Rename edata data members (AMICI-dev#3079)

* rename edata members

* fixup

* fixup

* fixup doc

* rename measurement error to noise scale

* fixup plotting

* fixup plural

* fixup + update doc

* Update src/model.cpp

---------

Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>

Author: FFroehlich

doc/examples/example_steady_states/ExampleEquilibrationLogic.ipynb

@@ -470,7 +470,7 @@
    "source": [
     "# create edata, with 3 timepoints and 2 observables:\n",
     "edata = ExpData(2, 0, 0, np.array([0.0, 0.1, 1.0]))\n",
-    "edata.set_observed_data([1.8] * 6)\n",
+    "edata.set_measurements([1.8] * 6)\n",
     "edata.fixed_parameters = np.array([3.0, 5.0])\n",
     "# set parameters for pre-equilibration\n",
     "edata.fixed_parameters_pre_equilibration = np.array([0.0, 2.0])\n",
@@ -765,7 +765,7 @@
     "# by setting an infinity timepoint\n",
     "# and creatíng an edata object, which is needed for adjoint computation\n",
     "edata = ExpData(2, 0, 0, np.array([float(\"inf\")]))\n",
-    "edata.set_observed_data([1.8] * 2)\n",
+    "edata.set_measurements([1.8] * 2)\n",
     "edata.fixed_parameters = np.array([3.0, 5.0])\n",
     "\n",
     "model_reduced.set_steady_state_sensitivity_mode(\n",
@@ -853,7 +853,7 @@
     "# No post-equilibration this time.\n",
     "# create edata, with 3 timepoints and 2 observables:\n",
     "edata = ExpData(2, 0, 0, np.array([0.0, 0.1, 1.0]))\n",
-    "edata.set_observed_data([1.8] * 6)\n",
+    "edata.set_measurements([1.8] * 6)\n",
     "edata.fixed_parameters = np.array([3.0, 5.0])\n",
     "# set parameters for pre-equilibration\n",
     "edata.fixed_parameters_pre_equilibration = np.array([0.0, 2.0])\n",

doc/examples/getting_started_extended/GettingStartedExtended.ipynb

@@ -1135,7 +1135,7 @@
     "edata.fixed_parameters = model.get_fixed_parameters()\n",
     "# set sigma to 1.0 except for observable 5, so that p[7] is used instead\n",
     "# (if we have sigma parameterized, the corresponding ExpData entries must NaN, otherwise they will override the parameter)\n",
-    "edata.set_observed_data_std_dev(\n",
+    "edata.set_noise_scales(\n",
     "    rdata[\"t\"] * 0 + np.nan,\n",
     "    list(model.get_observable_ids()).index(\"observable_x1withsigma\"),\n",
     ")\n",