From 0ea19e5500f081c37a74265b3530085d34742f10 Mon Sep 17 00:00:00 2001 From: Victor Engmark Date: Tue, 3 Sep 2024 12:55:30 +1200 Subject: [PATCH] chore(deps): Bump nixpkgs - Reintroduce now-working GitHub Workflows validation - Use Python 3.12 - Bump all Python packages - Work around argon2-cffi-bindings being incompatible with Python 3.12 - Patch sat-search and sat-stac for Python 3.12 compatibility - Add Poetry packages to `python` with multiple `withPackages` calls to avoid collisions - Avoid using very out of date sat-stac package --- .github/workflows/test.yml | 4 +- .pre-commit-config.yaml | 19 +- .../sentinel1_water_extraction/poetry.lock | 1726 +++++---- flooding/sentinel2_water_extraction/README.md | 4 +- .../sentinel2_water_extraction/poetry.lock | 3404 +++++++++-------- .../poetryPackages.nix | 5 + .../sentinel2_water_extraction.ipynb | 7 +- index.markdown | 3 +- nixpkgs.nix | 5 +- poetry2nix.nix | 95 +- shell.nix | 16 +- 11 files changed, 2755 insertions(+), 2533 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 13b80258..fcbd072c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -105,7 +105,7 @@ jobs: - windows-2022 python: - "3.9" - - "3.11" + - "3.12" sentinel: - "1" - "2" @@ -143,7 +143,7 @@ jobs: - name: Get GDAL Python package version run: | - GDAL_VERSION="$(grep --max-count=1 --only-matching 'file = "GDAL-.*\.tar\.gz"' poetry.lock)" + GDAL_VERSION="$(grep --max-count=1 --only-matching 'file = "gdal-.*\.tar\.gz"' poetry.lock)" # Use character removal compatible with macOS 12 GDAL_VERSION="${GDAL_VERSION#?????????????}" GDAL_VERSION="${GDAL_VERSION%????????}" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7d92b9b7..e1b20b2a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,16 +11,15 @@ repos: language: system stages: [commit] - # TODO: Reintroduce once https://github.com/NixOS/nixpkgs/pull/273831 is in use - # - id: check-github-workflows - # name: check-github-workflows - # description: Validate GitHub Workflows - # entry: check-jsonschema - # args: [--builtin-schema=vendor.github-workflows] - # files: ^\.github/workflows/[^/]+$ - # types: [yaml] - # language: system - # stages: [commit] + - id: check-github-workflows + name: check-github-workflows + description: Validate GitHub Workflows + entry: check-jsonschema + args: [--builtin-schema=vendor.github-workflows] + files: ^\.github/workflows/[^/]+$ + types: [yaml] + language: system + stages: [commit] - id: deadnix name: deadnix diff --git a/flooding/sentinel1_water_extraction/poetry.lock b/flooding/sentinel1_water_extraction/poetry.lock index 2334eace..f4d4ea69 100644 --- a/flooding/sentinel1_water_extraction/poetry.lock +++ b/flooding/sentinel1_water_extraction/poetry.lock @@ -2,53 +2,56 @@ [[package]] name = "anyio" -version = "3.6.2" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.8" files = [ - {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"}, - {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"}, + {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, + {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, ] [package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16,<0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "appnope" -version = "0.1.3" +version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - 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For each prerequisite, the - Linux (tested on Ubuntu 22.04, Jammy Jellyfish and 24.04, Noble Numbat) - macOS (tested on version 12, Monterey) - Windows (tested on Windows Server 2022) -- [Python](https://www.python.org/downloads/) (tested with 3.9 and 3.11) +- [Python](https://www.python.org/downloads/) (tested with 3.9 and 3.12) - [Poetry](https://python-poetry.org/docs/#installation) (tested with 1.8.3) -- [GDAL](https://gdal.org/download.html) (tested with 3.6.4) +- [GDAL](https://gdal.org/download.html) (tested