First set of tools (#1)

* First set of tools

.github/workflows/pythonpackage.yml

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+name: Python package
+
+on: [push]
+env:
+  POETRY_VERSION: 1.0
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: [3.8]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{matrix.PYTHON_VERSION}}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.PYTHON_VERSION}}
+    - name: Install poetry
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry==${{env.POETRY_VERSION}}
+    - name: Install deps
+      run: |
+        poetry install
+    - name: Run pytest
+      run: |
+        poetry run python -m pytest --cov=pyfgaws --cov-branch
+    - name: Style checking
+      run: |
+        poetry run black --line-length 99 --check pyfgaws
+    - name: Run lint
+      run: |
+        poetry run flake8 --config=ci/flake8.cfg pyfgaws
+    - name: Run mypy
+      run: |
+        poetry run mypy -p pyfgaws --config=ci/mypy.ini

.gitignore

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+# PyCharm
+.idea
+
+# Python compiled & optimized files
+*.pyc
+*.pyo
+
+# MyPy Cache directory
+.mypy_cache
+
+# for develop installs
+*.egg-info
+
+# venv set up
+.venv
+dist/

LICENSE

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+The MIT License
+
+Copyright (c) 2020 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

ci/check.sh

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+#!/bin/bash
+
+function banner() {
+    echo
+    echo "================================================================================"
+    echo $*
+    echo "================================================================================"
+    echo
+}
+
+#####################################################################
+# Takes two parameters, a "name" and a "command".
+# Runs the command and prints out whether it succeeded or failed, and
+# also tracks a list of failed steps in $failures.
+#####################################################################
+function run() {
+    local name=$1
+    local cmd=$2
+
+    banner "Running $name [$cmd]"
+    set +e
+    $cmd
+    exit_code=$?
+    set -e
+
+    if [[ $exit_code == 0 ]]; then
+        echo Passed $name: "[$cmd]"
+    else
+        echo Failed $name: "[$cmd]"
+        if [ -z "$failures" ]; then
+            failures="$failures $name"
+        else
+            failures="$failures, $name"
+        fi
+    fi
+}
+
+parent=$(cd $(dirname $0) && pwd -P)
+
+banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory ${root}"
+run "Unit Tests"     "python -m pytest -vv -r sx pyfgaws"
+run "Style Checking" "black --line-length 99 --check pyfgaws"
+run "Linting"        "flake8 --config=$parent/flake8.cfg pyfgaws"
+run "Type Checking"  "mypy -p pyfgaws --config $parent/mypy.ini"
+
+if [ -z "$failures" ]; then
+    banner "Checks Passed"
+else
+    banner "Checks Failed with failures in: $failures"
+    exit 1
+fi

ci/flake8.cfg

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+# flake8 config file
+
+[flake8]
+max_line_length = 100
+show-source = true
+ignore = E701 W504 W503

ci/mypy.ini

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+[mypy]
+strict_optional = False
+ignore_missing_imports = True
+disallow_untyped_decorators = False
+follow_imports = "silent"
+disallow_untyped_defs = True

conda-requirements.txt

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+# Setup python version and poetry
+python=3.8.2
+poetry=1.0.5