Configuration#
Using the command line you can see the available options using the --help flag. For example
!gotranx --help
Usage: gotranx [OPTIONS] COMMAND [ARGS]...
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --version Show version │
│ --license Show license │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy │
│ it or customize the installation. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────╮
│ convert │
│ cellml2ode │
│ ode2cellml │
│ ode2py │
│ ode2c │
│ ode2julia │
│ ode2cytozoo │
│ ode2mtk │
│ list-schemes │
│ inspect │
│ ode2md │
│ ode2ufl │
╰──────────────────────────────────────────────────────────────────────────────╯
or more specifically
!gotranx ode2py --help
Usage: gotranx ode2py [OPTIONS] [fname]
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ fname <file> │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --outname -o <str> Output name │
│ --remove-unused Remove unused │
│ variables │
│ --remove-singul… --no-remove-sin… Replace a small │
│ neighborhood of │
│ every removable │
│ singularity (e.g. │
│ x/(exp(x) - 1) at │
│ x = 0) with a │
│ truncated Taylor │
│ series │
│ [default: │
│ remove-singulari… │
│ --version Show version │
│ --license Show license │
│ --config -c <path> Read │
│ configuration │
│ options from a │
│ configuration │
│ file │
│ --verbose -v Verbose output │
│ --scheme <explicit_euler Numerical scheme │
│ |generalized_ru for solving the │
│ sh_larsen|forwa ODE │
│ rd_explicit_eul │
│ er|forward_gene │
│ ralized_rush_la │
│ rsen|hybrid_rus │
│ h_larsen> │
│ --stiff-states -s <str> Stiff states for │
│ the hybrid rush │
│ larsen scheme │
│ --delta <float> Delta value for │
│ the rush larsen │
│ schemes │
│ [default: 1e-08] │
│ --cse --no-cse Factor out │
│ subexpressions │
│ shared by the │
│ linearized │
│ expressions in │
│ the rush larsen │
│ schemes. --no-cse │
│ inlines them │
│ instead, emitting │
│ no temporaries │
│ [default: cse] │
│ --format -f <black|ruff|non Formatter for the │
│ e> output code │
│ [default: black] │
│ --backend -b <numpy|jax> Backend for the │
│ generated code │
│ [default: numpy] │
│ --shape -S <dynamic|single Shape of the │
│ |multiple> output arrays │
│ [default: │
│ dynamic] │
│ --help Show this message │
│ and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
Specify configurations in pyproject.toml#
It is also possible to specify the options in your pyproject.toml, e.g
# pyproject.toml
[tool.gotranx]
verbose = true
delta = 1e-6
scheme = [
"explicit_euler",
"generalized_rush_larsen",
"hybrid_rush_larsen",
]
stiff_states = [
"m",
"h",
"j",
]
cse = true
remove_singularities = true
[tool.gotranx.python]
format = "ruff"
[tool.gotranx.c]
format = "clang-format"
This will override any arguments passed from the command line. If you want to specify another configuration file, you can also pass the --config (or -c) flag where you specify a configuration file, e.g
gotranx ode2py file.ode -c folder/pyproject.toml
Options#
General options (under tool.gotranx)#
verbose(boolean, default:false): If True display more loggingscheme(list[str], default: []): Which schemes to include, see
!gotranx list-schemes
Scheme
┏━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Name ┃ Key ┃ Extra args ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ Explicit Euler │ explicit_euler │ [] │
│ Generalized Rush Larsen │ generalized_rush_larsen │ ['delta', 'cse'] │
│ Hybrid Rush Larsen │ hybrid_rush_larsen │ ['delta', │
│ │ │ 'stiff_states', 'cse'] │
└─────────────────────────┴─────────────────────────┴──────────────────────────┘
delta(float, default: 1e-8): Tolerance for zero division check in Rush-Larsen schemesstiff_states: (list[str], default: []): List of states where to apply the Rush-Larsen scheme for Hybrid Rush Larsencse(bool, default:true): Factor out subexpressions shared by the linearized expressions in the Rush-Larsen schemes, using one common-subexpression elimination pass across all states at once.falseinlines them instead, which emits no temporaries at all but costs far more operations — worth it only on the vectorized numpy backend, where every temporary is a live arrayremove_singularities(bool, default:true): Replace a small neighborhood of every removable singularity – a gate rate like(V + 10)/(exp((V + 10)/10) - 1)atV = -10, or a GHK flux atv = 0– with a truncated Taylor series. Without it the generated code divides by zero at exactly that point (numpy warns and returnsnan; numba crashes), and the Rush-Larsen linearization is wrong by an O(1) amount, possibly with the wrong sign, in a neighborhood of it.falseemits the expressions exactly as written. Must be a boolean:"false"is rejected rather than read as a truthy string
Python specific options (under tool.gotranx.python)#
format(str, default:black). Formatter to use for the python code
import gotranx
print(gotranx.codegen.PythonFormat._member_names_)
['black', 'ruff', 'none']
backend(str, default:numpy). Backend to use for the python code
import gotranx
print(gotranx.cli.gotran2py.Backend._member_names_)
['numpy', 'jax']
C specific options (under tool.gotranx.c)#
format(str, default:clang-format). Formatter to use for the C code
import gotranx
print(gotranx.codegen.CFormat._member_names_)
['clang_format', 'none']
to(str, default.h). Whether to save the C code to a.cor.hfile
CytoZoo specific options (under tool.gotranx.cytozoo)#
model_name(str, default: the ODE’s name in PascalCase). Name of the generated Julia struct. Must be a valid Julia identifier – an ODE named e.g.1962_noblepascal-cases to1962Noble, which is rejected rather than emitted as astructthat Julia cannot parsev_name(str, default:v). Name of the state holding the transmembrane potential