Merge pull request #3 from OPERA-Cal-Val/dev

v0.0.1

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,22 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+### The bug
+<!-- Please include a clear and concise description of what the bug is. Describe
+what actually happened *and* what you expected to happen. -->
+
+### To Reproduce
+<!-- Please include the steps to reproduce the behavior. E.g.,
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error -->
+
+ ### Additional context
+<!-- Add any other context or screenshots about the bug here. -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+### Background
+<!-- Please include a clear and concise description of *the problem* this feature would solve. -->
+
+### Describe the solution you'd like
+<!-- A clear and concise description of what you want to happen. -->
+
+### Alternatives
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+ ### Additional context
+<!-- Add any other context or screenshots about the feature request here. -->

.github/pull_request_template.md

@@ -0,0 +1,11 @@
+<!--
+If this is a pull request for a new release, please use the release template:
+   {{ cookiecutter.public_url }}/compare/main...develop?template=release.md
+ 
+If this PR does not include changes that should be reflected in CHANGELOG.md,
+please indicate so by affixing the `bumpless` label to this PR.
+
+NOTE: Pull requests should only be opened for merges to protected branches (required) and any 
+changes which you'd like reviewed. Do not open a pull request to update a feature or personal
+branch -- simply merge with `git`.
+-->

.github/workflows/changelog.yml

@@ -0,0 +1,18 @@
+name: Changelog updated?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-changelog-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.8.3
+    secrets:
+      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/distribute.yml

@@ -0,0 +1,37 @@
+name: Distribute to PyPI
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  distribute:
+    runs-on: ubuntu-latest
+    outputs:
+      SDIST_VERSION: ${{ steps.build.outputs.version }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v1
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools build "setuptools-scm[toml]"
+
+      - name: Build distribuion
+        id: build
+        run: |
+          git fetch origin +refs/tags/*:refs/tags/*
+          export SDIST_VERSION=$(python -m setuptools_scm)
+          echo "::set-output name=version::${SDIST_VERSION}"
+          python -m build
+
+      - name: upload to PyPI.org
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/labeled-pr.yml

@@ -0,0 +1,15 @@
+name: Is PR labeled?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+
+jobs:
+  call-labeled-pr-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.8.3

.github/workflows/release-github.yml

@@ -0,0 +1,16 @@
+name: Create Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  call-release-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.8.3
+    with:
+      release_prefix: tile-stitcher
+      develop_branch: dev
+      sync_pr_label: team-bot
+    secrets:
+      USER_TOKEN: ${{ secrets.OPERA_PST_GITHUB_TOKEN }}

.github/workflows/static-analysis.yml

@@ -0,0 +1,15 @@
+name: Static analysis
+
+on: push
+
+jobs:
+  call-flake8-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.8.3
+    with:
+      local_package_names: tile_stitcher
+
+  call-secrets-analysis-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.8.3
+
+  call-ruff-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.9.0

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+name: Test and Tag
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-name: tile-stitcher
+          environment-file: environment.yml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+
+      - name: Pytest in conda environment
+        shell: bash -l {0}
+        run: |
+          python -m pip install .
+          pytest . tests

.gitignore

@@ -20,13 +20,6 @@ notebooks_plots/
 # Test output
 tests/out/
 
-# Data Files
-*.zip
-*.tar.gz
-*.dat
-# Include the tile vector data
-!dem_stitcher/data/*.geojson.zip
-
 # .pyenv files
 .python-version
 
@@ -58,30 +51,27 @@ __pycache__/
 .envrc
 
 # Gdal and other image formats
-notebooks/*.tif
+*.tif
 *.xml
-notebooks/*.shp
-notebooks/*.sbx
-notebooks/*.sbn
-notebooks/*.shx
-notebooks/*.prj
-notebooks/*.qpj
-notebooks/*.dbf
-notebooks/*.cpg
-notebooks/*.msk
-notebooks/*.kmz
-notebooks/*.jpg
-notebooks/*.wld
-notebooks/*.geojson
-notebooks/**/*.tif
+*.shp
+*.sbx
+*.sbn
+*.shx
+*.prj
+*.qpj
+*.dbf
+*.cpg
+*.msk
+*.kmz
+*.jpg
+*.wld
+*.geojson
+*.tif
 
 # VRT
 *.vrt
 *.wgs84
 
-# Allow tif datacube to be added
-!dem_stitcher/data/geoid_18.tif
-
 # Log files
 *.log
 
