Remove support for legacy units and dynamic units selection (#2539)

* With v >=9.0, remove support for legacy units. Only modern units will be supported. * Issue warning is user is explicitly asking for a modern unit as it's no longer required * Error if the user is trying to use legacy unit via API or env variable * Add test for the same * update the test data for rxd tests Co-authored-by: adam newton <[email protected]>
neuronsimulator · Oct 6, 2023 · b3aa3d0 · b3aa3d0
1 parent 21c4afd
commit b3aa3d0
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Showing 46 changed files with 139 additions and 753 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -89,8 +89,6 @@ option(NRN_AVOID_ABSOLUTE_PATHS
        "Avoid embedding absolute paths in generated code (ccache optimisation)"
        ${NRN_AVOID_ABSOLUTE_PATHS_DEFAULT})
 mark_as_advanced(NRN_AVOID_ABSOLUTE_PATHS)
-option(NRN_DYNAMIC_UNITS_USE_LEGACY "Use legacy units as default for dynamic units"
-       ${NRN_DYNAMIC_UNITS_USE_LEGACY_DEFAULT})
 # note that if CoreNEURON is enabled then it is not necessary to enable this option
 option(NRN_ENABLE_MOD_COMPATIBILITY "Enable CoreNEURON compatibility for MOD files"
        ${NRN_ENABLE_MOD_COMPATIBILITY_DEFAULT})
@@ -499,9 +497,6 @@ if(NRN_ENABLE_CORENEURON)
   set(CORENRN_ENABLE_UNIT_TESTS
       ${NRN_ENABLE_TESTS}
       CACHE BOOL "" FORCE)
-  set(CORENRN_ENABLE_LEGACY_UNITS
-      ${NRN_DYNAMIC_UNITS_USE_LEGACY}
-      CACHE BOOL "" FORCE)
   if(NRN_ENABLE_PROFILING)
     if(NRN_PROFILER STREQUAL "caliper")
       set(CORENRN_ENABLE_CALIPER_PROFILING ON)
@@ -960,11 +955,6 @@ message(STATUS "CXX COMPILER  | ${CMAKE_CXX_COMPILER}")
 message(STATUS "BUILD_TYPE    | ${CMAKE_BUILD_TYPE} (allowed: ${allowableBuildTypes})")
 message(STATUS "COMPILE FLAGS | ${COMPILER_FLAGS}")
 message(STATUS "Shared        | ${NRN_ENABLE_SHARED}")
-if(NRN_DYNAMIC_UNITS_USE_LEGACY)
-  message(STATUS "Default units | legacy units")
-else()
-  message(STATUS "Default units | modern units (2019 nist constants)")
-endif()
 message(STATUS "MPI           | ${NRN_ENABLE_MPI}")
 if(NRN_ENABLE_MPI)
   message(STATUS "  DYNAMIC     | ${NRN_ENABLE_MPI_DYNAMIC}")
@@ -1035,9 +1025,6 @@ message(STATUS "CoreNEURON    | ${NRN_ENABLE_CORENEURON}")
 if(NRN_ENABLE_CORENEURON)
   message(STATUS "  PATH        | ${CORENEURON_DIR}")
   message(STATUS "  LINK FLAGS  | ${CORENRN_LIB_LINK_FLAGS}")
-  if(NOT coreneuron_FOUND)
-    message(STATUS "  Legacy Units| ${CORENRN_ENABLE_LEGACY_UNITS}")
-  endif()
 endif()
 if(NRN_UNIVERSAL2_BUILD)
   message(STATUS "CMAKE_OSX_ARCH| ${CMAKE_OSX_ARCHITECTURES}")

diff --git a/cmake/BuildOptionDefaults.cmake b/cmake/BuildOptionDefaults.cmake
@@ -26,7 +26,6 @@ set(NRN_ENABLE_MPI_DYNAMIC_DEFAULT OFF)
 set(NRN_ENABLE_MOD_COMPATIBILITY_DEFAULT OFF)
 set(NRN_ENABLE_REL_RPATH_DEFAULT OFF)
 set(NRN_AVOID_ABSOLUTE_PATHS_DEFAULT OFF)
-set(NRN_DYNAMIC_UNITS_USE_LEGACY_DEFAULT OFF)
 set(NRN_NMODL_CXX_FLAGS_DEFAULT "-O0")
 set(NRN_SANITIZERS_DEFAULT "")
 
@@ -68,7 +67,6 @@ set(NRN_OPTION_NAME_LIST
     NRN_MODULE_INSTALL_OPTIONS
     NRN_PYTHON_DYNAMIC
     NRN_MPI_DYNAMIC
-    NRN_DYNAMIC_UNITS_USE_LEGACY
     NRN_RX3D_OPT_LEVEL
     NRN_SANITIZERS
     CMAKE_BUILD_TYPE

diff --git a/cmake/ConfigFileSetting.cmake b/cmake/ConfigFileSetting.cmake
@@ -92,24 +92,6 @@ else()
   set(DISCRETE_EVENT_OBSERVER 0)
 endif()
 
-# No longer a user option. Default modern units. Controlled at launch by the environment variable
-# NRNUNIT_USE_LEGACY, and dynamically after launch by h.nrnunit_use_legacy(0or1). Left here solely
-# to obtain a nrnunits.lib file for modlunit. Nmodl uses the nrnunits.lib.in file.
-set(NRN_ENABLE_LEGACY_FR 0)
-if(NRN_ENABLE_LEGACY_FR)
-  set(LegacyFR 1)
-  set(LegacyY "")
-  set(LegacyN "/")
-  set(LegacyYPy "")
-  set(LegacyNPy "#")
-else()
-  set(LegacyFR 0)
-  set(LegacyY "/")
-  set(LegacyN "")
-  set(LegacyYPy "#")
-  set(LegacyNPy "")
-endif()
-
 if(NRN_ENABLE_MECH_DLL_STYLE)
   set(NRNMECH_DLL_STYLE 1)
 else()
@@ -126,12 +108,6 @@ if(NRN_ENABLE_PYTHON_DYNAMIC)
   list(APPEND NRN_COMPILE_DEFS NRNPYTHON_DYNAMICLOAD)
 endif()
 
-if(NRN_DYNAMIC_UNITS_USE_LEGACY)
-  set(DYNAMIC_UNITS_USE_LEGACY_DEFAULT 1)
-else()
-  unset(DYNAMIC_UNITS_USE_LEGACY_DEFAULT)
-endif()
-
 # =============================================================================
 # Dependencies option
 # =============================================================================
@@ -219,10 +195,8 @@ nrn_configure_file(nrnmpiuse.h src/oc)
 nrn_configure_file(nrnconfigargs.h src/nrnoc)
 nrn_configure_file(nrnneosm.h src/nrncvode)
 nrn_configure_file(sundials_config.h src/sundials)
-nrn_configure_dest_src(nrnunits.lib share/nrn/lib nrnunits.lib share/lib)
 nrn_configure_dest_src(nrn.defaults share/nrn/lib nrn.defaults share/lib)
-# NRN_DYNAMIC_UNITS requires nrnunits.lib.in be in same places as nrnunits.lib
-file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib.in
+file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib
      DESTINATION ${PROJECT_BINARY_DIR}/share/nrn/lib)
 
 if(NRN_MACOS_BUILD)
@@ -241,8 +215,6 @@ if(MINGW)
   set(nrnskip_rebase "#")
   nrn_configure_file(mknrndll.mak src/mswin/lib)
 endif()
-# TODO temporary workaround for mingw
-file(COPY ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib.in DESTINATION ${PROJECT_BINARY_DIR}/lib)
 
 # =============================================================================
 # If Interviews is not provided, configure local files

diff --git a/cmake_nrnconf.h.in b/cmake_nrnconf.h.in
@@ -91,9 +91,6 @@
 /* Define to 1 if you have the <unistd.h> header file. */
 #undef HAVE_UNISTD_H
 
-/* 1 for legacy, undef for NIST (as of 2017), for FARADAY and R */
-#undef LegacyFR
-
 /* define if using mingw */
 #undef MINGW
 

diff --git a/docs/cmake_doc/options.rst b/docs/cmake_doc/options.rst
@@ -597,20 +597,6 @@ NRN_ENABLE_DISCRETE_EVENT_OBSERVER:BOOL=ON
   Enable Observer to be a subclass of DiscreteEvent
   Can save space but a lot of component destruction may not notify other components that are watching it to no longer use that component. Useful only if one builds a model without needing to eliminate pieces of the model.
 
