Squashed commit of the following: (31f0d5b0) · Commits · 钟慕尧 / deepchem

.github/workflows/build.yml

0 → 100644

+125 −0

Original line number	Diff line number	Diff line
		name: Test for build scripts
		on:
		push: # ci work when pushing master branch
		branches:
		- master
		pull_request: # ci work when creating a PR to master branch
		branches:
		- master
		jobs:
		minimum-build:
		runs-on: ubuntu-latest
		strategy:
		fail-fast: false
		matrix:
		python-version: [3.7]
		steps:
		- uses: actions/checkout@v2
		- name: Cache pip modules for Linux
		uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Set up Python ${{ matrix.python-version }}
		uses: actions/setup-python@v2
		with:
		python-version: ${{ matrix.python-version }}
		- name: Build DeepChem
		run: \|
		python -m pip install --upgrade pip
		pip install tensorflow==2.3.0
		pip install -e .
		- name: Import checking
		run: python -c "import deepchem"

		bash-build:
		runs-on: ${{ matrix.os }}
		strategy:
		fail-fast: false
		matrix:
		os: [ubuntu-latest, macos-latest]
		python-version: [3.7]
		steps:
		- uses: actions/checkout@v2
		- name: Cache pip modules for Linux
		if: startsWith(runner.os, 'Linux')
		uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Cache pip modules for MacOS
		if: startsWith(runner.os, 'macOS')
		uses: actions/cache@v2
		with:
		path: ~/Library/Caches/pip
		key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Install miniconda
		uses: conda-incubator/setup-miniconda@v1
		with:
		miniconda-version: "latest"
		auto-update-conda: true
		python-version: ${{ matrix.python-version }}
		- name: Install dependencies (failure check)
		continue-on-error: true
		shell: bash -l {0}
		run: \|
		source scripts/install_deepchem_conda.bash
		- name: Install all dependencies
		shell: bash -l {0}
		run: \|
		source scripts/install_deepchem_conda.bash ${{ matrix.python-version }} cpu
		- name: Build DeepChem from source
		shell: bash -l {0}
		run: \|
		conda activate deepchem
		pip install -e .
		python -V
		python -c 'import deepchem; print(deepchem.__version__)'
		python -c 'import rdkit; print(rdkit.__version__)'
		python -c 'import torch; print(torch.__version__)'
		python -c 'import tensorflow; print(tensorflow.__version__)'

		powershell-build:
		runs-on: windows-latest
		strategy:
		fail-fast: false
		matrix:
		python-version: [3.7]
		steps:
		- uses: actions/checkout@v2
		- name: Cache pip packages for Windows
		uses: actions/cache@v2
		with:
		path: ~\AppData\Local\pip\Cache
		key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}
		- name: Install miniconda
		uses: conda-incubator/setup-miniconda@v1
		with:
		miniconda-version: "latest"
		auto-update-conda: true
		python-version: ${{ matrix.python-version }}
		- name: Install dependencies (failure check)
		continue-on-error: true
		shell: pwsh
		run: \|
		. .\scripts\install_deepchem_conda.ps1
		- name: Install dependencies
		shell: pwsh
		run: \|
		. .\scripts\install_deepchem_conda.ps1 ${{ matrix.python-version }} cpu
		- name: Build DeepChem from source
		shell: pwsh
		run: \|
		conda activate deepchem
		pip install -e .
		python -V
		python -c 'import deepchem; print(deepchem.__version__)'
		python -c 'import rdkit; print(rdkit.__version__)'
		python -c 'import torch; print(torch.__version__)'
		python -c 'import tensorflow; print(tensorflow.__version__)'

.github/workflows/docs.yml

0 → 100644

+55 −0

Original line number	Diff line number	Diff line
		name: Test for documents
		on:
		push: # ci work when pushing master branch
		branches:
		- master
		pull_request: # ci work when creating a PR to master branch
		branches:
		- master
		jobs:
		linux:
		runs-on: ubuntu-latest
		strategy:
		fail-fast: false
		matrix:
		python-version: [3.7]
		steps:
		- uses: actions/checkout@v2
		- name: Cache pip packages for Linux
		uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Set up Python ${{ matrix.python-version }}
		uses: actions/setup-python@v2
		with:
		python-version: ${{ matrix.python-version }}
		- name: Create env.yml
		run: \|
		python -m pip install --upgrade pip
		pip install conda-merge
		conda-merge env.common.yml env.cpu.yml env.test.yml > env.yml
		- uses: conda-incubator/setup-miniconda@v1
		with:
		miniconda-version: "latest"
		auto-update-conda: true
		activate-environment: deepchem
		channels: omnia,conda-forge,defaults
		python-version: ${{ matrix.python-version }}
		environment-file: env.yml
		- name: Install dependencies (docs)
		shell: bash -l {0}
		working-directory: ./docs
		run: pip install -r requirements.txt
		- name: Build docs
		shell: bash -l {0}
		working-directory: ./docs
		run: make clean html
		- name: DocTest
		shell: bash -l {0}
		working-directory: ./docs
		run: \|
		make doctest_tutorials
		make doctest_examples

.github/workflows/test.yml

0 → 100644

+83 −0

Original line number	Diff line number	Diff line
		name: Test for DeepChem core modules
		on:
		push: # ci work when pushing master branch
		branches:
		- master
		pull_request: # ci work when creating a PR to master branch
		branches:
		- master
		jobs:
		test:
		runs-on: ${{ matrix.os }}
		strategy:
		fail-fast: false
		matrix:
		os: [ubuntu-latest, macos-latest, windows-latest]
		python-version: [3.7]
		include:
		- os: ubuntu-latest
		python-version: 3.6
		steps:
		- uses: actions/checkout@v2
		- name: Cache pip packages for Linux
		if: startsWith(runner.os, 'Linux')
		uses: actions/cache@v2
		with:
		path: ~/.cache/pip
		key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Cache pip packages for MacOS
		if: startsWith(runner.os, 'macOS')
		uses: actions/cache@v2
		with:
		path: ~/Library/Caches/pip
		key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Cache pip packages for Windows
		if: startsWith(runner.os, 'Windows')
		uses: actions/cache@v2
		with:
		path: ~\AppData\Local\pip\Cache
		key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}
		restore-keys: \|
		${{ runner.os }}-pip-
		- name: Set up Python ${{ matrix.python-version }}
		uses: actions/setup-python@v2
		with:
		python-version: ${{ matrix.python-version }}
		- name: Install prerequisites for XGBoost and LightGBM (MacOS)
		if: startsWith(runner.os, 'macOS')
		run: brew update && brew install libomp
		- name: Create env.yml
		shell: bash
		run: \|
		python -m pip install --upgrade pip;
		pip install conda-merge;
		if [ "$(uname)" == 'Darwin' ]; then
		conda-merge env.common.yml env.cpu.mac.yml env.test.yml > env.yml
		else
		conda-merge env.common.yml env.cpu.yml env.test.yml > env.yml
		fi;
		- name: Install all dependencies
		uses: conda-incubator/setup-miniconda@v1
		with:
		miniconda-version: "latest"
		auto-update-conda: true
		activate-environment: deepchem
		channels: omnia,conda-forge,defaults
		python-version: ${{ matrix.python-version }}
		environment-file: env.yml
		- name: Install DeepChem
		shell: bash -l {0}
		run: pip install -e .
		- name: mypy
		shell: bash -l {0}
		run: mypy -p deepchem
		- name: doctest
		shell: bash -l {0}
		run: DGLBACKEND=pytorch pytest -v --ignore-glob='deepchem/*/test.py' --doctest-modules deepchem
		- name: pytest
		shell: bash -l {0}
		run: pytest -v -m "not slow" --cov=deepchem deepchem

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -101,4 +101,5 @@ datasets/pdbbind_v2019_refined.tar.gz
		datasets/qm8.csv

		.vscode/
		env.yml
		.python-version

.travis.yml

deleted100644 → 0

+0 −68

Original line number	Diff line number	Diff line
		jobs:
		include:
		- name: Linux Python 3.6
		language: python
		python: '3.6'
		sudo: required
		dist: xenial
		- name: Linux Python 3.7
		language: python
		python: '3.7'
		sudo: required
		dist: xenial
		env: NIGHTLY_PKG_PUBLISH=true
		- name: Windows Python 3.7
		language: c
		python: '3.7'
		os: windows
		- name: Documentation
		language: python
		python: '3.7'
		sudo: required
		dist: xenial
		env: CHECK_ONLY_DOCS=true
		cache: pip
		install:
		- if [[ "$TRAVIS_OS_NAME" != "windows" ]]; then
		wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
		export python_version=$TRAVIS_PYTHON_VERSION;
		bash miniconda.sh -b -p $HOME/miniconda;
		source "$HOME/miniconda/etc/profile.d/conda.sh";
		fi
		- if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then
		choco install miniconda3 --params="'/JustMe /AddToPath:1'";
		export PATH="/c/tools/miniconda3/:/c/tools/miniconda3/Scripts:/c/tools/miniconda3/Library/bin:$PATH";
		source /c/tools/miniconda3/etc/profile.d/conda.sh;
		fi
		- hash -r
		- conda config --set always_yes yes --set changeps1 no
		- conda update -q conda
		- bash scripts/install_deepchem_conda.sh cpu
		- conda activate deepchem
		- pip install -e .
		script:
		- if [[ "$CHECK_ONLY_DOCS" == "true" ]]; then
		cd docs && pip install -r requirements.txt;
		make clean html;
		make doctest_tutorials;
		make doctest_examples;
		travis_terminate $?;
		fi
		- bash devtools/run_yapf.sh
		- bash devtools/run_flake8.sh
		- mypy -p deepchem
		- pytest -v -m "not slow" --cov=deepchem deepchem
		- if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then
		pytest -v --ignore-glob='deepchem/*/test.py' --doctest-modules deepchem;
		fi
		after_success:
		- echo $TRAVIS_SECURE_ENV_VARS
		- coveralls
		deploy:
		provider: pypi
		username: __token__
		password:
		secure: 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
		edge: true
		on:
		condition: $NIGHTLY_PKG_PUBLISH = true

Admin message