Feat/binf 769 gitlab (#5) (#6)

* Python3.8 Upgrade

.cruft.json

@@ -0,0 +1,20 @@
+{
+    "template": "[email protected]:NCI-GDC/bio-python-template.git",
+    "commit": "a73c331723b3083eb17bcfe6d9ec13e9bb892bdd",
+    "context": {
+      "cookiecutter": {
+        "full_name": "Charles Czysz",
+        "email": "[email protected]",
+        "github_username": "czyszCTDS",
+        "project_name": "gdc-tosvc-tools",
+        "package_name": "gdc_tosvc_tools",
+        "project_short_description": "Tools for GDC Tumor-only Somatic Variant Calling Workflow",
+        "min_python_version": "3.8",
+        "github_repo": "https://github.com/NCI-GDC/gdc-tosvc-tools",
+        "commit": "a73c331723b3083eb17bcfe6d9ec13e9bb892bdd",
+        "_template": "[email protected]:NCI-GDC/bio-python-template.git"
+      }
+    },
+    "directory": null,
+    "checkout": null
+  }

.dockerignore

@@ -0,0 +1,110 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# direnv
+.envrc
+.direnv/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode/
+test-reports/

.gitignore

@@ -1,59 +1,114 @@
-.vagrant
-.DS_Store
-
-#bioinformatics stuff
-*.bam
-*.bai
-*.fa
-*.fastq
-*.fasta
-*.gtf
-*.tbi
-*.vcf
-*.fai
-*.bed
-*.bedGraph
-*.bw
-*.bigWig
-*.amb
-*.ann
-*.pac
-*.refmap
-
-#archives
-*.bz2
-*.gz
-*.zip
-*.tar
-*.Z
-
-# Logs
-logs
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
 *.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
 
-# Runtime data
-pids
-*.pid
-*.seed
+# virtualenv
+.venv
+venv/
+ENV/
 
-# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
+# direnv
+.envrc
+.direnv/
 
-# Coverage directory used by tools like istanbul
-coverage
+# Spyder project settings
+.spyderproject
+.spyproject
 
-# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
+# Rope project settings
+.ropeproject
 
-# node-waf configuration
-.lock-wscript
+# mkdocs documentation
+/site
 
-# Compiled binary addons (http://nodejs.org/api/addons.html)
-build/Release
+# mypy
+.mypy_cache/
 
-# Dependency directory
-# https://www.npmjs.org/doc/misc/npm-faq.html#should-i-check-my-node_modules-folder-into-git-
-node_modules
+# VSCode
+.vscode/
+test-reports/
 
-# Debug log from npm
-npm-debug.log
+# Gitlab CI - automatically created, break flit validation
+vars.env
+gl-code-quality-report.html

.gitlab-ci.yml

@@ -0,0 +1,54 @@
+---
+# To contribute improvements to CI/CD templates, please follow the Development guide at:
+# https://docs.gitlab.com/ee/development/cicd/templates.html
+# This specific template is located at:
+# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Python.gitlab-ci.yml
+include:
+  - project: nci-gdc/gitlab-templates
+    ref: master
+    file:
+      - templates/global/full.yaml
+      - templates/python/full.yaml
+
+variables:
+ BASE_CONTAINER_VERSION: "2.1.0"
+ DOCKER_BUILDKIT: 1
+ PIP_EXTRA_INDEX_URL: https://nexus.osdc.io/repository/pypi-all/simple
+ DOCKER_BUILD_OPTS: "--build-arg PIP_EXTRA_INDEX_URL=https://nexus.osdc.io/repository/pypi-all/simple"
+
+tox:
+  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+  before_script:
+    - mkdir -p /usr/share/man/man1
+
+release:
+  image: ${BASE_CONTAINER_REGISTRY}/${REPO_PY_VERSION}-builder:${BASE_CONTAINER_VERSION}
+
+.python_versions:
+  parallel:
+    matrix:
+      - REPO_PY_VERSION: [python3.8]
+
+docker_build:
+  rules:
+    - if: $CI_COMMIT_TAG
+      variables:
+        DOCKER_RELEASE_REGISTRY: "quay.io"
+    - if: $CI_COMMIT_REF_NAME =~ /main/
+      variables:
+        DOCKER_RELEASE_REGISTRY: "quay.io"
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+      variables:
+        DOCKER_RELEASE_REGISTRY: "quay.io"
+    - when: always
+  script:
+    - docker build . 
+      --file ./Dockerfile
+      ${DOCKER_BUILD_OPTS}
+      --build-arg http_proxy
+      --build-arg https_proxy
+      --build-arg BASE_CONTAINER_VERSION
+      -t ${DOCKER_RELEASE_REGISTRY}/ncigdc/${CI_PROJECT_NAME}:${VERSION}
+      -t ${DOCKER_RELEASE_REGISTRY}/ncigdc/${CI_PROJECT_NAME}:${CI_COMMIT_SHA}
+    - docker push ${DOCKER_PUSH_OPTS} ${DOCKER_RELEASE_REGISTRY}/ncigdc/${CI_PROJECT_NAME}:${VERSION}
+    - docker push ${DOCKER_PUSH_OPTS} ${DOCKER_RELEASE_REGISTRY}/ncigdc/${CI_PROJECT_NAME}:${CI_COMMIT_SHA}

.pre-commit-config.yaml

@@ -1,6 +1,34 @@
+default_stages: [commit, push]
+default_language_version:
+  python_venv: python3.8
+
 repos:
--   repo: git@github.com:Yelp/detect-secrets
-    rev: v0.13.1
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.2.0
     hooks:
-    -   id: detect-secrets
+      - id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: detect-aws-credentials
+        args: ["--allow-missing-credentials"]
+      - id: detect-private-key
+      - id: end-of-file-fixer
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: '4.0.1'
+    hooks:
+    -   id: flake8
+        additional_dependencies: [flake8-docstrings]