perf: Update python version and its dependencies (#1216)

.bumpversion.cfg

@@ -21,5 +21,8 @@ tag_name = v{new_version}
 [bumpversion:file:docs/install.rst]
 
 [bumpversion:file:docs/balsamic_methods.rst]
+
+[bumpversion:file:setup.py]
+
 search = {current_version}
 replace = {new_version}

.github/workflows/black_linter.yml

@@ -7,7 +7,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.7'
+          python-version: '3.11'
       - uses: psf/black@stable
         with:
           options: "--check --verbose"

.pytest.ini

@@ -1,4 +1,4 @@
 [pytest]
-testpaths = tests testpaths = tests
-addopts = -v -x addopts = -v -x
+testpaths = tests
+addopts = -v -x
 norecursedirs = '.*' 'dist' 'CVS' '_darcs' '{arch}' '*.egg' 'venv'

.readthedocs.yml

@@ -7,7 +7,7 @@ version: 2
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.7"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

BALSAMIC/assets/scripts/edit_vcf_info.py

@@ -1,10 +1,6 @@
-# vim: syntax=python tabstop=4 expandtab
-# coding: utf-8
-
-""" Script to include variant caller information to the VCF info field and output to new VCF file """
+""" Script to include variant caller information to the VCF info field and output to new VCF file."""
 
 import click
-import gzip
 from cyvcf2 import VCF, Writer
 
 

BALSAMIC/assets/scripts/generate_cnv_report.py

@@ -1,12 +1,11 @@
-#!/usr/bin/env python
+"""Script to generate CNV reports."""
 import os
 from pathlib import Path
 from typing import List, Tuple
 
 import click
-
-from fpdf import FPDF
 from PIL import Image
+from fpdf import FPDF
 
 
 @click.command(short_help="Merge statistics and plots into a single CNV report")
@@ -113,7 +112,7 @@ def add_plots_to_pdf(pdf: PDF, plot_paths: List[Path]) -> PDF:
 
         # Image position & resizing
         img = Image.open(path)
-        img.thumbnail(img_size, Image.ANTIALIAS)
+        img.thumbnail(img_size, Image.LANCZOS)
         pdf.image(img, img_xy[0], img_xy[1])
 
     return pdf

BALSAMIC/conda/balsamic.yaml

@@ -1,9 +1,8 @@
 channels:
   - conda-forge
-  - bioconda
   - defaults
 
 dependencies:
-  - conda-forge::python=3.7
+  - conda-forge::python=3.11
   - conda-forge::pip
   - conda-forge::pygraphviz

BALSAMIC/containers/balsamic/balsamic.sh

@@ -1,2 +1 @@
 conda env update -n base --file "${1}".yaml
-pip install --no-cache-dir fpdf2==2.4.6

BALSAMIC/containers/balsamic/balsamic.yaml

@@ -4,7 +4,6 @@ channels:
   - defaults
 
 dependencies:
-  - conda-forge::python=3.7
-  - conda-forge::pip
-  - conda-forge::pygraphviz
-  - conda-forge::pillow
+  - conda-forge::python=3.11
+  - conda-forge::pip==23.2.1
+  - conda-forge::pygraphviz==1.11

BALSAMIC/utils/rule.py

@@ -407,18 +407,6 @@ def get_swegen_sv(config: dict) -> str:
     return Path(config["reference"]["swegen_sv_frequency"]).as_posix()
 
 
-def get_toml(annotation: dict) -> str:
-    """Returns annotation in toml format
-
-    Args:
-        annotation: a dict containing annotation resource
-
-    Returns:
-        toml_annotation: a string in toml format
-    """
-    return toml.dumps(annotation)
-
-
 def dump_toml(annotations: list) -> str:
     """Returns list of converted annotation in toml format
 
@@ -430,5 +418,5 @@ def dump_toml(annotations: list) -> str:
     """
     toml_annotations = ""
     for annotation in annotations:
-        toml_annotations += get_toml(annotation)
+        toml_annotations += toml.dumps(annotation)
     return toml_annotations

CHANGELOG.rst

@@ -22,6 +22,7 @@ Changed:
 * Balsamic init workflow refactoring https://github.com/Clinical-Genomics/BALSAMIC/pull/1188
 * Updated cryptography version to 41.0.2 https://github.com/Clinical-Genomics/BALSAMIC/pull/1205
 * Refactor snakemake executable command generation https://github/Clinical-Genomics/BALSAMIC/pull/1211
+* Updated Python version to 3.11 and its dependencies https://github.com/Clinical-Genomics/BALSAMIC/pull/1216
 
 Fixed:
 ^^^^^^

docs/README.rst

@@ -8,7 +8,7 @@ Create a conda environment:
 
 .. code-block::
 
