Merge pull request #406 from 4dn-dcic/python-3.12

Support for Python 3.12

.github/workflows/main.yml

@@ -143,3 +143,34 @@ jobs:
       - name: QA (unit)
         run: |
           poetry run invoke test --no-flake
+
+  build_3_12:
+    needs: build_3_11
+    # The type of runner that the job will run on
+    runs-on: ubuntu-22.04
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.12'
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install Deps
+        run: |
+          make install
+          
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - name: QA (unit)
+        run: |
+          poetry run invoke test --no-flake

CHANGELOG.rst

@@ -3,6 +3,12 @@
 Change Log
 ==========
 
+5.4.0
+=====
+
+* Support for Python 3.12.
+
+
 5.3.0
 =====
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "tibanna"
-version = "5.3.0"
+version = "5.4.0"
 description = "Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud."
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -26,19 +26,20 @@ classifiers = [
   'Programming Language :: Python :: 3.9',
   'Programming Language :: Python :: 3.10',
   'Programming Language :: Python :: 3.11',
+  'Programming Language :: Python :: 3.12'
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"
+python = ">=3.8,<3.13"
 python-lambda-4dn = "0.12.3"
-boto3 = "^1.28.56"
-botocore = "^1.31.56"
+boto3 = "^1.34.136"
+botocore = "^1.34.136"
 Benchmark-4dn = "^0.5.24"
 tomlkit = "^0.11.0"
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.28.56"
-botocore-stubs = "^1.31.56"
+boto3-stubs = "^1.34.136"
+botocore-stubs = "^1.34.136"
 invoke = "^2.2.0"
 flake8 = "^3.9.0"
 

tibanna/awsem.py

@@ -393,15 +393,15 @@ def as_dict(self):
 
 def file2cwlfile(filename, dirname, unzip):
     if unzip:
-        filename = re.match('(.+)\.{0}$'.format(unzip), filename).group(1)
+        filename = re.match(r'(.+)\.{0}$'.format(unzip), filename).group(1)
     if dirname.endswith('/'):
         dirname = dirname.rstrip('/')
     return {"class": 'File', "path": dirname + '/' + filename}
 
 
 def file2wdlfile(filename, dirname, unzip):
     if unzip:
-        filename = re.match('(.+)\.{0}$'.format(unzip), filename).group(1)
+        filename = re.match(r'(.+)\.{0}$'.format(unzip), filename).group(1)
     if dirname.endswith('/'):
         dirname = dirname.rstrip('/')
     return dirname + '/' + filename