Merge pull request #16 from czbiohub/pranathi-gh

add github actions

.github/pull_request_template.md

@@ -0,0 +1,11 @@
+Many thanks to contributing to czbiohub/xicor!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
+
+## PR checklist
+ - [ ] This comment contains a description of changes (with reason)
+ - [ ] If you've fixed a bug or added code that should be tested, add tests!
+ - [ ] Ensure the test suite passes with [pytest](https://docs.pytest.org/en/latest/) . (command to run: `pytest` or `make coverage` if you want to see which lines don't have tests yet)
+ - [ ] Make sure your code is linted and autoformatted using [black](https://github.com/psf/black) (`black . --check`).
+ - [ ] Documentation in `usage.md` is updated
+ - [ ] `README.md` is updated

.github/workflows/ci.yml

@@ -0,0 +1,40 @@
+name: Pytest
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on: [push, pull_request]
+
+jobs:
+  test:
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and current latest
+        python-version: ['3.5']
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies with Python ${{ matrix.python-version }}
+        shell: bash -l {0}
+        run: |
+          conda env create -n testenv --file environment.yml
+          conda activate testenv
+          pip install .
+      - name: Run tests with coverage
+        shell: bash -l {0}
+        run: |
+          conda activate testenv
+          pip install -r requirements.txt
+          make coverage
+      - name: Send coverage to codecov.io
+        shell: bash -l {0}
+        run: |
+          pip install codecov
+          bash <(curl -s https://codecov.io/bash)

.github/workflows/linting.yml

@@ -0,0 +1,21 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# black code formatter github action: https://github.com/marketplace/actions/black-code-formatter
+
+name: Linting
+
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+  check_formatting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: black
+      uses: psf/black@stable
+      with:
+        args: ". --check"

.github/workflows/publish-pypi.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

environment.yml

@@ -5,13 +5,9 @@ channels:
   - r
   - defaults
 dependencies:
-  - flake8
   - pandas
   - pytest-cov
   - seaborn
   - numpy
   - scipy
   - ipykernel
-  - pip:
-    - xicor
-prefix: /Users/olgabot/opt/anaconda3/envs/xicor

