From fd2c217f8e7baabc8b4e48ebd2560a59ff809ffa Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Wed, 25 Mar 2026 18:49:00 +0100 Subject: [PATCH 01/44] Update README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7e4f03c..823046b 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ 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 @@ -64,7 +64,7 @@ Data is hosted remotely on a SurfDrive managed by the Parcels developers. You wi 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" +pixi run benchmark-setup add-dataset --name "Name for your dataset" --file "Path to ZIP archive in the SurfDrive" ``` 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. From b75d0b332ea0d4768d3fa98f55e7836d839c1089 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Wed, 25 Mar 2026 18:50:20 +0100 Subject: [PATCH 02/44] Update gitignore --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 6860f1e..d6114d4 100644 --- a/.gitignore +++ b/.gitignore @@ -10,6 +10,5 @@ credentials.json *.egg-info __pycache__ build/ -parcels/ .asv/ html/ From 295cb7bd10eab4b43bfa4a07eedcff0ec6ea0f26 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Wed, 25 Mar 2026 18:51:16 +0100 Subject: [PATCH 03/44] Add Parcels as submodule --- .gitmodules | 3 +++ Parcels | 1 + asv.conf.json | 2 +- 3 files changed, 5 insertions(+), 1 deletion(-) create mode 100644 .gitmodules create mode 160000 Parcels 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/asv.conf.json b/asv.conf.json index ab7af9b..d14c1d0 100644 --- a/asv.conf.json +++ b/asv.conf.json @@ -2,7 +2,7 @@ "version": 1, "project": "parcels", "project_url": "https://github.com/Parcels-Code/parcels", - "repo": "https://github.com/Parcels-Code/parcels.git", + "repo": "./Parcels", "branches": ["main"], "environment_type": "rattler", "conda_channels": [ From 98855a5f5a1cd36533f31f8b29bc38f5a758877c Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Wed, 25 Mar 2026 19:05:26 +0100 Subject: [PATCH 04/44] Add sandbox environment --- sandbox/.gitattributes | 2 ++ sandbox/.gitignore | 4 ++++ sandbox/pixi.toml | 14 ++++++++++++++ 3 files changed, 20 insertions(+) create mode 100644 sandbox/.gitattributes create mode 100644 sandbox/.gitignore create mode 100644 sandbox/pixi.toml diff --git a/sandbox/.gitattributes b/sandbox/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/sandbox/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/sandbox/.gitignore b/sandbox/.gitignore new file mode 100644 index 0000000..60c96b1 --- /dev/null +++ b/sandbox/.gitignore @@ -0,0 +1,4 @@ +# pixi environments +.pixi/* +!.pixi/config.toml +pixi.lock diff --git a/sandbox/pixi.toml b/sandbox/pixi.toml new file mode 100644 index 0000000..eaed168 --- /dev/null +++ b/sandbox/pixi.toml @@ -0,0 +1,14 @@ +# We couldn't have the parcels dependency in the root as it would cause unnecessary noise in the lockfile +[workspace] +authors = ["parcels-benchmarks contributors"] +channels = ["conda-forge"] +name = "sandbox" +platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] +preview = ['pixi-build'] + +[dependencies] + +parcels = { path = '../Parcels' } + +[pypi-dependencies] +parcels_benchmarks = { path = "..", editable = true } From bb967c68070cffb4cfaf5075b9cea8f621ea9ccf Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 10:38:41 +0100 Subject: [PATCH 05/44] Rename benchmarks.json to datasets.json --- README.md | 2 +- parcels_benchmarks/benchmark_setup.py | 2 +- parcels_benchmarks/{benchmarks.json => datasets.json} | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename parcels_benchmarks/{benchmarks.json => datasets.json} (100%) diff --git a/README.md b/README.md index 823046b..caa61ee 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ Once your data is hosted in the shared SurfDrive, you can easily add your datase pixi run benchmark-setup add-dataset --name "Name for your dataset" --file "Path to ZIP archive in the SurfDrive" ``` -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. +During this process, the dataset will be downloaded and a complete entry will be added to the [parcels_benchmarks/datasets.json](./parcels_benchmarks/datasets.json) manifest file. Once updated, this file can be committed to this repository and contributed via a pull request. ### Writing the benchmarks diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index 6996c2a..f137fbe 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -12,7 +12,7 @@ if PARCELS_DATADIR is not None: PARCELS_DATADIR = Path(PARCELS_DATADIR) -DEFAULT_MANIFEST = Path(__file__).with_name("benchmarks.json") +DEFAULT_MANIFEST = Path(__file__).with_name("datasets.json") def _load_manifest(path: Path) -> dict: diff --git a/parcels_benchmarks/benchmarks.json b/parcels_benchmarks/datasets.json similarity index 100% rename from parcels_benchmarks/benchmarks.json rename to parcels_benchmarks/datasets.json From 4d59a440dd7201d107163f30a23149deadc0ae83 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 10:56:32 +0100 Subject: [PATCH 06/44] typo --- parcels_benchmarks/benchmark_setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index f137fbe..4c4ee9e 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -234,7 +234,7 @@ def list_datasets( List datasets in the manifest. """ m = _load_manifest(manifest) - by_name = _dataset_by_name(m) # noqa: F821 + by_name = _datasets_by_name(m) 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')})") From 1f8777cc33975c9201bd9a34718a508e1020c9a0 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 10:57:32 +0100 Subject: [PATCH 07/44] update function name --- parcels_benchmarks/benchmark_setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index 4c4ee9e..2411f5c 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -89,9 +89,9 @@ def _get_pooch(manifest: dict, data_home: Path | None = None) -> pooch.Pooch: 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 + """Load a dataset listed in the provided manifest - This function provides quick access to a small number of example datasets + This function provides quick access to a small number of datasets that are useful in documentation and testing in parcels. Parameters From 96b3646f02aa617e5c5dfaa98dde7b7e77b54697 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 10:58:32 +0100 Subject: [PATCH 08/44] No need to have this default here Just expect it to be provided in the datasets.json --- parcels_benchmarks/benchmark_setup.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index 2411f5c..ed47f89 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -24,11 +24,6 @@ def _load_manifest(path: Path) -> dict: 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 From c56cf69e75c066e76e95f0205589ec42f389b100 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 11:00:56 +0100 Subject: [PATCH 09/44] Add pydantic --- pixi.lock | 76 ++++++++++++++++++++++++++++++++++++++++++++++++-- pyproject.toml | 1 + 2 files changed, 75 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 3f10ffb..2b34023 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5,6 +5,8 @@ environments: - 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conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda sha256: 032271135bca55aeb156cee361c81350c6f3fb203f57d024d7e5a1fc9ef18731 md5: 0caa1af407ecff61170c9437a808404d diff --git a/pyproject.toml b/pyproject.toml index ce6abe4..438f56b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,6 +12,7 @@ dependencies = [ "xarray", "pooch", "typer>=0.9", + "pydantic", ] # This creates an installable CLI command: `benchmark-setup ...