Update Python version to 3.13 in Dockerfile and Pipfile

.github/workflows/ci.yml

@@ -11,14 +11,24 @@ on:
       - master
 
 jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      python_version: ${{ steps.read_python_version.outputs.python_version }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Read Python version
+        id: read_python_version
+        run: echo "::set-output name=python_version::$(cat .python-version)"
   black:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -37,12 +47,13 @@ jobs:
           python -m black --check .
   flake8:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -61,12 +72,13 @@ jobs:
           flake8
   mypy:
     runs-on: ubuntu-latest
+    needs: setup
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -84,6 +96,7 @@ jobs:
           python -m mypy .
   test:
     runs-on: ubuntu-latest
+    needs: setup
     services:
       postgres:
         image: postgres:14.5
@@ -103,7 +116,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: ${{ needs.setup.outputs.python_version }}
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip

.gitignore

@@ -81,9 +81,6 @@ target/
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
 #   However, in case of collaboration, if having platform-specific dependencies or dependencies

.python-version

@@ -0,0 +1 @@
+3.13.0

Dockerfile

@@ -1,5 +1,5 @@
 # Use slim for a smaller image size and install only the required packages
-FROM python:3.8-slim
+FROM python:3.13-slim
 
 # > Setting PYTHONUNBUFFERED to a non empty value ensures that the python output is sent straight to
 # > terminal (e.g. your container log) without being first buffered and that you can see the output

Pipfile

@@ -28,7 +28,7 @@ sqlalchemy = "~=2.0"
 flask-migrate = "*"
 
 [requires]
-python_version = "3.8"
+python_version = "3.13"
 
 [pipenv]
 allow_prereleases = true

baracoda/barcodes.py

@@ -36,7 +36,7 @@ def get_new_barcode_group(prefix: str) -> Tuple[Any, int]:
         - OtherError: HTTP 500 with JSON representation of error.
     """
     try:
-        logger.debug(f"Creating a barcode group for '{ prefix }'")
+        logger.debug(f"Creating a barcode group for '{prefix}'")
         count = get_count_param()
 
         operator = BarcodeOperations(prefix=prefix)
@@ -70,7 +70,7 @@ def get_new_barcode(prefix: str) -> Tuple[Any, int]:
         - OtherError: HTTP 500 with JSON representation of error.
     """
     try:
-        logger.debug(f"Creating a barcode for '{ prefix }'")
+        logger.debug(f"Creating a barcode for '{prefix}'")
         text = get_text_param()
         operator = BarcodeOperations(prefix=prefix, text=text)
         barcode = operator.create_barcode()
@@ -98,7 +98,7 @@ def get_last_barcode(prefix: str) -> Tuple[Any, int]:
         - OtherError: HTTP 500 with JSON representation of error.
     """
     try:
-        logger.debug(f"Obtaining last from '{ prefix }'")
+        logger.debug(f"Obtaining last from '{prefix}'")
         operator = BarcodeOperations(prefix=prefix)
 
         barcode = operator.get_last_barcode(prefix)

baracoda/formats/sequencescape.py

@@ -73,4 +73,4 @@ def barcode_with_checksum(self, barcode: str) -> str:
         Returns:
             str -- the same barcode but with the suffix attached separated by '-'
         """
-        return f"{ barcode }-{ self.suffix(barcode) }"
+        return f"{barcode}-{self.suffix(barcode)}"

migrations/versions/bc442d63d7d3_move_forward_current_value_for_heron.py

@@ -25,7 +25,7 @@ def __DANGER_restart_sequence_with(value):
         )
         raise ValueError(description)
     # Last value in database is 2564197, we want to move forward past this value
-    op.execute(f"ALTER SEQUENCE heron RESTART WITH { value };")
+    op.execute(f"ALTER SEQUENCE heron RESTART WITH {value};")
 
 
 def upgrade():