diff --git a/.github/dependabot.yml b/.github/dependabot.yml index b57086b1..779abe4c 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -4,6 +4,10 @@ updates: directory: / schedule: interval: daily + - package-ecosystem: pip + directory: /flooding/sentinel1_water_extraction + schedule: + interval: daily - package-ecosystem: pip directory: /flooding/sentinel2_water_extraction schedule: diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 21f3d68b..3bc0f8e6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -56,12 +56,19 @@ jobs: - name: Run test run: nix-shell --pure --run 'LC_MESSAGES=C TZ=UTC mocha' - test-sentinel2-water-extraction-nix: - name: Test Sentinel-2 water extraction using Nix + test-sentinel-water-extraction-nix: + name: Test Sentinel-${{ matrix.sentinel }} using Nix runs-on: ubuntu-22.04 defaults: run: - working-directory: flooding/sentinel2_water_extraction + working-directory: + flooding/sentinel${{ matrix.sentinel }}_water_extraction + strategy: + fail-fast: false + matrix: + sentinel: + - "1" + - "2" steps: - name: Check out repository uses: actions/checkout@v3.5.0 @@ -76,17 +83,18 @@ jobs: - name: Run test run: nix-shell --pure --run 'jupyter nbconvert --debug --execute --inplace - --to=notebook sentinel2_water_extraction.ipynb' + --to=notebook sentinel${{ matrix.sentinel }}_water_extraction.ipynb' - test-sentinel2-water-extraction-poetry: + test-sentinel-water-extraction-poetry: name: - Test on ${{ matrix.runner }}, using Poetry with Python ${{ matrix.python - }} + Test Sentinel-${{ matrix.sentinel }} on ${{ matrix.runner }}, using Poetry + with Python ${{ matrix.python }} runs-on: ${{ matrix.runner }} defaults: run: shell: bash --login -o errexit {0} # https://github.com/conda-incubator/setup-miniconda/tree/7e642bb2e4ca56ff706818a0febf72bb226d348d#use-a-default-shell - working-directory: flooding/sentinel2_water_extraction + working-directory: + flooding/sentinel${{ matrix.sentinel }}_water_extraction strategy: fail-fast: false matrix: @@ -99,6 +107,9 @@ jobs: - "3.9" - "3.10" - "3.11" + sentinel: + - "1" + - "2" include: - runner: macos-12 pip-cache-dir: ~/Library/Caches/pip @@ -116,8 +127,8 @@ jobs: path: ${{ matrix.pip-cache-dir }} key: ${{ runner.os }}-pip-${{ secrets.CACHE_SEED }}-${{ matrix.python - }}-${{ - hashFiles('./flooding/sentinel2_water_extraction/poetry.lock') }} + }}-${{ hashFiles('./flooding/sentinel${{ matrix.sentinel + }}_water_extraction/poetry.lock') }} restore-keys: ${{ runner.os }}-pip-${{ secrets.CACHE_SEED }}-${{ matrix.python }} @@ -150,8 +161,8 @@ jobs: with: timeout_minutes: 9999 # Workaround for https://github.com/nick-fields/retry/issues/107 max_attempts: 6 - command: bash --login -o errexit -c 'cd - flooding/sentinel2_water_extraction && poetry install --only=main + command: bash --login -o errexit -c 'cd flooding/sentinel${{ + matrix.sentinel }}_water_extraction && poetry install --only=main --no-root' # Workaround for https://github.com/python-poetry/poetry/issues/7363 / https://github.com/nick-fields/retry/issues/89 shell: bash if: ${{ startsWith(runner.os, 'Windows') }} @@ -159,15 +170,15 @@ jobs: - name: Run test run: poetry run jupyter nbconvert --debug --execute --inplace --to=notebook - sentinel2_water_extraction.ipynb + sentinel${{ matrix.sentinel }}_water_extraction.ipynb