Update CI/CD for Python 3.7/3.10/3.13/3.14 and fix compatibility issues

- Update test matrix to [3.7, 3.10, 3.13, 3.14]
- Update actions/checkout to v4 and actions/setup-python to v5
- Replace deprecated logger.warn() with logger.warning()
- Remove future package dependency (Python 2 compat layer)
- Replace setup.py sdist bdist_wheel with python -m build
- Add PEP 517/518 build-system config to pyproject.toml
- Update black target-version in pyproject.toml

Agent-Logs-Url: https://github.com/murphycj/AGFusion/sessions/e49f3a3e-549d-48df-8578-155ae7490dfb

Co-authored-by: murphycj <3837196+murphycj@users.noreply.github.com>

Author: Copilot

.github/workflows/deploy-pypi.yaml

@@ -14,17 +14,17 @@ jobs:
       - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: "3.10"
 
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel build
           pip install .
       - name: Build the distribution
-        run: python setup.py sdist bdist_wheel
+        run: python -m build
 
       - name: Publish AGFusion to PyPI
         if: github.repository == 'murphycj/AGFusion'

.github/workflows/test.yaml

@@ -8,10 +8,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.10", "3.13", "3.14"]
     steps:
       - name: Checkout source code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -32,4 +36,4 @@ jobs:
       - name: Test build bundle for pip
         run: |
           pip install setuptools wheel build
-          python setup.py sdist bdist_wheel
+          python -m build

agfusion/cli.py

@@ -10,9 +10,6 @@
 from os.path import exists, join, split
 from pathlib import Path
 
-from future.standard_library import install_aliases
-
-install_aliases()
 from urllib.error import HTTPError
 from urllib.request import urlopen
 
@@ -154,7 +151,7 @@ def batch_mode(args, agfusion_db, pyensembl_data, rename, colors):
     if not exists(args.out):
         mkdir(args.out)
     else:
-        agfusion_db.logger.warn(f"Output directory {args.out} already exists! Overwriting...")
+        agfusion_db.logger.warning(f"Output directory {args.out} already exists! Overwriting...")
 
     if not Path(args.file).exists():
         raise FileNotFoundError(f"File not found {args.file}")
@@ -528,7 +525,7 @@ def parse_names_and_colors(args, agfusion_db):
             assert len(pair) == 2, " did not properly specify --rename"
 
             if pair[0] in rename:
-                agfusion_db.logger.warn(f"WARNING - you rename {pair[0]} twice.")
+                agfusion_db.logger.warning(f"WARNING - you rename {pair[0]} twice.")
 
             rename[pair[0]] = pair[1]
 
@@ -539,7 +536,7 @@ def parse_names_and_colors(args, agfusion_db):
             assert len(pair) == 2, " did not properly specify --colors"
 
             if pair[0] in colors:
-                agfusion_db.logger.warn(f"You specified colors for {pair[0]} twice.")
+                agfusion_db.logger.warning(f"You specified colors for {pair[0]} twice.")
 
             if pair[0] in rename:
                 colors[rename[pair[0]]] = pair[1]

agfusion/parsers.py

@@ -675,7 +675,7 @@ def __init__(self, infile, logger):
             line = line.strip().split("\t")
 
             if line[data_indices["genes_1"]] == "none" or line[data_indices["genes_2"]] == "none":
-                self.logger.warn(
+                self.logger.warning(
                     f"Skipping fusion on line {n} because one or more "
                     + "of the provided gene names under 'gene_1' and"
                     + " 'gene_2' is listed as 'none'."

pyproject.toml

@@ -1,4 +1,8 @@
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [tool.black]
 line-length = 100
-target-version = ['py36', 'py37', 'py38']
+target-version = ['py37', 'py310', 'py311', 'py312', 'py313']
 include = '\.pyi?$'

requirements.txt

@@ -1,6 +1,5 @@
 matplotlib>=3.9.2
 pandas==2.2.3
 biopython>=1.79
-future>=0.16.0
 pyensembl>=2.3.13
 numpy<2

setup.py

@@ -35,7 +35,6 @@
         "matplotlib>=1.5.0",
         "pandas>=0.18.1",
         "biopython>=1.67",
-        "future>=0.16.0",
         "pyensembl>=1.1.0",
     ],
 )