diff --git a/.gitignore b/.gitignore index 6860f1e..c1a039b 100644 --- a/.gitignore +++ b/.gitignore @@ -10,6 +10,9 @@ credentials.json *.egg-info __pycache__ build/ -parcels/ .asv/ html/ +.DS_Store + +data +.env diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..c3ecd2c --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "Parcels"] + path = Parcels + url = git@github.com:Parcels-code/Parcels diff --git a/Parcels b/Parcels new file mode 160000 index 0000000..c6f11dc --- /dev/null +++ b/Parcels @@ -0,0 +1 @@ +Subproject commit c6f11dc1a6aaac843db455d4ecf11d4fdc26a456 diff --git a/README.md b/README.md index 7e4f03c..1ea22d3 100644 --- a/README.md +++ b/README.md @@ -6,15 +6,30 @@ This repository houses performance benchmarks for [Parcels](https://github.com/O ## Development instructions +This project uses a combination of [Pixi](https://pixi.sh/dev/installation/), [ASV](https://asv.readthedocs.io/), and [intake-xarray](https://github.com/intake/intake-xarray) to coordinate the setting up and running of benchmarks. + +- Scripts are used to download the datasets required into the correct location +- intake-xarray is used to define data catalogues which can be easily accessed from within benchmark scripts +- ASV is used to run the benchmarks (see the [Writing the benchmarks](#writing-the-benchmarks) section). +- Pixi is used to orchestrate all the above into a convenient, user friendly workflow + +You can run `pixi task list` to see the list of available tasks in the workspace. + +In brief, you can set up the data and run the benchmarks by doing: + - [install Pixi](https://pixi.sh/dev/installation/) `curl -fsSL https://pixi.sh/install.sh | bash` - `pixi install` -- `pixi run asv run` +- `PARCELS_BENCHMARKS_DATA_FOLDER=./data pixi run benchmarks` -You can run the linting with `pixi run lint` +> [!NOTE] +> The syntax `PARCELS_BENCHMARKS_DATA_FOLDER=./data pixi run ...` set's the environment variable for the task, but you can set environment variables [in other ways](https://askubuntu.com/a/58828) as well. > [!IMPORTANT] -> The default path for the benchmark data is set by [pooch.os_cache](https://www.fatiando.org/pooch/latest/api/generated/pooch.os_cache.html), which typically is a subdirectory of your home directory. Currently, you will need at least 50GB of disk space available to store the benchmark data. -> To change the location of the benchmark data cache, you can set the environment variable `PARCELS_DATADIR` to a preferred location to store the benchmark data. +> Currently, you will need at least 50GB of disk space available to store the unzipped benchmark data. Since the zips are deleted after downloaded and extracted, this ends up being about 80GB of disk space needed. +> You need to be explicit to determine where the benchmark data will be saved by +> setting the `PARCELS_BENCHMARKS_DATA_FOLDER` environment variable. This +> environment variable is used in the downloading of the data and definition of +> the benchmarks. To view the benchmark data @@ -34,7 +49,7 @@ Members of the Parcels community can contribute benchmark data using the followi 2. Clone your fork onto your system ``` -git clone git@github.com:/parcels-benchmarks.git ~/parcels-benchmarks +git clone --recurse-submodules git@github.com:/parcels-benchmarks.git ``` 3. Run the benchmarks @@ -61,13 +76,9 @@ Adding benchmarks for parcels typically involves adding a dataset and defining t ### Adding new data Data is hosted remotely on a SurfDrive managed by the Parcels developers. You will need to open an issue on this repository to start the process of getting your data hosted in the shared SurfDrive. -Once your data is hosted in the shared SurfDrive, you can easily add your dataset to the benchmark dataset manifest using - -``` -pixi run benchmark-setup pixi add-dataset --name "Name for your dataset" --file "Path to ZIP archive in the SurfDrive" -``` +Once your data is hosted in the shared SurfDrive, you can easily add your dataset to the benchmark dataset catalogue by modifying `catalogs/parcels-benchmarks/catalog.yml`. -During this process, the dataset will be downloaded and a complete entry will be added to the [parcels_benchmarks/benchmarks.json](./parcels_benchmarks/benchmarks.json) manifest file. Once updated, this file can be committed to this repository and contributed via a pull request. +In the benchmark you can now use this catalogue entry. ### Writing the benchmarks diff --git a/asv.conf.json b/asv.conf.json deleted file mode 100644 index ab7af9b..0000000 --- a/asv.conf.