diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index cb3e5b9..41261b4 100644 --- a/.github/workflows/python-package.yml +++ b/.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 diff --git a/CHANGES.rst b/CHANGES.rst index 81d9ff5..8eb46ad 100755 --- a/CHANGES.rst +++ b/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 \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 05ed91b..87a6099 100644 --- a/Dockerfile +++ b/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 ########################## diff --git a/README.rst b/README.rst index dd6ee5e..3452296 100755 --- a/README.rst +++ b/README.rst @@ -34,7 +34,7 @@ Required Packages ================= We require that you install: -:python: `v3.10.14 `_ +:python: `v3.10 `_ :pandas: `v2.2.2 `_ :biopython: `v1.84 `_ :Pillow: `v10.4.0 `_ diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..12237e5 --- /dev/null +++ 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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 diff --git a/setup.py b/setup.py index ccd1b44..b80af85 100755 --- a/setup.py +++ b/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',