pt3dstyle logical connection should be at center of soma section (instead of center of contour).

[nrnhines]

Closes #2973

The logical connection after import3d neurolucida3 file should be invariant on h.define_shape().
That is, the location of the rest of the tree should not change relative to the soma.

This is accomplished by updating the logical connection point of dendrites at instantiation when the actual 3-d soma section points are known (after processing the contour).

The two (related) substantive changes in this PR are noted in the comments.

Test added

[azure-pipelines]

✔️ 528f82d -> Azure artifacts URL

[azure-pipelines]

✔️ 528f82d -> Azure artifacts URL

[azure-pipelines]

✔️ 7b96538 -> Azure artifacts URL

[azure-pipelines]

✔️ 5cd3295 -> Azure artifacts URL

[azure-pipelines]

✔️ efc9f28 -> Azure artifacts URL

[nrnhines]

The many CI failures are perplexing. On my machine I have similar errors for ninja testfor this pr but also for the master. ie. Ubuntu 24.04, gcc version 13.2.0 (Ubuntu 13.2.0-23ubuntu4), Python 3.12.3 (via pyenv)

The following tests FAILED:
	  3 - unit_tests::benchmarks (Failed)
	 86 - parallel::subworld (Failed)
	 88 - parallel::netpar (Failed)
	 89 - parallel::bas (Failed)
	 90 - parallel::nrntest_fast (Failed)
	 92 - nmodl_tests::test_disc (Failed)
	 93 - nmodl_tests::test_function_table (Failed)
	 94 - nmodl_tests::test_kinetic (Failed)
	123 - pyinit::nrniv_py3.12_python_check_sys_path (Failed)
	125 - pyinit::nrniv_py3.12_nrnpython_check_sys_path (Failed)
	127 - pyinit::nrniv_py3.12_python_check_sys_prefix (Failed)
	129 - pyinit::nrniv_py3.12_nrnpython_check_sys_prefix (Failed)
	131 - pyinit::nrniv_py3.12_python_check_sys_exec_prefix (Failed)
	133 - pyinit::nrniv_py3.12_nrnpython_check_sys_exec_prefix (Failed)
	159 - pyinit::nrniv_pydef_python_check_sys_path (Failed)
	161 - pyinit::nrniv_pydef_nrnpython_check_sys_path (Failed)
	163 - pyinit::nrniv_pydef_python_check_sys_prefix (Failed)
	165 - pyinit::nrniv_pydef_nrnpython_check_sys_prefix (Failed)
	167 - pyinit::nrniv_pydef_python_check_sys_exec_prefix (Failed)
	169 - pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix (Failed)
	194 - external_nrntest (Failed)
	207 - testcorenrn_vecevent::compare_results (Failed)

[azure-pipelines]

✔️ 3e38a26 -> Azure artifacts URL

[sonarcloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[azure-pipelines]

✔️ d6fd24b -> Azure artifacts URL

[bbpbuildbot]

Logfiles from GitLab pipeline #225622 (:no_entry:) have been uploaded here!

Status and direct links:

• ✅ mac_m1_cmake_build: [cmake, ON, OFF, OFF, address]
• ✅ spack_setup
• ✅ build:nmodl
• ✅ build:neuron:nmodl:intel:legacy
• ✅ build:neuron:nmodl:intel:shared
• ✅ build:neuron:nmodl:nvhpc:acc:legacy
• ✅ build:neuron:nmodl:nvhpc:acc:shared
• ✅ build:neuron:nmodl:nvhpc:omp:legacy
• ✅ build:neuron:nmodl:nvhpc:omp
• ✅ test:neuron:nmodl:intel:legacy
• ✅ test:neuron:nmodl:intel:shared
• ✅ test:neuron:nmodl:nvhpc:acc:legacy
• ✅ test:neuron:nmodl:nvhpc:acc:shared
• ✅ test:neuron:nmodl:nvhpc:omp:legacy
• ✅ test:neuron:nmodl:nvhpc:omp