finalise: if: always() needs: - lint - test-machine-readable-to-human-readable-date-time - - test-sentinel2-water-extraction-nix - - test-sentinel2-water-extraction-poetry + - test-sentinel-water-extraction-nix + - test-sentinel-water-extraction-poetry runs-on: ubuntu-22.04 steps: - name: Decide whether the needed jobs succeeded or failed diff --git a/README.md b/README.md index 257d149a..e803bdf0 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,10 @@ support emergency events Current automated processes -### [Flood Water Extraction](flooding/sentinel2_water_extraction/README.md) +### [Radar Flood Water Extraction](flooding/sentinel2_water_extraction/README.md) -Jupyter Notebook for extracting water from Sentinel 2 imagery. +Jupyter Notebook for extracting water from Sentinel 1 radar imagery. + +### [Optical Flood Water Extraction](flooding/sentinel2_water_extraction/README.md) + +Jupyter Notebook for extracting water from Sentinel 2 optical imagery. diff --git a/flooding/sentinel2_water_extraction/CODING.md b/flooding/CODING.md similarity index 100% rename from flooding/sentinel2_water_extraction/CODING.md rename to flooding/CODING.md diff --git a/flooding/sentinel1_water_extraction/.envrc b/flooding/sentinel1_water_extraction/.envrc new file mode 100644 index 00000000..82b2b9ef --- /dev/null +++ b/flooding/sentinel1_water_extraction/.envrc @@ -0,0 +1,9 @@ +#!/usr/bin/env bash +# the shebang is ignored, but nice for editors + +if type -P lorri &>/dev/null; then + eval "$(lorri direnv)" +else + echo 'while direnv evaluated .envrc, could not find the command "lorri" [https://github.com/nix-community/lorri]' + use nix +fi diff --git a/flooding/sentinel1_water_extraction/README.md b/flooding/sentinel1_water_extraction/README.md new file mode 100644 index 00000000..cec952cb --- /dev/null +++ b/flooding/sentinel1_water_extraction/README.md @@ -0,0 +1 @@ +# Sentinel-1 Water Extraction diff --git a/flooding/sentinel1_water_extraction/out/.gitignore b/flooding/sentinel1_water_extraction/out/.gitignore new file mode 100644 index 00000000..120f485d --- /dev/null +++ b/flooding/sentinel1_water_extraction/out/.gitignore @@ -0,0 +1,2 @@ +* +!/.gitignore diff --git a/flooding/sentinel1_water_extraction/poetry.lock b/flooding/sentinel1_water_extraction/poetry.lock new file mode 100644 index 00000000..54f0b204 --- /dev/null +++ b/flooding/sentinel1_water_extraction/poetry.lock @@ -0,0 +1,2193 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "22.1.0" +description = "File support 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+python-versions = ">=3.7" +files = [ + {file = "zipp-3.14.0-py3-none-any.whl", hash = "sha256:188834565033387710d046e3fe96acfc9b5e86cbca7f39ff69cf21a4128198b7"}, + {file = "zipp-3.14.0.tar.gz", hash = "sha256:9e5421e176ef5ab4c0ad896624e87a7b2f07aca746c9b2aa305952800cb8eecb"}, +] + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.8" +content-hash = "48a028685edbb6a87424d997e15f29de5aaa8cdc8edd0e2e8dc25dc3599916a0" diff --git a/flooding/sentinel1_water_extraction/poetryPackages.nix b/flooding/sentinel1_water_extraction/poetryPackages.nix new file mode 100644 index 00000000..56c50f5d --- /dev/null +++ b/flooding/sentinel1_water_extraction/poetryPackages.nix @@ -0,0 +1,11 @@ +{ + pkgs, + python, +}: +pkgs.poetry2nix.mkPoetryPackages { + inherit python; + projectDir = builtins.path { + path = ./.; + name = "sentinel1_water_extraction_packages"; + }; +} diff --git a/flooding/sentinel1_water_extraction/pyproject.toml b/flooding/sentinel1_water_extraction/pyproject.toml new file mode 100644 index 00000000..ed2c8c98 --- /dev/null +++ b/flooding/sentinel1_water_extraction/pyproject.toml @@ -0,0 +1,19 @@ +[tool.poetry] +name = "sentinel1-water-extraction" +version = "0.1.0" +description = "" +authors = [ + "Matthew Wightman ", + "Victor Engmark ", +] +license = "MIT" +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.8" +gdal = "*" +jupyterlab = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/flooding/sentinel1_water_extraction/sentinel1_water_extraction.ipynb b/flooding/sentinel1_water_extraction/sentinel1_water_extraction.ipynb new file mode 100644 index 00000000..a5721bd7 --- /dev/null +++ b/flooding/sentinel1_water_extraction/sentinel1_water_extraction.ipynb @@ -0,0 +1,31 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "afd1fc79", + "metadata": { + "collapsed": false + }, + "source": [ + "# Sentinel-1 Water Extraction\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "08f4d272", + "metadata": {}, + "outputs": [], + "source": [ + "\"\"\"Sentinel-1 Water Extraction.\"\"\"\n" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/flooding/sentinel1_water_extraction/shell.nix b/flooding/sentinel1_water_extraction/shell.nix new file mode 100644 index 00000000..68e0ff19 --- /dev/null +++ b/flooding/sentinel1_water_extraction/shell.nix @@ -0,0 +1,17 @@ +let + sources = import ../../nix/sources.nix; + pkgs = import sources.nixpkgs {}; + python = import ../../python.nix { + inherit pkgs; + }; + poetryPackages = import ./poetryPackages.nix { + inherit pkgs python; + }; +in + pkgs.mkShell { + packages = + [ + pkgs.cacert + ] + ++ poetryPackages.poetryPackages; + } diff --git a/flooding/sentinel2_water_extraction/poetry.lock b/flooding/sentinel2_water_extraction/poetry.lock index a8a44fa0..9f30a010 100644 --- a/flooding/sentinel2_water_extraction/poetry.lock +++ b/flooding/sentinel2_water_extraction/poetry.lock @@ -196,18 +196,18 @@ css = ["tinycss2 (>=1.1.0,<1.2)"] [[package]] name = "boto3" -version = "1.26.75" +version = "1.26.76" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.26.75-py3-none-any.whl", hash = "sha256:0bbc318e8c4a6006de0069b99810780962f53fed591830fee9ab670aa4ec56ef"}, - {file = "boto3-1.26.75.tar.gz", hash = "sha256:702efaf333ddd9a1520283a22bd74b6c3a890ab38df5afcf4e821a2f3d707688"}, + {file = "boto3-1.26.76-py3-none-any.whl", hash = "sha256:b4c2969b7677762914394b8273cc1905dfe5b71f250741c1a575487ae357e729"}, + {file = "boto3-1.26.76.tar.gz", hash = "sha256:30c7d967ed1c6b5a05643e42cae9d4d36c3f1cb6782637ddc7007a104cfd9027"}, ] [package.dependencies] -botocore = ">=1.29.75,<1.30.0" +botocore = ">=1.29.76,<1.30.