` From 2cec8b44965975ad68b211df0dcf349c6b64be88 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 11:07:44 +0100 Subject: [PATCH 10/44] Migrate to pydantic --- parcels_benchmarks/benchmark_setup.py | 83 +++++++++++++++------------ 1 file changed, 46 insertions(+), 37 deletions(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index ed47f89..8a941ad 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -1,10 +1,31 @@ -import json import os from pathlib import Path -from typing import Any import pooch import typer +from pydantic import BaseModel, Field, HttpUrl + + +class Dataset(BaseModel): + """A single dataset entry in the manifest.""" + + name: str = Field(..., description="Unique name for the dataset") + file: str = Field(..., description="Filename of the dataset zip file") + known_hash: str | None = Field( + None, description="SHA256 hash of the file in format 'sha256:xxxxx'" + ) + + +class DatasetsManifest(BaseModel): + """Root manifest structure containing all datasets.""" + + data_url: HttpUrl = Field( + ..., description="Base URL where dataset files are hosted" + ) + datasets: list[Dataset] = Field( + default_factory=list, description="List of available datasets" + ) + app = typer.Typer(add_completion=False) @@ -15,23 +36,18 @@ DEFAULT_MANIFEST = Path(__file__).with_name("datasets.json") -def _load_manifest(path: Path) -> dict: +def _load_manifest(path: Path) -> DatasetsManifest: 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") - - return manifest + return DatasetsManifest.model_validate_json(f.read()) -def _save_manifest(path: Path, manifest: dict[str, Any]) -> None: +def _save_manifest(path: Path, manifest: DatasetsManifest) -> None: # keep stable ordering by dataset name - manifest["datasets"] = sorted(manifest["datasets"], key=lambda d: d.get("name", "")) + manifest.datasets = sorted(manifest.datasets, key=lambda d: d.name) with path.open("w", encoding="utf-8") as f: - json.dump(manifest, f, indent=2) + f.write(manifest.model_dump_json(indent=2)) f.write("\n") @@ -41,42 +57,35 @@ def _cache_dir(data_home: Path | None) -> Path: 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, - } +def _datasets_by_name(manifest: DatasetsManifest) -> dict[str, Dataset]: + out: dict[str, Dataset] = {} + for dataset in manifest.datasets: + if dataset.name in out: + raise ValueError(f"Duplicate dataset name in manifest: {dataset.name}") + out[dataset.name] = dataset return out -def _create_pooch_registry(manifest: dict) -> dict[str, str | None]: +def _create_pooch_registry(manifest: DatasetsManifest) -> 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") + for dataset in manifest.datasets: + registry[dataset.file] = dataset.known_hash return registry -def _get_pooch(manifest: dict, data_home: Path | None = None) -> pooch.Pooch: +def _get_pooch( + manifest: DatasetsManifest, 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"], + base_url=str(manifest.data_url), registry=registry, ) @@ -114,7 +123,7 @@ def download_example_dataset( + ", ".join(datasets.keys()) ) odie = _get_pooch(manifest, data_home=data_home) - zip_name = datasets[dataset]["file"] + 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, @@ -177,13 +186,13 @@ def add_dataset( 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"]} + existing_files = {d.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"] + base_url = str(m.data_url) cache_dir = _cache_dir(data_home) url = f"{base_url}{file}" cache_dir.mkdir(parents=True, exist_ok=True) @@ -214,7 +223,7 @@ def add_dataset( typer.echo(f" Unzipped -> {common_parent_dir}") # Append to manifest - m["datasets"].append({"name": name, "file": file, "known_hash": known_hash}) + m.datasets.append(Dataset(name=name, file=file, known_hash=known_hash)) _save_manifest(manifest, m) typer.echo(f"Added {name!r} to {manifest}") @@ -231,7 +240,7 @@ def list_datasets( m = _load_manifest(manifest) by_name = _datasets_by_name(m) 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')})") + typer.echo(f"{name}: {entry.file} ({entry.known_hash or 'no-hash'})") def main() -> None: From 64fd72cc0f089550e0506454fcf167fcd7799bde Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 11:09:52 +0100 Subject: [PATCH 11/44] Assert no duplicate dataset names --- parcels_benchmarks/benchmark_setup.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index 8a941ad..15c65c7 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -3,7 +3,7 @@ import pooch import typer -from pydantic import BaseModel, Field, HttpUrl +from pydantic import BaseModel, Field, HttpUrl, model_validator class Dataset(BaseModel): @@ -26,6 +26,18 @@ class DatasetsManifest(BaseModel): default_factory=list, description="List of available datasets" ) + @model_validator(mode="after") + def validate_unique_names(self) -> "DatasetsManifest": + """Ensure all dataset names are unique.""" + names = [dataset.name for dataset in self.datasets] + duplicates = [name for name in names if names.count(name) > 1] + if duplicates: + unique_duplicates = sorted(set(duplicates)) + raise ValueError( + f"Duplicate dataset name(s) in manifest: {', '.join(unique_duplicates)}" + ) + return self + app = typer.Typer(add_completion=False) @@ -60,8 +72,6 @@ def _cache_dir(data_home: Path | None) -> Path: def _datasets_by_name(manifest: DatasetsManifest) -> dict[str, Dataset]: out: dict[str, Dataset] = {} for dataset in manifest.datasets: - if dataset.name in out: - raise ValueError(f"Duplicate dataset name in manifest: {dataset.name}") out[dataset.name] = dataset return out From b281743484654cf123a430bf9d8e9f558e9e1bd7 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 11:13:28 +0100 Subject: [PATCH 12/44] refactor --- parcels_benchmarks/benchmark_setup.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index 15c65c7..a1cbd65 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -70,10 +70,7 @@ def _cache_dir(data_home: Path | None) -> Path: def _datasets_by_name(manifest: DatasetsManifest) -> dict[str, Dataset]: - out: dict[str, Dataset] = {} - for dataset in manifest.datasets: - out[dataset.name] = dataset - return out + return {dataset.name: dataset for dataset in manifest.datasets} def _create_pooch_registry(manifest: DatasetsManifest) -> dict[str, str | None]: From 96e24a7e5084fb5a7ffa81d03d35c778a17fef02 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 11:14:23 +0100 Subject: [PATCH 13/44] Rename function All datasets are "example" datasets --- benchmarks/fesom2.py | 6 +++--- benchmarks/moi_curvilinear.py | 10 ++++------ parcels_benchmarks/benchmark_setup.py | 4 ++-- 3 files changed, 9 insertions(+), 11 deletions(-) diff --git a/benchmarks/fesom2.py b/benchmarks/fesom2.py index e7bd735..027bc18 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -1,5 +1,6 @@ import numpy as np import uxarray as ux + from parcels import ( FieldSet, Particle, @@ -7,8 +8,7 @@ convert, ) from parcels.kernels import AdvectionRK2_3D - -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_example_dataset +from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_dataset runtime = np.timedelta64(1, "D") dt = np.timedelta64(2400, "s") @@ -29,7 +29,7 @@ class FESOM2: 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( + self.datapath = download_dataset( "FESOM-baroclinic-gyre", data_home=PARCELS_DATADIR ) diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index dcc1f27..c705772 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -1,12 +1,12 @@ from glob import glob import numpy as np -import parcels import xarray as xr import xgcm -from parcels.interpolators import XLinear -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_example_dataset +import parcels +from parcels.interpolators import XLinear +from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_dataset runtime = np.timedelta64(2, "D") dt = np.timedelta64(15, "m") @@ -72,9 +72,7 @@ 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/parcels_benchmarks/benchmark_setup.py b/parcels_benchmarks/benchmark_setup.py index a1cbd65..61ab784 100644 --- a/parcels_benchmarks/benchmark_setup.py +++ b/parcels_benchmarks/benchmark_setup.py @@ -97,7 +97,7 @@ def _get_pooch( ) -def download_example_dataset( +def download_dataset( dataset: str, manifest_path: Path = DEFAULT_MANIFEST, data_home: Path | None = None ) -> Path: """Load a dataset listed in the provided manifest @@ -158,7 +158,7 @@ def download_all( dataset_folders: dict[str, Path] = {} for dataset_name in datasets.keys(): - folder = download_example_dataset( + folder = download_dataset( dataset_name, manifest_path=manifest_path, data_home=data_home ) dataset_folders[dataset_name] = folder From 2d83e26dcf6d4dc01a7eed3188369474747feb95 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 13:47:57 +0100 Subject: [PATCH 14/44] Add download-catalogue option --- catalogue.yaml | 25 ++++++++++++++ download_catalogue.py | 79 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 catalogue.yaml create mode 100644 download_catalogue.py diff --git a/catalogue.yaml b/catalogue.yaml new file mode 100644 index 0000000..8a46d68 --- /dev/null +++ b/catalogue.yaml @@ -0,0 +1,25 @@ +# zip_url: https://surfdrive.surf.nl/index.php/s/cmdSy8wBtCLDaGJ/download?path=%2F&files= +plugins: + source: + - module: intake_xarray +sources: + croco: + description: CROCO_idealized + driver: netcdf + #cache: + # - argkey: urlpath + # regex: '' + # type: file + args: + urlpath: "{{ CATALOG_DIR }}/parcels-examples/CROCOidealized_data/CROCO_idealized.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + GlobCurrent_example_data: + description: GlobCurrent_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/parcels-examples/GlobCurrent_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" diff --git a/download_catalogue.py b/download_catalogue.py new file mode 100644 index 0000000..51b5cf1 --- /dev/null +++ b/download_catalogue.py @@ -0,0 +1,79 @@ +#!