feat: Release v13.0.0

.bumpversion.cfg

@@ -6,8 +6,6 @@ tag_name = v{new_version}
 
 [bumpversion:file:CITATION.cff]
 
-[bumpversion:file:BALSAMIC/containers/balsamic/Dockerfile]
-
 [bumpversion:file:BALSAMIC/__version__.py]
 
 [bumpversion:file:BALSAMIC/__init__.py]
@@ -21,5 +19,8 @@ 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"

.github/workflows/docker_build_publish_develop.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
+        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, purecn, somalier, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout
@@ -39,6 +39,11 @@ jobs:
           tags: clinicalgenomics/balsamic:develop-${{ matrix.container-name }}
           build-args: CONTAINER_NAME=${{ matrix.container-name }}
           provenance: false
+      - name: Prune containers
+        id: docker_prune_containers
+        shell: bash
+        run: |
+          docker system prune -a -f
       - name: Test container
         id: docker_test_container
         shell: bash

.github/workflows/docker_build_publish_release.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        container-name: [align_qc, annotate, coverage_qc, varcall_cnvkit, varcall_py27, varcall_py3, balsamic, delly, vcf2cytosure, cnvpytor, somalier, ascatNgs]
+        container-name: [align_qc, annotate, ascatNgs, cadd, cnvkit, cnvpytor, coverage_qc, delly, gatk, htslib, purecn, somalier, varcall_py3, varcall_py27, vcf2cytosure]
     steps:
       - name: Git checkout
         id: git_checkout
@@ -39,6 +39,11 @@ jobs:
           tags: clinicalgenomics/balsamic:${{ steps.get_branch_name.outputs.branch }}-${{ matrix.container-name }}
           build-args: CONTAINER_NAME=${{ matrix.container-name }}
           provenance: false
+      - name: Prune containers
+        id: docker_prune_containers
+        shell: bash
+        run: |
+          docker system prune -a -f
       - name: Test container
         id: docker_test_container
         shell: bash

.github/workflows/pytest_and_coveralls.yml

@@ -27,6 +27,8 @@ jobs:
         with:
           activate-environment: balsamic
           environment-file: BALSAMIC/conda/balsamic.yaml
+      - name: Install the HTML to PDF renderer
+        run: sudo apt-get update && sudo apt-get install -y wkhtmltopdf
       # Install BALSAMIC
       - name: Install BALSAMIC
         id: install_balsamic

.github/workflows/urls_check.yml

@@ -15,5 +15,5 @@ jobs:
       - name: Link Checker
         uses: lycheeverse/lychee-action@v1.8.0
         with:
-          args: --verbose './BALSAMIC/constants/reference.py' './docs/*.rst'
+          args: --verbose './BALSAMIC/constants/cache.py' './docs/*.rst'
           fail: true

.lycheeignore

@@ -1,4 +1,6 @@
 https:\/\/gatk\.broadinstitute\.org\/hc\/.*
 https:\/\/cancer\.sanger\.ac\.uk\/cosmic\/file_download\/.*
 https:\/\/doi.org\/10.1073\/pnas.*
+https:\/\/doi.org\/10.1093\/bioinformatics\/.*
+https:\/\/drive.google.com\/.*
 https://doi.org/10.1002/cpbi.17

.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

@@ -5,9 +5,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
-    python: "3.7"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

BALSAMIC/assets/__init__.py

@@ -1,9 +0,0 @@
-import pkg_resources
-
-##### FILES #####
-
-cg_logo = "assets/cg.png"
-
-##### Paths #####
-
-cg_logo_path = pkg_resources.resource_filename("BALSAMIC", cg_logo)