Merge pull request #43 from cancervariants/issue-42

Issue 42

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+source =
+   variant/
+   tests/
+omit =
+   setup.py
+   docs/*

.ebextensions/00sample_log.config

@@ -0,0 +1,8 @@
+files:
+  "/opt/elasticbeanstalk/tasks/bundlelogs.d/01-sample-app.conf":
+    content: |
+      /tmp/sample-app*
+
+  "/opt/elasticbeanstalk/tasks/taillogs.d/01-sample-app.conf":
+    content: |
+      /tmp/sample-app.log

.flake8

@@ -0,0 +1,9 @@
+[flake8]
+ignore = D205, D400
+exclude =
+  .git
+  venv
+  __pycache__
+  source
+  outputs
+  docs/*

.github/workflows/github-actions.yml

@@ -0,0 +1,20 @@
+name: github-actions
+on: [push, pull_request]
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Setup Python
+              uses: actions/setup-python@v1
+              with:
+                  python-version: 3.7
+
+            - name: Install dependencies
+              run: |
+                  python3 -m pip install pipenv
+                  pipenv install --dev
+
+            - run: pipenv run flake8
+            - run: pipenv run pytest tests/

.gitignore

@@ -5,6 +5,7 @@ instance/
 
 .pytest_cache/
 .coverage
+.coverage.*
 htmlcov/
 .vim/
 
@@ -16,4 +17,14 @@ dist/
 .mypy_cache/
 
 
-varlexapp/data/seqrepo/
+variant/data/seqrepo/
+variant/data/notebooks
+
+Pipfile.lock
+
+.python-version
+
+pyproject.toml
+
+# Jupyter Notebook
+.ipynb_checkpoints/

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.4.0
+    hooks:
+    - id: flake8
+      additional_dependencies: [flake8-docstrings]
+    - id: check-added-large-files
+    - id: detect-private-key

EBSampleApp-Python.iml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="GoLibraries">
+    <option name="urls">
+      <set>
+        <option value="file://$MODULE_DIR$" />
+      </set>
+    </option>
+  </component>
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/build" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 3.6 (NEWRELEASE)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

Pipfile

@@ -4,93 +4,95 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
+pytest = "*"
+jupyterlab = "*"
+pytest-cov = "*"
+flake8 = "*"
+coveralls = "*"
+coverage = "*"
+flake8-docstrings = "*"
+pre-commit = "*"
+variant-normalization = {editable = true, path = "."}
 