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "version": 1, - "project": "parcels", - "project_url": "https://github.com/Parcels-Code/parcels", - "repo": "https://github.com/Parcels-Code/parcels.git", - "branches": ["main"], - "environment_type": "rattler", - "conda_channels": [ - "conda-forge", - "defaults", - "https://repo.prefix.dev/parcels" - ], - "default_benchmark_timeout": 1800, - "env_dir": ".asv/env", - "results_dir": "results", - "html_dir": "html", - "build_command": [], - "install_command": [ - "in-dir={conf_dir} python -m pip install .", - "in-dir={build_dir} python -m pip install ." - ], - "uninstall_command": [ - "return-code=any python -m pip uninstall -y parcels parcels_benchmarks" - ] -} diff --git a/asv.conf.jsonc b/asv.conf.jsonc new file mode 100644 index 0000000..fd7e57b --- /dev/null +++ b/asv.conf.jsonc @@ -0,0 +1,31 @@ +{ + "version": 1, + "project": "parcels", + "project_url": "https://github.com/Parcels-Code/parcels", + "repo": "./Parcels", + "dvcs": "git", + "branches": ["main"], + "environment_type": "rattler", + "conda_channels": [ + "conda-forge", + "defaults", + "https://repo.prefix.dev/parcels", + ], + "default_benchmark_timeout": 1800, + "env_dir": ".asv/env", + "results_dir": "results", + "html_dir": "html", + "build_command": ["python -m build --wheel -o {build_cache_dir} {build_dir}"], + // "install_command": [ + // "in-dir={conf_dir} python -m pip install .", + // "in-dir={build_dir} python -m pip install ." + // ], + // "uninstall_command": [ + // "return-code=any python -m pip uninstall -y parcels parcels_benchmarks" + // ] + "matrix": { + "req": { + "intake-xarray": [], + }, + }, +} diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index e69de29..6bf489b 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -0,0 +1,27 @@ +import logging +import os +from pathlib import Path + +logger = logging.getLogger(__name__) + +PIXI_PROJECT_ROOT = os.environ.get("PIXI_PROJECT_ROOT") +if PIXI_PROJECT_ROOT is not None: + PIXI_PROJECT_ROOT = Path(PIXI_PROJECT_ROOT) + +PIXI_PROJECT_ROOT: Path | None + +try: + PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) +except KeyError: + # Default to `./data` + PARCELS_BENCHMARKS_DATA_FOLDER = Path("./data") + logger.info("PARCELS_BENCHMARKS_DATA_FOLDER was not set. Defaulting to `./data`") + +if not PARCELS_BENCHMARKS_DATA_FOLDER.is_absolute(): + if PIXI_PROJECT_ROOT is None: + raise RuntimeError( + "PARCELS_BENCHMARKS_DATA_FOLDER is a relative path, but PIXI_PROJECT_ROOT env variable is not set. We don't know where to store the data." + ) + PARCELS_BENCHMARKS_DATA_FOLDER = PIXI_PROJECT_ROOT / str( + PARCELS_BENCHMARKS_DATA_FOLDER + ) diff --git a/benchmarks/catalogs.py b/benchmarks/catalogs.py new file mode 100644 index 0000000..36a1c5a --- /dev/null +++ b/benchmarks/catalogs.py @@ -0,0 +1,12 @@ +import intake + +from . import PARCELS_BENCHMARKS_DATA_FOLDER + + +class Catalogs: + CAT_EXAMPLES = intake.open_catalog( + f"{PARCELS_BENCHMARKS_DATA_FOLDER}/surf-data/parcels-examples/catalog.yml" + ) + CAT_BENCHMARKS = intake.open_catalog( + f"{PARCELS_BENCHMARKS_DATA_FOLDER}/surf-data/parcels-benchmarks/catalog.yml" + ) diff --git a/benchmarks/fesom2.py b/benchmarks/fesom2.py index e7bd735..3b4b2aa 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -1,5 +1,6 @@ import numpy as np import uxarray as ux +import xarray as xr from parcels import ( FieldSet, Particle, @@ -8,39 +9,38 @@ ) from