Update parameters dependency to modelfit_parameters

Also clang-format everything again

README.rst

@@ -14,8 +14,8 @@ package - but it can be used for any kind of image or domain.
 *gauss2dfit* is provided in two parts; a C++ shared library (libgauss2dfit) and
 optional Python bindings. Both depend on the base package
 `gauss2d <https://github.com/lsst-dm/gauss2d/>`, as well as the
-`parameters <https://github.com/lsst-dm/parameters/>` package for defining
-parameters with limits and transformations.
+`modelfit_parameters <https://github.com/lsst/modelfit_parameters/>` package
+for defining parameters with limits and transformations.
 
 *gauss2dfit* is built with `Meson <https://github.com/mesonbuild>`_ and uses
 `pkg-config <https://github.com/pkgconf/pkgconf>`_ to store package

include/model.h

@@ -500,7 +500,7 @@ class Model : public ParametricModel {
         unsigned int n_obsired = map_extra_weak.expired() + map_grad_weak.expired()
                                  + factors_grad_weak.expired() + factors_extra_weak.expired();
         const bool expired = n_obsired == 4;
-        if(print) {
+        if (print) {
             std::cout << "expired=" << expired << "\n";
         }
         if (!((n_obsired == 0) || expired)) {
@@ -770,9 +770,9 @@ class Model : public ParametricModel {
                 std::vector<double> loglike_new_plus;
                 std::vector<double> loglike_new_minus;
                 try {
-                    param.set_value_transformed(value + diff/2.);
+                    param.set_value_transformed(value + diff / 2.);
                     loglike_new_plus = this->evaluate();
-                    param.set_value_transformed(value - diff/2.);
+                    param.set_value_transformed(value - diff / 2.);
                     loglike_new_minus = this->evaluate();
                 } catch (std::runtime_error& e) {
                     param.set_value_transformed(value + diff);
@@ -1192,8 +1192,7 @@ class Model : public ParametricModel {
                           std::vector<std::vector<std::shared_ptr<Image>>> outputs = {},
                           std::vector<std::shared_ptr<Image>> residuals = {},
                           std::vector<std::shared_ptr<Image>> outputs_prior = {},
-                          std::shared_ptr<Image> residuals_prior = nullptr,
-                          bool force = false,
+                          std::shared_ptr<Image> residuals_prior = nullptr, bool force = false,
                           bool print = false) {
         const size_t n_outputs = outputs.size();
         const bool has_outputs = n_outputs > 0;

include/param_defs.h

@@ -3,7 +3,9 @@
 
 #include <vector>
 
-#include "parameters/parameter.h"
+#include "lsst/modelfit/parameters.h"
+
+namespace parameters = lsst::modelfit::parameters;
 
 namespace gauss2d::fit {
 using ParamBase = parameters::ParameterBase<double>;

include/parameters.h

@@ -8,8 +8,9 @@
 #include <cfloat>
 #include <iostream>
 
-#include "parameters/parameter.h"
-#include "parameters/unit.h"
+#include "lsst/modelfit/parameters.h"
+
+namespace parameters = lsst::modelfit::parameters;
 
 namespace gauss2d::fit {
 

include/sersicmixcomponent.h

@@ -1,7 +1,7 @@
 #ifndef GAUSS2D_FIT_SERSICMIXCOMPONENT_H
 #define GAUSS2D_FIT_SERSICMIXCOMPONENT_H
 
-#include <parameters/parameter.h>
+#include "lsst/modelfit/parameters.h"
 
 #include "channel.h"
 #include "ellipticalcomponent.h"
@@ -68,7 +68,7 @@ class SersicParametricEllipseHolder {
     }
 };
 
-// TODO: Add ref to derivation of weights, when publicized
+// TODO: Add ref to derivation of weights, when published
 /**
  * @brief A Gaussian mixture approximation to a Sersic profile Component.
  *
@@ -81,7 +81,8 @@ class SersicParametricEllipseHolder {
  * but deliberately excludes the very inner and outermost regions.
  *
  * @note See https://ned.ipac.caltech.edu/level5/March05/Graham/Graham2.html
- *       for a useful summary of various properties of the Sersic profile.
+ *       (Graham & Driver 2005) for a useful summary of various properties
+ *       of the Sersic profile.
  */
 class SersicMixComponent : private SersicParametricEllipseHolder, public EllipticalComponent {
 private:

include/transforms.h

@@ -1,21 +1,13 @@
-//
-// Created by dtaranu on 4/8/21.
-//
-
 #ifndef GAUSS2D_FIT_TRANSFORMS_H
 #define GAUSS2D_FIT_TRANSFORMS_H
 
