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prelude #63

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kaizu opened this issue Jul 4, 2019 · 0 comments
Closed

prelude #63

kaizu opened this issue Jul 4, 2019 · 0 comments
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@kaizu
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kaizu commented Jul 4, 2019

See https://doc.rust-lang.org/std/prelude/index.html

from ecell4.prelude import *
#behaves as
from ecell4 import *
from ecell4_base.core import *
from ecell4_base import *
@kaizu kaizu added the proposal label Jul 4, 2019
kaizu added a commit to kaizu/ecell4 that referenced this issue Jan 21, 2020
@kaizu
Add prelude ecell#63
e79c79d
kaizu added a commit that referenced this issue Feb 3, 2020
@kaizu
Interface (#74)
67ec462 
* Add prelude #63

* Make a step plot

* Add a new interface, Session

* Check dimensionality

* #19 Support a new keyword, proceed

* #19 Enable to extend reserved keywords

* Implement ensemble

* session.Result is picklable

* Use run_ensemble

* Move ecell4.util.viz -> ecell4.plotting

* ecell4.util.viz will be deprecated

* get_range_of_world and get_range_of_trajectories are moved into _core

* Copy deep

* Add plotting._plotly

* Add a datasource for STRING

* Add idmapping using UniProt
@kaizu kaizu mentioned this issue Apr 29, 2020
Merged
kozo2 pushed a commit that referenced this issue May 2, 2020
@kaizu
New interfaces (#84)
bf39870 
* Interface (#74)

* Add prelude #63

* Make a step plot

* Add a new interface, Session

* Check dimensionality

* #19 Support a new keyword, proceed

* #19 Enable to extend reserved keywords

* Implement ensemble

* session.Result is picklable

* Use run_ensemble

* Move ecell4.util.viz -> ecell4.plotting

* ecell4.util.viz will be deprecated

* get_range_of_world and get_range_of_trajectories are moved into _core

* Copy deep

* Add plotting._plotly

* Add a datasource for STRING

* Add idmapping using UniProt

* Interface2 (#75)

* Set method

* Add more options

* Fix silly mistakes

* #11 Enable rich display

* Session.run accepts numpy.ndarray as t

* Arithmetic representations in y

* Enable to set own observable in _plotly

* Split elegans-based plot functions into _elegans

* Format before assignment

* Rename plotting.default -> BACKEND

* Enable rule-based descriptions in observables

* Enable observables in plotting.plot_number_observer (#77)

* Session.run accepts numpy.ndarray as t

* Arithmetic representations in y

* Enable to set own observable in _plotly

* Split elegans-based plot functions into _elegans

* Format before assignment

* Rename plotting.default -> BACKEND

* Enable rule-based descriptions in observables

* Load submodules

* Skip some submodules

* Remove a duplicated file

* Remove all

* Update version

* Import all from submodules

* Set __all__

* Rather use the common name

* Update the relative module path

* Move display_anim into _core

* Enable ndiv

* Fix for pi

* Enable to change figsize in _matplotlib

* Add DOI

* Add citation

* Update the citation outputs

* Import citation in prelude

* Put a space after a comma

* load_world is already imported

* Cast to an integer

* Enable to fetch an abstract

* Remove an unnecessary module

* Simplify run_simulation and ensemble_simulations, and deprecate old implementations

* The config yaml is loaded if existing

* Add plot_trajectory in _plotly

* Change the default renderer on Google Colab

* Try STL visualization in Plotly

* Set opacity

* Use default colorscale

* Update

* Enable to show stl

* Enable to check dimensionality of units in a model
@kaizu kaizu closed this as completed May 10, 2020
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