Merge pull request #55 from NCI-GDC/feat/binf-726-template

[BINF-726] Apply cookiecutter template

.cruft.json

@@ -0,0 +1,20 @@
+{
+    "template": "[email protected]:NCI-GDC/bio-python-template.git",
+    "commit": "2538d116b1c2f3cf68b734c5a5179a4fc70acc9f",
+    "context": {
+      "cookiecutter": {
+        "full_name": "Charles Czysz",
+        "email": "[email protected]",
+        "github_username": "czyszCTDS",
+        "project_name": "maf-lib",
+        "package_name": "maflib",
+        "project_short_description": "Python package for processing and creating MAF files for the GDC",
+        "min_python_version": "3.8",
+        "github_repo": "https://github.com/NCI-GDC/maf-lib",
+        "commit": "2538d116b1c2f3cf68b734c5a5179a4fc70acc9f",
+        "_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

@@ -109,5 +109,5 @@ ENV/
 .vscode/
 test-reports/
 
-# Gitlab
+# Gitlab CI
 vars.env

.gitlab-ci.yml

@@ -1,3 +1,4 @@
+---
 # 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:
@@ -26,27 +27,26 @@ release:
 .python_versions:
   parallel:
     matrix:
-      - REPO_PY_VERSION: [python3.8, python3.10]
+      - REPO_PY_VERSION: [python3.8]
 
 docker_build:
   rules:
-    - when: always
-    - if: '$CI_PIPELINE_SOURCE == "schedule"'
-      when: never
-    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_TAG
       variables:
-        RELEASE_REGISTRY: containers.osdc.io/ncigdc  # Override globally-defined RELEASE_REGISTRY
+        DOCKER_RELEASE_REGISTRY: "quay.io"
     - if: $CI_COMMIT_REF_NAME =~ /main/
       variables:
-        RELEASE_REGISTRY: containers.osdc.io/ncigdc
+        DOCKER_RELEASE_REGISTRY: "quay.io"
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+      variables:
+        DOCKER_RELEASE_REGISTRY: "quay.io"
+    - when: always
   script:
-    - echo "docker build ${DOCKER_BUILD_OPTS} -t ${RELEASE_REGISTRY}/$CI_PROJECT_NAME:$VERSION ."
-    - echo "docker push ${DOCKER_PUSH_OPTS} ${RELEASE_REGISTRY}/$CI_PROJECT_NAME:$VERSION"
     - docker build . 
       --file ./Dockerfile
       ${DOCKER_BUILD_OPTS}
       --build-arg http_proxy
       --build-arg https_proxy
       --build-arg BASE_CONTAINER_VERSION
-      -t ${RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}
-    - docker push ${DOCKER_PUSH_OPTS} ${RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}
+      -t ${DOCKER_RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}
+    - docker push ${DOCKER_PUSH_OPTS} ${DOCKER_RELEASE_REGISTRY}/${CI_PROJECT_NAME}:${VERSION}

.secrets.baseline

@@ -1,19 +1,18 @@
 {
-  "exclude": {
-    "files": null,
-    "lines": null
-  },
-  "generated_at": "2020-07-23T15:23:24Z",
+  "version": "1.2.0",
   "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
     {
       "name": "AWSKeyDetector"
     },
     {
-      "name": "ArtifactoryDetector"
+      "name": "AzureStorageKeyDetector"
     },
     {
-      "base64_limit": 4.5,
-      "name": "Base64HighEntropyString"
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
     },
     {
       "name": "BasicAuthDetector"
@@ -22,8 +21,11 @@
       "name": "CloudantDetector"
     },
     {
-      "hex_limit": 3,
-      "name": "HexHighEntropyString"
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3
     },
     {
       "name": "IbmCloudIamDetector"
@@ -35,32 +37,94 @@
       "name": "JwtTokenDetector"
     },
     {
-      "keyword_exclude": null,
-      "name": "KeywordDetector"
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
     },
     {
       "name": "MailchimpDetector"
     },
+    {
+      "name": "NpmDetector"
+    },
     {
       "name": "PrivateKeyDetector"
     },
+    {
+      "name": "SendGridDetector"
+    },
     {
       "name": "SlackDetector"
     },
     {
       "name": "SoftlayerDetector"
     },
+    {
+      "name": "SquareOAuthDetector"
+    },
     {
       "name": "StripeDetector"
     },
     {
       "name": "TwilioKeyDetector"
     }
   ],
-  "results": {},
-  "version": "0.13.1",
-  "word_list": {
-    "file": null,
-    "hash": null
-  }
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    },
+    {
+      "path": "detect_secrets.filters.regex.should_exclude_file",
+      "pattern": [
+        "^.secrets.baseline$"
+      ]
+    }
+  ],
+  "results": {
+    ".cruft.json": [
+      {
+        "type": "Hex High Entropy String",
+        "filename": ".cruft.json",
+        "hashed_secret": "7379565c0e0821137830796e10f09f31692c2ad2",
+        "is_verified": false,
+        "line_number": 3,
+        "is_secret": false
+      }
+    ]
+  },
+  "generated_at": "2022-10-03T14:39:09Z"
 }

Dockerfile

@@ -1,4 +1,4 @@
-ARG REGISTRY=quay.io
+ARG REGISTRY=docker.osdc.io
 ARG BASE_CONTAINER_VERSION=2.0.1
 
 FROM ${REGISTRY}/ncigdc/python3.8-builder:${BASE_CONTAINER_VERSION} as builder
@@ -11,14 +11,14 @@ RUN pip install tox && tox -e build
 
 FROM ${REGISTRY}/ncigdc/python3.8:${BASE_CONTAINER_VERSION}
 
-COPY --from=builder /opt/dist/*.tar.gz /opt
-COPY requirements.txt /opt
+COPY --from=builder /opt/dist/*.whl /opt/
+COPY requirements.txt /opt/
 
 WORKDIR /opt
 
 RUN pip install --no-deps -r requirements.txt \
-	&& pip install --no-deps *.tar.gz \
-	&& rm -f *.tar.gz requirements.txt
+	&& pip install --no-deps *.whl \
+	&& rm -f *.whl requirements.txt
 
 ENTRYPOINT ["maflib"]