 #include <cmath>
 #include <iostream>
 #include <memory>
 
-#ifndef PARAMETERS_LIMITS_H
-#include "parameters/limits.h"
-#endif
+#include "lsst/modelfit/parameters.h"
 
-#ifndef PARAMETERS_TRANSFORM_H
-#include "parameters/transform.h"
-#endif
+namespace parameters = lsst::modelfit::parameters;
 
 namespace gauss2d::fit {
 #pragma GCC diagnostic push

meson.build

@@ -19,20 +19,20 @@ if gsl_dep.found()
 endif
 
 if use_eups
-    gauss2d_eupsdir = run_command('eups', 'list', '-d', 'gauss2d', check: true).stdout().strip()
+    gauss2d_eupsdir = run_command('sh', '-c', 'echo $GAUSS2D_DIR', check: true, capture: true).stdout().strip()
     cpp = meson.get_compiler('cpp')
     gauss2d_dep = declare_dependency(
         dependencies: [cpp.find_library('gauss2d', dirs: [gauss2d_eupsdir + '/build-release/lib64']),],
         include_directories: gauss2d_eupsdir + '/build-release/include',
     )
 
-    parameters_eupsdir = run_command('eups', 'list', '-d', 'parameters', check: true).stdout().strip()
+    parameters_eupsdir = run_command('sh', '-c', 'echo $MODELFIT_PARAMETERS_DIR', check: true, capture: true).stdout().strip()
     parameters_dep = declare_dependency(
         include_directories: parameters_eupsdir + '/build-release/include',
     )
 else
     gauss2d_dep = dependency('gauss2d')
-    parameters_dep = dependency('parameters')
+    parameters_dep = dependency('lsst_modelfit_parameters')
 endif
 
 inc = include_directories('include')

python/gauss2d/fit/parameters.cc

@@ -33,7 +33,7 @@
 #include "gauss2d/fit/parameters.h"
 #include "gauss2d/fit/transforms.h"
 #include "gauss2d/fit/util.h"
-#include "parameters/transform.h"
+#include "lsst/modelfit/parameters.h"
 
 #include "parameters.h"
 #include "pybind11.h"
@@ -71,7 +71,7 @@ void bind_parameters(py::module &m) {
     declare_sizeparameter<double, g2f::SigmaYParameter, g2f::SizeYParameter>(m, "SigmaY");
     declare_parameter<double, g2f::StdDevParameter>(m, "StdDev");
     declare_transform_base<double>(m);
-    declare_transform<double, parameters::UnitTransform<double>>(m, "Unit");
+    declare_transform<double, lsst::modelfit::parameters::UnitTransform<double>>(m, "Unit");
     declare_transform<double, g2f::InverseTransform>(m, "Inverse");
     declare_transform<double, g2f::JanskyToABMagTransform>(m, "JanskyToABMag");
     declare_transform<double, g2f::NanojanskyToABMagTransform>(m, "NanojanskyToABMag");

python/gauss2d/fit/parameters.h

@@ -34,8 +34,7 @@
 
 #include "gauss2d/fit/parameters.h"
 #include "gauss2d/fit/transforms.h"
-#include "parameters/limits.h"
-#include "parameters/transform.h"
+#include "lsst/modelfit/parameters.h"
 
 #include "pybind11.h"
 #include "utils.h"
@@ -44,6 +43,7 @@ namespace py = pybind11;
 using namespace pybind11::literals;
 
 namespace g2f = gauss2d::fit;
+namespace parameters = lsst::modelfit::parameters;
 
 template <typename T>
 void declare_limits(py::module &m) {

python/gauss2d/fit/sersicmixcomponent.cc

@@ -31,9 +31,9 @@
 #include "gauss2d/fit/parameters.h"
 #include "gauss2d/fit/sersicmixcomponent.h"
 #include "gauss2d/fit/sersicparametricellipse.h"
+#include "lsst/modelfit/parameters.h"
 