-NRN_DYNAMIC_UNITS_USE_LEGACY:BOOL=OFF
-----------------------------
-  Default is to use modern faraday, R, etc. from 2019 nist constants.
-  When Off or ON, and in the absence of the ``NRNUNIT_USE_LEGACY=0or1``
-  environment variable, the default dynamic value of ``h.nrnunit_use_legacy()``
-  will be 0 or 1 respectively.
-
-  At launch time (or import neuron),
-  use of legacy or modern units can be specified with the
-  ``NRNUNIT_USE_LEGACY=0or1`` environment variable. The use of legacy or
-  modern units can be dynamically specified after launch with the
-  ``h.nrnunit_use_legacy(0or1)`` function (with no args, returns the
-  current use flag).
-
 NRN_ENABLE_MECH_DLL_STYLE:BOOL=ON
 ---------------------------------
   Dynamically load nrnmech shared library

diff --git a/docs/hoc/modelspec/programmatic/mechanisms/nmodl.rst b/docs/hoc/modelspec/programmatic/mechanisms/nmodl.rst
@@ -285,12 +285,7 @@ Description:
     the UNIX units database. This can increase legibility and convenience, and is helpful both as a
     reminder to the user and as a means for automating the process of checking for consistency of
     units.
-    The UNIX units database taken into account is defined in the `nrnunits.lib file <https://github.com/neuronsimulator/nrn/blob/master/share/lib/nrnunits.lib.in>`_.
-    This file includes two versions of the units due to the updates in the values of their base
-    units. Currently there are legacy and modern units that contain the changes after the updates
-    introduced on 2019 to the nist constants. The selection between those two versions can be done
-    using the ``NRN_DYNAMIC_UNITS_USE_LEGACY`` CMake variable or a call to
-    ``h.nrnunit_use_legacy(bool)`` during runtime.
+    The UNIX units database (based on the 2019 updated NIST constants) taken into account is defined in the `nrnunits.lib file <https://github.com/neuronsimulator/nrn/blob/master/share/lib/nrnunits.lib>`_.
 
     New units can be defined in terms of default units and previously defined units by placing
     definitions in the UNITS block. e.g.

diff --git a/docs/python/envvariables.rst b/docs/python/envvariables.rst
@@ -61,26 +61,3 @@ NEURON_MODULE_OPTIONS
     os.environ["NEURON_MODULE_OPTIONS"] = nrn_options
     from neuron import h
     assert(nrn_options in h.nrnversion(7))
-
-
-
-NRNUNIT_USE_LEGACY
-------------------
-  When set to 1, legacy unit values for FARADAY, R, and a few other constants
-  are used. See ``nrn/share/lib/nrnunits.lib.in`` lines which begin with
-  ``@LegacyY@``, ``nrn/src/oc/hoc_init.c`` in the code section
-  ``static struct { /* Modern, Legacy units constants */``, and
-  ``nrn/src/nrnoc/eion.c``.
-
-  When set to 0, (default), values from codata2018 are used.
-  See ``nrn/share/lib/nrnunits.lib.in`` lines that begin with
-  ``@LegacyN@`` and ``nrn/src/oc/nrnunits_modern.h``.
-
-  Switching between legacy and modern units can also be done after launch
-  with the top level HOC function :func:`nrnunit_use_legacy`.
-
-  The purpose of allowing legacy unit values is to easily validate
-  results of old models (double precision identity).
-
-  This environment variable takes precedence over the CMake option
-  ``NRN_DYNAMIC_UNITS_USE_LEGACY``.
diff --git a/docs/python/modelspec/programmatic/mechanisms/nmodl.rst b/docs/python/modelspec/programmatic/mechanisms/nmodl.rst
@@ -283,12 +283,7 @@ Description:
     the UNIX units database. This can increase legibility and convenience, and is helpful both as a
     reminder to the user and as a means for automating the process of checking for consistency of
     units.
-    The UNIX units database taken into account is defined in the `nrnunits.lib file <https://github.com/neuronsimulator/nrn/blob/master/share/lib/nrnunits.lib.in>`_.
-    This file includes two versions of the units due to the updates in the values of their base
-    units. Currently there are legacy and modern units that contain the changes after the updates
-    introduced on 2019 to the nist constants. The selection between those two versions can be done
-    using the ``NRN_DYNAMIC_UNITS_USE_LEGACY`` CMake variable or a call to
-    ``h.nrnunit_use_legacy(bool)`` during runtime.
+    The UNIX units database (based on the 2019 updated NIST constants) taken into account is defined in the `nrnunits.lib file <https://github.com/neuronsimulator/nrn/blob/master/share/lib/nrnunits.lib>`_.
 
