Merge branch 'release/1.3.0'

.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

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

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

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.3.0
 commit = True
 tag = True
 

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,
 )

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