 #include "parameters.h"
-#include "parameters/parameter.h"
 #include "pybind11.h"
 
 namespace py = pybind11;

python/meson.build

@@ -22,7 +22,7 @@ if gsl_dep.found()
 endif
 
 if use_eups
-    gauss2d_eupsdir = run_command('eups', 'list', '-d', 'gauss2d', check: true).stdout().strip()
+    gauss2d_eupsdir = run_command('sh', '-c', 'echo $GAUSS2D_DIR', check: true, capture: true).stdout().strip()
     cpp = meson.get_compiler('cpp')
     gauss2d_dep = declare_dependency(
         dependencies: [cpp.find_library('gauss2d', dirs: [gauss2d_eupsdir + '/build-release/lib64']),],
@@ -32,7 +32,7 @@ if use_eups
         include_directories: gauss2d_eupsdir + '/python/lib/build-release/include',
     )
     gauss2dfit_eupsdir = gauss2dfit_eups.stdout().strip()
-    parameters_eupsdir = run_command('eups', 'list', '-d', 'parameters', check: true).stdout().strip()
+    parameters_eupsdir = run_command('sh', '-c', 'echo $MODELFIT_PARAMETERS_DIR', check: true, capture: true).stdout().strip()
     # TODO: Can this dependency be extracted from '../meson.build' somehow
     gauss2dfit_dep = declare_dependency(
         dependencies: [cpp.find_library('gauss2dfit', dirs: [gauss2dfit_eupsdir + '/build-release/lib64']),],

src/gaussianprior.cc

@@ -39,9 +39,7 @@ PriorEvaluation GaussianPrior::evaluate(bool calc_jacobians, bool normalize) con
     std::map<ParamBaseCRef, std::vector<double>> jacobians = {};
     // dresidual/dx = d((x - mean)/stddev)/dx = 1/stddev
     if (calc_jacobians) {
-        jacobians[*_param] = {
-            1.0 / (_stddev*(_transformed ? 1.0 : _param->get_transform_derivative()))
-        };
+        jacobians[*_param] = {1.0 / (_stddev * (_transformed ? 1.0 : _param->get_transform_derivative()))};
     }
 
     return PriorEvaluation{prior, {residual}, jacobians};

src/sersicmixcomponent.cc

@@ -376,9 +376,7 @@ ParamCRefs& SersicMixComponent::get_parameters_const(ParamCRefs& params, ParamFi
     return params;
 }
 
-double SersicMixComponent::get_sersicindex() const {
-    return this->_sersicindex->get_value();
-}
+double SersicMixComponent::get_sersicindex() const { return this->_sersicindex->get_value(); }
 
 SersicMixComponentIndexParameter& SersicMixComponent::get_sersicindex_param() const {
     return *(this->_sersicindex);
@@ -451,9 +449,7 @@ void SersicMixComponent::set_grad_param_factors(const Channel& channel, GradPara
     }
 }
 
-void SersicMixComponent::set_sersicindex(double value) {
-    this->_sersicindex->set_value(value);
-}
+void SersicMixComponent::set_sersicindex(double value) { this->_sersicindex->set_value(value); }
 
 std::string SersicMixComponent::repr(bool name_keywords) const {
     return "SersicMixComponent(" + EllipticalComponent::repr(name_keywords) + ", "

tests/test_model.cc

@@ -45,9 +45,8 @@ typedef std::vector<std::shared_ptr<const g2f::Channel>> Channels;
 const auto CHANNEL_NONE = g2f::Channel::NONE_PTR();
 Channels CHANNELS_NONE = {CHANNEL_NONE};
 
-std::shared_ptr<Data> make_data(Channels channels, const size_t n_x, const size_t n_y,
-                                const size_t dn_x = 0., const size_t dn_y = 0.,
-                                const double sigma_inv_value = 1.) {
+std::shared_ptr<Data> make_data(Channels channels, const size_t n_x, const size_t n_y, const size_t dn_x = 0.,
+                                const size_t dn_y = 0., const double sigma_inv_value = 1.) {
     std::vector<std::shared_ptr<const Observation>> observations;
     double dx_min = 0., dy_min = 0.;
     for (const auto& channel_ptr : channels) {
@@ -214,26 +213,23 @@ void verify_model(Model& model, const std::vector<std::shared_ptr<const g2f::Cha
 