     New units can be defined in terms of default units and previously defined units by placing
     definitions in the UNITS block. e.g.

diff --git a/docs/python/programming/math/constants.rst b/docs/python/programming/math/constants.rst
@@ -15,16 +15,13 @@ The following mathematical and physical constants are available through the ``h`
     
     h.PHI       1.61803398874989484820 (golden ratio)
     
-    h.FARADAY   96484.56 (coulombs/mole) (legacy value)
     h.FARADAY   96485.3321233100141 (modern value. derived from mole and electron charge)
     
-    h.R         8.31441 (molar gas constant, joules/mole/deg-K) (legacy value)
     h.R         8.3144626181532395 (modern value. derived from boltzmann constant and mole)
 
     h.Avogadro_constant  6.02214076e23 (codata2018 value, introduced version 8.0)
 
 As of Version 8.0 (circa October, 2020) modern units are the default.
-See :func:`nrnunit_use_legacy`
 
 .. warning::
     Constants are not treated specially by the interpreter and 
@@ -37,10 +34,4 @@ See :func:`nrnunit_use_legacy`
     If assignment takes
     place due to execution of a hoc interpreter statement, the warning occurs
     only once but cannot be avoided.
-
-    The legacy FARADAY is a bit different than the legacy faraday of the units database. 
-    The legacy faraday in a :file:`.mod` mechanism is 96520.
-
-
-
 
diff --git a/docs/python/simctrl/programmatic.rst b/docs/python/simctrl/programmatic.rst
@@ -214,22 +214,6 @@ Functions
 
 ----
 
-.. function:: nrnunit_use_legacy
-
-  Syntax:
-    ``bool = h.nrnunit_use_legacy(bool)``
-
-  Description:
-    | Return current units usage as 0 or 1.
-    | An argument is not required.
-    | Arg, False uses modern codata2018 units for FARADAY, R, etc. (default as of version 8.0)
-    | Arg, True uses legacy units (default prior to October, 2020)
-
-  .. seealso::
-    :ref:`NRNUNIT_USE_LEGACY` :ref:`CONSTANTS`
-
-----
-
 .. data:: secondorder
 
 

diff --git a/share/lib/nrnunits.lib.in → share/lib/nrnunits.lib b/share/lib/nrnunits.lib.in → share/lib/nrnunits.lib
@@ -68,10 +68,8 @@ pi			3.14159265358979323846
 c			2.99792458+8 m/sec fuzz
 g			9.80665 m/sec2
 au			1.49597871+11 m fuzz
-@LegacyY@mole			6.022169+23 fuzz
-@LegacyN@mole			6.02214076+23 fuzz
-@LegacyY@e			1.6021917-19 coul fuzz
-@LegacyN@e			1.602176634-19 coul fuzz
+mole			6.02214076+23 fuzz
+e			1.602176634-19 coul fuzz
 energy			c2
 force			g
 mercury			1.33322+5 kg/m2-sec2
@@ -394,8 +392,7 @@ ev			e-volt
 / faraday			9.652000+04 coul
 / faraday  from  host: physics.nist.gov
 /          	 path: /PhysRefData/fundconst/html/keywords.html
-@LegacyY@faraday		9.6485309+4 coul
-@LegacyN@faraday		e-mole
+faraday		e-mole
 fathom			6 ft
 fermi			1-15 m
 fifth			4|5 qt
@@ -431,8 +428,7 @@ hyl			gm force sec2/m
 hz			/sec
 imaginarycubicfoot	1.4 ft3
 jeroboam		4|5 gal
-@LegacyY@boltzmann		1.38064852-23 joule/K
-@LegacyN@boltzmann		1.380649-23 joule/K
+boltzmann		1.380649-23 joule/K
 k			boltzmann
 karat			1|24
 kcal			kilocal
@@ -501,8 +497,7 @@ quarter			9 in
 quartersection		1|4 mi2
 quintal			100 kg
 quire			25
-@LegacyY@gasconstant		8.3144598 joule/K
-@LegacyN@gasconstant		k-mole
+gasconstant		k-mole
 R			gasconstant
 rad			100 erg/gm
 ream			500
@@ -571,10 +566,8 @@ tex			.001 gram / m
 englishell		45 inch
 scottishell		37.2 inch
 flemishell		27 inch
-@LegacyY@planck			6.626-34 joule-sec
-@LegacyN@planck			6.62607015-34 joule-sec
-@LegacyY@hbar			1.055-34 joule-sec
-@LegacyN@hbar			planck/two-pi
+planck			6.62607015-34 joule-sec
+hbar			planck/two-pi
 electronmass		9.1095-31 kg
 protonmass		1.6726-27 kg
 neutronmass		1.6606-27 kg

