add basic ci setup

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: daily
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "daily"

.github/workflows/main.yaml

@@ -0,0 +1,91 @@
+name: CI
+
+on:
+  push:
+    branches: "*"
+  pull_request:
+    branches: main
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - uses: actions/setup-python@v2.2.2
+      - uses: pre-commit/action@v2.0.3
+
+  test:
+    name: ${{ matrix.python-version }}-build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+          activate-environment: datatree
+          environment-file: ci/environment.yml
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Install datatree
+        shell: bash -l {0}
+        run: |
+          python -m pip install --no-deps -e .
+          python -m pip list
+      - name: Running Tests
+        shell: bash -l {0}
+        run: |
+          python -m pytest --cov=./ --cov-report=xml --verbose
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v2.0.2
+      #   if: ${{ matrix.python-version }} == 3.8
+      #   with:
+      #     file: ./coverage.xml
+      #     fail_ci_if_error: false
+
+  test-upstream:
+    name: ${{ matrix.python-version }}-dev-build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9]
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+          activate-environment: datatree
+          environment-file: ci/environment.yml
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Install dev reqs
+        shell: bash -l {0}
+        run: |
+          python -m pip install --no-deps --upgrade \
+            git+https://github.com/pydata/xarray \
+            git+https://github.com/Unidata/netcdf4-python \
+            git+https://github.com/c0fec0de/anytree
+          python -m pip install --no-deps -e .
+          python -m pip list
+      - name: Running Tests
+        shell: bash -l {0}
+        run: |
+          python -m pytest --verbose

.github/workflows/pypipublish.yaml

@@ -0,0 +1,26 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - name: Set up Python
+        uses: actions/setup-python@v2.2.1
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools setuptools-scm 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/*

.pre-commit-config.yaml

@@ -0,0 +1,56 @@
+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+  # isort should run before black as black sometimes tweaks the isort output
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.9.3
+    hooks:
+      - id: isort
+  # https://github.com/python/black#version-control-integration
+  - repo: https://github.com/psf/black
+    rev: 21.7b0
+    hooks:
+      - id: black
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.4
+    hooks:
+      - id: blackdoc
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.9.2
+    hooks:
+      - id: flake8
+  # - repo: https://github.com/Carreau/velin
+  #   rev: 0.0.8
+  #   hooks:
+  #     - id: velin
+  #       args: ["--write", "--compact"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+      - id: mypy
+        # Copied from setup.cfg
+        exclude: "properties|asv_bench"
+        additional_dependencies: [
+            # Type stubs
+            types-python-dateutil,
+            types-pkg_resources,
+            types-PyYAML,
+            types-pytz,
+            # Dependencies that are typed
+            numpy,
+            typing-extensions==3.10.0.0,
+          ]
+  # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
+  # - repo: https://github.com/asottile/pyupgrade
+  #   rev: v1.22.1
+  #   hooks:
+  #     - id: pyupgrade
+  #       args:
+  #         - "--py3-only"
+  #         # remove on f-strings in Py3.7
+  #         - "--keep-percent-format"

ci/environment.yml

@@ -0,0 +1,13 @@
+name: datatree
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - xarray >=0.19.0
+  - netcdf4
+  - anytree
+  - pytest
+  - flake8
+  - black
+  - codecov
+  - pytest-cov

datatree/_version.py

@@ -1 +1 @@
-__version__ = "0.1.dev9+g805d97f.d20210817"
+__version__ = "0.1.dev46+g415cbb7.d20210825"

dev-requirements.txt

@@ -0,0 +1,6 @@
+pytest
+flake8
+black
+codecov
+pytest-cov
+-r requirements.txt

requirements.txt

@@ -0,0 +1,4 @@
+xarray>=0.19.0
+netcdf4
+anytree
+future

setup.py

@@ -1,24 +1,21 @@
+from os.path import exists
 from setuptools import find_packages, setup
 
-install_requires = [
-    "xarray>=0.19.0",
-    "netcdf4"
-    "anytree",
-    "future",
-]
 
-extras_require = {'tests':
-    [
-        "pytest",
-        "flake8",
-        "black",
-        "codecov",
-    ]
-}
+with open('requirements.txt') as f:
+    install_requires = f.read().strip().split('\n')
+
+if exists('README.rst'):
+    with open('README.rst') as f:
+        long_description = f.read()
+else:
+    long_description = ''
+
 
 setup(
     name="datatree",
     description="Hierarchical tree-like data structures for xarray",
+    long_description=long_description,
     url="https://github.com/TomNicholas/datatree",
     author="Thomas Nicholas",
     author_email="thomas.nicholas@columbia.edu",
@@ -29,11 +26,13 @@
         "Topic :: Scientific/Engineering",
         "License :: OSI Approved :: Apache License",
         "Operating System :: OS Independent",
+        "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
     ],
     packages=find_packages(exclude=["docs", "tests", "tests.*", "docs.*"]),
     install_requires=install_requires,
-    extras_require=extras_require,
     python_requires=">=3.7",
     setup_requires="setuptools_scm",
     use_scm_version={