/usr/bin/env python3 +"""Download and extract a catalogue zip archive.""" + +import argparse +import shutil +import zipfile +from pathlib import Path + +import requests + + +def extract_zip_url(catalogue_path: Path) -> str: + with catalogue_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: + response = requests.get(url, stream=True) + response.raise_for_status() + cd = response.headers.get("Content-Disposition", "") + filename = "archive.zip" + if "filename=" in cd: + filename = cd.split("filename=")[-1].strip().strip('"') + if not filename.endswith(".zip"): + filename += ".zip" + dest = dest_dir / filename + print(f"Downloading {url} -> {dest}") + with dest.open("wb") as f: + for chunk in response.iter_content(chunk_size=8192): + f.write(chunk) + 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 + print(f"found={found}") + for zip_path in found: + print(f"Extracting {zip_path}") + extract_to = zip_path.parent + with zipfile.ZipFile(zip_path) as zf: + zf.extractall(extract_to) + zip_path.unlink() + print(f"Deleted {zip_path}") + # recurse in case extracted zips contained more zips + unzip_recursive(directory) + + +def main() -> None: + parser = argparse.ArgumentParser( + description="Download and extract a catalogue archive." + ) + parser.add_argument("catalogue", type=Path, help="Path to catalogue.yml") + parser.add_argument("output_dir", type=Path, help="Directory to extract into") + args = parser.parse_args() + + if not args.catalogue.is_file(): + raise SystemExit(f"catalogue file not found: {args.catalogue}") + + args.output_dir.mkdir(parents=True, exist_ok=True) + + url = extract_zip_url(args.catalogue) + download_file(url, args.output_dir) + unzip_recursive(args.output_dir) + + shutil.copy(args.catalogue, args.output_dir / args.catalogue.name) + print("Done.") + + +if __name__ == "__main__": + main() From 45703682f2ca194c18fe9b444deb5ea5656f81de Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 14:06:46 +0100 Subject: [PATCH 15/44] Update catalogue --- .gitignore | 3 +++ catalogue.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) diff --git a/.gitignore b/.gitignore index d6114d4..62caba4 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,6 @@ __pycache__ build/ .asv/ html/ +.DS_Store + +output diff --git a/catalogue.yaml b/catalogue.yaml index 8a46d68..581846d 100644 --- a/catalogue.yaml +++ b/catalogue.yaml @@ -1,4 +1,5 @@ # 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 @@ -23,3 +24,41 @@ sources: chunks: {} xarray_kwargs: engine: "netcdf4" + MITgcm_example_data: + description: MITgcm_example_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/parcels-examples/MITgcm_example_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + MovingEddies_data: + description: MovingEddies_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/parcels-examples/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 }}/parcels-examples/SWASH_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" + WOA_data: + description: WOA_data + driver: netcdf + args: + urlpath: "{{ CATALOG_DIR }}/parcels-examples/WOA_data/*.nc" + chunks: {} + xarray_kwargs: + engine: "netcdf4" From 9fa1963bc5879a302ccc6e4bfef3cf860c9157c5 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 14:43:51 +0100 Subject: [PATCH 16/44] Move files and add tasks --- .../parcels-examples/catalogue.yaml | 12 ++++++------ download_catalogue.py => download-catalogue.py | 12 +++++------- pixi.toml | 18 ++++++++++++++++++ 3 files changed, 29 insertions(+), 13 deletions(-) rename catalogue.yaml => catalogues/parcels-examples/catalogue.yaml (73%) rename download_catalogue.py => download-catalogue.py (88%) diff --git a/catalogue.yaml b/catalogues/parcels-examples/catalogue.yaml similarity index 73% rename from catalogue.yaml rename to catalogues/parcels-examples/catalogue.yaml index 581846d..90f919c 100644 --- a/catalogue.yaml +++ b/catalogues/parcels-examples/catalogue.yaml @@ -12,7 +12,7 @@ sources: # regex: '' # type: file args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/CROCOidealized_data/CROCO_idealized.nc" + urlpath: "{{ CATALOG_DIR }}/data/CROCOidealized_data/CROCO_idealized.nc" chunks: {} xarray_kwargs: engine: "netcdf4" @@ -20,7 +20,7 @@ sources: description: GlobCurrent_example_data driver: netcdf args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/GlobCurrent_example_data/*.nc" + urlpath: "{{ CATALOG_DIR }}/data/GlobCurrent_example_data/*.nc" chunks: {} xarray_kwargs: engine: "netcdf4" @@ -28,7 +28,7 @@ sources: description: MITgcm_example_data driver: netcdf args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/MITgcm_example_data/*.nc" + urlpath: "{{ CATALOG_DIR }}/data/MITgcm_example_data/*.nc" chunks: {} xarray_kwargs: engine: "netcdf4" @@ -36,7 +36,7 @@ sources: description: MovingEddies_data driver: netcdf args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/MovingEddies_data/*.nc" + urlpath: "{{ CATALOG_DIR }}/data/MovingEddies_data/*.nc" chunks: {} xarray_kwargs: engine: "netcdf4" @@ -50,7 +50,7 @@ sources: description: SWASH_data driver: netcdf args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/SWASH_data/*.nc" + urlpath: "{{ CATALOG_DIR }}/data/SWASH_data/*.nc" chunks: {} xarray_kwargs: engine: "netcdf4" @@ -58,7 +58,7 @@ sources: description: WOA_data driver: netcdf args: - urlpath: "{{ CATALOG_DIR }}/parcels-examples/WOA_data/*.nc" + urlpath: "{{ CATALOG_DIR }}/data/WOA_data/*.nc" chunks: {} xarray_kwargs: engine: "netcdf4" diff --git a/download_catalogue.py b/download-catalogue.py similarity index 88% rename from download_catalogue.py rename to download-catalogue.py index 51b5cf1..3927441 100644 --- a/download_catalogue.py +++ b/download-catalogue.py @@ -23,13 +23,7 @@ def extract_zip_url(catalogue_path: Path) -> str: def download_file(url: str, dest_dir: Path) -> Path: response = requests.get(url, stream=True) response.raise_for_status() - cd = response.headers.get("Content-Disposition", "") - filename = "archive.zip" - if "filename=" in cd: - filename = cd.split("filename=")[-1].strip().strip('"') - if not filename.endswith(".zip"): - filename += ".zip" - dest = dest_dir / filename + dest = dest_dir / "data.zip" print(f"Downloading {url} -> {dest}") with dest.open("wb") as f: for chunk in response.iter_content(chunk_size=8192): @@ -62,6 +56,10 @@ def main() -> None: parser.add_argument("output_dir", type=Path, help="Directory to extract into") args = parser.parse_args() + if args.output_dir.exists(): + print("Output directory already exists! Exiting...") + return + if not args.catalogue.is_file(): raise SystemExit(f"catalogue file not found: {args.catalogue}") diff --git a/pixi.toml b/pixi.toml index 8b1cb52..6612212 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,6 +7,20 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] [tasks] lint = "pre-commit run --all-files" +download-catalogue = { cmd = "python download-catalogue.py {{ catalogue_file }} {{ output_dir }}", args = [ + "catalogue_file", + "output_dir", +] } + +[tasks.benchmark] +cmd = "asv run" +depends-on = [ + # Downloads the datasets. The catalogue files in the scripts will live at (e.g.,) `data/parcels-examples/catalogue.yaml` + { task = "download-catalogue", args = [ + { catalogue_file = "parcels-examples.catalogue.yaml" }, + { output_dir = "data/parcels-examples" }, + ] }, +] [dependencies] @@ -15,6 +29,10 @@ asv = ">=0.6.5" pooch = ">=1.8.2" pre_commit = "*" py-rattler = "0.15.*" +intake-xarray = ">=2.0.0,<3" +parcels = ">=3.1.4,<4" +ipython = ">=9.11.0,<10" +netcdf4 = ">=1.7.4,<2" [pypi-dependencies] parcels_benchmarks = { path = ".", editable = true } From bddcbdc7171847e2c2978646cd584f7e19507118 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 14:48:49 +0100 Subject: [PATCH 17/44] Add catalogue --- .gitignore | 2 +- catalogues/parcels-benchmarks/catalogue.yaml | 64 ++++++++++++++++++++ pixi.toml | 6 +- 3 files changed, 70 insertions(+), 2 deletions(-) create mode 100644 catalogues/parcels-benchmarks/catalogue.yaml diff --git a/.gitignore b/.gitignore index 62caba4..4aa2ea9 100644 --- a/.gitignore +++ b/.gitignore @@ -14,4 +14,4 @@ build/ html/ .DS_Store -output +data diff --git a/catalogues/parcels-benchmarks/catalogue.yaml b/catalogues/parcels-benchmarks/catalogue.yaml new file mode 100644 index 0000000..46656fc --- /dev/null +++ b/catalogues/parcels-benchmarks/catalogue.yaml @@ -0,0 +1,64 @@ +# 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 + 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/pixi.toml b/pixi.toml index 6612212..e2b5b7d 100644 --- a/pixi.toml +++ b/pixi.toml @@ -17,9 +17,13 @@ cmd = "asv run" depends-on = [ # Downloads the datasets. The catalogue files in the scripts will live at (e.g.,) `data/parcels-examples/catalogue.yaml` { task = "download-catalogue", args = [ - { catalogue_file = "parcels-examples.catalogue.yaml" }, + { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, { output_dir = "data/parcels-examples" }, ] }, + { task = "download-catalogue", args = [ + { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, + { output_dir = "data/parcels-benchmarks" }, + ] }, ] [dependencies] From 99cf82d47f882cce66c04500731c6761c314263a Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:08:05 +0100 Subject: [PATCH 18/44] Move file --- pixi.toml | 16 +++++++++------- .../download-catalogue.py | 0 2 files changed, 9 insertions(+), 7 deletions(-) rename download-catalogue.py => scripts/download-catalogue.py (100%) diff --git a/pixi.toml b/pixi.toml index e2b5b7d..8a67b54 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,15 +7,13 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] [tasks] lint = "pre-commit run --all-files" -download-catalogue = { cmd = "python download-catalogue.py {{ catalogue_file }} {{ output_dir }}", args = [ +# Downloads the datasets. The catalogue file which should be used will be housed at `output_dir/catalogue_file.name` +download-catalogue = { cmd = "python scripts/download-catalogue.py {{ catalogue_file }} {{ output_dir }}", args = [ "catalogue_file", "output_dir", ] } -[tasks.benchmark] -cmd = "asv run" -depends-on = [ - # Downloads the datasets. The catalogue files in the scripts will live at (e.g.,) `data/parcels-examples/catalogue.yaml` +setup-data = { depends-on = [ { task = "download-catalogue", args = [ { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, { output_dir = "data/parcels-examples" }, @@ -23,8 +21,12 @@ depends-on = [ { task = "download-catalogue", args = [ { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, { output_dir = "data/parcels-benchmarks" }, - ] }, -] + ] } +]} + +[tasks.benchmark] +cmd = "asv run" +depends-on = ["setup-data"] [dependencies] diff --git a/download-catalogue.py b/scripts/download-catalogue.py similarity index 100% rename from download-catalogue.py rename to scripts/download-catalogue.py From 070bcf0c79b5b5cb336afc0cc5bf069b597fbc7a Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:10:24 +0100 Subject: [PATCH 19/44] Update folder location --- pixi.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.toml b/pixi.toml index 8a67b54..4ae06fd 100644 --- a/pixi.toml +++ b/pixi.toml @@ -16,11 +16,11 @@ download-catalogue = { cmd = "python scripts/download-catalogue.py {{ catalogue_ setup-data = { depends-on = [ { task = "download-catalogue", args = [ { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, - { output_dir = "data/parcels-examples" }, + { output_dir = "surf-data/parcels-examples" }, ] }, { task = "download-catalogue", args = [ { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, - { output_dir = "data/parcels-benchmarks" }, + { output_dir = "surf-data/parcels-benchmarks" }, ] } ]} From 96b97d81e003d434a63ed797e0d6b0f4192b0eeb Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:24:04 +0100 Subject: [PATCH 20/44] Add PARCELS_BENCHMARKS_DATA_FOLDER env var --- .env.example | 2 ++ .gitignore | 1 + scripts/download-catalogue.py | 19 ++++++++++++------- 3 files changed, 15 insertions(+), 7 deletions(-) create mode 100644 .env.example diff --git a/.env.example b/.env.example new file mode 100644 index 0000000..ed309eb --- /dev/null +++ b/.env.example @@ -0,0 +1,2 @@ +# Target location for the data to be downloaded to +PARCELS_BENCHMARKS_DATA_FOLDER='./data' \ No newline at end of file diff --git a/.gitignore b/.gitignore index 4aa2ea9..0c3c80f 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,4 @@ html/ .DS_Store data +.env \ No newline at end of file diff --git a/scripts/download-catalogue.py b/scripts/download-catalogue.py index 3927441..0b53203 100644 --- a/scripts/download-catalogue.py +++ b/scripts/download-catalogue.py @@ -7,7 +7,12 @@ from pathlib import Path import requests +import os +try: + PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) +except KeyError as e: + raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data should be downloaded.") from e def extract_zip_url(catalogue_path: Path) -> str: with catalogue_path.open() as f: @@ -53,23 +58,23 @@ def main() -> None: description="Download and extract a catalogue archive." ) parser.add_argument("catalogue", type=Path, help="Path to catalogue.yml") - parser.add_argument("output_dir", type=Path, help="Directory to extract into") + parser.add_argument("output_dir", type=str, help="Subdirectory in PARCELS_BENCHMARKS_DATA_FOLDER to extract into") args = parser.parse_args() - - if args.output_dir.exists(): + output_dir = PARCELS_BENCHMARKS_DATA_FOLDER / args.output_dir + if output_dir.exists(): print("Output directory already exists! Exiting...") return if not args.catalogue.is_file(): raise SystemExit(f"catalogue file not found: {args.catalogue}") - args.output_dir.mkdir(parents=True, exist_ok=True) + output_dir.mkdir(parents=True, exist_ok=True) url = extract_zip_url(args.catalogue) - download_file(url, args.output_dir) - unzip_recursive(args.output_dir) + download_file(url, output_dir) + unzip_recursive(output_dir) - shutil.copy(args.catalogue, args.output_dir / args.catalogue.name) + shutil.copy(args.catalogue, output_dir / args.catalogue.name) print("Done.") From 98bb9e78cd0cdea90f940b0d9d92ad2e4f192f2c Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:38:54 +0100 Subject: [PATCH 21/44] Use curl instead --- pixi.toml | 3 ++- scripts/download-catalogue.py | 8 ++------ 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/pixi.toml b/pixi.toml index 4ae06fd..6513401 100644 --- a/pixi.toml +++ b/pixi.toml @@ -15,7 +15,7 @@ download-catalogue = { cmd = "python scripts/download-catalogue.py {{ catalogue_ setup-data = { depends-on = [ { task = "download-catalogue", args = [ - { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, + { catalogue_file = "catalogues/parcels-examples/catalogue.yaml" }, { output_dir = "surf-data/parcels-examples" }, ] }, { task = "download-catalogue", args = [ @@ -39,6 +39,7 @@ intake-xarray = ">=2.0.0,<3" parcels = ">=3.1.4,<4" ipython = ">=9.11.0,<10" netcdf4 = ">=1.7.4,<2" +curl = "*" [pypi-dependencies] parcels_benchmarks = { path = ".", editable = true } diff --git a/scripts/download-catalogue.py b/scripts/download-catalogue.py index 0b53203..df61d53 100644 --- a/scripts/download-catalogue.py +++ b/scripts/download-catalogue.py @@ -6,7 +6,7 @@ import zipfile from pathlib import Path -import requests +import subprocess import os try: @@ -26,13 +26,9 @@ def extract_zip_url(catalogue_path: Path) -> str: def download_file(url: str, dest_dir: Path) -> Path: - response = requests.get(url, stream=True) - response.raise_for_status() dest = dest_dir / "data.zip" print(f"Downloading {url} -> {dest}") - with dest.open("wb") as f: - for chunk in response.iter_content(chunk_size=8192): - f.write(chunk) + subprocess.run(["curl", "-L", "-o", str(dest), url], check=True) return dest From 42d7f5371154a31f2601649751be7fb0f1cda9c7 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:52:44 +0100 Subject: [PATCH 22/44] Rename files (catalogue to catalog and yaml->yml) --- benchmarks/__init__.py | 11 ++++++++++ .../parcels-benchmarks/catalog.yml | 0 .../parcels-examples/catalog.yml | 0 pixi.toml | 14 ++++++------- ...nload-catalogue.py => download-catalog.py} | 21 +++++++++---------- 5 files changed, 28 insertions(+), 18 deletions(-) rename catalogues/parcels-benchmarks/catalogue.yaml => catalogs/parcels-benchmarks/catalog.yml (100%) rename catalogues/parcels-examples/catalogue.yaml => catalogs/parcels-examples/catalog.yml (100%) rename scripts/{download-catalogue.py => download-catalog.py} (76%) diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index e69de29..a63e3e3 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -0,0 +1,11 @@ +import os +from pathlib import Path +import intake + +try: + PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) +except KeyError as e: + raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded.") from e + +CAT_EXAMPLES = intake.open_catalog('surf-data/parcels-examples/catalog.yml') +CAT_BENCHMARKS = intake.open_catalog('surf-data/parcels-benchmarks/catalog.yml') \ No newline at end of file diff --git a/catalogues/parcels-benchmarks/catalogue.yaml b/catalogs/parcels-benchmarks/catalog.yml similarity index 100% rename from catalogues/parcels-benchmarks/catalogue.yaml rename to catalogs/parcels-benchmarks/catalog.yml diff --git a/catalogues/parcels-examples/catalogue.yaml b/catalogs/parcels-examples/catalog.yml similarity index 100% rename from catalogues/parcels-examples/catalogue.yaml rename to catalogs/parcels-examples/catalog.yml diff --git a/pixi.toml b/pixi.toml index 6513401..51021ce 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,19 +7,19 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] [tasks] lint = "pre-commit run --all-files" -# Downloads the datasets. The catalogue file which should be used will be housed at `output_dir/catalogue_file.name` -download-catalogue = { cmd = "python scripts/download-catalogue.py {{ catalogue_file }} {{ output_dir }}", args = [ - "catalogue_file", +# Downloads the datasets. The catalog file which should be used will be housed at `output_dir/catalog_file.name` +download-catalog = { cmd = "python scripts/download-catalog.py {{ catalog_file }} {{ output_dir }}", args = [ + "catalog_file", "output_dir", ] } setup-data = { depends-on = [ - { task = "download-catalogue", args = [ - { catalogue_file = "catalogues/parcels-examples/catalogue.yaml" }, + { task = "download-catalog", args = [ + { catalog_file = "catalogs/parcels-examples/catalog.yml" }, { output_dir = "surf-data/parcels-examples" }, ] }, - { task = "download-catalogue", args = [ - { catalogue_file = "catalogues/parcels-benchmarks/catalogue.yaml" }, + { task = "download-catalog", args = [ + { catalog_file = "catalogs/parcels-benchmarks/catalog.yml" }, { output_dir = "surf-data/parcels-benchmarks" }, ] } ]} diff --git a/scripts/download-catalogue.py b/scripts/download-catalog.py similarity index 76% rename from scripts/download-catalogue.py rename to scripts/download-catalog.py index df61d53..90744f2 100644 --- a/scripts/download-catalogue.py +++ b/scripts/download-catalog.py @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -"""Download and extract a catalogue zip archive.""" +"""Download and extract a catalog zip archive.""" import argparse import shutil @@ -12,10 +12,10 @@ try: PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) except KeyError as e: - raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data should be downloaded.") from e + raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded.") from e -def extract_zip_url(catalogue_path: Path) -> str: - with catalogue_path.open() as f: +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}") @@ -37,7 +37,6 @@ def unzip_recursive(directory: Path) -> None: found = list(directory.rglob("*.zip")) if not found: return - print(f"found={found}") for zip_path in found: print(f"Extracting {zip_path}") extract_to = zip_path.parent @@ -51,9 +50,9 @@ def unzip_recursive(directory: Path) -> None: def main() -> None: parser = argparse.ArgumentParser( - description="Download and extract a catalogue archive." + description="Download and extract a catalog archive." ) - parser.add_argument("catalogue", type=Path, help="Path to catalogue.yml") + 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 @@ -61,16 +60,16 @@ def main() -> None: print("Output directory already exists! Exiting...") return - if not args.catalogue.is_file(): - raise SystemExit(f"catalogue file not found: {args.catalogue}") + if not args.catalog.is_file(): + raise SystemExit(f"catalog file not found: {args.catalog}") output_dir.mkdir(parents=True, exist_ok=True) - url = extract_zip_url(args.catalogue) + url = extract_zip_url(args.catalog) download_file(url, output_dir) unzip_recursive(output_dir) - shutil.copy(args.catalogue, output_dir / args.catalogue.name) + shutil.copy(args.catalog, output_dir / args.catalog.name) print("Done.") From fc3718689806eb492cda124c6f803412fb43bcaf Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 13:43:56 +0100 Subject: [PATCH 23/44] Add task descriptions --- pixi.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.toml b/pixi.toml index 51021ce..00325a6 100644 --- a/pixi.toml +++ b/pixi.toml @@ -7,11 +7,10 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] [tasks] lint = "pre-commit run --all-files" -# Downloads the datasets. The catalog file which should be used will be housed at `output_dir/catalog_file.name` download-catalog = { cmd = "python scripts/download-catalog.py {{ catalog_file }} {{ output_dir }}", args = [ "catalog_file", "output_dir", -] } +], description = "Downloads the datasets. 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 = [ @@ -22,11 +21,12 @@ setup-data = { depends-on = [ { 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] From e582cff2ca7c97021ef419a81255ca7112544e74 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:04:31 +0100 Subject: [PATCH 24/44] Update readme --- README.md | 29 +++++++++++++++++++---------- pixi.toml | 2 +- 2 files changed, 20 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index caa61ee..3c38054 100644 --- a/README.md +++ b/README.md @@ -6,15 +6,28 @@ 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` > [!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 benchmark data. +> 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 @@ -61,13 +74,9 @@ 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 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/datasets.json](./parcels_benchmarks/datasets.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/pixi.toml b/pixi.toml index 00325a6..af87575 100644 --- a/pixi.toml +++ b/pixi.toml @@ -10,7 +10,7 @@ lint = "pre-commit run --all-files" download-catalog = { cmd = "python scripts/download-catalog.py {{ catalog_file }} {{ output_dir }}", args = [ "catalog_file", "output_dir", -], description = "Downloads the datasets. The catalog file which should be used in scripts will be housed at `output_dir/catalog_file.name`"} +], description = "Downloads and upzips data corresponding with an Intake catalogue. 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 = [ From 2a064be91422029e11d5e625ad14f9aa515a3b67 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:04:49 +0100 Subject: [PATCH 25/44] Remove parcels_benchmarks internal package --- parcels_benchmarks/__init__.py | 1 - parcels_benchmarks/benchmark_setup.py | 258 -------------------------- parcels_benchmarks/datasets.json | 20 -- pyproject.toml | 31 ---- 4 files changed, 310 deletions(-) delete mode 100644 parcels_benchmarks/__init__.py delete mode 100644 parcels_benchmarks/benchmark_setup.py delete mode 100644 parcels_benchmarks/datasets.json 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 61ab784..0000000 --- a/parcels_benchmarks/benchmark_setup.py +++ /dev/null @@ -1,258 +0,0 @@ -import os -from pathlib import Path - -import pooch -import typer -from pydantic import BaseModel, Field, HttpUrl, model_validator - - -class Dataset(BaseModel): - """A single dataset entry in the manifest.""" - - name: str = Field(..., description="Unique name for the dataset") - file: str = Field(..., description="Filename of the dataset zip file") - known_hash: str | None = Field( - None, description="SHA256 hash of the file in format 'sha256:xxxxx'" - ) - - -class DatasetsManifest(BaseModel): - """Root manifest structure containing all datasets.""" - - data_url: HttpUrl = Field( - ..., description="Base URL where dataset files are hosted" - ) - datasets: list[Dataset] = Field( - default_factory=list, description="List of available datasets" - ) - - @model_validator(mode="after") - def validate_unique_names(self) -> "DatasetsManifest": - """Ensure all dataset names are unique.""" - names = [dataset.name for dataset in self.datasets] - duplicates = [name for name in names if names.count(name) > 1] - if duplicates: - unique_duplicates = sorted(set(duplicates)) - raise ValueError( - f"Duplicate dataset name(s) in manifest: {', '.join(unique_duplicates)}" - ) - return self - - -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("datasets.json") - - -def _load_manifest(path: Path) -> DatasetsManifest: - if not path.is_file(): - raise FileNotFoundError(f"Manifest not found: {path}") - with path.open("r", encoding="utf-8") as f: - return DatasetsManifest.model_validate_json(f.read()) - - -def _save_manifest(path: Path, manifest: DatasetsManifest) -> None: - # keep stable ordering by dataset name - manifest.datasets = sorted(manifest.datasets, key=lambda d: d.name) - with path.open("w", encoding="utf-8") as f: - f.write(manifest.model_dump_json(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: DatasetsManifest) -> dict[str, Dataset]: - return {dataset.name: dataset for dataset in manifest.datasets} - - -def _create_pooch_registry(manifest: DatasetsManifest) -> 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 dataset in manifest.datasets: - registry[dataset.file] = dataset.known_hash - return registry - - -def _get_pooch( - manifest: DatasetsManifest, 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=str(manifest.data_url), - registry=registry, - ) - - -def download_dataset( - dataset: str, manifest_path: Path = DEFAULT_MANIFEST, data_home: Path | None = None -) -> Path: - """Load a dataset listed in the provided manifest - - This function provides quick access to a small number of 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_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.