Merging from dev

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.10.14]
+        python-version: [3.10]
 
     steps:
     - name: Checkout github repo (+ download lfs dependencies)
@@ -39,6 +39,6 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with nosetest
+    - name: Test with poetry
       run: |
-        nosetests -v --with-coverage --cover-tests
+        poetry export --format requirements.txt --output requirements.txt --without-hashes

CHANGES.rst

@@ -25,3 +25,5 @@ RS:Added functionality to kinase domain involvement in the annotation
 RS:Bug fix for running auto selection mode and upgrading requirements
 ## v1.2.1
 GJ:Bug fix for selection of transcript, error when MT chromosome. 
+## v1.3.0
+RS: Adding generate_fusion_peptides Utilities and update for python 3

Dockerfile

@@ -1,5 +1,5 @@
 ################## Base Image ##########
-ARG PYTHON_VERSION="3.10.14"
+ARG PYTHON_VERSION="3.10"
 FROM --platform=linux/amd64 python:${PYTHON_VERSION}
 
 ################## ARGUMENTS/Environments ##########
@@ -21,7 +21,7 @@ LABEL org.opencontainers.image.created=${BUILD_DATE} \
     org.opencontainers.image.vcs-url="https://github.com/rhshah/iAnnotateSV.git" \
     org.opencontainers.image.vcs-ref=${VCS_REF}
 
-LABEL org.opencontainers.image.description="This container uses python 3.10.14 as the base image to build \
+LABEL org.opencontainers.image.description="This container uses python 3.10 as the base image to build \
     iAnnotateSV version ${iAnnotateSV_VERSION}"
 
 ################## INSTALL ##########################

README.rst

@@ -34,7 +34,7 @@ Required Packages
 =================
 We require that you install:
 
-:python: `v3.10.14 <https://www.python.org/downloads/release/>`_
+:python: `v3.10 <https://www.python.org/downloads/release/>`_
 :pandas: `v2.2.2 <http://pandas.pydata.org/>`_
 :biopython: `v1.84 <http://biopython.org/wiki/Main_Page>`_
 :Pillow: `v10.4.0 <https://pypi.python.org/pypi/Pillow/>`_

pyproject.toml

@@ -11,7 +11,7 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.10.14"
+python = "^3.10"
 biopython = "1.84"
 numpy = "2.1.0"
 pandas = "2.2.2"
@@ -23,9 +23,6 @@ coloredlogs = "15.0.1"
 [tool.poetry.dev-dependencies]
 flake8 = "*"
 ruff = "*"
-codecov = "*"
-coverage = "*"
-nose = "*"
 sphinx = "*"
 
 [build-system]

requirements-dev.txt

@@ -7,7 +7,4 @@ biopython==1.84
 reportlab==3.6.13
 flake8
 ruff
-codecov
-coverage
-nose
 sphinx

setup.cfg

@@ -7,7 +7,7 @@ keywords = structural, variants, NGS, MSK-IMPACT, MSK-ACCESS
 license = Apache Software License
 classifiers =
     Programming Language :: Python
-    Programming Language :: Python :: 3.10.14
+    Programming Language :: Python :: 3.10
     License :: OSI Approved :: Apache License
     Operating System :: OS Independent
     Intended Audience :: Science/Research

setup.py

@@ -48,7 +48,7 @@ def read(*filenames, **kwargs):
       zip_safe=False,
       classifiers=(
         'Programming Language :: Python',
-        'Programming Language :: Python :: 3.10.14',
+        'Programming Language :: Python :: 3.10',
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: OS Independent',
         'Intended Audience :: Science/Research',