Kazunari Kaizu
Kazunari Kaizu
`Species`'s `count`, `num_units`, and `deserialize` are deprecated. `Species::count` could be replaced with `count_species_matches`. To count the number of unit species, check the size of a list given by `Species::units`. Function...
Close this. If not fixed, please reopen.
It is hard to support an infinite rate in `ode`. `egfrd` seems supporting it already, but not correctly working with multiple reactions with infinite rates. ```python with reaction_rules(): A +...
- `World` -> `ParticleContainerBase` -> `ParticleContainer` -> `ecell4::Space`. - `Transaction` -> `ParticleContainer`, and `TransactionImpl` -> `Transaction`. - `MultiParticleContainer` -> `ParticleContainer`. - `ParticleContainerBase` stores `MatrixSpace` as its member variable. - `Multi`...
 The benchmark shows `ParticleSpace` properly replaces `MatrixSpace`. See also https://github.com/ecell/ecell4/blob/4-1-stable/misc/benchmark.png
- `ode` Ordinary Differential Equations. "Explicit Euler", "Cash-Karp", or "Controlled Rosenbrock 4". See Boost.Numeric.Odeint https://www.boost.org/doc/libs/release/libs/numeric/odeint/ - `gillespie` The Gillespie algorithm. The direct method. https://doi.org/10.1021/j100540a008 - `meso` The spatial Gillespie algorithm....
Moved to https://github.com/ecell/ecell4_docs/issues/23
This issue requests to update docstring. Reopen.
The project version is given here: https://github.com/ecell/ecell4-base/blob/master/CMakeLists.txt#L4 This also works as the version of Python pacage `ecell4_base`. Thus, it must be consistent with the style.
The version scheme in PEP 440 is `[N!]N(.N)*[{a|b|rc}N][.postN][.devN]`. The current implementation only accepts `N.N.N`. Here is a proposal: `N.N.[dev]N` - No epoch - At least two release numbers are required....