-   conda create -n balsamic_doc -c bioconda -c conda-forge python=3.7 pip pygraphviz
+   conda create -n balsamic_doc -c bioconda -c conda-forge python=3.11 pip pygraphviz
    conda activate balsamic_doc
 
 Install Sphinx and extensions:

docs/install.rst

@@ -10,8 +10,8 @@ Software Requirements
 ~~~~~~~~~~~~~~~~~~~~~
 
 - Conda >=version 4.5.0: For detailed software and python requirements please see ``setup.py`` and ``BALSAMIC/conda/balsamic.yaml``
-- Singularity >=version 3.0.0: BALSAMIC uses singularity to run vairous parts of the workflow. 
-- Python 3.6
+- Singularity >=version 3.0.0: BALSAMIC uses singularity to run vairous parts of the workflow.
+- Python 3.11
 - BALSAMIC is dependent on third-party bioinformatics software ``Sentieon-tools``. Example: for running wgs variant calling using ``TNScope``, and to execute ``UMIworkflow``.
 
 ``Note: Set Sentieon envionment variables in your ~/.bashrc file by adding following two lines``
@@ -28,18 +28,18 @@ Step 1. Installing BALSAMIC
 
 ::
 
-    conda create -c conda-forge -c defaults --name S_BALSAMIC python==3.7 pip pygraphviz
+    conda create -c conda-forge -c defaults --name S_balsamic python==3.11 pip pygraphviz
 
 
-2. Activate environment: 
+2. Activate environment:
 
 ::
 
     conda activate S_BALSAMIC
 
 
 
-3. Install BALSAMIC using ``pip`` within the newly created environment: 
+3. Install BALSAMIC using ``pip`` within the newly created environment:
 
 ::
 

requirements-dev.txt

@@ -1,7 +1,5 @@
-pytest==7.1.3
-pytest-cov==2.8.1
-coveralls
-pylint==2.13.9
-black==22.3.0
-pillow>=8.4.0
-fpdf2==2.4.6
+black==23.7.0
+bump2version==1.0.1
+coveralls==3.3.1
+pytest-cov==4.1.0
+pytest==7.4.0

setup.py

@@ -1,51 +1,133 @@
+"""Description of the Balsamic package."""
 import os
-from setuptools import setup, find_packages
+from typing import List
 
-here = os.path.abspath(os.path.dirname(__file__))
+from setuptools import setup, find_packages
 
-# Load the package's __version__.py module as a dictionary.
-about = {}
-with open(os.path.join(here, "BALSAMIC", "__version__.py")) as f:
-    exec(f.read(), about)
+NAME: str = "BALSAMIC"
+AUTHOR: str = "Clinical Genomics"
+URL: str = "https://github.com/Clinical-Genomics/BALSAMIC"
+EMAIL: str = "support@clinicalgenomics.se"
+REQUIRES_PYTHON: str = ">=3.11.0"
 
 # Requirements
-requirements = [
-    "click==8.1.3",
-    "colorclass>=2.2.0",
-    "coloredlogs>=14.0",
-    "graphviz==0.16",
-    "gsutil==5.23",
-    "jinja2>=2.11.2",
-    "matplotlib==3.5.2",
-    "networkx>=2.6.3",
-    "numpy>=1.21.6",
-    "pandas>=1.1.5",
-    "psutil>=5.7.0",
-    "pydantic>=1.9.0,<2.0",
-    "pygments>=2.6.1",
-    "pyyaml>=5.3.1",
-    "six>=1.12.0",
-    "snakemake==7.25.0",
-    "yapf>=0.30.0",
-    "h5py>=3.6.0",
-    "PyPDF2>=1.26.0",
-    "markdown==3.3.3",
-    "cryptography==41.0.2",
-    "tabulate==0.8.10",
+requirements: List[str] = [
+    "aiohttp==3.8.5",
+    "aiosignal==1.3.1",
+    "appdirs==1.4.4",
+    "argcomplete==3.1.1",
+    "async-timeout==4.0.2",
+    "attrs==23.1.0",
+    "boto==2.49.0",
+    "cachetools==5.3.1",
+    "certifi==2023.7.22",
+    "cffi==1.15.1",
+    "charset-normalizer==3.2.0",
+    "click==8.1.6",
+    "colorclass==2.2.2",
+    "coloredlogs==15.0.1",
+    "ConfigArgParse==1.7",
+    "connection-pool==0.0.3",
+    "contourpy==1.1.0",
+    "crcmod==1.7",
+    "cryptography==41.0.3",
+    "cycler==0.11.0",
+    "cyvcf2==0.30.22",
+    "datrie==0.8.2",
+    "defusedxml==0.7.1",
+    "docutils==0.20.1",
+    "dpath==2.1.6",
+    "fasteners==0.18",
