Skip to content

BiorthBasis parameter 'subsamp' and 'samplesz' are duplicates! #222

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
The9Cat merged 11 commits into from
May 29, 2026
Merged

BiorthBasis parameter 'subsamp' and 'samplesz' are duplicates! #222

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
c967fca
Use 'subsamp' as a proxy for 'samplesz' and deprecate 'subsamp' with …
May 28, 2026
a347a3b
Potential fix for pull request finding
The9Cat May 28, 2026
bb96362
Potential fix for pull request finding
The9Cat May 28, 2026
219ac1a
Potential fix for pull request finding
The9Cat May 28, 2026
43c919f
Potential fix for pull request finding
The9Cat May 28, 2026
3f1bd24
Potential fix for pull request finding
The9Cat May 28, 2026
20e3ec2
Fix Cube valid_keys entries for samplesz suggestion
Copilot May 28, 2026
5cffe13
chore: finalize targeted review-comment handling
Copilot May 28, 2026
be2cd3a
remove some build files along for the ride
michael-petersen May 29, 2026
ad182a3
Merge branch 'devel' into covarianceParameterConfusion
michael-petersen May 29, 2026
f8e8c48
Add explicit version number to deprecation warning
May 29, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
69 changes: 55 additions & 14 deletions expui/BiorthBasis.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -275,9 +275,19 @@ namespace BasisClasses
if (conf["M0_ONLY"]) M0_only = conf["M0_ONLY"].as<bool>();
if (conf["pcavar"]) pcavar = conf["pcavar"].as<bool>();
if (conf["subsamp"]) sampT = conf["subsamp"].as<int>();
if (conf["samplesz"]) sampT = conf["samplesz"].as<int>();

sampT = std::max(1, sampT); // Sanity
}

// Deprecation warning
if (conf["subsamp"]) {
if (myid==0)
std::cout << "---- Spherical: parameter 'subsamp' is deprecated. "
<< "It works, but will be removed in version >= 7.11. "
<< "Please use 'samplesz' instead."
<< std::endl;
}
}
catch (YAML::Exception & error) {
if (myid==0) std::cout << "Error parsing parameter stanza for <"
<< name << ">: "
Expand Down Expand Up @@ -1522,6 +1532,7 @@ namespace BasisClasses
if (conf["pyproj" ]) pyproj = conf["pyproj" ].as<std::string>();
if (conf["pcavar"] ) pcavar = conf["pcavar" ].as<bool>();
if (conf["subsamp"] ) sampT = conf["subsamp" ].as<int>();
if (conf["samplesz" ]) sampT = conf["samplesz" ].as<int>();

// Sanity
sampT = std::max(1, sampT);
Expand All @@ -1537,14 +1548,23 @@ namespace BasisClasses
// Deprecation warning
if (conf["eof_file"]) {
if (myid==0)
std::cout << "Cylinder: parameter 'eof_file' is deprecated. "
<< "and will be removed in a future release. Please "
std::cout << "Cylindrical: parameter 'eof_file' is deprecated. "
<< "and will be removed in version >= 7.11. Please "
<< "use 'cachename' instead."
<< std::endl;

conf["cachename"] = conf["eof_file"];
}

// Deprecation warning
if (conf["subsamp"]) {
if (myid==0)
std::cout << "---- Cylindrical: parameter 'subsamp' is deprecated. "
<< "It works, but will be removed in version >= 7.11. "
<< "Please use 'samplesz' instead."
<< std::endl;
}

}
catch (YAML::Exception & error) {
if (myid==0) std::cout << "Error parsing 'force' for Component <"
Expand Down Expand Up @@ -2482,8 +2502,18 @@ namespace BasisClasses
if (conf["M0_ONLY"]) M0_only = conf["M0_ONLY"].as<bool>();
if (conf["pcavar"]) pcavar = conf["pcavar"].as<bool>();
if (conf["subsamp"]) sampT = conf["subsamp"].as<int>();
if (conf["samplesz"]) sampT = conf["samplesz"].as<int>();

sampT = std::max(1, sampT); // Sanity

if (conf["subsamp"]) {
if (myid==0)
std::cout << "---- FlatDisk: parameter 'subsamp' is deprecated. "
<< "It works, but will be removed in version >= 7.11. "
<< "Please use 'samplesz' instead."
<< std::endl;
}

}
catch (YAML::Exception & error) {
if (myid==0) std::cout << "Error parsing parameter stanza for <"
Expand Down Expand Up @@ -4362,8 +4392,9 @@ namespace BasisClasses
"verbose",
"check",
"method",
"pcavar,"
"pcavar",
"subsamp",
"samplesz",
"nint",
"totalCovar",
"fullCovar"
Expand Down Expand Up @@ -4422,20 +4453,30 @@ namespace BasisClasses
// Assign values from YAML
//
try {
if (conf["nminx"]) nminx = conf["nminx" ].as<int>();
if (conf["nminy"]) nminy = conf["nminy" ].as<int>();
if (conf["nminz"]) nminz = conf["nminz" ].as<int>();
if (conf["nminx"]) nminx = conf["nminx" ].as<int>();
if (conf["nminy"]) nminy = conf["nminy" ].as<int>();
if (conf["nminz"]) nminz = conf["nminz" ].as<int>();

if (conf["nmaxx"]) nmaxx = conf["nmaxx" ].as<int>();
if (conf["nmaxy"]) nmaxy = conf["nmaxy" ].as<int>();
if (conf["nmaxz"]) nmaxz = conf["nmaxz" ].as<int>();
if (conf["nmaxx"]) nmaxx = conf["nmaxx" ].as<int>();
if (conf["nmaxy"]) nmaxy = conf["nmaxy" ].as<int>();
if (conf["nmaxz"]) nmaxz = conf["nmaxz" ].as<int>();

if (conf["knots"]) knots = conf["knots" ].as<int>();
if (conf["knots"]) knots = conf["knots" ].as<int>();

if (conf["check"]) check = conf["check" ].as<bool>();

if (conf["pcavar"]) pcavar = conf["pcavar" ].as<bool>();
if (conf["subsamp"]) sampT = conf["subsamp" ].as<int>();
if (conf["samplesz"]) sampT = conf["samplesz"].as<int>();
Comment thread
The9Cat marked this conversation as resolved.

if (conf["check"]) check = conf["check" ].as<bool>();
if (conf["subsamp"]) {
if (myid==0)
std::cout << "---- Cube: parameter 'subsamp' is deprecated. "
<< "It works, but will be removed in version >= 7.11. "
<< "Please use 'samplesz' instead."
<< std::endl;
}

if (conf["pcavar"]) pcavar = conf["pcavar" ].as<bool>();
if (conf["subsamp"]) sampT = conf["subsamp"].as<int>();
}
catch (YAML::Exception & error) {
if (myid==0) std::cout << "Error parsing parameter stanza for <"
Expand Down
8 changes: 4 additions & 4 deletions pyEXP/BasisWrappers.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,9 +137,9 @@ void BasisFactoryClasses(py::module &m)
support for computing the coefficieint covariance from subsamples of
particles. This is implemented by the enableCoefCovariance() method
for each of these supported bases. The force configuration must
contain the parameters 'pcavar' (boolean) and 'subsamp' (integer) keys.
contain the parameters 'pcavar' (boolean) and 'samplesz' (integer) keys.
The 'pcavar' parameter turns on the covariance computation. The
'subsamp' parameter sets the number of partions or subsamples for each
'samplesz' parameter sets the number of partitions or subsamples for each
coefficient creation. There are two additional control parameters that
may be optionally specified with the enableCoefCovariance() call. The
'total' parameters enables computing the total covariance matrices only
Expand Down Expand Up @@ -176,11 +176,11 @@ void BasisFactoryClasses(py::module &m)
counts, the sample masses, the coefficient means and the coefficient
covariance matrices. The first two elements are vectors of length
equal to the number of subsamples. The third element is a 4D array
with dimensions (subsamp, Nlm, nmax) where subsamp is the number of
with dimensions (samplesz, Nlm, nmax) where samplesz is the number of
subsamples, Nlm, is the number of harmonics (e.g. l, m values or m
values for the spherical and cylindrical bases), and nmax is the number
of coefficients. The fourth element is a 4D array with dimensions
(subsamp, Nlm, nmax, namx) containing the covariance matrices for each
(samplesz, Nlm, nmax, namx) containing the covariance matrices for each
subsample in the last two dimensions.

Typical usage might be:
Expand Down
Loading