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 = str(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(Dataset(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 = _datasets_by_name(m) - for name, entry in sorted(by_name.items(), key=lambda kv: kv[0]): - typer.echo(f"{name}: {entry.file} ({entry.known_hash or 'no-hash'})") - - -def main() -> None: - app() - - -if __name__ == "__main__": - main() diff --git a/parcels_benchmarks/datasets.json b/parcels_benchmarks/datasets.json deleted file mode 100644 index fb93639..0000000 --- a/parcels_benchmarks/datasets.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/pyproject.toml b/pyproject.toml index 438f56b..7941833 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,34 +1,3 @@ -[build-system] -requires = ["setuptools>=61", "wheel"] -build-backend = "setuptools.build_meta" - -[project] -name = "parcels_benchmarks" -version = "0.1.0" -description = "Helper utilities for Parcels benchmarks" -requires-python = ">=3.10" -authors = [{ name = "Parcels team" }] -dependencies = [ - "xarray", - "pooch", - "typer>=0.9", - "pydantic", -] - -# 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"] - - [tool.ruff.lint] select = [ "E", # Error From c3299ba55f5a03085ec5046e56cf87b96ae0bf2a Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:05:13 +0100 Subject: [PATCH 26/44] Update script to unpack zips correctly --- scripts/download-catalog.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/scripts/download-catalog.py b/scripts/download-catalog.py index 90744f2..a67a93c 100644 --- a/scripts/download-catalog.py +++ b/scripts/download-catalog.py @@ -39,11 +39,18 @@ def unzip_recursive(directory: Path) -> None: return for zip_path in found: print(f"Extracting {zip_path}") - extract_to = zip_path.parent + 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) From 0f3a93a68d40d15e9e491878ef36763b1b2e6f17 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:25:18 +0100 Subject: [PATCH 27/44] Update toml and lock --- pixi.lock | 12960 +++++++++++++++++++++++++++++++++++++++++++++------- pixi.toml | 5 +- 2 files changed, 11278 insertions(+), 1687 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2b34023..2e15f46 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3,329 +3,1075 @@ environments: default: channels: - 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__osx >=11.0 + - libcxx >=19 + license: Zlib + license_family: Other + purls: [] + size: 94375 + timestamp: 1770168363685 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 diff --git a/pixi.toml b/pixi.toml index af87575..aae7d09 100644 --- a/pixi.toml +++ b/pixi.toml @@ -39,7 +39,4 @@ intake-xarray = ">=2.0.0,<3" parcels = ">=3.1.4,<4" ipython = ">=9.11.0,<10" netcdf4 = ">=1.7.4,<2" -curl = "*" - -[pypi-dependencies] -parcels_benchmarks = { path = ".", editable = true } +curl = "*" \ No newline at end of file From 9a25838733738b01bce5a11e6ab74ac3715befd3 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:25:25 +0100 Subject: [PATCH 28/44] Add comment --- scripts/download-catalog.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/download-catalog.py b/scripts/download-catalog.py index a67a93c..6b34cb4 100644 --- a/scripts/download-catalog.py +++ b/scripts/download-catalog.py @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -"""Download and extract a catalog zip archive.""" +"""Download and extract a catalog zip archive, unzipping all zip archives contained within.""" import argparse import shutil From 0c2cd03d34a5c8672c1695d28b9a2b0bf930356c Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:28:46 +0100 Subject: [PATCH 29/44] Update catalogs regardless of folder existing --- scripts/download-catalog.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/scripts/download-catalog.py b/scripts/download-catalog.py index 6b34cb4..9ac1d19 100644 --- a/scripts/download-catalog.py +++ b/scripts/download-catalog.py @@ -63,20 +63,24 @@ def main() -> None: 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 - if output_dir.exists(): - print("Output directory already exists! Exiting...") - return + 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, exist_ok=True) + 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) - shutil.copy(args.catalog, output_dir / args.catalog.name) print("Done.") From 0c2b6cf8b975ddeabacf5a170332552e88b7f233 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:55:15 +0100 Subject: [PATCH 30/44] Fix catalogues --- benchmarks/__init__.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index a63e3e3..5ba3ff9 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -2,10 +2,16 @@ from pathlib import Path import intake +PARCELS_BENCHMARKS_DATA_FOLDER: str +PROJECT_ROOT = Path(__file__).parent.parent.resolve() + try: PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) except KeyError as e: raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded.") from e -CAT_EXAMPLES = intake.open_catalog('surf-data/parcels-examples/catalog.yml') -CAT_BENCHMARKS = intake.open_catalog('surf-data/parcels-benchmarks/catalog.yml') \ No newline at end of file +if not PARCELS_BENCHMARKS_DATA_FOLDER.is_absolute(): + PARCELS_BENCHMARKS_DATA_FOLDER = PROJECT_ROOT / str(PARCELS_BENCHMARKS_DATA_FOLDER) + +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') \ No newline at end of file From c2eb313c51837ec4dd854f5304a1131ea0dd861a Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:55:59 +0100 Subject: [PATCH 31/44] Migrate fesom ingestion to intake --- benchmarks/fesom2.py | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/benchmarks/fesom2.py b/benchmarks/fesom2.py index 027bc18..1887daf 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -7,40 +7,36 @@ ParticleSet, convert, ) +import xarray as xr from parcels.kernels import AdvectionRK2_3D -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_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_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) From b4da9468847b99290d1d3b6d3bf62ad4ad11e124 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:56:58 +0100 Subject: [PATCH 32/44] Update MOI With placeholder code. Will fix in another PR --- benchmarks/moi_curvilinear.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index c705772..bbae20f 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -6,12 +6,17 @@ import parcels from parcels.interpolators import XLinear -from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_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""" From 6fb1b7f91222d96128bb883f7fb188cbcebc4490 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:57:09 +0100 Subject: [PATCH 33/44] Update ASV conf --- asv.conf.json | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/asv.conf.json b/asv.conf.json index d14c1d0..2b6d875 100644 --- a/asv.conf.json +++ b/asv.conf.json @@ -3,6 +3,7 @@ "project": "parcels", "project_url": "https://github.com/Parcels-Code/parcels", "repo": "./Parcels", + "dvcs": "git", "branches": ["main"], "environment_type": "rattler", "conda_channels": [ @@ -14,12 +15,17 @@ "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" - ] + "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": [] + } +} } From 515b76732d4155984ea09e583b63fac5bf76d779 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:11:26 +0000 Subject: [PATCH 34/44] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .env.example | 2 +- .gitignore | 2 +- README.md | 1 - asv.conf.json | 6 +++--- benchmarks/__init__.py | 13 ++++++++++--- benchmarks/fesom2.py | 14 +++++++++----- benchmarks/moi_curvilinear.py | 7 +++---- pixi.toml | 8 ++++---- scripts/download-catalog.py | 16 +++++++++++----- 9 files changed, 42 insertions(+), 27 deletions(-) diff --git a/.env.example b/.env.example index ed309eb..ff797d4 100644 --- a/.env.example +++ b/.env.example @@ -1,2 +1,2 @@ # Target location for the data to be downloaded to -PARCELS_BENCHMARKS_DATA_FOLDER='./data' \ No newline at end of file +PARCELS_BENCHMARKS_DATA_FOLDER='./data' diff --git a/.gitignore b/.gitignore index 0c3c80f..c1a039b 100644 --- a/.gitignore +++ b/.gitignore @@ -15,4 +15,4 @@ html/ .DS_Store data -.env \ No newline at end of file +.env diff --git a/README.md b/README.md index 3c38054..05a3c74 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,6 @@ In brief, you can set up the data and run the benchmarks by doing: - `pixi install` - `PARCELS_BENCHMARKS_DATA_FOLDER=./data pixi run benchmarks` - > [!IMPORTANT] > Currently, you will need at least 50GB of disk space available to store the benchmark data. > You need to be explicit to determine where the benchmark data