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -216,14 +216,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.29.75" +version = "1.29.76" description = "Low-level, data-driven core of boto 3." category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.29.75-py3-none-any.whl", hash = "sha256:b6e50fc7aacdcc7fa345cc2c55f53e61db8165bdca4d8ca57323e22cac2671c6"}, - {file = "botocore-1.29.75.tar.gz", hash = "sha256:eef47ca90d02dbc92296208e24ac5e02bdf5cfa45f10d160fdc19612e141bce2"}, + {file = "botocore-1.29.76-py3-none-any.whl", hash = "sha256:70735b00cd529f152992231ca6757e458e5ec25db43767b3526e9a35b2f143b7"}, + {file = "botocore-1.29.76.tar.gz", hash = "sha256:c2f67b6b3f8acf2968eafca06526f07b9fb0d27bac4c68a635d51abb675134a7"}, ] [package.dependencies] @@ -1179,14 +1179,14 @@ test = ["codecov", "coverage", "ipykernel (>=5.5.6)", "ipython", "jedi (<0.18)", [[package]] name = "jupyter-console" -version = "6.6.0" +version = "6.6.1" description = "Jupyter terminal console" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "jupyter_console-6.6.0-py3-none-any.whl", hash = "sha256:545ba4f0b3c8aa64108cb9d35532253b814c7d4f25e2bffb3f0aec56b183a371"}, - {file = "jupyter_console-6.6.0.tar.gz", hash = "sha256:0ce8b5596df6b2453d56d1127aaa3e7b0e3c8fb73d48dcc77162753019b78215"}, + {file = "jupyter_console-6.6.1-py3-none-any.whl", hash = "sha256:b32b5cb673a90909911988a2f1906ced005b07e8dadab6c8664d3f5de44a8191"}, + {file = "jupyter_console-6.6.1.tar.gz", hash = "sha256:5931212d5cbc1f956f6fd615755b5e15f389a8eaa697288dbbe4377017615ecc"}, ] [package.dependencies] @@ -2067,14 +2067,14 @@ twisted = ["twisted"] [[package]] name = "prompt-toolkit" -version = "3.0.36" +version = "3.0.37" description = "Library for building powerful interactive command lines in Python" category = "main" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7.0" files = [ - {file = "prompt_toolkit-3.0.36-py3-none-any.whl", hash = "sha256:aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305"}, - {file = "prompt_toolkit-3.0.36.tar.gz", hash = "sha256:3e163f254bef5a03b146397d7c1963bd3e2812f0964bb9a24e6ec761fd28db63"}, + {file = "prompt_toolkit-3.0.37-py3-none-any.whl", hash = "sha256:6a2948ec427dfcc7c983027b1044b355db6aaa8be374f54ad2015471f7d81c5b"}, + {file = "prompt_toolkit-3.0.37.tar.gz", hash = "sha256:d5d73d4b5eb1a92ba884a88962b157f49b71e06c4348b417dd622b25cdd3800b"}, ] [package.dependencies] @@ -2718,14 +2718,14 @@ win32 = ["pywin32"] [[package]] name = "setuptools" -version = "67.3.3" +version = "67.4.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "setuptools-67.3.3-py3-none-any.whl", hash = "sha256:9d3de8591bd6f6522594406fa46a6418eabd0562dacb267f8556675762801514"}, - {file = "setuptools-67.3.3.tar.gz", hash = "sha256:ed4e75fafe103c79b692f217158ba87edf38d31004b9dbc1913debb48793c828"}, + {file = "setuptools-67.4.0-py3-none-any.whl", hash = "sha256:f106dee1b506dee5102cc3f3e9e68137bbad6d47b616be7991714b0c62204251"}, + {file = "setuptools-67.4.0.tar.gz", hash = "sha256:e5fd0a713141a4a105412233c63dc4e17ba0090c8e8334594ac790ec97792330"}, ] [package.extras] diff --git a/flooding/sentinel2_water_extraction/poetryPackages.nix b/flooding/sentinel2_water_extraction/poetryPackages.nix index 5bc21313..6f3fef27 100644 --- a/flooding/sentinel2_water_extraction/poetryPackages.nix +++ b/flooding/sentinel2_water_extraction/poetryPackages.nix @@ -1,6 +1,9 @@ -{pkgs}: +{ + pkgs, + python, +}: pkgs.poetry2nix.mkPoetryPackages { - python = pkgs.python3; + inherit python; projectDir = builtins.path { path = ./.; name = "sentinel2_water_extraction_packages"; diff --git a/flooding/sentinel2_water_extraction/shell.nix b/flooding/sentinel2_water_extraction/shell.nix index 7e0ac200..68e0ff19 