with 3.9.2) Once you have all of the above, `cd [emergency-management-tools path]/flooding/sentinel2_water_extraction` and diff --git a/flooding/sentinel2_water_extraction/poetry.lock b/flooding/sentinel2_water_extraction/poetry.lock index fa2348b4..bd4832c6 100644 --- a/flooding/sentinel2_water_extraction/poetry.lock +++ b/flooding/sentinel2_water_extraction/poetry.lock @@ -15,95 +15,69 @@ files = [ dev = ["coveralls", "flake8", "pydocstyle"] test = ["pytest (>=4.6)", "pytest-cov"] -[[package]] -name = "aiofiles" -version = "22.1.0" -description = "File support for asyncio." -optional = false -python-versions = ">=3.7,<4.0" -files = [ - 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"sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" diff --git a/flooding/sentinel2_water_extraction/poetryPackages.nix b/flooding/sentinel2_water_extraction/poetryPackages.nix index a9471ba1..65b37913 100644 --- a/flooding/sentinel2_water_extraction/poetryPackages.nix +++ b/flooding/sentinel2_water_extraction/poetryPackages.nix @@ -8,4 +8,9 @@ poetry2nix.mkPoetryPackages { path = ./.; name = "sentinel2_water_extraction_packages"; }; + overrides = poetry2nix.overrides.withDefaults (_final: prev: { + argon2-cffi-bindings = prev.argon2-cffi-bindings.override { + preferWheel = true; + }; + }); } diff --git a/flooding/sentinel2_water_extraction/sentinel2_water_extraction.ipynb b/flooding/sentinel2_water_extraction/sentinel2_water_extraction.ipynb index d4be9f7f..347d0586 100644 --- a/flooding/sentinel2_water_extraction/sentinel2_water_extraction.ipynb +++ b/flooding/sentinel2_water_extraction/sentinel2_water_extraction.ipynb @@ -96,7 +96,7 @@ "# suppress warnings - raised by external rasterio library\n", "import warnings\n", "from datetime import date\n", - "from typing import Annotated, List, Optional, Tuple, TypedDict\n", + "from typing import Annotated, Any, List, Optional, Tuple, TypedDict\n", "\n", "import geopandas as gpd\n", "import matplotlib.pyplot as plt\n", @@ -108,7 +108,6 @@ "from rasterio.plot import show\n", "from rio_tiler.io import COGReader\n", "from satsearch import Search\n", - "from satstac import ItemCollection\n", "from shapely.geometry import shape\n", "from typing_extensions import NotRequired\n", "\n", @@ -268,7 +267,7 @@ "metadata": {}, "outputs": [], "source": [ - "def image_search(bbox: Annotated[List[float], 4], date_range: str) -> ItemCollection:\n", + "def image_search(bbox: Annotated[List[float], 4], date_range: str) -> Any:\n", " \"\"\"Use SatSearch to find all Sentinel-2 images that meet our criteria.\"\"\"\n", " # Note, we are not querying cloud cover and accepting\n", " # all images irrelevant of cloud metadata.\n", @@ -286,7 +285,7 @@ " print(\"NO IMAGE FOUND\")\n", " sys.exit()\n", "\n", - " return search.items()" + " return search.collections()" ] }, { diff --git a/index.markdown b/index.markdown index a4bc5ef0..bd6ea3e9 100644 --- a/index.markdown +++ b/index.markdown @@ -4,5 +4,4 @@ layout: default - [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 }}) +- [Convert date/time from machine-readable to human-readable]({{ 'machine-readable-to-human-readable-date-time/' | relative_url }}) diff --git a/nixpkgs.nix b/nixpkgs.nix index fcc35fbe..4eb300e1 100644 --- a/nixpkgs.nix +++ b/nixpkgs.nix @@ -1,6 +1,7 @@ import ( builtins.fetchTarball { - url = "https://github.com/nixos/nixpkgs/archive/2057814051972fa1453ddfb0d98badbea9b83c06.tar.gz"; - sha256 = "1a8jafyawg8mysv787q0cwghkza9kahbbniism7v2rcxas89b575"; + name = "nixos-unstable-2024-09-06"; + url = "https://github.com/nixos/nixpkgs/archive/ad416d066ca1222956472ab7d0555a6946746a80.tar.gz"; + sha256 = "0b9x5sghija7gy4lzf6l9s2kchdwj0zxs37ndlms2r8z1g3gwa7v"; } ) {} diff --git a/poetry2nix.nix b/poetry2nix.nix index 6a6480b2..9f62b5a8 100644 --- a/poetry2nix.nix +++ b/poetry2nix.nix @@ -1,10 +1,85 @@ -{pkgs}: -import ( - builtins.fetchTarball { - name = "poetry2nix-2024.8.2346599"; - url = "https://github.com/nix-community/poetry2nix/archive/7619e43c2b48c29e24b88a415256f09df96ec276.tar.gz"; - sha256 = "10nf9213h7vkzrqhrgk88r5sd2rq19cvdpnn59f65ifak790sgc0"; - } -) { - inherit pkgs; -} +{pkgs}: let + poetry2nix = + import ( + builtins.fetchTarball { + url = "https://github.com/nix-community/poetry2nix/archive/2024.9.285936.tar.gz"; + sha256 = "11a3wd1lgcq4qknh3almy9pcyqgm9f1q9iihdvy08g2hvmj2zris"; + } + ) { + inherit pkgs; + }; +in + poetry2nix.overrideScope (_finalPoetry2nix: prevPoetry2nix: { + defaultPoetryOverrides = prevPoetry2nix.defaultPoetryOverrides.extend (final: prev: { + jupyter-server = prev.jupyter-server.overridePythonAttrs (old: { + # Already in poetry2nix but needed here because we're mixing old and new versions of jupyter-server + nativeBuildInputs = (old.nativeBuildInputs or []) ++ [final.jupyter-packaging]; + }); + sat-search = prev.sat-search.overridePythonAttrs (old: { + # https://github.com/sat-utils/sat-search/pull/136 + patches = + (old.patches or []) + ++ pkgs.lib.optionals (!(old.src.isWheel or false)) [ + (pkgs.writeText "sat-search-importlib.patch" '' + --- a/setup.py + +++ b/setup.py + @@ -1,9 +1,20 @@ + #!/usr/bin/env python + +import importlib.util + +import importlib.machinery + from setuptools import setup, find_packages + -from imp import load_source + from os import path + import io + + +def load_source(modname, filename): + + loader = importlib.machinery.SourceFileLoader(modname, filename) + + spec = importlib.util.spec_from_file_location(modname, filename, loader=loader) + + module = importlib.util.module_from_spec(spec) + + # The module is always executed and not cached in sys.modules. + + # Uncomment the following line to cache the module. + + # sys.modules[module.__name__] = module + + loader.exec_module(module) + + return module + + + __version__ = load_source('satsearch.version', 'satsearch/version.py').__version__ + + here = path.abspath(path.dirname(__file__)) + '') + ]; + }); + sat-stac = prev.sat-stac.overridePythonAttrs (old: { + # https://github.com/sat-utils/sat-stac/pull/75 + patches = + (old.patches or []) + ++ pkgs.lib.optionals (!(old.src.isWheel or false)) [ + (pkgs.writeText "sat-stac-importlib.patch" '' + --- a/setup.py + +++ b/setup.py + @@ -1,9 +1,20 @@ + #!/usr/bin/env python + +import importlib.util + +import importlib.machinery + from setuptools import setup, find_packages + -from imp import load_source + from os import path + import io + + +def load_source(modname, filename): + + loader = importlib.machinery.SourceFileLoader(modname, filename) + + spec = importlib.util.spec_from_file_location(modname, filename, loader=loader) + + module = importlib.util.module_from_spec(spec) + + # The module is always executed and not cached in sys.modules. + + # Uncomment the following line to cache the module. + + # sys.modules[module.__name__] = module + + loader.exec_module(module) + + return module + + + __version__ = load_source('satstac.version', 'satstac/version.py').__version__ + + here = path.abspath(path.dirname(__file__)) + '') + ]; + }); + }); + }) diff --git a/shell.nix b/shell.nix index f3be3452..3310a1dc 100644 --- a/shell.nix +++ b/shell.nix @@ -14,23 +14,19 @@ let }; pythonWithAllPackages = ( - python.withPackages ( - ps: - [ + ( + python.withPackages ( + ps: [ ps.mypy ps.pip ps.pylint ps.types-python-dateutil ] - ++ sentinel1WaterExtractionPoetryPackages.poetryPackages - ++ sentinel2WaterExtractionPoetryPackages.poetryPackages + ) ) + .withPackages (_ps: sentinel1WaterExtractionPoetryPackages.poetryPackages) ) - .override ( - _args: { - ignoreCollisions = true; - } - ); + .withPackages (_ps: sentinel2WaterExtractionPoetryPackages.poetryPackages); in pkgs.mkShell { packages = [