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Merged
robjmcgibbon merged 1 commit into from
Jun 3, 2026
Merged

Update location of files for flamingo test #216

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2 changes: 1 addition & 1 deletion SOAP/core/swift_cells.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ def __call__(self, data, cache):
np.s_[mem_start:mem_end, ...],
)
except OSError as e:
print(f'Error reading {dataset_name}')
print(f"Error reading {dataset_name}")
raise e


Expand Down
73 changes: 39 additions & 34 deletions SOAP/property_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4938,11 +4938,15 @@ def add_properties(self, halo_property: HaloProperty, halo_type: str):
units = unyt.unyt_quantity(1, units=prop.unit)
if not prop.output_physical:
units = units * unyt.Unit("a") ** prop.a_scale_exponent
prop_unit = units.units.latex_repr.replace(
"\\rm{km} \\cdot \\rm{kpc}", "\\rm{kpc} \\cdot \\rm{km}"
).replace(
"\\frac{\\rm{km}^{2}}{\\rm{s}^{2}}", "\\rm{km}^{2} / \\rm{s}^{2}"
).rstrip()
prop_unit = (
units.units.latex_repr.replace(
"\\rm{km} \\cdot \\rm{kpc}", "\\rm{kpc} \\cdot \\rm{km}"
)
.replace(
"\\frac{\\rm{km}^{2}}{\\rm{s}^{2}}", "\\rm{km}^{2} / \\rm{s}^{2}"
)
.rstrip()
)

prop_dtype = prop.dtype.__name__

Expand Down Expand Up @@ -5336,9 +5340,9 @@ def replace_math(match):
# Map from internal snap_* unit names to human-readable physical equivalents.
# Values are validated against the live unyt registry by _validate_snap_unit_map.
_snap_unit_map = {
"snap_mass": "(1e10*Msun)",
"snap_length": "Mpc",
"snap_time": "(s*Mpc/km)",
"snap_mass": "(1e10*Msun)",
"snap_length": "Mpc",
"snap_time": "(s*Mpc/km)",
"snap_temperature": "K",
}

Expand All @@ -5359,8 +5363,9 @@ def _resolve_snap_units(self, prop_name: str, prop: dict) -> str:

units = unyt.unyt_quantity(1, units=prop_unit)
latex = (
units.units.latex_repr
.replace("\\rm{km} \\cdot \\rm{kpc}", "\\rm{kpc} \\cdot \\rm{km}")
units.units.latex_repr.replace(
"\\rm{km} \\cdot \\rm{kpc}", "\\rm{kpc} \\cdot \\rm{km}"
)
.replace("\\frac{\\rm{km}^{2}}{\\rm{s}^{2}}", "\\rm{km}^{2} / \\rm{s}^{2}")
.replace(r"1.0 \times ", "")
.rstrip()
Expand Down Expand Up @@ -5450,10 +5455,7 @@ def get_footnotes_rst(self, name: str) -> tuple[list[int], str]:
self.footnotes.append(fnote)
footnote_nums.append(i + 1)
if footnote_nums:
refs = " ".join(
f"`[{n}] <footnote-{n}_>`_"
for n in sorted(footnote_nums)
)
refs = " ".join(f"`[{n}] <footnote-{n}_>`_" for n in sorted(footnote_nums))
return footnote_nums, refs
return [], ""

Expand Down Expand Up @@ -5529,7 +5531,9 @@ def enumerate_to_rst(match):
# Convert inline math and non-breaking spaces within the
# item text now, before the block is stashed as a
# placeholder (the main conversion steps run before restore)
item = re.sub(r"\$([^\n\$]+?)\$", lambda m: f":math:`{m.group(1)}`", item)
item = re.sub(
r"\$([^\n\$]+?)\$", lambda m: f":math:`{m.group(1)}`", item
)
item = item.replace("~", " ")
rst_items.append(f"#. {item}")
block = "\n\n" + "\n".join(rst_items) + "\n\n"
Expand Down Expand Up @@ -5640,24 +5644,24 @@ def _build_rst_table(self, prop_names: list, lines: list):