release.md

@@ -90,7 +90,7 @@ deactivate
 source bin/activate
 pip install -U setuptools
 # install as much as possible from non-test server!
-pip install pytest pytest-cov scipy numpy flake8
+pip install pytest pytest-cov scipy numpy
 pip install -i https://test.pypi.org/simple --pre xicor
 ```
 5\. Do any final testing:

requirements.txt

@@ -2,4 +2,4 @@ scipy>=1.4.1
 pytest
 pytest-cov
 numpy
-flake8
+black

setup.py

@@ -1,17 +1,15 @@
 import setuptools
 
-with open('README.md') as readme_file:
+with open("README.md") as readme_file:
     readme = readme_file.read()
 
-with open('HISTORY.md') as history_file:
-    history = history_file.read().replace('.. :changelog:', '')
+with open("HISTORY.md") as history_file:
+    history = history_file.read().replace(".. :changelog:", "")
 
-with open('requirements.txt') as requirements_file:
+with open("requirements.txt") as requirements_file:
     requirements = requirements_file.read()
 
-test_requirements = [
-    'pytest', 'coverage', "pytest-cov"
-]
+test_requirements = ["pytest", "coverage", "pytest-cov"]
 
 
 setuptools.setup(
@@ -25,25 +23,23 @@
     long_description_content_type="text/markdown",
     url="https://github.com/czbiohub/xicor/",
     packages=setuptools.find_packages(
-        exclude=[
-            "tests",
-            "*.tests",
-            "*.tests.*",
-            "tests.*",
-            "test_*"]),
+        exclude=["tests", "*.tests", "*.tests.*", "tests.*", "test_*"]
+    ),
     include_package_data=True,
     install_requires=requirements,
     setup_requires=[
-        "setuptools>=38.6.0", "setuptools_scm", 'setuptools_scm_git_archive'],
+        "setuptools>=38.6.0",
+        "setuptools_scm",
+        "setuptools_scm_git_archive",
+    ],
     license="MIT",
     zip_safe=False,
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    use_scm_version={
-        'write_to': 'xicor/version.py'},
-    test_suite='tests',
-    extras_require={'test': test_requirements}
+    use_scm_version={"write_to": "xicor/version.py"},
+    test_suite="tests",
+    extras_require={"test": test_requirements},
 )

tests/conftest.py

@@ -9,19 +9,10 @@ def anscombes_quartet():
         "x_2": [10, 8, 13, 9, 11, 14, 6, 4, 12, 7, 5],
         "x_3": [0, 0, 0, 0, 1, 1, 2, 3],
         "x_4": [8, 8, 8, 8, 8, 8, 8, 19, 8, 8, 8],
-        "y_1": [
-            8.04, 6.95, 7.58, 8.81, 8.33,
-            9.96, 7.24, 4.26, 10.84, 4.82, 5.68
-        ],
-        "y_2": [
-            9.14, 8.14, 8.74, 8.77, 9.26, 8.1,
-            6.13, 3.1, 9.13, 7.26, 4.74
-        ],
+        "y_1": [8.04, 6.95, 7.58, 8.81, 8.33, 9.96, 7.24, 4.26, 10.84, 4.82, 5.68],
+        "y_2": [9.14, 8.14, 8.74, 8.77, 9.26, 8.1, 6.13, 3.1, 9.13, 7.26, 4.74],
         "y_3": [0, 1, 2, 3, 4, 5, 6, 7],
-        "y_4": [
-            6.58, 5.76, 7.71, 8.84,
-            8.47, 7.04, 5.25, 12.5, 5.56, 7.91, 6.89
-        ]
+        "y_4": [6.58, 5.76, 7.71, 8.84, 8.47, 7.04, 5.25, 12.5, 5.56, 7.91, 6.89],
     }
 
     return anscombes_quartet

tests/xi_test.py

@@ -4,7 +4,7 @@
 
 from xicor.xicor import Xi
 
-'''
+"""
 From Wikipedia:
 Anscombe's quartet comprises four data sets that have nearly
 identical simple descriptive statistics, yet have very different distributions
@@ -13,7 +13,7 @@
 statistician Francis Anscombe to demonstrate both the importance of graphing
 data before analyzing it and the effect of outliers and other influential
 observations on statistical properties.
-'''
+"""
 
 
 @pytest.fixture
@@ -43,11 +43,19 @@ def test_p_val_asymptotic(anscombes_xis):
     random.seed(2020)
     np.random.seed(2020)
     # values taken from R code
-    assert anscombes_xis["xi_1"].pval_asymptotic(
-        ties=False, nperm=1000) == 0.07841556446646347
-    assert anscombes_xis["xi_2"].pval_asymptotic(
-        ties=False, nperm=1000) == 0.0010040217037570187
-    assert anscombes_xis["xi_3"].pval_asymptotic(
-        ties=False, nperm=1000) == 0.04989192742513937
-    assert anscombes_xis["xi_4"].pval_asymptotic(
-        ties=False, nperm=1000) == 0.2599336349448975
+    assert (
+        anscombes_xis["xi_1"].pval_asymptotic(ties=False, nperm=1000)
+        == 0.07841556446646347
+    )
+    assert (
+        anscombes_xis["xi_2"].pval_asymptotic(ties=False, nperm=1000)
+        == 0.0010040217037570187
+    )
+    assert (
+        anscombes_xis["xi_3"].pval_asymptotic(ties=False, nperm=1000)
+        == 0.04989192742513937
+    )
+    assert (
+        anscombes_xis["xi_4"].pval_asymptotic(ties=False, nperm=1000)
+        == 0.2599336349448975
+    )

xicor/__init__.py

@@ -1,19 +1,19 @@
 from pkg_resources import get_distribution, DistributionNotFound
 
 
-__version__ = '0.1.0dev0'
+__version__ = "0.1.0dev0"
 
 
-__title__ = 'xicor'
-__description__ = 'xi correlation for tied data'
-__uri__ = 'https://github.com/czbiohub/xicor'
-__doc__ = __description__ + ' <' + __uri__ + '>'
+__title__ = "xicor"
+__description__ = "xi correlation for tied data"
+__uri__ = "https://github.com/czbiohub/xicor"
+__doc__ = __description__ + " <" + __uri__ + ">"
 
-__author__ = 'Phoenix Logan'
-__email__ = '[email protected]'
+__author__ = "Phoenix Logan"
+__email__ = "[email protected]"
 
-__license__ = 'MIT License'
-__copyright__ = 'Copyright (c) 2020 Chan Zuckerberg Biohub'
+__license__ = "MIT License"
+__copyright__ = "Copyright (c) 2020 Chan Zuckerberg Biohub"
 
 
 try: