diff --git a/.github/workflows/test_ubg.yaml b/.github/workflows/test_ubg.yaml index 44eaee4..939ef13 100644 --- a/.github/workflows/test_ubg.yaml +++ b/.github/workflows/test_ubg.yaml @@ -16,15 +16,15 @@ jobs: max-parallel: 1 matrix: platform: [ubuntu-latest] - python-version: [3.6] + python-version: ['3.10'] steps: - name: Checkout repo - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: ref: ${{ github.head_ref }} submodules: recursive - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name : Set up NodeJS @@ -34,24 +34,13 @@ jobs: [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh" # This loads nvm [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion" # This loads nvm bash_completion nvm install node - - name: Setup Docker - uses: docker-practice/actions-setup-docker@master - with: - docker_channel: nightly - # this value please see https://github.com/AkihiroSuda/moby-snapshot/releases - docker_nightly_version: snapshot-20201109 - env: - PLATFORM: ${{ matrix.platform }} - - name: Login to GitHub Container Registry - uses: docker/login-action@v1 - with: - registry: ghcr.io - username: ${{ github.repository_owner }} - password: ${{ secrets.RS_PAT }} - name: Install Python dependencies run: | python -m pip install --upgrade pip pip install tox tox-gh-actions + - name: Install Test data + run: | + bash install_data.sh - name: Test with tox id: run-tox run: tox -vv diff --git a/command_line_tools b/command_line_tools index 3c3cbdb..082f3a3 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 3c3cbdbf59daef7f34114468e127c744fb3a2580 +Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e diff --git a/install_data.sh b/install_data.sh index 50c0c4e..c7a6fae 100755 --- a/install_data.sh +++ b/install_data.sh @@ -9,9 +9,10 @@ filename=test_uncollapsed_bam_generation.tar.gz # Skip if already have test data [[ -f $filename ]] && exit 0 -curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null +#curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null +#curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} -curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename} +curl -L "https://drive.usercontent.google.com/download?id=${fileid}&confirm=xxx" -o ${filename} if [[ "$OSTYPE" == "linux-gnu" ]]; then tar --warning=no-unknown-keyword -xzvf $filename diff --git a/requirements.txt b/requirements.txt index 03be6c8..042c5b7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,10 +1,6 @@ -toil[cwl] -pip -pytz -typing -bumpversion -flake8 -tox -twine -pytest -pytest-runner +coloredlogs==15.0.1 +pytest==7.2.0 +setuptools==65.4.1 +toil[cwl]==5.10.0 +pytest-runner==6.0.1 +tox==3.27.1 diff --git a/setup.cfg b/setup.cfg index 2283863..6215d14 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.0 +current_version = 1.3.0 commit = True tag = True diff --git a/setup.py b/setup.py index b0209b9..cdc0366 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ with open('README.md') as readme_file: readme = readme_file.read() -requirements = ['toil[cwl]==5.5.0', ] +requirements = ['toil[cwl]==5.10.0', ] setup_requirements = ['pytest-runner', ] @@ -22,7 +22,7 @@ 'Intended Audience :: Developers', 'License :: OSI Approved :: Apache Software License', 'Natural Language :: English', - 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.10', ], description="Workflow for making MSK-ACCESS standard binary alignment mapping file.", install_requires=requirements, @@ -36,6 +36,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/msk-access/uncollapsed_bam_generation', - version='1.2.0', + version='1.3.0', zip_safe=False, ) diff --git a/subworkflows b/subworkflows index e6aa311..aeb7fec 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit e6aa31182783696debaa222c100087f3d9210ac0 +Subproject commit aeb7fec838db8abdfbdae7fbc617e2dd6bc5ae9c diff --git a/tox.ini b/tox.ini index 655f6a9..e05ffb2 100644 --- a/tox.ini +++ b/tox.ini @@ -1,13 +1,13 @@ [tox] -envlist = py{36}-{linux} +envlist = py{310}-{linux} [travis] python = - 3.6: py36 + 3.10: py310 [gh-actions] python = - 3.6: py36 + 3.10: py310 [gh-actions:env] PLATFORM = @@ -28,14 +28,6 @@ deps = passenv = gh-actions -whitelist_externals = - wget - chmod - tar - goodls - -commands_pre = ./install_data.sh - commands = py.test --capture=sys --basetemp={envtmpdir} tests