+    "fastjsonschema==2.18.0",
+    "fonttools==4.42.0",
+    "fpdf2==2.7.4",
+    "frozenlist==1.4.0",
+    "gcs-oauth2-boto-plugin==3.0",
+    "gitdb==4.0.10",
+    "GitPython==3.1.32",
+    "google-apitools==0.5.32",
+    "google-auth==2.22.0",
+    "google-reauth==0.1.1",
+    "graphviz==0.20.1",
+    "gsutil==5.25",
+    "h5py==3.9.0",
+    "httplib2==0.20.4",
+    "humanfriendly==10.0",
+    "idna==3.4",
+    "importlib-metadata==6.8.0",
+    "iniconfig==2.0.0",
+    "Jinja2==3.1.2",
+    "jsonschema==4.18.6",
+    "jsonschema-specifications==2023.7.1",
+    "jupyter_core==5.3.1",
+    "kiwisolver==1.4.4",
+    "MarkupSafe==2.1.3",
+    "matplotlib==3.7.2",
+    "monotonic==1.6",
+    "multidict==6.0.4",
+    "nbformat==5.9.2",
+    "numpy==1.25.2",
+    "oauth2client==4.1.3",
+    "packaging==23.1",
+    "pandas==2.0.3",
+    "Pillow==10.0.0",
+    "plac==1.3.5",
+    "platformdirs==3.10.0",
+    "pluggy==1.2.0",
+    "psutil==5.9.5",
+    "PuLP==2.7.0",
+    "pyasn1==0.5.0",
+    "pyasn1-modules==0.3.0",
+    "pycparser==2.21",
+    "pydantic==1.10.12",
+    "Pygments==2.15.1",
+    "pyOpenSSL==23.2.0",
+    "pyparsing==3.0.9",
+    "PyPDF2==3.0.1",
+    "pytest==7.4.0",
+    "python-dateutil==2.8.2",
+    "pytz==2023.3",
+    "pyu2f==0.1.5",
+    "PyYAML==6.0.1",
+    "referencing==0.30.0",
+    "requests==2.31.0",
+    "reretry==0.11.8",
+    "retry-decorator==1.1.1",
+    "rpds-py==0.9.2",
+    "rsa==4.7.2",
+    "six==1.16.0",
+    "smart-open==6.3.0",
+    "smmap==5.0.0",
+    "snakemake==7.32.0",
+    "stopit==1.1.2",
+    "tabulate==0.9.0",
+    "throttler==1.2.2",
     "toml==0.10.2",
+    "tomli==2.0.1",
+    "toposort==1.10",
+    "traitlets==5.9.0",
+    "typing_extensions==4.7.1",
+    "tzdata==2023.3",
+    "urllib3==1.26.16",
+    "wrapt==1.15.0",
+    "yapf==0.40.1",
+    "yarl==1.9.2",
+    "yte==1.5.1",
+    "zipp==3.16.2",
 ]
 
 # The C libraries required to build numpy are not available on RTD
 if not os.getenv("READTHEDOCS"):
     requirements.extend(["cyvcf2==0.30.22"])
 
 setup(
-    name="BALSAMIC",
-    version=about["__version__"],
-    url="https://github.com/Clinical-Genomics/BALSAMIC",
-    author="Hassan Foroughi Asl",
-    author_email="hassan.foroughi@scilifelab.se",
+    name=NAME,
+    version="12.0.2",
+    url=URL,
+    author=AUTHOR,
+    author_email=EMAIL,
     install_requires=requirements,
+    python_requires=REQUIRES_PYTHON,
     packages=find_packages(),
     package_data={
         "": [

tests/commands/init/test_init.py

@@ -11,6 +11,7 @@
 from BALSAMIC.constants.cache import GenomeVersion
 from BALSAMIC.constants.cluster import ClusterAccount
 from BALSAMIC.constants.constants import EXIT_SUCCESS, EXIT_FAIL
+from BALSAMIC.utils.exc import BalsamicError
 
 
 def test_init_hg(
@@ -176,7 +177,7 @@ def test_init_hg_graph_exception(
     # GIVEN a temporary output directory and a COSMIC key
 
     # WHEN invoking the init command
-    with mock.patch.object(Source, "render"):
+    with mock.patch.object(Source, "render", side_effect=BalsamicError("Test error")):
         result: Result = invoke_cli(
             [
                 "init",
@@ -189,7 +190,7 @@ def test_init_hg_graph_exception(
             ]
         )
 
-    # THEN the human reference generation workflow should have successfully started
+    # THEN the human reference generation workflow should fail
     assert "Workflow graph generation failed" in result.output
     assert Path(tmp_path, balsamic_version, GenomeVersion.HG19, config_json).exists()
     assert not Path(