From 98fa5431f1bfddde4a530e118747e249d00acdd0 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 6 Sep 2024 16:48:03 -0400 Subject: [PATCH 1/3] Updating submodules and actions --- .github/workflows/test_nucleo.yaml | 12 ++++++------ .travis.yml | 4 ++-- bam_collapsing | 2 +- command_line_tools | 2 +- requirements.txt | 2 +- setup.cfg | 2 +- setup.py | 6 +++--- tox.ini | 14 ++++++++------ uncollapsed_bam_generation | 2 +- 9 files changed, 24 insertions(+), 22 deletions(-) diff --git a/.github/workflows/test_nucleo.yaml b/.github/workflows/test_nucleo.yaml index a10f381..4f21cd2 100644 --- a/.github/workflows/test_nucleo.yaml +++ b/.github/workflows/test_nucleo.yaml @@ -16,25 +16,25 @@ jobs: max-parallel: 1 matrix: platform: [ubuntu-latest] - python-version: [3.9] + 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: ${{ matrix.python-version }} - name : Set up NodeJS run: | curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.37.2/install.sh | bash - export NVM_DIR="$HOME/.nvm" + export NVM_DIR="$HOME/.nvm" [ -s "$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 + - name: Setup Docker uses: docker-practice/actions-setup-docker@master with: docker_channel: nightly @@ -43,7 +43,7 @@ jobs: env: PLATFORM: ${{ matrix.platform }} - name: Login to GitHub Container Registry - uses: docker/login-action@v1 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} diff --git a/.travis.yml b/.travis.yml index c09cb40..457f8de 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: python python: -- 3.9 +- 3.10 install: pip install -U tox-travis script: tox deploy: @@ -14,4 +14,4 @@ deploy: on: tags: true repo: msk-access/nucleo - python: 3.9 + python: 3.10 diff --git a/bam_collapsing b/bam_collapsing index f49d5d4..003ed9c 160000 --- a/bam_collapsing +++ b/bam_collapsing @@ -1 +1 @@ -Subproject commit f49d5d4091d8867847aaf4d5a8500cfff0617fce +Subproject commit 003ed9cdab7610cfbb77ccbef8498e9d9b3d69a7 diff --git a/command_line_tools b/command_line_tools index 28551d5..082f3a3 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 28551d5bfbbcd4cd2e6755395a01c7494fa244a1 +Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e diff --git a/requirements.txt b/requirements.txt index 666cb2d..e0396a6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -toil[cwl]==5.7.1 +toil[cwl]==5.10.0 pytz==2022.6 bumpversion==0.6.0 flake8==6.0.0 diff --git a/setup.cfg b/setup.cfg index e2d50fe..95006dc 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 3.0.4 +current_version = 3.1.0 commit = True tag = True diff --git a/setup.py b/setup.py index 2d2e674..d3e7b9b 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 :: 3.9', + 'Programming Language :: Python :: 3.10', ], description="Workflow that creates all the bam files for the MSK-ACCESS fastq file", install_requires=requirements, @@ -36,6 +36,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/msk-access/nucleo', - version='3.0.4', + version='3.1.0', zip_safe=False, ) diff --git a/tox.ini b/tox.ini index 8ea6ea5..ae891ec 100644 --- a/tox.ini +++ b/tox.ini @@ -1,9 +1,9 @@ [tox] -envlist = py{39}-{linux}, flake8 +envlist = py{310}-{linux}, flake8 [travis] python = - 3.9: py39 + 3.10: py310 [testenv:flake8] basepython = python @@ -12,7 +12,7 @@ commands = flake8 nucleo [gh-actions] python = - 3.9: py39 + 3.10: py310 [gh-actions:env] PLATFORM = @@ -32,14 +32,16 @@ deps = passenv = {gh-actions,pytest} -whitelist_externals = +allowlist_externals = wget chmod tar goodls + sh + bash + tar -commands_pre = ./install_data.sh +commands_pre = bash ./install_data.sh commands = py.test --capture=sys --basetemp={envtmpdir} tests - diff --git a/uncollapsed_bam_generation b/uncollapsed_bam_generation index e55c072..6576bfc 160000 --- a/uncollapsed_bam_generation +++ b/uncollapsed_bam_generation @@ -1 +1 @@ -Subproject commit e55c072d59343c55581261a8ff84ebed71404500 +Subproject commit 6576bfceadd14adc0655c1cc7f82a0045c0fd09b From da983b05e26c9194ae777e9d16e1374a1f7a4d44 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 6 Sep 2024 17:00:04 -0400 Subject: [PATCH 2/3] Remove bam_collapsing submodule --- .gitmodules | 4 ---- bam_collapsing | 1 - 2 files changed, 5 deletions(-) delete mode 160000 bam_collapsing diff --git a/.gitmodules b/.gitmodules index 7e7de8b..094b11a 100644 --- a/.gitmodules +++ b/.gitmodules @@ -6,10 +6,6 @@ path = subworkflows url = https://github.com/msk-access/cwl_subworkflows.git branch = develop -[submodule "bam_collapsing"] - path = bam_collapsing - url = https://github.com/msk-access/bam_collapsing.git - branch = develop [submodule "uncollapsed_bam_generation"] path = uncollapsed_bam_generation url = https://github.com/msk-access/uncollapsed_bam_generation.git diff --git a/bam_collapsing b/bam_collapsing deleted file mode 160000 index 003ed9c..0000000 --- a/bam_collapsing +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 003ed9cdab7610cfbb77ccbef8498e9d9b3d69a7 From c4219d6c4b1baca87b6fc95f77298f820feb434f Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 6 Sep 2024 17:08:36 -0400 Subject: [PATCH 3/3] update --- .gitmodules | 4 ++++ bam_collapsing | 1 + 2 files changed, 5 insertions(+) create mode 160000 bam_collapsing diff --git a/.gitmodules b/.gitmodules index 094b11a..9509fc6 100644 --- a/.gitmodules +++ b/.gitmodules @@ -10,3 +10,7 @@ path = uncollapsed_bam_generation url = https://github.com/msk-access/uncollapsed_bam_generation.git branch = develop +[submodule "bam_collapsing"] + path = bam_collapsing + url = https://github.com/msk-access/bam_collapsing.git + branch = develop diff --git a/bam_collapsing b/bam_collapsing new file mode 160000 index 0000000..003ed9c --- /dev/null +++ b/bam_collapsing @@ -0,0 +1 @@ +Subproject commit 003ed9cdab7610cfbb77ccbef8498e9d9b3d69a7