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 ───────────────────────────────────────────────────────────────────╮
│ cellml2ode │
│ convert │
│ inspect │
│ list-schemes │
│ ode2c │
│ ode2py │
╰──────────────────────────────────────────────────────────────────────────────╯
or more specifically
!gotranx ode2py --help
Usage: gotranx ode2py [OPTIONS] [FNAME]
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ fname [FNAME] [default: None] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --outname -o TEXT Output name │
│ [default: None] │
│ --remove-unused Remove unused variables │
│ --version Show version │
│ --license Show license │
│ --config -c PATH Read configuration │
│ options from a │
│ configuration file │
│ [default: None] │
│ --verbose -v Verbose output │
│ --scheme [explicit_euler|generali Numerical scheme for │
│ zed_rush_larsen|forward_ solving the ODE │
│ explicit_euler|forward_g │
│ eneralized_rush_larsen|h │
│ ybrid_rush_larsen] │
│ --stiff-states -s TEXT Stiff states for the │
│ hybrid rush larsen scheme │
│ --delta FLOAT Delta value for the rush │
│ larsen schemes │
│ [default: 1e-08] │
│ --format -f [black|ruff|none] Formatter for the output │
│ code │
│ [default: black] │
│ --backend -b [numpy|jax] Backend for the generated │
│ code │
│ [default: numpy] │
│ --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",
]
[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'] │
│ Hybrid Rush Larsen │ hybrid_rush_larsen │ ['delta', │
│ │ │ 'stiff_states'] │
└─────────────────────────┴─────────────────────────┴──────────────────────────┘
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 Larsen
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