100644 --- a/flooding/sentinel2_water_extraction/shell.nix +++ b/flooding/sentinel2_water_extraction/shell.nix @@ -1,9 +1,12 @@ let sources = import ../../nix/sources.nix; pkgs = import sources.nixpkgs {}; - poetryPackages = import ./poetryPackages.nix { + python = import ../../python.nix { inherit pkgs; }; + poetryPackages = import ./poetryPackages.nix { + inherit pkgs python; + }; in pkgs.mkShell { packages = diff --git a/index.markdown b/index.markdown index 5165ca58..a4bc5ef0 100644 --- a/index.markdown +++ b/index.markdown @@ -2,6 +2,7 @@ layout: default --- -- [Flood Water Extraction](https://github.com/linz/emergency-management-tools/tree/master/flooding/sentinel2_water_extraction) +- [Radar Flood Water Extraction](https://github.com/linz/emergency-management-tools/tree/master/flooding/sentinel1_water_extraction) +- [Optical Flood Water Extraction](https://github.com/linz/emergency-management-tools/tree/master/flooding/sentinel2_water_extraction) - [Convert date/time from machine-readable to human-readable]({{ 'machine-readable-to-human-readable-date-time/' | relative_url }}) diff --git a/python.nix b/python.nix new file mode 100644 index 00000000..2c252db7 --- /dev/null +++ b/python.nix @@ -0,0 +1,2 @@ +{pkgs}: +pkgs.python3 diff --git a/shell.nix b/shell.nix index d7c6b2fc..0e6a449d 100644 --- a/shell.nix +++ b/shell.nix @@ -1,40 +1,50 @@ let sources = import ./nix/sources.nix; pkgs = import sources.nixpkgs {}; - sentinel2WaterExtractionPoetryPackages = import ./flooding/sentinel2_water_extraction/poetryPackages.nix { + python = import ./python.nix { inherit pkgs; }; - python = sentinel2WaterExtractionPoetryPackages.python.withPackages ( - ps: - [ - ( - ps.buildPythonPackage rec { - pname = "nbqa"; - version = "1.6.4"; - src = ps.fetchPypi { - inherit pname version; - hash = "sha256-H7y+N+9TBJW9fwjlO7g4qGmwdKD771eF7ScNNwphPrA="; - }; - buildInputs = [ - ps.ipython - ps.tomli - ps.tokenize-rt - ]; - propagatedBuildInputs = [ - ps.tokenize-rt - ]; - } - ) - ps.mypy - ps.pylint - ps.types-python-dateutil - ] - ++ sentinel2WaterExtractionPoetryPackages.poetryPackages + sentinel1WaterExtractionPoetryPackages = import ./flooding/sentinel1_water_extraction/poetryPackages.nix { + inherit pkgs python; + }; + pythonWithSentinel1WaterExtractionPoetryPackages = python.withPackages ( + _ps: sentinel1WaterExtractionPoetryPackages.poetryPackages + ); + sentinel2WaterExtractionPoetryPackages = import ./flooding/sentinel2_water_extraction/poetryPackages.nix { + inherit pkgs python; + }; + pythonWithSentinel1And2WaterExtractionPoetryPackages = pythonWithSentinel1WaterExtractionPoetryPackages.withPackages ( + _ps: sentinel2WaterExtractionPoetryPackages.poetryPackages + ); + pythonWithAllPackages = pythonWithSentinel1And2WaterExtractionPoetryPackages.withPackages ( + ps: [ + ( + ps.buildPythonPackage rec { + pname = "nbqa"; + version = "1.6.4"; + src = ps.fetchPypi { + inherit pname version; + hash = "sha256-H7y+N+9TBJW9fwjlO7g4qGmwdKD771eF7ScNNwphPrA="; + }; + buildInputs = [ + ps.ipython + ps.tomli + ps.tokenize-rt + ]; + propagatedBuildInputs = [ + ps.tokenize-rt + ]; + } + ) + ps.mypy + ps.pylint + ps.types-python-dateutil + ] ); in pkgs.mkShell { packages = [ - python + pythonWithAllPackages pkgs.alejandra pkgs.black pkgs.cacert