 [packages]
-apispec = "==2.0.2"
-apispec-oneofschema = "==2.1.0"
-apispec-webframeworks = "==0.4.0"
-appdirs = "==1.4.3"
-appnope = "==0.1.0"
-astroid = "==2.2.5"
-atomicwrites = "==1.3.0"
-attrs = "==19.3.0"
-beautifulsoup4 = "==4.8.0"
-"biocommons.seqrepo" = "==0.5.1"
-biopython = "==1.69"
-bioutils = "==0.5.0"
-bs4 = "==0.0.1"
-certifi = "==2019.9.11"
-chardet = "==3.0.4"
-click = "==7.0"
-coloredlogs = "==10.0"
-configparser = "==4.0.2"
-cssselect = "==1.0.3"
-decorator = "==4.4.1"
-enum34 = "==1.1.6"
-fake-useragent = "==0.1.11"
-hgvs = "==1.3.0.post0"
-humanfriendly = "==4.18"
-idna = "==2.8"
-importlib-metadata = "==0.23"
-iniherit = "==0.3.9"
-ipython = "==5.8.0"
-isort = "==4.3.21"
-itsdangerous = "==1.1.0"
-jedi = "==0.15.1"
-lazy-object-proxy = "==1.4.2"
-lxml = "==4.3.4"
-marshmallow = "==3.2.0"
-marshmallow-enum = "==1.5.1"
-marshmallow-oneofschema = "==2.0.1"
-mccabe = "==0.6.1"
-more-itertools = "==7.2.0"
-mypy = "==0.761"
-mypy-extensions = "==0.4.3"
-numpy = "==1.17.2"
-parse = "==1.12.0"
-parso = "==0.5.1"
-pexpect = "==4.7.0"
-pickleshare = "==0.7.5"
-pluggy = "==0.13.0"
-prompt-toolkit = "==1.0.18"
-psycopg2-binary = "==2.8.4"
-ptyprocess = "==0.6.0"
-py = "==1.8.0"
-pyee = "==6.0.0"
-pylint = "==2.3.1"
-pyparsing = "==2.4.5"
-pyppeteer = "==0.0.25"
-pyquery = "==1.4.0"
-pysam = "==0.15.2"
-pytest = "==5.2.2"
-requests = "==2.22.0"
-requests-html = "==0.10.0"
-seqrepo = "==0.0.0"
-simplegeneric = "==0.8.1"
-six = "==1.12.0"
-soupsieve = "==1.9.2"
-text-unidecode = "==1.2"
-tqdm = "==4.32.2"
-traitlets = "==4.3.3"
-typed-ast = "==1.4.0"
-typing-extensions = "==3.7.4.1"
-urllib3 = "==1.25.3"
-w3lib = "==1.20.0"
-wcwidth = "==0.1.7"
-websockets = "==8.0.1"
-wrapt = "==1.11.2"
-yoyo-migrations = "==6.1.0"
-zipp = "==0.6.0"
-Flask = "==1.1.1"
-Flask-Cors = "==3.0.8"
-ipython_genutils = "==0.2.0"
-Jinja2 = "==2.10.1"
-MarkupSafe = "==1.1.1"
-Parsley = "==1.3"
-Pygments = "==2.4.2"
-PyYAML = "==5.1.2"
-uWSGI = "==2.0.18"
-Werkzeug = "==0.16.0"
-
-[requires]
-python_version = "3.7"
+appdirs = "*"
+appnope = "*"
+astroid = "*"
+atomicwrites = "*"
+beautifulsoup4 = "*"
+biopython = "*"
+bioutils = "*"
+bs4 = "*"
+certifi = "*"
+chardet = "*"
+click = "*"
+coloredlogs = "*"
+configparser = "*"
+cssselect = "*"
+decorator = "*"
+enum34 = "*"
+fake-useragent = "*"
+hgvs = "*"
+humanfriendly = "*"
+idna = "*"
+importlib-metadata = "*"
+iniherit = "*"
+isort = "*"
+itsdangerous = "*"
+jedi = "*"
+lazy-object-proxy = "*"
+lxml = "*"
+mccabe = "*"
+more-itertools = "*"
+mypy = "*"
+mypy-extensions = "*"
+numpy = "*"
+parse = "*"
+parso = "*"
+pexpect = "*"
+pickleshare = "*"
+prompt-toolkit = "*"
+psycopg2-binary = "*"
+ptyprocess = "*"
+pyee = "*"
+pylint = "*"
+pyppeteer = "*"
+pyquery = "*"
+pysam = "*"
+requests = "*"
+requests-html = "*"
+seqrepo = "*"
+simplegeneric = "*"
+six = "*"
+soupsieve = "*"
+text-unidecode = "*"
+tqdm = "*"
+traitlets = "*"
+typed-ast = "*"
+typing-extensions = "*"
+urllib3 = "*"
+w3lib = "*"
+wcwidth = "*"
+websockets = "*"
+wrapt = "*"
+yoyo-migrations = "*"
+zipp = "*"
+ipython_genutils = "*"
+Jinja2 = "*"
+MarkupSafe = "*"
+Parsley = "*"
+PyYAML = "*"
+"biocommons.seqrepo" = "*"
+fastapi = "*"
+uvicorn = "*"
+pydantic = "*"
+pluggy = "*"
+attrs = "*"
+pyparsing = "*"
+uvloop = "*"
+httptools = "*"
+py = "*"
+python-dotenv = "*"
+twine = "*"
+werkzeug = "*"
+"ga4gh.vrs" = {extras = ["extras"], version = "*"}