parcels.kernels import AdvectionRK2_3D -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_example_dataset +from . import PARCELS_BENCHMARKS_DATA_FOLDER runtime = np.timedelta64(1, "D") dt = np.timedelta64(2400, "s") -def _load_ds(datapath): +def _load_ds(): """Helper function to load uxarray dataset from datapath""" - grid_file = f"{datapath}/mesh/fesom.mesh.diag.nc" - data_files = f"{datapath}/*.nc" - return ux.open_mfdataset(grid_file, data_files, combine="by_coords") + grid_file = xr.open_mfdataset( + f"{PARCELS_BENCHMARKS_DATA_FOLDER}/surf-data/parcels-benchmarks/data/Parcelsv4_Benchmarking_data/Parcels_Benchmarks_FESOM-baroclinic-gyre/data/mesh/fesom.mesh.diag.nc" + ) + data_files = xr.open_mfdataset( + f"{PARCELS_BENCHMARKS_DATA_FOLDER}/surf-data/parcels-benchmarks/data/Parcelsv4_Benchmarking_data/Parcels_Benchmarks_FESOM-baroclinic-gyre/data/*.nc" + ) + + grid = ux.open_grid(grid_file) + return ux.UxDataset(data_files, uxgrid=grid) class FESOM2: params = ([10000], [AdvectionRK2_3D]) param_names = ["npart", "integrator"] - def setup(self, npart, integrator): - # Ensure the dataset is downloaded in the desired data_home - # and obtain the path to the dataset - self.datapath = download_example_dataset( - "FESOM-baroclinic-gyre", data_home=PARCELS_DATADIR - ) - def time_load_data(self, npart, integrator): - ds = _load_ds(self.datapath) + ds = _load_ds() for i in range(min(ds.coords["time"].size, 2)): _u = ds["u"].isel(time=i).compute() _v = ds["v"].isel(time=i).compute() def pset_execute(self, npart, integrator): - ds = _load_ds(self.datapath) + ds = _load_ds() ds = convert.fesom_to_ugrid(ds) fieldset = FieldSet.from_ugrid_conventions(ds) diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index dcc1f27..baf9f18 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -6,12 +6,16 @@ import xgcm from parcels.interpolators import XLinear -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_example_dataset - runtime = np.timedelta64(2, "D") dt = np.timedelta64(15, "m") +PARCELS_DATADIR = ... # TODO: Replace with intake + + +def download_dataset(*args, **kwargs): ... # TODO: Replace with intake + + def _load_ds(datapath, chunk): """Helper function to load xarray dataset from datapath with or without chunking""" @@ -72,9 +76,7 @@ class MOICurvilinear: ] def setup(self, interpolator, chunk, npart): - self.datapath = download_example_dataset( - "MOi-curvilinear", data_home=PARCELS_DATADIR - ) + self.datapath = download_dataset("MOi-curvilinear", data_home=PARCELS_DATADIR) def time_load_data_3d(self, interpolator, chunk, npart): """Benchmark that times loading the 'U' and 'V' data arrays only for 3-D""" diff --git a/catalogs/parcels-benchmarks/catalog.yml b/catalogs/parcels-benchmarks/catalog.yml new file mode 100644 index 0000000..b502b94 --- /dev/null +++ b/catalogs/parcels-benchmarks/catalog.yml @@ -0,0 +1,63 @@ +# zip_url: https://surfdrive.surf.nl/index.php/s/7xlfdOFaUGDEmpD/download?path=%2F&files= +# ^ Do not remove this line! Used by the download script to find the data source +plugins: + source: + - module: intake_xarray +sources: #!TODO Update + croco: + description: CROCO_idealized + driver: netcdf + #cache: + # - argkey: urlpath + # regex: '' + # type: file + args: + urlpath: "{{ CATALOG_DIR }}/data/CROCOidealized_data/CROCO_idealized.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + GlobCurrent_example_data: + description: GlobCurrent_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/GlobCurrent_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + MITgcm_example_data: + description: MITgcm_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/MITgcm_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + MovingEddies_data: + description: MovingEddies_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/MovingEddies_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + + # NemoCurvilinear_data: + # NemoNorthSeaORCA025-N006_data: + # OFAM_example_data + # Peninsula_data + SWASH_data: + description: SWASH_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/SWASH_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + WOA_data: + description: WOA_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/WOA_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" diff --git a/catalogs/parcels-examples/catalog.yml b/catalogs/parcels-examples/catalog.yml new file mode 100644 index 0000000..90f919c --- /dev/null +++ b/catalogs/parcels-examples/catalog.yml @@ -0,0 +1,64 @@ +# zip_url: https://surfdrive.surf.nl/index.php/s/cmdSy8wBtCLDaGJ/download?path=%2F&files= +# ^ Do not remove this line! Used by the download script to find the data source +plugins: + source: + - module: intake_xarray +sources: + croco: + description: CROCO_idealized + driver: netcdf + #cache: + # - argkey: urlpath + # regex: '' + # type: file + args: + urlpath: "{{ CATALOG_DIR }}/data/CROCOidealized_data/CROCO_idealized.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + GlobCurrent_example_data: + description: GlobCurrent_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/GlobCurrent_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + MITgcm_example_data: + description: MITgcm_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/MITgcm_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + MovingEddies_data: + description: MovingEddies_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/MovingEddies_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + + # NemoCurvilinear_data: + # NemoNorthSeaORCA025-N006_data: + # OFAM_example_data + # Peninsula_data + # SWASH_data + SWASH_data: + description: SWASH_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/SWASH_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + WOA_data: + description: WOA_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/data/WOA_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" diff --git a/parcels_benchmarks/__init__.py b/parcels_benchmarks/__init__.py deleted file mode 100644 index 25ba20c..0000000 --- a/parcels_benchmarks/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# parcels_benchmarks/benchmark_utils diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py deleted file mode 100644 index 6996c2a..0000000 --- a/parcels_benchmarks/benchmark_setup.py +++ /dev/null @@ -1,247 +0,0 @@ -import json -import os -from pathlib import Path -from typing import Any - -import pooch -import typer - -app = typer.Typer(add_completion=False) - -PARCELS_DATADIR = os.getenv("PARCELS_DATADIR", default=None) -if PARCELS_DATADIR is not None: - PARCELS_DATADIR = Path(PARCELS_DATADIR) - -DEFAULT_MANIFEST = Path(__file__).with_name("benchmarks.json") - - -def _load_manifest(path: Path) -> dict: - if not path.is_file(): - raise FileNotFoundError(f"Manifest not found: {path}") - with path.open("r", encoding="utf-8") as f: - manifest = json.load(f) - - if "datasets" not in manifest or not isinstance(manifest["datasets"], list): - raise ValueError("Manifest must contain a top-level 'datasets' list") - - # Provide default URL if omitted - manifest.setdefault( - "data_url", - "https://surfdrive.surf.nl/index.php/s/7xlfdOFaUGDEmpD/download?path=%2F&files=", - ) - return manifest - - -def _save_manifest(path: Path, manifest: dict[str, Any]) -> None: - # keep stable ordering by dataset name - manifest["datasets"] = sorted(manifest["datasets"], key=lambda d: d.get("name", "")) - with path.open("w", encoding="utf-8") as f: - json.dump(manifest, f, indent=2) - f.write("\n") - - -def _cache_dir(data_home: Path | None) -> Path: - if data_home is None: - return Path(pooch.os_cache("parcels-benchmarks")) - return Path(data_home) - - -def _datasets_by_name(manifest: dict) -> dict[str, dict]: - out: dict[str, dict] = {} - for d in manifest["datasets"]: - name = d.get("name") - file = d.get("file") - known_hash = d.get("known_hash") - if not name or not file: - raise ValueError(f"Each dataset needs at least 'name' and 'file': {d}") - if name in out: - raise ValueError(f"Duplicate dataset