Clean up package dependencies (backport #1574) (#1576)

Previously, package dependencies were moved from separate
requirements*.txt files into pyproject.toml, but the old files were not
removed. This situation left to the old files accidentally being edited
instead of pyproject.toml. Here the old files are removed and dependency
changes that had been made to them are carried over to pyproject.toml
(just bumping minimum versions and dropping qiskit-dynamics).<hr>This is
an automatic backport of pull request #1574 done by
[Mergify](https://mergify.com).

Co-authored-by: Will Shanks <willshanks@us.ibm.com>

Author: mergify[bot]

pyproject.toml

@@ -9,9 +9,9 @@ description = "Software for developing quantum computing programs"
 dependencies = [
     "numpy>=1.17",
     "scipy>=1.4",
-    "qiskit>=0.45",
+    "qiskit>=1.3",
     "qiskit-ibm-experiment>=0.4.6",
-    "qiskit_ibm_runtime>=0.29.0",
+    "qiskit_ibm_runtime>=0.34.0",
     "matplotlib>=3.4",
     "uncertainties",
     "lmfit",
@@ -54,23 +54,14 @@ extras = [
     "cvxpy>=1.3.2", # for tomography
     "scikit-learn", # for discriminators
     "qiskit-aer>=0.13.2",
-    "qiskit-dynamics>=0.4.0", # for the PulseBackend
 ]
 
 [project.entry-points."qiskit.synthesis"]
 "clifford.rb_default" = "qiskit_experiments.library.randomized_benchmarking.clifford_synthesis:RBDefaultCliffordSynthesis"
 
 [dependency-groups]
 formatting = ["black~=22.0"]
-devbase = [
-    # Extra dependencies for tests/documentation code
-    # qiskit-ibm-runtime 0.34 and qiskit 1.3 are needed to pass run options through
-    # qiskit_ibm_runtime.SamplerV2 to test backends' backend.run calls.
-    # Earlier versions work okay when using physical backends or not passing run
-    # options.
-    "qiskit-ibm-runtime>=0.34",  # see above
-    "qiskit>=1.3",  # see above
-]
+devbase = []
 testing = [
     {include-group = "devbase"},
     # Test runner tools