diff --git a/share/lib/python/neuron/expect_hocerr.py b/share/lib/python/neuron/expect_hocerr.py
@@ -41,7 +41,7 @@ def expect_hocerr(callable, args, sec=None):
 
     original_stderr = sys.stderr
     sys.stderr = my_stderr = StringIO()
-    err = 0
+    err = False
     pyerrmes = False
     try:
         if sec:
@@ -50,7 +50,7 @@ def expect_hocerr(callable, args, sec=None):
             callable(*args)
             printerr("expect_hocerr: no err for %s%s" % (str(callable), str(args)))
     except Exception as e:
-        err = 1
+        err = True
         errmes = my_stderr.getvalue()
         if errmes:
             errmes = errmes.splitlines()[0]
@@ -70,12 +70,12 @@ def expect_err(stmt):
     """
     here = inspect.currentframe()
     caller = here.f_back
-    err = 0
+    err = False
     checking(stmt)
     try:
         exec(stmt, caller.f_globals, caller.f_locals)
         printerr("expect_err: no err for-- " + stmt)
     except Exception as e:
-        err = 1
+        err = True
         printerr(e)
     assert err
diff --git a/share/lib/python/neuron/rxd/constants.py b/share/lib/python/neuron/rxd/constants.py
@@ -1,23 +1,18 @@
-# Avogadro's number (approximation before 2019 redefinition)
-NA_legacy = 6.02214129e23
 NA_modern = 6.02214076e23
 
 
 def NA():
     try:
         from neuron import h
 
-        # val = NA_legacy if h.nrnunit_use_legacy() else NA_modern
         val = h.Avogadro_constant
-        # Note: h.Avogadro_constant is consistent with the above NA legacy and
-        # modern values.
     except:
         val = NA_modern
     return val
 
 
 def molecules_per_mM_um3():
     # converting from mM um^3 to molecules
-    # = 6.02214129e23 * 1000. / 1.e18 / 1000
+    # = 6.02214076e23 * 1000. / 1.e18 / 1000
     # = avogadro * (L / m^3) * (m^3 / um^3) * (mM / M)
     return NA() / 1e18
diff --git a/share/lib/python/neuron/rxd/rxd.py b/share/lib/python/neuron/rxd/rxd.py
@@ -254,8 +254,6 @@ def byeworld():
 
 last_diam_change_cnt = None
 last_structure_change_cnt = None
-last_nrn_legacy_units = h.nrnunit_use_legacy()
-
 
 _all_reactions = []
 
@@ -570,10 +568,8 @@ def _cxx_compile(formula):
 
 
 def _setup_units(force=False):
-    global last_nrn_legacy_units
     if initializer.is_initialized():
-        if force or last_nrn_legacy_units != h.nrnunit_use_legacy():
-            last_nrn_legacy_units = h.nrnunit_use_legacy()
+        if force:
             clear_rates()
             _setup_memb_currents()
             _compile_reactions()

diff --git a/share/lib/python/neuron/rxdtests/do_test.py b/share/lib/python/neuron/rxdtests/do_test.py
@@ -23,7 +23,6 @@ def do_test(test_to_run, results_location, num_record=10):
 
     import itertools
 
-    h.nrnunit_use_legacy(True)
     data = {"record_count": 0, "data": []}
     do_test.data = data
     record_count = 0