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update test branch to new changes in master #29

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Merged
m-herbold merged 11 commits into from
Oct 14, 2025
Merged

update test branch to new changes in master #29

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136765f
Merge pull request #22 from cramirezpe/mherbold_test_branch
m-herbold Jul 31, 2025
fdddf7b
Merge pull request #23 from cramirezpe/mherbold_test_branch
m-herbold Aug 15, 2025
372fb2c
Merge pull request #24 from cramirezpe/mherbold_test_branch
m-herbold Aug 15, 2025
77e1b8e
Merge pull request #25 from cramirezpe/mherbold_test_branch
m-herbold Aug 19, 2025
9f84db5
Merge pull request #26 from cramirezpe/mherbold_test_branch
m-herbold Aug 27, 2025
274fbf6
updating bookkeeper to use picca covariance scripts, update readme wi…
Oct 3, 2025
7c5d9f5
update example config to reflect changes from covariance scripts
Oct 3, 2025
3d2f9a0
new baseline default configs
m-herbold Oct 14, 2025
157d5e3
Merge pull request #28 from igmhub/m-herbold-patch-1
m-herbold Oct 14, 2025
130ca82
updated tests
Oct 14, 2025
4502157
Merge pull request #27 from igmhub/abby-dev
m-herbold Oct 14, 2025
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29 changes: 18 additions & 11 deletions picca_bookkeeper/bookkeeper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3732,6 +3732,7 @@ def get_covariance_matrix_tasker(
cross_correlations = []

args = {}
correlations = []
for auto_correlation in auto_correlations:
absorber, region, absorber2, region2 = auto_correlation.replace(
"-", "."
Expand All @@ -3745,11 +3746,13 @@ def get_covariance_matrix_tasker(
self.paths.cf_fname(
absorber, region, absorber2, region2).resolve()
)

args[f"{region}-{region2}"] = str(
self.paths.cf_fname("lya", region, "lya", region2).resolve()
)

correlations.append(str(
self.paths.cf_fname(absorber, region, absorber2, region2).resolve()
))
#args[f"{region}-{region2}"] = str(
# self.paths.cf_fname("lya", region, "lya", region2).resolve()
# )

for cross_correlation in cross_correlations:
(
tracer,
Expand All @@ -3764,11 +3767,15 @@ def get_covariance_matrix_tasker(
input_files.append(self.paths.xcf_fname(
absorber, region, tracer).resolve())

args[f"{region}-qso"] = str(
self.paths.xcf_fname("lya", region, tracer).resolve()
)

#args[f"{region}-qso"] = str(
# self.paths.xcf_fname("lya", region, tracer).resolve()
# )
correlations.append(str(
self.paths.xcf_fname(absorber, region, tracer).resolve()
))

# Now slurm args
args['correlations'] = " ".join(correlations)
command = "write_full_covariance.py"

updated_extra_args = self.generate_extra_args(
Expand Down Expand Up @@ -3798,7 +3805,7 @@ def get_covariance_matrix_tasker(
args = DictUtils.merge_dicts(args, updated_extra_args)

return get_Tasker(updated_system)(
command="/global/cfs/cdirs/desicollab/science/lya/y1-kp6/iron-tests/correlations/scripts/write_full_covariance_matrix_flex_size.py",
command="picca_write_full_covariance.py",
command_args=args,
packages=["picca"],
slurm_header_args=slurm_header_args,
Expand Down Expand Up @@ -3983,7 +3990,7 @@ def get_smooth_covariance_tasker(
args = DictUtils.merge_dicts(args, updated_extra_args)

return get_Tasker(updated_system)(
command="/global/cfs/cdirs/desicollab/science/lya/y1-kp6/iron-tests/correlations/scripts/write_smooth_covariance_flex_size.py",
command="picca_write_smooth_covariance.py",
command_args=args,
packages=["picca"],
slurm_header_args=slurm_header_args,
Expand Down
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