@@ -92,22 +82,4 @@ notebooks/**/*.tif
 *.pdf
 
 # Ignore json
-*.json
-
-# Ignore Experimental Directories
-notebooks/experimental/
-tests/notebooks/
-
-# Notebooks
-*.ipynb
-!notebooks/Basic_Demo.ipynb
-!notebooks/Comparing_DEMs.ipynb
-!notebooks/Staging_a_DEM_for_ISCE2.ipynb
-!notebooks/organize_tile_data/0_Format_and_Organize_Data.ipynb
-!notebooks/organize_tile_data/1_Missing_glo-30_tiles.ipynb
-!notebooks/analysis_and_comparison/0_Alignment_with_original_DEM_tiles.ipynb
-!notebooks/analysis_and_comparison/1_Comparison_with_ISCE2_dem.ipynb
-!notebooks/Filling_in_missing_glo-30_tiles_with_glo-90_tiles.ipynb
-!notebooks/Merging_DEM_Tiles_into_a_VRT.ipynb
-
-notebooks/analysis_and_comparison/la_test/
+*.json

.trufflehog.txt

@@ -0,0 +1,3 @@
+CHANGELOG.md
+.*.ipynb$
+.*README.md

CHANGELOG.md

@@ -0,0 +1,16 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
+and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.1]
+* First release of `tile_stitcher` with following datasets (See readme for links):
+    - ESA 10m worldcover 2020 and 2021; 
+    - Pekel 30m water occurence 2021; 
+    - S1 coherence from 2020;  
+    - Hansen annual mosaics 2000, 2013 - present
+    - Cop 100m Landcover 2015-2019
+* Includes workflows for static analysis, release to PyPI, and integration testing.

README.md

@@ -5,13 +5,28 @@ This tool provides a tool to create continuous rasters of global publicly availa
 
 The API can be summarized as
 ```
+from tile_stitcher import get_raster_from_tiles
+
+bounds = [-120.55, 34.85, -120.25, 35.15]
+X, p = get_raster_from_tiles(bounds, tile_shortname='esa_world_cover_2021')
+
+# X is an c x m x n numpy array, where c is the number of channels specified by `count`
+# p is a dictionary (or a rasterio profile) including relevant GIS metadata; CRS is epsg:4326
 ```
+
 The rasters are returned in the global lat/lon projection `epsg:4326` and the API assumes that bounds are supplied in this format.
 
+```
+import rasterio
+
+with rasterio.open('esa_worlf_cover_2021_subset.tif', 'w', **p) as ds:
+   ds.write(X)
+```
+
 # Installation
 
 In order to easily manage dependencies, we recommend using dedicated project environments
-via [Anaconda/Miniconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html).
+via [Anaconda/Miniconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
 or [Python virtual environments](https://docs.python.org/3/tutorial/venv.html).
 
 1. Clone the repository and navigate to it in the ternmal.
@@ -20,10 +35,10 @@ or [Python virtual environments](https://docs.python.org/3/tutorial/venv.html).
 4. Install the library with `pip`
 
 ```
-python -m pip install dem_stitcher
+python -m pip install .
 ```
 
-Python 3.10+ is supported.
+You can also install for development with `python -m pip install -e .`. Python 3.10+ is supported.
 
 # Notebooks
 
@@ -36,22 +51,30 @@ We have notebooks to demonstrate common usage:
 
 The datasets supported are:
 
-1. Pekel
-2. ESA World Cover (10 m) 2020 and 2021
+```
+In [1]: from tile_stitcher.stitcher import DATASET_SHORTNAMES
+
+In [2]: DATASET_SHORTNAMES
+Out[2]: ['peckel_water_occ_2021',
+ 'esa_world_cover_2020',
+ 'esa_world_cover_2021',
+ 'hansen_annual_mosaic',
+ 's1_coherence_2020',
+ 'cop_100_lulc_discrete']
+```
+These correspond to
++ Pekel: https://global-surface-water.appspot.com/download
++ ESA World Cover (10 m) for 2020 and 2021: https://aws.amazon.com/marketplace/pp/prodview-7oorylcamixxc
++ Hansen annual mosaic: https://data.globalforestwatch.org/documents/941f17325a494ed78c4817f9bb20f33a/explore
++ S1 Coherence from December 2019 - Nov 2020: https://aws.amazon.com/marketplace/pp/prodview-iz6lnjbdlgcwa#resources
++ The copernicus 100 m LULC dataset from 2015 - 2019: https://land.copernicus.eu/global/content/annual-100m-global-land-cover-maps-available
+
+See these [notebooks](notebooks/tile_creation) to see how these tiles are generated and organized.
 
 # Dateline support
 
 None curently.
 
-# For Development
-
-This is almost identical to normal installation:
-
-1. Clone this repo `git clone https://github.com/ACCESS-Cloud-Based-InSAR/dem-stitcher.git`
-2. Navigate with your terminal to the repo.
-3. Create a new environment and install requirements using `conda env update --file environment.yml` (or use [`mamba`](https://github.com/mamba-org/mamba) to speed the install up)
-4. Install the package from cloned repo using `python -m pip install -e .`
-
 # Contributing
 
 We welcome contributions to this open-source package. To do so: