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Merge pull request #35 from cindytsai/libyt-dev
Support dim 2/1 and Fix Stuff
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‎.github/workflows/build-test.yml‎

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@@ -28,7 +28,7 @@ jobs:
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- version: "3.12"
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toxenv: "py312"
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include:
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- os: ubuntu-20.04
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- os: ubuntu-22.04
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python: { version: "3.7", toxenv: "py37" }
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steps:
@@ -40,6 +40,15 @@ jobs:
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run: |
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python -m pip install --upgrade pip
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python -m pip install tox
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- name: Get test dataset
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uses: actions/cache@v4
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id: cache_dataset
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with:
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path: ${{ github.workspace }}/tests/data
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key: ${{ hashFiles('tests/data/**') }}
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- if: steps.cache_dataset.outputs.cache-hit != 'true'
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working-directory: ${{ github.workspace }}/tests/data
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run: sh get_test_data.sh
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- name: Run pytest
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run: tox -e ${{ matrix.python.toxenv }} -- --html=report.html --self-contained-html
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- name: Upload pytest report

‎.gitignore‎

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.idea/
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report.html
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tests/data/gamer/*
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tests/data/enzo/*

‎README.md‎

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@@ -1,6 +1,8 @@
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# libyt frontend for yt
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[![PyPI version](https://badge.fury.io/py/yt-libyt.svg)](https://badge.fury.io/py/yt-libyt)
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[![Run Tests](https://github.com/data-exp-lab/yt_libyt/actions/workflows/build-test.yml/badge.svg)](https://github.com/data-exp-lab/yt_libyt/actions/workflows/build-test.yml)
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[![Style Check](https://github.com/data-exp-lab/yt_libyt/actions/workflows/style-check.yml/badge.svg)](https://github.com/data-exp-lab/yt_libyt/actions/workflows/style-check.yml)
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This is a [`yt`](https://yt-project.org/) frontend for [`libyt`](https://github.com/yt-project/libyt).
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‎setup.cfg‎

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@@ -66,6 +66,8 @@ ignore =
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E741,
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# Line break occurred before a binary operator (black compatibility)
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W503,
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# Except handlers should only be names of exception classes
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B030,
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################### tox env ###################
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# Test -- pytest (Default)
@@ -85,6 +87,8 @@ deps =
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pytest-html
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pytest-cov
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pytest-randomly
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h5py
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libconf
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commands =
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pytest {posargs}
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‎tests/data/get_test_data.sh‎

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#!/bin/bash
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# This script downloads test data for yt_libyt
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# Run this script inside the tests/data directory: sh get-test-data.sh
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# gamer
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mkdir -p gamer
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curl -o "gamer/Plummer.tar.gz" "https://yt-project.org/data/Plummer.tar.gz"
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tar -xvzf "gamer/Plummer.tar.gz" -C gamer
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# enzo
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mkdir -p enzo
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curl -o "enzo/IsolatedGalaxy.tar.gz" "https://yt-project.org/data/IsolatedGalaxy.tar.gz"
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tar -xvzf "enzo/IsolatedGalaxy.tar.gz" -C enzo
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curl -o "enzo/EnzoKelvinHelmholtz.tar.gz" "https://yt-project.org/data/EnzoKelvinHelmholtz.tar.gz"
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tar -xvzf "enzo/EnzoKelvinHelmholtz.tar.gz" -C enzo

‎tests/stubs/libyt_v_0_2_stub.py‎

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import types
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3+
import numpy as np
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import yt
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LIBYT_VERSION = (0, 2, 0)
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8+
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def create_libyt_stub(
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simulation: str,
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fig_base_name: str,
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test_data: str,
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get_code_params: dict,
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field_list: dict,
15+
particle_list: dict,
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simulation_field_to_yt_field,
17+
) -> types.ModuleType:
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"""
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Returns a stub module that mimics libyt with a specific simulation.
20+
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:note: yt store the data structure in 3d, which is if the simulation is 2d, an additional dimension is added.
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hierarchy is stored in 3d as well in a continuous array with 0 as the first grid, if dimensionality is 2,
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the third dimension is set to 1.
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grid_data stores the grid id starting from the index offset.
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When extracting the data using yt, the data is always in 3d, so if the simulation is 2d, we need to extract it.
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:param simulation: simulation name, e.g., "gamer", "enzo", etc.
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:param fig_base_name: figure base name
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:param test_data: the absolute path to the test data.
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:param get_code_params: the code parameters defined in the simulation frontend, and how to get it.
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{
34+
"code_params": [(param_name, default_value), ...],
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"method": (function to get the parameter)
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"expected_error": Exception type that is expected to be raised if the parameter is not found
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}
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:param field_list: libyt-v0.2 defined field list
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:param particle_list: libyt-v0.2 defined particle list
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:param simulation_field_to_yt_field: mapping field_list and particle_list name to yt field name
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"""
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# Mock libyt module based on libyt version 0.x.0
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stub = types.ModuleType("libyt")
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stub.libyt_info = {
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"version": LIBYT_VERSION,
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"SERIAL_MODE": True,
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"INTERACTIVE_MODE": False,
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"JUPYTER_KERNEL": False,
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"SUPPORT_TIMER": False,
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}
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stub.param_yt = {
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"frontend": simulation,
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"fig_basename": fig_base_name,
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"current_time": None,
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"current_redshift": None,
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"omega_lambda": None,
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"omega_matter": None,
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"hubble_constant": None,
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"length_unit": None,
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"mass_unit": None,
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"time_unit": None,
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"magnetic_unit": None,
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"cosmological_simulation": None,
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"dimensionality": None,
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"refine_by": None,
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"velocity_unit": None,
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"domain_left_edge": None,
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"domain_right_edge": None,
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"periodicity": None,
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"domain_dimensions": None,
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"num_grids": None,
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"index_offset": None,
73+
"field_list": None,
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"particle_list": None,
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}
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stub.param_user = {}
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stub.hierarchy = {
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"grid_left_edge": None,
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"grid_right_edge": None,
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"grid_dimensions": None,
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"grid_parent_id": None,
82+
"grid_levels": None,
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"proc_num": None,
84+
# "par_count_list": None, # This is optional, which is a bad design choice.
85+
}
86+
stub.grid_data = {}
87+
stub.particle_data = {}
88+
89+
ds = yt.load(test_data)
90+
# Fill in param_user
91+
for param in get_code_params["code_params"]:
92+
try:
93+
stub.param_user[param[0]] = get_code_params["method"](ds, param[0])
94+
except get_code_params["expected_error"]:
95+
stub.param_user[param[0]] = param[1]
96+
97+
# Fill in param_yt
98+
for param in ds.__dict__.keys():
99+
if param in stub.param_yt and stub.param_yt[param] is None:
100+
stub.param_yt[param] = getattr(ds, param)
101+
if stub.param_yt["velocity_unit"] is None:
102+
stub.param_yt["velocity_unit"] = stub.param_yt["length_unit"] / stub.param_yt["time_unit"]
103+
stub.param_yt["domain_left_edge"] = ds.domain_left_edge
104+
stub.param_yt["domain_right_edge"] = ds.domain_right_edge
105+
stub.param_yt["periodicity"] = ds.periodicity
106+
stub.param_yt["domain_dimensions"] = ds.domain_dimensions
107+
stub.param_yt["num_grids"] = ds.index.num_grids
108+
stub.param_yt["index_offset"] = ds._index_class.grid._id_offset
109+
stub.param_yt["field_list"] = field_list
110+
stub.param_yt["particle_list"] = particle_list
111+
112+
# Fill in hierarchy
113+
stub.hierarchy["grid_left_edge"] = ds.index.grid_left_edge
114+
stub.hierarchy["grid_right_edge"] = ds.index.grid_right_edge
115+
stub.hierarchy["grid_dimensions"] = ds.index.grid_dimensions
116+
stub.hierarchy["grid_levels"] = ds.index.grid_levels
117+
stub.hierarchy["proc_num"] = np.zeros((stub.param_yt["num_grids"], 1), dtype=np.int32)
118+
stub.hierarchy["grid_parent_id"] = np.ones((stub.param_yt["num_grids"], 1), dtype=np.int32) * -1
119+
for g in ds.index.grids:
120+
if g.Parent is not None:
121+
stub.hierarchy["grid_parent_id"][g.id - stub.param_yt["index_offset"]] = g.Parent.id
122+
123+
# Fill in grid_data
124+
for gid in range(stub.param_yt["num_grids"]):
125+
if gid + stub.param_yt["index_offset"] not in stub.grid_data:
126+
stub.grid_data[gid + stub.param_yt["index_offset"]] = {}
127+
for field in field_list.keys():
128+
# TODO: assume cell-centered fields
129+
ghost_cells = field_list[field]["ghost_cell"]
130+
allocate_dim = stub.hierarchy["grid_dimensions"][gid][
131+
: stub.param_yt["dimensionality"]
132+
].copy()
133+
if field_list[field]["contiguous_in_x"]:
134+
allocate_dim = np.flip(allocate_dim)
135+
for d in range(2 * stub.param_yt["dimensionality"]):
136+
allocate_dim[int(d / 2)] += ghost_cells[d]
137+
stub.grid_data[gid + stub.param_yt["index_offset"]][field] = (
138+
np.ones(allocate_dim, dtype=np.float64) * np.nan
139+
)
140+
141+
if field_list[field]["contiguous_in_x"]:
142+
if stub.param_yt["dimensionality"] == 3:
143+
stub.grid_data[gid + stub.param_yt["index_offset"]][field][
144+
ghost_cells[0] : allocate_dim[0] - ghost_cells[1],
145+
ghost_cells[2] : allocate_dim[1] - ghost_cells[3],
146+
ghost_cells[4] : allocate_dim[2] - ghost_cells[5],
147+
] = (
148+
ds.index.grids[gid][simulation_field_to_yt_field[field]]
149+
.swapaxes(0, 2)
150+
.in_base("code")
151+
)
152+
elif stub.param_yt["dimensionality"] == 2:
153+
stub.grid_data[gid + stub.param_yt["index_offset"]][field][
154+
ghost_cells[0] : allocate_dim[0] - ghost_cells[1],
155+
ghost_cells[2] : allocate_dim[1] - ghost_cells[3],
156+
] = np.squeeze(
157+
ds.index.grids[gid][simulation_field_to_yt_field[field]].in_base("code")
158+
).swapaxes(
159+
0, 1
160+
)
161+
else:
162+
stub.grid_data[gid + stub.param_yt["index_offset"]][field][
163+
ghost_cells[0] : allocate_dim[0] - ghost_cells[1]
164+
] = ds.index.grids[gid][simulation_field_to_yt_field[field]].in_base("code")
165+
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return stub

‎tests/test_enzo.py‎

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import os
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import sys
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import yt
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from stubs.libyt_v_0_2_stub import create_libyt_stub
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7+
import yt_libyt
8+
9+
10+
def test_enzo_isolated_galaxy():
11+
# Create libyt stub and make it importable
12+
simulation = "enzo"
13+
problem = "IsolatedGalaxy"
14+
fig_base_name = f"{simulation}-{problem}"
15+
test_data_path = os.path.join(
16+
os.path.dirname(__file__), "data", simulation, f"{problem}/galaxy0030/galaxy0030"
17+
)
18+
code_param_list = {
19+
"code_params": [
20+
("HydroMethod", None),
21+
("MultiSpecies", None),
22+
("DualEnergyFormalism", None),
23+
],
24+
"method": (lambda ds, code_param: ds.parameters[code_param]),
25+
"expected_error": KeyError,
26+
}
27+
field_list = {
28+
"Density": {
29+
"attribute": ["", [], None],
30+
"field_type": "cell-centered",
31+
"contiguous_in_x": True,
32+
"ghost_cell": [3, 3, 3, 3, 3, 3],
33+
}
34+
}
35+
particle_list = {}
36+
simulation_field_to_yt_field = {"Density": ("gas", "density")}
37+
38+
libyt_stub = create_libyt_stub(
39+
simulation,
40+
fig_base_name,
41+
test_data_path,
42+
code_param_list,
43+
field_list,
44+
particle_list,
45+
simulation_field_to_yt_field,
46+
)
47+
sys.modules["libyt"] = libyt_stub
48+
49+
# Run yt_libyt code
50+
ds = yt_libyt.libytDataset()
51+
slc = yt.SlicePlot(ds, "z", ("enzo", "Density"))
52+
slc.save(f"{fig_base_name}-libyt.png")
53+
54+
# Compare to post-processing results
55+
ds_post = yt.load(test_data_path)
56+
slc_post = yt.SlicePlot(ds_post, "z", ("enzo", "Density"))
57+
slc_post.save(f"{fig_base_name}-post.png")
58+
fig_size = slc_post.data_source["enzo", "Density"].size
59+
60+
assert (
61+
sum(slc.data_source["enzo", "Density"] - slc_post.data_source["enzo", "Density"]) / fig_size
62+
< 1e-2
63+
)
64+
65+
66+
def test_enzo_kelvin_helmholtz():
67+
# Create libyt stub and make it importable
68+
simulation = "enzo"
69+
problem = "EnzoKelvinHelmholtz"
70+
fig_base_name = f"{simulation}-{problem}"
71+
test_data_path = os.path.join(
72+
os.path.dirname(__file__), "data", simulation, f"{problem}/DD0000/DD0000"
73+
)
74+
code_param_list = {
75+
"code_params": [
76+
("HydroMethod", None),
77+
("MultiSpecies", None),
78+
("DualEnergyFormalism", None),
79+
],
80+
"method": (lambda ds, code_param: ds.parameters[code_param]),
81+
"expected_error": KeyError,
82+
}
83+
field_list = {
84+
"Density": {
85+
"attribute": ["", [], None],
86+
"field_type": "cell-centered",
87+
"contiguous_in_x": True,
88+
"ghost_cell": [3, 3, 3, 3, 0, 0],
89+
}
90+
}
91+
particle_list = {}
92+
simulation_field_to_yt_field = {"Density": ("gas", "density")}
93+
94+
libyt_stub = create_libyt_stub(
95+
simulation,
96+
fig_base_name,
97+
test_data_path,
98+
code_param_list,
99+
field_list,
100+
particle_list,
101+
simulation_field_to_yt_field,
102+
)
103+
sys.modules["libyt"] = libyt_stub
104+
105+
# Run yt_libyt code
106+
ds = yt_libyt.libytDataset()
107+
slc = yt.SlicePlot(ds, "z", ("enzo", "Density"))
108+
slc.save(f"{fig_base_name}-libyt.png")
109+
110+
# Compare to post-processing results
111+
ds_post = yt.load(test_data_path)
112+
slc_post = yt.SlicePlot(ds_post, "z", ("enzo", "Density"))
113+
slc_post.save(f"{fig_base_name}-post.png")
114+
fig_size = slc_post.data_source["enzo", "Density"].size
115+
116+
assert (
117+
sum(slc.data_source["enzo", "Density"] - slc_post.data_source["enzo", "Density"]) / fig_size
118+
< 1e-2
119+
)

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