will be saved by diff --git a/asv.conf.json b/asv.conf.json index 2b6d875..9c4740a 100644 --- a/asv.conf.json +++ b/asv.conf.json @@ -15,7 +15,7 @@ "env_dir": ".asv/env", "results_dir": "results", "html_dir": "html", - "build_command": [ "python -m build --wheel -o {build_cache_dir} {build_dir}"], + "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 ." @@ -25,7 +25,7 @@ // ] "matrix": { "req": { - "intake-xarray": [] + "intake-xarray": [] } -} + } } diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index 5ba3ff9..264263a 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -1,5 +1,6 @@ import os from pathlib import Path + import intake PARCELS_BENCHMARKS_DATA_FOLDER: str @@ -8,10 +9,16 @@ try: PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) except KeyError as e: - raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded.") from e + raise RuntimeError( + "Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded." + ) from e if not PARCELS_BENCHMARKS_DATA_FOLDER.is_absolute(): PARCELS_BENCHMARKS_DATA_FOLDER = PROJECT_ROOT / str(PARCELS_BENCHMARKS_DATA_FOLDER) -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') \ No newline at end of file +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 1887daf..3b4b2aa 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -1,14 +1,14 @@ import numpy as np import uxarray as ux - +import xarray as xr from parcels import ( FieldSet, Particle, ParticleSet, convert, ) -import xarray as xr from parcels.kernels import AdvectionRK2_3D + from . import PARCELS_BENCHMARKS_DATA_FOLDER runtime = np.timedelta64(1, "D") @@ -18,11 +18,15 @@ def _load_ds(): """Helper function to load uxarray dataset from datapath""" - 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_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) + return ux.UxDataset(data_files, uxgrid=grid) class FESOM2: diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index bbae20f..baf9f18 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -1,20 +1,19 @@ from glob import glob import numpy as np +import parcels import xarray as xr import xgcm - -import parcels from parcels.interpolators import XLinear 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 +PARCELS_DATADIR = ... # TODO: Replace with intake +def download_dataset(*args, **kwargs): ... # TODO: Replace with intake def _load_ds(datapath, chunk): diff --git a/pixi.toml b/pixi.toml index aae7d09..483b413 100644 --- a/pixi.toml +++ b/pixi.toml @@ -10,7 +10,7 @@ lint = "pre-commit run --all-files" download-catalog = { cmd = "python scripts/download-catalog.py {{ catalog_file }} {{ output_dir }}", args = [ "catalog_file", "output_dir", -], description = "Downloads and upzips data corresponding with an Intake catalogue. If target folder already exists - skips. The catalog file which should be used in scripts will be housed at `output_dir/catalog_file.name`"} +], description = "Downloads and upzips data corresponding with an Intake catalogue. 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 = [ @@ -20,8 +20,8 @@ setup-data = { depends-on = [ { 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."} + ] }, +], description = "Setup all data to be used in the benchmarks." } [tasks.benchmark] cmd = "asv run" @@ -39,4 +39,4 @@ intake-xarray = ">=2.0.0,<3" parcels = ">=3.1.4,<4" ipython = ">=9.11.0,<10" netcdf4 = ">=1.7.4,<2" -curl = "*" \ No newline at end of file +curl = "*" diff --git a/scripts/download-catalog.py b/scripts/download-catalog.py index 9ac1d19..9c7aa50 100644 --- a/scripts/download-catalog.py +++ b/scripts/download-catalog.py @@ -2,17 +2,19 @@ """Download and extract a catalog zip archive, unzipping all zip archives contained within.""" import argparse +import os import shutil +import subprocess import zipfile from pathlib import Path -import subprocess -import os - try: PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) except KeyError as e: - raise RuntimeError("Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded.") from e + raise RuntimeError( + "Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded." + ) from e + def extract_zip_url(catalog_path: Path) -> str: with catalog_path.open() as f: @@ -60,7 +62,11 @@ def main() -> None: 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") + 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 From 4365e7b865c425f640a41b647cd9968b94563bfa Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 09:08:34 +0200 Subject: [PATCH 35/44] Default PARCELS_BENCHMARKS_DATA_FOLDER to ./data - Rafactor path variables and move catalogue definitions to separate file - Since the downloading script now relies on the --- benchmarks/__init__.py | 33 ++++++++++++++++++--------------- benchmarks/catalogs.py | 12 ++++++++++++ scripts/download-catalog.py | 8 +------- 3 files changed, 31 insertions(+), 22 deletions(-) create mode 100644 benchmarks/catalogs.py diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py index 264263a..6bf489b 100644 --- a/benchmarks/__init__.py +++ b/benchmarks/__init__.py @@ -1,24 +1,27 @@ +import logging import os from pathlib import Path -import intake +logger = logging.getLogger(__name__) -PARCELS_BENCHMARKS_DATA_FOLDER: str -PROJECT_ROOT = Path(__file__).parent.parent.resolve() +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 as e: - raise RuntimeError( - "Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded." - ) from e +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(): - PARCELS_BENCHMARKS_DATA_FOLDER = PROJECT_ROOT / str(PARCELS_BENCHMARKS_DATA_FOLDER) - -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" -) + 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/scripts/download-catalog.py b/scripts/download-catalog.py index 9c7aa50..c8401b1 100644 --- a/scripts/download-catalog.py +++ b/scripts/download-catalog.py @@ -2,18 +2,12 @@ """Download and extract a catalog zip archive, unzipping all zip archives contained within.""" import argparse -import os import shutil import subprocess import zipfile from pathlib import Path -try: - PARCELS_BENCHMARKS_DATA_FOLDER = Path(os.environ["PARCELS_BENCHMARKS_DATA_FOLDER"]) -except KeyError as e: - raise RuntimeError( - "Set the PARCELS_BENCHMARKS_DATA_FOLDER environment variable to specify where the data is/should be downloaded." - ) from e +from benchmarks import PARCELS_BENCHMARKS_DATA_FOLDER def extract_zip_url(catalog_path: Path) -> str: From 5c981072163a172a5f4b244e7ccc63665c4a2343 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 09:45:28 +0200 Subject: [PATCH 36/44] Clean out dependencies Using the `pyproject.toml` file to specify the project dependencies (including the local dependency with Parcels). This helps ensure that dependencies are available in a way available to ASV as well. Maybe this ASV <-> pixi thing needs to be further investigated... ASV's own environment management is something I find confusing --- pixi.lock | 16321 ++++++++++++++++++----------------------------- pixi.toml | 9 +- pyproject.toml | 17 + 3 files changed, 6064 insertions(+), 10283 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2e15f46..fdd1fe6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3,1075 +3,784 @@ environments: default: channels: - 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/noarch/asciitree-0.3.3-py_2.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/asv-0.6.5-py312h1289d80_3.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/asv_runner-0.2.1-pyhd8ed1ab_0.conda - 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pypi: https://files.pythonhosted.org/packages/2a/2d/d4bf65e47cea8ff2c794a600c4fd1273a7902f268757c531e0ee9f18aa58/pooch-1.9.0-py3-none-any.whl - - pypi: https://files.pythonhosted.org/packages/4c/e1/011b49f954b3bcc773f81d73f4ee873d21d8e394366df316e66e857fedfe/py_rattler-0.23.2-cp38-abi3-win_amd64.whl + - pypi: https://files.pythonhosted.org/packages/2e/e7/3732ea0d57c658f17b16ac38d5ad6ea3e6778587f7343adefcba2b448667/py_rattler-0.15.0-cp38-abi3-win_amd64.whl - pypi: https://files.pythonhosted.org/packages/f6/70/1fdda42d65b28b078e93d75d371b2185a61da89dda4def8ba6ba41ebdeb4/pyarrow-23.0.1-cp312-cp312-win_amd64.whl - pypi: https://files.pythonhosted.org/packages/8c/b2/23f4032cd1c9744aa8e9ecda43cd4d755fcb209f7f40fae035248f31a679/pyct-0.6.0-py3-none-any.whl - pypi: https://files.pythonhosted.org/packages/79/4f/a6a2e2b202d7fd97eadfe90979845b8706676b41cbd3b42ba75adf329d1f/Pympler-1.1-py3-none-any.whl @@ -1404,12 +1404,12 @@ packages: - pypi: ./ name: benchmarks version: 0.1.0 - sha256: 65ccbd7a76df77e2a582558448481dd616333c37090714805373f6b399b9d383 + sha256: 78444b1cf3dd42c88f261a8b56dae925863671bc5aa9724d17c8604a070e96fe requires_dist: - intake-xarray - parcels @ file:///Users/Hodgs004/coding/repos/parcels-benchmarks/Parcels - - asv - - py-rattler + - asv>=0.6.5 + - py-rattler==0.15.