name in manifest: {name}") - out[name] = { - "name": name, - "file": file, - "known_hash": known_hash, - } - return out - - -def _create_pooch_registry(manifest: dict) -> dict[str, str | None]: - """Collapses the mapping of dataset names to filenames into a pooch registry. - - Hashes are set to None for all files. - """ - registry: dict[str, str | None] = {} - for data in manifest["datasets"]: - registry[data["file"]] = data.get("known_hash") - return registry - - -def _get_pooch(manifest: dict, data_home: Path | None = None) -> pooch.Pooch: - cache_dir = _cache_dir(data_home) - registry = _create_pooch_registry(manifest) - cache_dir.parent.mkdir(parents=True, exist_ok=True) - return pooch.create( - path=cache_dir, - base_url=manifest["data_url"], - registry=registry, - ) - - -def download_example_dataset( - dataset: str, manifest_path: Path = DEFAULT_MANIFEST, data_home: Path | None = None -) -> Path: - """Load an example dataset listed in the provided manifest - - This function provides quick access to a small number of example datasets - that are useful in documentation and testing in parcels. - - Parameters - ---------- - dataset : str - Name of the dataset to load. - manifest_path: Path - Fully qualified path to a parcels-benchmarks manifest file - data_home : pathlike, optional - The directory in which to cache data. If not specified, defaults to wherever - pooch.os_cache("parcels-benchmarks") goes on your system. - - Returns - ------- - dataset_folder : Path - Path to the folder containing the downloaded dataset files. - """ - manifest = _load_manifest(manifest_path) - datasets = _datasets_by_name(manifest) - - # Dev note: `dataset` is assumed to be a folder name with netcdf files - if dataset not in datasets: - raise ValueError( - f"Dataset {dataset!r} not found. Available datasets are: " - + ", ".join(datasets.keys()) - ) - odie = _get_pooch(manifest, data_home=data_home) - zip_name = datasets[dataset]["file"] - listing = odie.fetch(zip_name, processor=pooch.Unzip()) - - # as pooch currently returns a file listing while we want a dir, - # we find the common parent dir to all files - common_parent_dir = min( - [Path(f) for f in listing], key=lambda f: len(f.parents) - ).parent - - return common_parent_dir - - -@app.command("download-all") -def download_all( - manifest_path: Path = typer.Option( - DEFAULT_MANIFEST, help="Path to benchmarks manifest JSON." - ), - data_home: Path | None = typer.Option( - PARCELS_DATADIR, help="Override cache directory." - ), -) -> None: - """Download all datasets listed in benchmarks manifest file.""" - - manifest = _load_manifest(manifest_path) - datasets = _datasets_by_name(manifest) - - dataset_folders: dict[str, Path] = {} - for dataset_name in datasets.keys(): - folder = download_example_dataset( - dataset_name, manifest_path=manifest_path, data_home=data_home - ) - dataset_folders[dataset_name] = folder - return dataset_folders - - -@app.command("add-dataset") -def add_dataset( - name: str = typer.Option(..., help="New dataset name to add to the manifest."), - file: str = typer.Option( - ..., help="Zip filename available at data_url (e.g. Foo.zip)." - ), - manifest: Path = typer.Option( - DEFAULT_MANIFEST, help="Path to benchmarks manifest JSON." - ), - data_home: Path | None = typer.Option( - PARCELS_DATADIR, help="Override cache directory." - ), -) -> None: - """ - Download a NEW dataset whose zip exists at data_url but is not yet in the manifest. - - We assume the sha256 is unknown ahead of time: - - download with known_hash=None - - compute sha256 of the downloaded zip - - append {name,file,known_hash} to the manifest - """ - m = _load_manifest(manifest) - datasets = _datasets_by_name(m) - - if name in datasets: - raise typer.BadParameter(f"Dataset {name!r} already exists in manifest.") - - # Also prevent duplicates by file - existing_files = {d.get("file") for d in m["datasets"]} - if file in existing_files: - raise typer.BadParameter( - f"File {file!r} is already