Add CI testing of unittests and linting

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 120
+ignore = E203

.github/workflows/ci-tests.yml

@@ -0,0 +1,44 @@
+# 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
+
+name: Unit tests
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+  # Run on main because caches are inherited from parent branches
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7"]
+
+    # Set default shell to allow conda activate env to be passed from one step to the next
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Miniconda with Python ${{ matrix.python-version }}
+      uses: conda-incubator/[email protected]
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: environment.yml
+        clean-patched-environment-file: false
+    - name: Check Conda configuration
+      run: |
+        conda info -a
+        python --version
+    - name: Install repo using pip
+      run: |
+        python -m pip install .
+    - name: Test with pytest
+      run: |
+        # Limit to just the most problematic test during debugging
+        pytest --durations=0

.github/workflows/pre-commit.yml

@@ -0,0 +1,41 @@
+---
+# Adapted from https://github.com/alan-turing-institute/Python-quality-tools
+name: pre-commit action
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+  # Run on main because caches are inherited from parent branches
+env:
+  # This should be the default but we'll be explicit
+  PRE_COMMIT_HOME: ~/.caches/pre-commit
+jobs:
+  pre-commit_job:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.7"
+      - name: Install Pre-Commit
+        shell: bash
+        run: |
+          python -m pip install pre-commit
+      - name: Cache Pre-Commit Hooks
+        id: cache
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.PRE_COMMIT_HOME }}
+          key: ${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+      - name: Install Pre-Commit Hooks
+        shell: bash
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pre-commit install-hooks
+      - name: Run Pre-Commit Hooks
+        shell: bash
+        run: |
+          pre-commit run --all-files

.gitignore

@@ -113,4 +113,10 @@ pyveg/azure_config.py
 #docs things
 docs/build
 docs/source/_static
-docs/source/_templates
+docs/source/_templates
+
+# Test data
+pyveg/testdata/test_ne_england/
+
+# Virtual Environments
+env/

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+# Ignore RVeg and Notebooks for now
+exclude: (^rveg|^notebooks|^binder)
+default_language_version:
+    # force all unspecified python hooks to run python3
+    python: python3.7
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-xml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+    -   id: black
+        exclude: (^pyveg/configs|^pyveg/zenodo_config_template.py|^pyveg/azure_config_template.py)
+-   repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: 'v1.6.0'  # Use the sha / tag you want to point at
+    hooks:
+    -   id: autopep8
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    -   id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+# Ignore type checking for now, as this would require non-trival change to the code
+# in order to pass `mypy` tests
+# -   repo: https://github.com/pre-commit/mirrors-mypy
+#     rev: 'v0.960'  # Use the sha / tag you want to point at
+#     hooks:
+#     -   id: mypy

CONTRIBUTING.md

@@ -11,13 +11,17 @@ Don't let trying to be perfect get in the way of being good - exciting ideas are
 
 ## Table of contents
 
-- [Where to start: issues](#where-to-start-issues)
-- [Making a change with a pull request](#making-a-change-with-a-pull-request)
-  - [1. Comment on an existing issue or open a new issue referencing your addition](#1-comment-on-an-existing-issue-or-open-a-new-issue-referencing-your-addition)
-  - [2. Create a new branch (if you have *write* access to the repository) or fork the repository to your profile (if you don't currently have _write_ access)](#2-create-a-new-branch-or-fork-the-repository-to-your-profile)
-  - [3. Make the changes you've discussed](#3-make-the-changes-youve-discussed)
-  - [4. Submit a pull request](#4-submit-a-pull-request)
-- [Style guide](#style-guide)
+- [Contributing to monitoring-ecosystem-resilience (the repo!)](#contributing-to-monitoring-ecosystem-resilience-the-repo)
+  - [Table of contents](#table-of-contents)
+  - [Where to start: issues](#where-to-start-issues)
+  - [Making a change with a pull request](#making-a-change-with-a-pull-request)
+    - [1. Comment on an existing issue or open a new issue referencing your addition](#1-comment-on-an-existing-issue-or-open-a-new-issue-referencing-your-addition)
+    - [2. Create a new branch to your profile](#2-create-a-new-branch-or-forkgithub-fork-the-monitoring-ecosystem-resilience-repositorymonitoring-ecosystem-resilience-repo-to-your-profile)
+      - [2a) Create a branch](#2a-create-a-branch)
+      - [2b. Fork the repository](#2b-fork-the-repository)
+    - [3. Make the changes you've discussed](#3-make-the-changes-youve-discussed)
+    - [4. Submit a pull request](#4-submit-a-pull-request)
+  - [Style Guide](#style-guide)
 
 ## Where to start: issues
 
@@ -138,8 +142,7 @@ Simply make your edits on their files and open a pull request to their branch!
 
 What happens if the continuous integration (CI) fails (for example, if the pull request notifies you that "Some checks were not successful")?
 The CI could fail for a number of reasons.
-At the bottom of the pull request, where it says whether your build passed or failed, you can click “Details” next to the test, which takes you to the Travis page.
-You can view the log or rerun the checks if you have write access to the repo by clicking the “Restart build” button in the top right (you must be logged in to Travis CI with your GitHub account see the “Restart build” button).
+At the bottom of the pull request, where it says whether your build passed or failed, you can click “Details” next to the test, which takes you to the [GitHub Actions](https://github.com/urbangrammarai/gee_pipeline/actions) page. From there you can view the log or rerun the checks (if you have write-access to the repo).
 
 GitHub has a [nice introduction][github-flow] to the pull request workflow, but please get in touch if you have any questions.
 

LICENSE.md

@@ -4,4 +4,4 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
 
 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.
+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.

MANIFEST.in

@@ -1 +1 @@
-include pyveg/testdata/*
+include pyveg/testdata/*

binder/requirements.txt

@@ -12,4 +12,4 @@ earthengine-api==0.1.210
 geetools
 pillow
 imageio
-opencv-python
+opencv-python

docs/source/conf.py

@@ -12,66 +12,67 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../pyveg'))
+
+sys.path.insert(0, os.path.abspath("../../pyveg"))
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyveg'
-copyright = '2020, Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton.'
-author = 'Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton.'
+project = "pyveg"
+copyright = "2020, Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton."
+author = "Nick Barlow, Camila Rangel Smith, Samuel Van Stroud, Jesse F. Abrams, Chris Boulton, Joshua Buxton."
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
-master_doc = 'index'
+master_doc = "index"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "recommonmark",
 ]
 
 napoleon_use_ivar = True
 
 # for Sphinx-1.3
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'y'
+language = "y"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

environment.yml

@@ -0,0 +1,9 @@
+name: gee_pipeline
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.7
+  - earthengine-api
+  - rasterio
+  - coverage