# swiftsimio name
snake_name = ".".join(
self._camel_to_snake(part) for part in prop['name'].split("/")
self._camel_to_snake(part) for part in prop["name"].split("/")
)

# HDF5 output name (prepend InputHalos/ where applicable)
output_name = prop["name"]
if output_name.split("/")[0] in ("HBTplus", "VR", "FOF"):
output_name = "InputHalos/" + output_name
snake_name = 'input_halos_' + snake_name
snake_name = "input_halos_" + snake_name

prop_units_rst = self._resolve_snap_units(prop_name, prop)
prop_comp_rst = self._compression_to_rst(
self.compression_description[prop["compression"]]
)
prop_filter = prop['category']
prop_filter = prop["category"]
output_types = self._get_output_types_rst(prop)
if 'DummyProperties' in prop['types']:
prop_filter = 'basic'
output_types = r'\-'
if "DummyProperties" in prop["types"]:
prop_filter = "basic"
output_types = r"\-"
description = prop["description"].format(
label="satisfying a spherical overdensity criterion.",
core_excision="excised core",
Expand Down Expand Up @@ -5713,9 +5717,11 @@ def generate_rst_files(self, output_dir: str):
prop_names_sorted = sorted(
self.properties.keys(),
key=lambda key: (
category_order.index(self.properties[key]["category"])
if self.properties[key]["category"] in category_order
else len(category_order),
(
category_order.index(self.properties[key]["category"])
if self.properties[key]["category"] in category_order
else len(category_order)
),
self.properties[key]["name"].lower(),
),
)
Expand All @@ -5726,11 +5732,11 @@ def generate_rst_files(self, output_dir: str):
dmo_props = []
hydro_props = []
for n in prop_names_sorted:
if self.properties[n]['category'] == 'InputHalos':
if self.properties[n]["category"] == "InputHalos":
input_basic_props.append(n)
elif 'DummyProperties' in self.properties[n]['types']:
elif "DummyProperties" in self.properties[n]["types"]:
input_copied_props.append(n)
elif self.properties[n]['dmo']:
elif self.properties[n]["dmo"]:
dmo_props.append(n)
else:
hydro_props.append(n)
Expand All @@ -5740,16 +5746,16 @@ def generate_rst_files(self, output_dir: str):
self.footnotes = []

# Introduction
with open(f'documentation/property_table_intro.rst') as file:
with open(f"documentation/property_table_intro.rst") as file:
lines = [line.rstrip() for line in file.readlines()]

# Tables
for props, table_title in [
(input_basic_props, "Input halo properties"),
(dmo_props, "Dark matter only properties"),
(hydro_props, "Hydrodynamical properties"),
(input_copied_props, "Copied properties"),
]:
(input_basic_props, "Input halo properties"),
(dmo_props, "Dark matter only properties"),
(hydro_props, "Hydrodynamical properties"),
(input_copied_props, "Copied properties"),
]:

lines.append(table_title)
lines.append("-" * len(table_title))
Expand Down Expand Up @@ -5778,7 +5784,6 @@ def generate_rst_files(self, output_dir: str):
ofile.write("\n".join(lines))



class DummyProperties:
"""
Dummy HaloProperty object used to include properties which are not computed
Expand Down
2 changes: 1 addition & 1 deletion tests/FLAMINGO/parameters_HYDRO.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ GroupMembership:
filename: "{sim_dir}/{sim_name}/SOAP-HBT/membership_{snap_nr:04d}/membership_{snap_nr:04d}.{file_nr}.hdf5"

ExtraInput:
xrays: "/cosma8/data/dp004/dc-mcgi1/FLAMINGO/Xray/{sim_name}/xray/flamingo_{snap_nr:04}/xray_{snap_nr:04}.{file_nr}.hdf5"
xrays: "/cosma8/data/dp004/dc-mcgi1/SOAP/TEST_DATA/Xray/{sim_name}/xray/flamingo_{snap_nr:04}/xray_{snap_nr:04}.{file_nr}.hdf5"

HaloProperties:
# Where to write the halo properties file
Expand Down
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