referenced in the manifest." - ) - - base_url = m["data_url"] - cache_dir = _cache_dir(data_home) - url = f"{base_url}{file}" - cache_dir.mkdir(parents=True, exist_ok=True) - - typer.echo(f"Downloading (no hash verification): {url}") - # Download the zip WITHOUT verifying hash. - result = pooch.retrieve( - url=url, - known_hash=None, - path=cache_dir, - processor=None, - ) - typer.echo(f" Downloaded zip -> {Path(result)}") - - digest = pooch.file_hash(Path(result)) - known_hash = f"sha256:{digest}" - typer.echo(f" Computed {known_hash}") - - typer.echo("Unzipping...") - result = pooch.retrieve( - url=url, - known_hash=known_hash, - path=cache_dir, - processor=pooch.Unzip(), - ) - files = [Path(p) for p in result] - common_parent_dir = min(files, key=lambda p: len(p.parents)).parent - typer.echo(f" Unzipped -> {common_parent_dir}") - - # Append to manifest - m["datasets"].append({"name": name, "file": file, "known_hash": known_hash}) - _save_manifest(manifest, m) - typer.echo(f"Added {name!r} to {manifest}") - - -@app.command("list") -def list_datasets( - manifest: Path = typer.Option( - DEFAULT_MANIFEST, help="Path to benchmarks manifest JSON." - ), -) -> None: - """ - List datasets in the manifest. - """ - m = _load_manifest(manifest) - by_name = _dataset_by_name(m) # noqa: F821 - for name, entry in sorted(by_name.items(), key=lambda kv: kv[0]): - typer.echo(f"{name}: {entry['file']} ({entry.get('known_hash', 'no-hash')})") - - -def main() -> None: - app() - - -if __name__ == "__main__": - main() diff --git a/parcels_benchmarks/benchmarks.json b/parcels_benchmarks/benchmarks.json deleted file mode 100644 index fb93639..0000000 --- a/parcels_benchmarks/benchmarks.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "data_url": "https://surfdrive.surf.nl/index.php/s/7xlfdOFaUGDEmpD/download?path=%2F&files=", - "datasets": [ - { - "name": "FESOM-baroclinic-gyre", - "file": "Parcels_Benchmarks_FESOM-baroclinic-gyre_v2025.10.2.2.zip", - "known_hash": "sha256:8d849df2996e3cecf95344e6cde6ed873919d33d731b5fbed4ecacf1a57fbce3" - }, - { - "name": "Global ICON Data", - "file": "Parcels_Benchmarks_ICON.zip", - "known_hash": "sha256:06e80941050d16b89ddce758fb6a1030e3facaba9d32bf9085f1e1e497731903" - }, - { - "name": "MOi-curvilinear", - "file": "Parcels_Benchmarks_MOi_data.zip", - "known_hash": "sha256:f7816d872897c089eeb07a4e32b7fbcc96a0023ef01ac6c3792f88d8d8893885" - } - ] -} diff --git a/pixi.lock b/pixi.lock index 3f10ffb..8f2f4dd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5,309 +5,782 @@ environments: - url: https://conda.anaconda.org/conda-forge/ indexes: - https://pypi.org/simple + options: + pypi-prerelease-mode: if-necessary-or-explicit packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/asv-0.6.5-py312h1289d80_3.conda - 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If target folder already exists - skips. The catalog file which should be used in scripts will be housed at `output_dir/catalog_file.name`" } + +setup-data = { depends-on = [ + { task = "download-catalog", args = [ + { catalog_file = "catalogs/parcels-examples/catalog.yml" }, + { output_dir = "surf-data/parcels-examples" }, + ] }, + { task = "download-catalog", args = [ + { catalog_file = "catalogs/parcels-benchmarks/catalog.yml" }, + { output_dir = "surf-data/parcels-benchmarks" }, + ] }, +], description = "Setup all data to be used in the benchmarks." } + +[tasks.benchmark] +cmd = "asv run" +depends-on = ["setup-data"] +description = "Run the benchmarks, setting up the data first." [dependencies] python = "3.12.*" -asv = ">=0.6.5" -pooch = ">=1.8.2" pre_commit = "*" -py-rattler = "0.15.