Merge branch 'release/1.3.0'

.github/workflows/docker-publish.yml

@@ -0,0 +1,64 @@
+name: Publish Docker image to ghcr.io
+on:
+  push:
+    tags:
+      - "*"
+jobs:
+  push_to_registries:
+    name: Build and publish Docker image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Prepare
+        # In this preparation step, a few configurations are made
+        # according to tags that will be used to export the image
+        # for Docker Hub, as well as the name of the image itself
+        id: prep
+        run: |
+          DOCKER_IMAGE=ghcr.io/rhshah/iAnnotateSV
+          VERSION=noop
+          if [ "${{ github.event_name }}" = "schedule" ]; then
+            VERSION=nightly
+          elif [[ $GITHUB_REF == refs/tags/* ]]; then
+            VERSION=${GITHUB_REF#refs/tags/}
+          elif [[ $GITHUB_REF == refs/heads/* ]]; then
+            VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
+          fi
+          TAGS="${DOCKER_IMAGE}:${VERSION}"
+          if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+            MINOR=${VERSION%.*}
+            MAJOR=${MINOR%.*}
+            TAGS="$TAGS,${DOCKER_IMAGE}:latest"
+          elif [[ $VERSION =~ ^v[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+            VERSION=$(echo ${VERSION#v})
+            TAGS="${DOCKER_IMAGE}:${VERSION}"
+          elif [ "${{ github.event_name }}" = "push" ]; then
+            TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
+          fi
+          echo ::set-output name=version::${VERSION}
+          echo ::set-output name=tags::${TAGS}
+      - name: Login to GitHub Container Registry
+        #if: github.event_name != 'pull_request'
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.RS_PAT }}
+      - name: Push to GitHub Packages
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.prep.outputs.tags }}
+          build-args: |
+            iAnnotateSV_VERSION=${{ steps.prep.outputs.version }}
+          labels: |
+            org.opencontainers.image.title=${{ github.event.repository.name }}
+            org.opencontainers.image.description=${{ github.event.repository.description }}
+            org.opencontainers.image.version=${{ steps.prep.outputs.version }}

.github/workflows/python-package.yml

@@ -15,17 +15,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7.18]
+        python-version: [3.10.14]
 
     steps:
     - name: Checkout github repo (+ download lfs dependencies)
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         lfs: true
     - name: Checkout LFS objects
       run: git lfs checkout
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/python-publish.yml

@@ -0,0 +1,19 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Publish package to PyPI
+
+on:
+    push:
+        tags:
+            - "*.*.*"
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+            - name: Build and publish to pypi
+              uses: JRubics/poetry-publish@v1.11
+              with:
+                  pypi_token: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -90,4 +90,7 @@ ENV/
 
 # IDE settings
 .vscode/
-.idea/
+.idea/
+.DS_Store
+iAnnotateSV/.DS_Store
+iAnnotateSV/data/.DS_Store

Dockerfile

@@ -0,0 +1,39 @@
+################## Base Image ##########
+ARG PYTHON_VERSION="3.10.14"
+FROM --platform=linux/amd64 python:${PYTHON_VERSION}
+
+################## ARGUMENTS/Environments ##########
+ARG BUILD_DATE
+ARG BUILD_VERSION
+ARG LICENSE="Apache-2.0"
+ARG iAnnotateSV_VERSION
+ARG VCS_REF
+
+################## METADATA ########################
+LABEL org.opencontainers.image.vendor="MSKCC"
+LABEL org.opencontainers.image.authors="Ronak Shah (shahr2@mskcc.org)"
+
+LABEL org.opencontainers.image.created=${BUILD_DATE} \
+    org.opencontainers.image.version=${BUILD_VERSION} \
+    org.opencontainers.image.licenses=${LICENSE} \
+    org.opencontainers.image.version.pvs=${iAnnotateSV_VERSION} \
+    org.opencontainers.image.source.pv="https://pypi.org/project/iAnnotateSV" \
+    org.opencontainers.image.vcs-url="https://github.com/rhshah/iAnnotateSV.git" \
+    org.opencontainers.image.vcs-ref=${VCS_REF}
+
+LABEL org.opencontainers.image.description="This container uses python 3.10.14 as the base image to build \
+    iAnnotateSV version ${iAnnotateSV_VERSION}"
+
+################## INSTALL ##########################
+
+WORKDIR /app
+ADD . /app
+
+# install iAnnotateSV 
+
+RUN apt-get update && apt-get install --no-install-recommends -y gcc g++ zlib1g-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && make deps-install \ 
+    && poetry build \
+    && pip install dist/iAnnotateSV-*-py3-none-any.whl