* requires_python: '>=3.12' - pypi: https://files.pythonhosted.org/packages/cd/3a/577b549de0cc09d95f11087ee63c739bba856cd3952697eec4c4bb91350a/bleach-6.3.0-py3-none-any.whl name: bleach @@ -6363,20 +6363,20 @@ packages: - pkg:pypi/pure-eval?source=hash-mapping size: 16668 timestamp: 1733569518868 -- pypi: https://files.pythonhosted.org/packages/3a/39/e6e984b7ca34a2e30f1a984bd40cb1ef561a705bc1b36b9e960c975234f3/py_rattler-0.23.2-cp38-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl +- pypi: https://files.pythonhosted.org/packages/2e/e7/3732ea0d57c658f17b16ac38d5ad6ea3e6778587f7343adefcba2b448667/py_rattler-0.15.0-cp38-abi3-win_amd64.whl name: py-rattler - version: 0.23.2 - sha256: 87be072cae015d9323dbb2eee3adcb0fef85db6a96b3a0dfd4e2e71603544636 + version: 0.15.0 + sha256: d8a060e9821c764282ab245cac871c53478f9eea33242710090c07fd7369d5a3 requires_python: '>=3.8' -- pypi: https://files.pythonhosted.org/packages/4c/e1/011b49f954b3bcc773f81d73f4ee873d21d8e394366df316e66e857fedfe/py_rattler-0.23.2-cp38-abi3-win_amd64.whl +- pypi: https://files.pythonhosted.org/packages/52/40/cf00e0612bb52142876726a92f7bdeaad27ec108c8979384de8f4803d306/py_rattler-0.15.0-cp38-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl name: py-rattler - version: 0.23.2 - sha256: dcf730a9af43aba38bad0c047e39e669fd120d41faa247e455aafa4e3ef6623c + version: 0.15.0 + sha256: 7dcd3413ab85a89b35dc9e8597ebe6765e1eb982b5cf497198330fb989ea1e57 requires_python: '>=3.8' -- pypi: https://files.pythonhosted.org/packages/5a/86/6e0202ddd5ffc1c9cb1be80c9981a67061413e05ab6073939fa9c9dc0821/py_rattler-0.23.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl +- pypi: https://files.pythonhosted.org/packages/63/af/658ab85515ffd470f6fe845cbdf2a4099a718b8304ebaa15c7826dcb8ea7/py_rattler-0.15.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl name: py-rattler - version: 0.23.2 - sha256: a502192d3f3c13a6c332e1d790e85c49bd8cbdf814c6d312841586b5b5988acb + version: 0.15.0 + sha256: 19ccd381bfcaa8eddcdc0edef684c78797719ca36489b0c109285e1975571aa7 requires_python: '>=3.8' - pypi: https://files.pythonhosted.org/packages/2c/a5/da83046273d990f256cb79796a190bbf7ec999269705ddc609403f8c6b06/pyarrow-23.0.1-cp312-cp312-manylinux_2_28_x86_64.whl name: pyarrow diff --git a/pyproject.toml b/pyproject.toml index 3e34039..aaf7ec5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,8 +7,8 @@ requires-python = ">=3.12" dependencies = [ "intake-xarray", "parcels @ file:///${PROJECT_ROOT}/Parcels", - "asv", - "py-rattler", + "asv>=0.6.5", + "py-rattler==0.15.*", ] From d46f4b1775b33dbb51eae0ed81b0c9c51f4ebd9a Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:25:54 +0200 Subject: [PATCH 38/44] run pre-commit --- benchmarks/fesom2.py | 1 + benchmarks/moi_curvilinear.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/benchmarks/fesom2.py b/benchmarks/fesom2.py index 3b4b2aa..00c34cc 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -1,6 +1,7 @@ import numpy as np import uxarray as ux import xarray as xr + from parcels import ( FieldSet, Particle, diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index baf9f18..e419d34 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -1,9 +1,10 @@ from glob import glob import numpy as np -import parcels import xarray as xr import xgcm + +import parcels from parcels.interpolators import XLinear runtime = np.timedelta64(2, "D") From b1d3bc5018485733d120f4f18289848b29190ded Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:27:46 +0200 Subject: [PATCH 39/44] Rename asv.conf.json to .jsonc (comment supported format) --- asv.conf.json => asv.conf.jsonc | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename asv.conf.json => asv.conf.jsonc (90%) diff --git a/asv.conf.json b/asv.conf.jsonc similarity index 90% rename from asv.conf.json rename to asv.conf.jsonc index 9c4740a..fd7e57b 100644 --- a/asv.conf.json +++ b/asv.conf.jsonc @@ -9,7 +9,7 @@ "conda_channels": [ "conda-forge", "defaults", - "https://repo.prefix.dev/parcels" + "https://repo.prefix.dev/parcels", ], "default_benchmark_timeout": 1800, "env_dir": ".asv/env", @@ -25,7 +25,7 @@ // ] "matrix": { "req": { - "intake-xarray": [] - } - } + "intake-xarray": [], + }, + }, } From 0675afebc9947e60c8589e2b82b33a47eec55120 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 2 Apr 2026 13:28:31 +0000 Subject: [PATCH 40/44] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- benchmarks/fesom2.py | 1 - benchmarks/moi_curvilinear.py | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/benchmarks/fesom2.py b/benchmarks/fesom2.py index 00c34cc..3b4b2aa 100644 --- a/benchmarks/fesom2.py +++ b/benchmarks/fesom2.py @@ -1,7 +1,6 @@ import numpy as np import uxarray as ux import xarray as xr - from parcels import ( FieldSet, Particle, diff --git a/benchmarks/moi_curvilinear.py b/benchmarks/moi_curvilinear.py index e419d34..baf9f18 100644 --- a/benchmarks/moi_curvilinear.py +++ b/benchmarks/moi_curvilinear.py @@ -1,10 +1,9 @@ from glob import glob import numpy as np +import parcels import xarray as xr import xgcm - -import parcels from parcels.interpolators import XLinear runtime = np.timedelta64(2, "D") From f992e3a5f5fac19d0f087cbcd34e58ecc85abf6c Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:33:27 +0200 Subject: [PATCH 41/44] Review feedback --- .env.example | 2 -- sandbox/.gitattributes | 2 -- sandbox/.gitignore | 4 ---- sandbox/pixi.toml | 14 -------------- 4 files changed, 22 deletions(-) delete mode 100644 .env.example delete mode 100644 sandbox/.gitattributes delete mode 100644 sandbox/.gitignore delete mode 100644 sandbox/pixi.toml diff --git a/.env.example b/.env.example deleted file mode 100644 index ff797d4..0000000 --- a/.env.example +++ /dev/null @@ -1,2 +0,0 @@ -# Target location for the data to be downloaded to -PARCELS_BENCHMARKS_DATA_FOLDER='./data' diff --git a/sandbox/.gitattributes b/sandbox/.gitattributes deleted file mode 100644 index 997504b..0000000 --- a/sandbox/.gitattributes +++ /dev/null @@ -1,2 +0,0 @@ -# SCM syntax highlighting & preventing 3-way merges -pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/sandbox/.gitignore b/sandbox/.gitignore deleted file mode 100644 index 60c96b1..0000000 --- a/sandbox/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# pixi environments -.pixi/* -!.pixi/config.toml -pixi.lock diff --git a/sandbox/pixi.toml b/sandbox/pixi.toml deleted file mode 100644 index eaed168..0000000 --- a/sandbox/pixi.toml +++ /dev/null @@ -1,14 +0,0 @@ -# We couldn't have the parcels dependency in the root as it would cause unnecessary noise in the lockfile -[workspace] -authors = ["parcels-benchmarks contributors"] -channels = ["conda-forge"] -name = "sandbox" -platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"] -preview = ['pixi-build'] - -[dependencies] - -parcels = { path = '../Parcels' } - -[pypi-dependencies] -parcels_benchmarks = { path = "..", editable = true } From 10f4c967dd1cb54392f0725969ed042079c76884 Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:39:55 +0200 Subject: [PATCH 42/44] update readme --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 05a3c74..1ea22d3 100644 --- a/README.md +++ b/README.md @@ -21,8 +21,11 @@ In brief, you can set up the data and run the benchmarks by doing: - `pixi install` - `PARCELS_BENCHMARKS_DATA_FOLDER=./data pixi run benchmarks` +> [!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] -> Currently, you will need at least 50GB of disk space available 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 From cbbc1802edd66d8148ba7e353777d25eebd19efd Mon Sep 17 00:00:00 2001 From: Vecko <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:43:45 +0200 Subject: [PATCH 43/44] Disable isort --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index aaf7ec5..b0b275f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ include = ["benchmarks*"] 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 From c116a3c9dd197209d9d613010d7f9b300ae1b08a Mon Sep 17 00:00:00 2001 From: Nick Hodgskin <36369090+VeckoTheGecko@users.noreply.github.com> Date: Thu, 2 Apr 2026 15:44:19 +0200 Subject: [PATCH 44/44] Update catalogs/parcels-benchmarks/catalog.yml Co-authored-by: Erik van Sebille --- catalogs/parcels-benchmarks/catalog.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/catalogs/parcels-benchmarks/catalog.yml b/catalogs/parcels-benchmarks/catalog.yml index 46656fc..b502b94 100644 --- a/catalogs/parcels-benchmarks/catalog.yml +++ b/catalogs/parcels-benchmarks/catalog.yml @@ -45,7 +45,6 @@ sources: #!TODO Update # NemoNorthSeaORCA025-N006_data: # OFAM_example_data # Peninsula_data - # SWASH_data SWASH_data: description: SWASH_data driver: netcdf