*" +ipython = ">=9.11.0,<10" +netcdf4 = ">=1.7.4,<2" +curl = "*" +proj = "*" [pypi-dependencies] -parcels_benchmarks = { path = ".", editable = true } +benchmarks = { path = "." } diff --git a/pyproject.toml b/pyproject.toml index ce6abe4..b0b275f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,38 +1,25 @@ -[build-system] -requires = ["setuptools>=61", "wheel"] -build-backend = "setuptools.build_meta" - [project] -name = "parcels_benchmarks" +name = "benchmarks" version = "0.1.0" -description = "Helper utilities for Parcels benchmarks" -requires-python = ">=3.10" -authors = [{ name = "Parcels team" }] +description = "Add your description here" +readme = "README.md" +requires-python = ">=3.12" dependencies = [ - "xarray", - "pooch", - "typer>=0.9", + "intake-xarray", + "parcels @ file:///${PROJECT_ROOT}/Parcels", + "asv>=0.6.5", + "py-rattler==0.15.*", ] -# This creates an installable CLI command: `benchmark-setup ...` -[project.scripts] -benchmark-setup = "parcels_benchmarks.benchmark_setup:main" - [tool.setuptools.packages.find] -where = ["."] -include = ["parcels_benchmarks"] - -# Include the benchmarks manifest in the wheel/sdist -[tool.setuptools.package-data] -parcels_benchmarks = ["*.json"] - +include = ["benchmarks*"] [tool.ruff.lint] select = [ "E", # Error "F", # pyflakes - "I", # isort + # "I", # isort #? Pre-commit in CI was wrestling with the local install "B", # Bugbear "UP", # pyupgrade "LOG", # logging diff --git a/scripts/download-catalog.py b/scripts/download-catalog.py new file mode 100644 index 0000000..c8401b1 --- /dev/null +++ b/scripts/download-catalog.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python3 +"""Download and extract a catalog zip archive, unzipping all zip archives contained within.""" + +import argparse +import shutil +import subprocess +import zipfile +from pathlib import Path + +from benchmarks import PARCELS_BENCHMARKS_DATA_FOLDER + + +def extract_zip_url(catalog_path: Path) -> str: + with catalog_path.open() as f: + first_line = f.readline().strip() + if not first_line.startswith("# zip_url:"): + raise ValueError(f"First line must be '# zip_url: ', got: {first_line!r}") + url = first_line.removeprefix("# zip_url:").strip() + if not url: + raise ValueError("zip_url is empty") + return url + + +def download_file(url: str, dest_dir: Path) -> Path: + dest = dest_dir / "data.zip" + print(f"Downloading {url} -> {dest}") + subprocess.run(["curl", "-L", "-o", str(dest), url], check=True) + return dest + + +def unzip_recursive(directory: Path) -> None: + """Recursively find and extract all zip files, deleting originals.""" + found = list(directory.rglob("*.zip")) + if not found: + return + for zip_path in found: + print(f"Extracting {zip_path}") + extract_to = zip_path.parent / zip_path.stem + extract_to.mkdir(exist_ok=True) + with zipfile.ZipFile(zip_path) as zf: + zf.extractall(extract_to) + zip_path.unlink() + print(f"Deleted {zip_path}") + # Collapse data/data -> data if the only child is a same-named folder + sole_child = extract_to / zip_path.stem + if sole_child.is_dir() and len(list(extract_to.iterdir())) == 1: + for item in sole_child.iterdir(): + item.rename(extract_to / item.name) + sole_child.rmdir() + # recurse in case extracted zips contained more zips + unzip_recursive(directory) + + +def main() -> None: + parser = argparse.ArgumentParser( + description="Download and extract a catalog archive." + ) + parser.add_argument("catalog", type=Path, help="Path to catalog.yml") + parser.add_argument( + "output_dir", + type=str, + help="Subdirectory in PARCELS_BENCHMARKS_DATA_FOLDER to extract into", + ) + args = parser.parse_args() + output_dir = PARCELS_BENCHMARKS_DATA_FOLDER / args.output_dir + catalog_path = output_dir / args.catalog.name + + if not args.catalog.is_file(): + raise SystemExit(f"catalog file not found: {args.catalog}") + if output_dir.exists(): + shutil.copy(args.catalog, catalog_path) + print(f"Copied catalogue across to {catalog_path}") + print("Output directory already exists! Exiting...") + return + + output_dir.mkdir(parents=True) + shutil.copy(args.catalog, catalog_path) + print(f"Copied catalogue across to {catalog_path}") + + url = extract_zip_url(args.catalog) + download_file(url, output_dir) + unzip_recursive(output_dir) + + print("Done.") + + +if __name__ == "__main__": + main()