                         // TODO: Determine less arbitrary thresholds
                         double is_close_threshold = 2e-3;
-                        if(
-                            (name_row == g2f::ReffXParameter::_name)
+                        if ((name_row == g2f::ReffXParameter::_name)
                             || (name_row == g2f::ReffYParameter::_name)
                             || (name_col == g2f::ReffXParameter::_name)
                             || (name_col == g2f::ReffYParameter::_name)
                             || (name_row == g2f::SersicIndexParameter::_name)
-                            || (name_col == g2f::SersicIndexParameter::_name)
-                        ) {
+                            || (name_col == g2f::SersicIndexParameter::_name)) {
                             is_close_threshold *= 10.;
                         }
 
-                        if (!(
-                              (skip_rho && (name_row == g2f::RhoParameter::_name))
+                        if (!((skip_rho && (name_row == g2f::RhoParameter::_name))
                               || (skip_rho && (name_col == g2f::RhoParameter::_name)))) {
                             auto value2 = hessian2->get_value(row, col);
-                            auto msg = g2f::isclose(
-                                value, value2, is_close_threshold, is_close_threshold/10
-                            ).isclose;
-                            CHECK_MESSAGE(msg, "hessian[", row,
-                                          ",", col, "]=(", value, ")!= hessian2 value=(", value2,
+                            auto msg
+                                    = g2f::isclose(value, value2, is_close_threshold, is_close_threshold / 10)
+                                              .isclose;
+                            CHECK_MESSAGE(msg, "hessian[", row, ",", col, "]=(", value,
+                                          ")!= hessian2 value=(", value2,
                                           ") for params_free[row], params_free[col]=", param_str_row.str(),
                                           param_str_col.str());
                         }
@@ -474,10 +470,7 @@ TEST_CASE("Model") {
     double frac_value = 0.3;
     for (const auto& channel : channels) {
         auto frac1 = std::make_shared<g2f::ProperFractionParameter>(
-            frac_value,
-            nullptr,
-            g2f::get_transform_default<g2f::Log10Transform>()
-        );
+                frac_value, nullptr, g2f::get_transform_default<g2f::Log10Transform>());
         auto frac2 = std::make_shared<g2f::ProperFractionParameter>(1.0, nullptr, nullptr, nullptr, true);
         data_frac1.emplace_back(*channel, frac1);
         data_frac2.emplace_back(*channel, frac2);
@@ -538,9 +531,9 @@ TEST_CASE("Model PSF") {
 
         comps.emplace_back(std::make_shared<g2f::GaussianComponent>(
                 std::make_shared<g2f::GaussianParametricEllipse>(
-                    std::make_shared<g2f::SigmaXParameter>(size, nullptr, transform_log10),
-                    std::make_shared<g2f::SigmaYParameter>(size, nullptr, transform_log10),
-                    std::make_shared<g2f::RhoParameter>(0, nullptr, transform_rho)),
+                        std::make_shared<g2f::SigmaXParameter>(size, nullptr, transform_log10),
+                        std::make_shared<g2f::SigmaYParameter>(size, nullptr, transform_log10),
+                        std::make_shared<g2f::RhoParameter>(0, nullptr, transform_rho)),
                 cens, last));
     }
     g2f::Components psfcomps = {g2f::GaussianComponent::make_uniq_default_gaussians({0.})};
@@ -602,8 +595,7 @@ TEST_CASE("Model with priors") {
             std::make_shared<g2f::ReffXParameter>(1.475109), std::make_shared<g2f::ReffYParameter>(1.469544),
             std::make_shared<g2f::RhoParameter>(-0.020842));
 
-    auto ell_g2
-            = g2::Ellipse(ellipse_src->get_size_x(), ellipse_src->get_size_y(), ellipse_src->get_rho());
+    auto ell_g2 = g2::Ellipse(ellipse_src->get_size_x(), ellipse_src->get_size_y(), ellipse_src->get_rho());
     auto ell_maj = g2::EllipseMajor(ell_g2);
     double axrat = ell_maj.get_axrat();
     double size_ell = sqrt(std::pow(ell_maj.get_r_major(), 2) * axrat);

ups/eupspkg.cfg.sh

@@ -15,6 +15,11 @@ build()
     (build_cc && build_py)
 }
 
+clean()
+{
+    ./clean.sh
+}
+
 config_cc()
 {
     ([ -d "$GAUSS2DFIT_DIR" ] && ./clean-cc.sh && meson setup --prefix="$GAUSS2DFIT_DIR/build-release" \