Merge branch 'master' into speedup-retrieval-of-analyses

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 19.0.8
+current_version = 19.0.9
 commit = True
 tag = True
 tag_name = {new_version}

.github/workflows/black.yml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - uses: psf/black@stable
         with:
           options: ". --check --line-length 100"

.github/workflows/production_install.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.11
 
     - name: Test install
       run: |

.github/workflows/publish_to_pypi.yaml

@@ -16,7 +16,7 @@ jobs:
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
-      python-version: 3.8
+      python-version: 3.11
 
    - name: Install build tools
      run: >-

.github/workflows/test_and_coverage.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.11
 
     - name: Install Trailblazer
       run: |

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8-slim-bullseye
+FROM python:3.11-slim-bullseye
 
 ENV GUNICORN_WORKERS=1
 ENV GUNICORN_TREADS=1

README.md

@@ -10,7 +10,7 @@ Trailblazer is a tool that aims to provide:
 
 ## Installation
 
-Trailblazer is written in Python 3.8 and is available on the [Python Package Index][pypi] (PyPI).
+Trailblazer is written in Python 3.11 and is available on the [Python Package Index][pypi] (PyPI).
 
 ```bash
 pip install trailblazer

setup.py

@@ -52,7 +52,7 @@ def parse_reqs(req_path="./requirements.txt"):
 
 setup(
     name=NAME,
-    version="19.0.8",
+    version="19.0.9",
     description=DESCRIPTION,
     long_description=LONG_DESCRIPTION,
     long_description_content_type="text/markdown",
@@ -77,7 +77,7 @@ def parse_reqs(req_path="./requirements.txt"):
     classifiers=[
         "License :: OSI Approved :: MIT License",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.11",
         "Environment :: Console",
     ],
 )

trailblazer/constants.py

@@ -1,4 +1,4 @@
-from enum import Enum
+from enum import Enum, StrEnum
 from typing import Dict, List, Tuple
 
 ONE_MONTH_IN_DAYS: int = 31
@@ -12,13 +12,13 @@
 TYPES: Tuple = ("other", "rna", "tgs", "wes", "wgs", "wts")
 
 
-class FileFormat(str, Enum):
+class FileFormat(StrEnum):
     CSV: str = "csv"
     JSON: str = "json"
     YAML: str = "yaml"
 
 
-class FileExtension(str, Enum):
+class FileExtension(StrEnum):
     CSV: str = ".csv"
     JSON: str = ".json"
     YAML: str = ".yaml"
@@ -35,7 +35,7 @@ def list(cls) -> List:
         return [task.value for task in cls]
 
 
-class Pipeline(str, Enum):
+class Pipeline(StrEnum):
     """Analysis pipeline names."""
 
     BALSAMIC: str = "BALSAMIC"
@@ -44,7 +44,7 @@ class Pipeline(str, Enum):
     SARS_COV_2: str = "SARS-COV-2"
 
 
-class SlurmSqueueHeader(str, Enum):
+class SlurmSqueueHeader(StrEnum):
     """SLURM squeue output headers."""
 
     JOBID: str = "JOBID"
@@ -55,7 +55,7 @@ class SlurmSqueueHeader(str, Enum):
     TIME_LIMIT: str = "TIME_LIMIT"
 
 
-class SlurmJobStatus(str, Enum):
+class SlurmJobStatus(StrEnum):
     """SLURM allowed status."""
 
     CANCELLED: str = "cancelled"
@@ -75,13 +75,13 @@ def ongoing_statuses(cls) -> Tuple:
         return cls.PENDING.value, cls.RUNNING.value, cls.COMPLETING.value
 
 
-class CharacterFormat(str, Enum):
+class CharacterFormat(StrEnum):
     """Define character encoding/decoding to use."""
 
     UNICODE_TRANSFORMATION_FORMAT_8: str = "utf-8"
 
 
-class TrailblazerStatus(str, Enum):
+class TrailblazerStatus(StrEnum):
     """Trailblazer allowed status."""
 
     CANCELLED: str = "cancelled"
@@ -102,7 +102,7 @@ def ongoing_statuses(cls) -> Tuple[str, str, str, str]:
         return cls.PENDING.value, cls.RUNNING.value, cls.COMPLETING.value, cls.ERROR.value
 
 
-class TrailblazerStatusColor(str, Enum):
+class TrailblazerStatusColor(StrEnum):
     """Trailblazer status colors."""
 
     COMPLETED: str = "green"