Feature/update submoudles

.github/workflows/test_bam_collapsing.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 get_test_data.sh
       - name: Test with tox
         id: run-tox
         run: tox -vv

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-- 3.6
+- 3.10
 install: pip install -U tox-travis
 script: tox
 deploy:
@@ -14,4 +14,4 @@ deploy:
   on:
     tags: true
     repo: msk-access/bam_collapsing
-    python: 3.6
+    python: 3.10

get_test_data.sh

@@ -8,10 +8,16 @@ filename=test_fgbio_bam_collapsing.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}
 
-tar --warning=no-unknown-keyword -xzvf $filename
+# Suppress linux warnings for MacOS tar.gz files
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    tar --warning=no-unknown-keyword -xzvf $filename
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    tar -xzvf $filename
+fi
 
 rm $filename

requirements.txt

@@ -1,16 +1,6 @@
-toil[cwl]==5.0.0
-pytz==2020.1
-typing==3.7.4.3
-ruamel.yaml==0.16.5
-pip==20.2.3
-bumpversion==0.6.0
-wheel==0.35.1
-watchdog==0.10.3
-flake8==3.8.4
-tox==3.20.0
-coverage==5.3
-twine==3.2.0
-pytest==6.1.1
-pytest-runner==5.2
-coloredlogs==10.0
-pytest-travis-fold==1.3.0
+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 = 1.0.0
+current_version = 1.1.0
 commit = True
 tag = True
 

setup.py

@@ -8,7 +8,7 @@
 with open('README.md') as readme_file:
     readme = readme_file.read()
 
-requirements = ['toil[all]==4.2.0', ]
+requirements = ['toil[all]==5.10.0', ]
 
 setup_requirements = [
     'pytest-runner', ]

tests/test_bam_collapsing.py

@@ -59,8 +59,8 @@ def setup_module():
 
         cmd = [
             "cwltool",
-            "--preserve-environment",
-            "PATH",
+#            "--preserve-environment",
+#            "PATH",
             "bam_collapsing.cwl",
             "test_fgbio_bam_collapsing/inputs/inputs.json",
         ]

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 =
@@ -30,11 +30,5 @@ deps =
 
 passenv = {gh-actions,pytest}
 
-whitelist_externals =
-    wget
-    chmod
-    tar
-    goodls
-commands_pre = ./get_test_data.sh
 commands =
     py.test --capture=sys --basetemp={envtmpdir} tests