Makefile

@@ -1,5 +1,14 @@
-init:
-	pip install -r requirements.txt
+# options
+.ONESHELL:
 
-test:
-	nosetests -v --with-coverage --cover-tests tests
+
+.PHONY: deps-install
+deps-install:  ## install dependencies
+	pip install poetry
+	poetry install 
+
+requirements.txt: poetry.lock
+	poetry export --format requirements.txt --output requirements.txt --without-hashes
+
+requirements-dev.txt: poetry.lock
+	poetry export --with dev --format requirements.txt --output requirements-dev.txt --without-hashes

README.rst

@@ -10,23 +10,9 @@ iAnnotateSV: Annotation of structural variants detected from NGS
 .. image:: https://img.shields.io/pypi/v/iAnnotateSV.svg
         :target: https://pypi.python.org/pypi/iAnnotateSV
 
-.. image:: https://landscape.io/github/rhshah/iAnnotateSV/master/landscape.svg?style=flat
-   :target: https://landscape.io/github/rhshah/iAnnotateSV/master
-   :alt: Code Health
-
-
 .. image:: https://zenodo.org/badge/18929/rhshah/iAnnotateSV.svg
    :target: https://zenodo.org/badge/latestdoi/18929/rhshah/iAnnotateSV
 
-
-.. image:: https://travis-ci.org/rhshah/iAnnotateSV.svg?branch=master
-    :target: https://travis-ci.org/rhshah/iAnnotateSV
-
-
-.. image:: https://codecov.io/gh/rhshah/iAnnotateSV/branch/master/graph/badge.svg
-  :target: https://codecov.io/gh/rhshah/iAnnotateSV
-
-
 iAnnotateSV is a Python library and command-line software toolkit to annotate and
 visualize structural variants detected from Next Generation DNA sequencing data. This works for majority is just re-writing of a tool called dRanger_annotate written in matlab by Mike Lawrence at Broad Institue. 
 But it also has some additional functionality and control over the annotation w.r.t the what transcripts to be used for annotation.
@@ -48,13 +34,18 @@ Required Packages
 =================
 We require that you install:
 
-:python: `v2.7.15 <https://www.python.org/downloads/release/python-2715/>`_
-:pandas: `v0.24.2 <http://pandas.pydata.org/>`_
-:biopython: `v1.76 <http://biopython.org/wiki/Main_Page>`_
-:Pillow: `v6.2.1 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
-:openpyxl: `v2.6.4 <https://pypi.python.org/pypi/openpyxl/2.6.4>`_
-:reportlab: `v3.5.2 <https://pypi.python.org/pypi/reportlab/3.5.2>`_
-:coloredlogs: `v14.0 <https://pypi.python.org/pypi/coloredlogs>`_
+:python: `v3.10.14 <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/>`_
+:openpyxl: `v3.1.5 <https://pypi.python.org/pypi/openpyxl/>`_
+:reportlab: `v3.6.13 <https://pypi.python.org/pypi/reportlab/>`_
+:coloredlogs: `v15.0.1 <https://pypi.python.org/pypi/coloredlogs>`_
+
+Utilities
+=========
+
+`Generate Fusion Peptides <./generate_fusion_peptides/README.md>`_ - Helen Xie
 
 Quick Usage
 ===========

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 9f362582164ff56ce148b5cb1ccd33fe
+config: 2053fac6e0c6125adcfdafa8b47c0de3
 tags: 645f666f9bcd5a90fca523b33c5a78b7