yml

* Move tools check to GitHub Actions

* Delete tools.yml

* Move docs to github actions

* Delete docs.yml

* Create install_dependencies.sh (#311)

* Rename install_dependencies.sh to ci/install_dependencies.sh

* +x

* Update and rename pythonpackage.yml to flake8.yml

* Delete flake8.yml

* Update flake8.yml