[pull] master from neuronsimulator:master #3
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e.g., we can now do ```python node.include_flux(ca * (1-ca)) ``` where `ca` is an `rxd.Species`
* initial partial API * nrnpy_set_pr_etal should be extern C * nrn_call_function leaves results on stack * segments, properties * including hocdec.h to try to avoid Datum errors on some systems * sectionlist and allsec hoc_Item getters * symbol and object introspection * symbol table getting and interating * object ref, push * Renamed files to avoid having two nrnapi.h files. On some systems (most? but not the one I used for everything else), some files tried to include the wrong nrnapi.h during the "make install" phase. * neuronapi.cpp no longer uses its .h, that is now a header for 3rd party tools * switched to enum for stack types * needed typedefs for C to be happy * test: sections.c * clang-format * replaced hoc_Item with new synonym nrn_Item * netcon example shows no need for dlsym * support for .so files in addition to .dylib * removed an excess const We'll still treat the pointer as const, but the user has no reason to care. * Add Robert's API tests to CTest (#2365) * build + run tests * fixups * different fixup * add -rdynamic * bugfix flagged by ASan * fix to header file name of api * hh_sim and sections work with handles don't have quantitative identity with the old hh_sim results, but very close. * rename stack_types_t per @olupton * replace param_handle with param * working vclamp * unified API property functions * getters use const args * forgot to commit sections * vector_capacity now on const obj * Several improvements - C/C++ api header included in implementation - signatures made compatible - public nrn_Item defined as inheriting from hoc_Item - dropped overlapping definitions. types are both fw declarations and opaque types * Make tests link against nrniv_lib, no dlopen * Address sonar lint reservations * Make comparisons be part of the test and account for fp innacuraciesa * Tests to find ref files * api: Make tests resilient to accumulated errors * Use in-test ref result, depending on NRN_ENABLE_CORENEURON * Use free for allocated c strings * Dont alloc Section Item to heap as its not used. NOTE: It seems that Sections are never freed. However we are lacking API to free Sections and Symbols in general. * Address intel compiler complain * Free memb_func[].dparam_semantics * Switch dparam_semantics to unique_ptr (no raw!) * Memb_list to do its memory management * Memb_list to be aware of its potential "view" condition and not free * Back pdata free * nrn_init to better initialize mpi * Addressed a number of warnings, inc avoidiing potential double free * Addressed sonarcloud issues * fix the merge with master * Fix test/api/netcon.cpp after merge with master - after RANDOM construct (#2627) was merged, netstim.mod uses Random123 by default - before this, netstim was using scoprand by default and reference results were from the same - now, explicitly use Random123 in the test and update reference results * fix warning [-Wimplicit-exception-spec-mismatch] --------- Co-authored-by: Olli Lupton <[email protected]> Co-authored-by: Fernando Pereira <[email protected]> Co-authored-by: Pramod Kumbhar <[email protected]> Co-authored-by: Nicolas Cornu <[email protected]> Co-authored-by: Michael Hines <[email protected]>
#2887) * add warning for 0 volume i region * add test for warning
The SoA no longer leaks the storage for the stable identifiers, instead it uses reference counting.
From https://linux.die.net/man/3/free: If ptr is NULL, no operation is performed.
* Give more CPU to jobs * For the FENV_ACCESS see the note here: https://eel.is/c++draft/cfenv.syn
* Pin numpy max version to <2
* Pin version of numpy in CI
* Pin tenacity package (plotly dep)
- The CI here: https://github.com/neuronsimulator/nrn/actions/runs/9543904495/job/26301425761 is failing with the error:
ModuleNotFoundError: No module named 'tenacity.asyncio'
- This is probably due to a new version of tenacity being released:
jd/tenacity@8.3.0...8.4.0
Doc is already on RTD (read the doc)
This PR introduces a wrapper of all C function that are registered with Python. The wrapper catches all exceptions, and converts them to Python exceptions, then it returns a value signaling an error.
* Rename `nmodl2` page under Python to `nmodl_neuron_extension` * Use absolute path references in NMODL pages under Python * Move NMODL pages under Python to `NMODLanguage` * Various updates to `nmodl_neuron_extension` page and `nmodl` page * Use mini tabs for Python/HOC fragments in NMODL pages
* Also accept len(sl)
…ystem` (#3292) * Replace `cleanup` and Win32 script with std::filesystem * Fixups * Remove from cmake * Update src/oc/hoc.cpp Co-authored-by: Nicolas Cornu <[email protected]> * Update src/oc/hoc.cpp Co-authored-by: Nicolas Cornu <[email protected]> * Put back Windows-specific part of cleanup * Use `noexcept` version of `fs::remove` * Declare the Windows function as `extern` --------- Co-authored-by: Nicolas Cornu <[email protected]>
Also remove unused setup.py.in
* use new Docker image tags (`manylinux_2_28_x86_64` and `manylinux_2_28_aarch64`) in CI for building wheels * use vendor-provided `flex`, `mpich`, and `openmpi` instead of building from source (still need custom `readline` and `ncurses` as the `*-static` versions do not use `-fPIC`) * unify MPI headers when building wheels * remove BBP-specific tests for wheels * show warning in Python wrapper if host machine is using GCC<10 * mention new min system requirements in docs when using a manylinux NEURON wheel
Plotly 6 requires anywidget
* Remove docs.yml CI * Enable readthedocs build on pull requests * Remove conda dependencies * Update docs build instructions
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