Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ecell/ecell4 issues and pull requests

#98 - Error installation

Issue - State: closed - Opened by onurburakozdemir 9 months ago - 1 comment

#97 - ecell4 1.2.0 does not work with ecell4_base 2.0.5

Issue - State: open - Opened by kozo2 about 4 years ago - 1 comment

#96 - AttributeError: 'ecell4_base.core.NetworkModel' object has no attribute 'is_static'

Issue - State: closed - Opened by kozo2 about 4 years ago - 1 comment

#95 - name must be determined first

Pull Request - State: closed - Opened by kaizu over 4 years ago

#94 - Feature/pysb

Pull Request - State: closed - Opened by kaizu over 4 years ago - 1 comment

#93 - Return a figure without showing it

Issue - State: open - Opened by kaizu over 4 years ago

#92 - cyjs doesn't properly work

Issue - State: open - Opened by kaizu over 4 years ago - 2 comments

#91 - Return figure

Pull Request - State: open - Opened by kaizu almost 5 years ago

#90 - :bookmark: Bump version to 1.2.0b1

Pull Request - State: closed - Opened by kozo2 almost 5 years ago

#89 - Minor changes

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#88 - Plotting time series in 3D

Issue - State: open - Opened by kaizu almost 5 years ago

#87 - Add new dependencies

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#86 - Adapt to the latest pint

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#85 - Fix a critical mistake

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#84 - New interfaces

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#82 - Use "ver or later" notation in install_requires

Pull Request - State: closed - Opened by kozo2 almost 5 years ago

#81 - Add extras_require to setup.py

Pull Request - State: closed - Opened by kozo2 almost 5 years ago

#80 - Move from TravisCI to GitHub Actions

Pull Request - State: closed - Opened by kozo2 almost 5 years ago

#79 - Create Action for PyPI publishing

Pull Request - State: closed - Opened by kozo2 almost 5 years ago

#78 - arXiv DataSource

Issue - State: open - Opened by kaizu almost 5 years ago

#77 - Enable observables in plotting.plot_number_observer

Pull Request - State: closed - Opened by kaizu almost 5 years ago

#76 - #16 Enable to export the PySB Model roughly

Pull Request - State: closed - Opened by kaizu about 5 years ago

#75 - Interface2

Pull Request - State: closed - Opened by kaizu about 5 years ago

#74 - Interface

Pull Request - State: closed - Opened by kaizu about 5 years ago

#73 - Transition from setup.py to pyproject.toml

Issue - State: closed - Opened by kozo2 about 5 years ago - 1 comment

#72 - Replacing GPL-2.0 to GPL-3.0

Issue - State: closed - Opened by kozo2 about 5 years ago - 2 comments

#71 - Testing with sbml-test-suite

Issue - State: open - Opened by kozo2 over 5 years ago

#70 - Enable abs

Pull Request - State: closed - Opened by kaizu over 5 years ago

#69 - enable to show SGFRD world

Pull Request - State: closed - Opened by ToruNiina over 5 years ago

#68 - :green_heart: use conda-forge on travis

Pull Request - State: closed - Opened by ToruNiina over 5 years ago

#67 - :pencil2: fix typo

Pull Request - State: closed - Opened by ToruNiina over 5 years ago

#66 - Integration tests with Papermill

Issue - State: open - Opened by kozo2 over 6 years ago

#65 - 📝 Update README for ecell4_base version 2.0.0

Pull Request - State: closed - Opened by kozo2 over 5 years ago

#64 - Prepare for building conda package

Pull Request - State: closed - Opened by 0ncorhynchus over 5 years ago

#63 - prelude

Issue - State: closed - Opened by kaizu over 5 years ago
Labels: proposal

#62 - Update ReactionRulePolicy

Pull Request - State: closed - Opened by kaizu over 5 years ago

#61 - Creating Conda package

Issue - State: closed - Opened by kozo2 over 5 years ago

#60 - Enable to set ReactionRule's attributes

Issue - State: closed - Opened by kaizu over 5 years ago - 1 comment
Labels: enhancement

#59 - Complete the web site.

Issue - State: closed - Opened by kaizu over 8 years ago - 2 comments

#58 - Add tools for metabolic control analysis #57

Pull Request - State: closed - Opened by kaizu over 5 years ago

#57 - Add tools for metabolic control analysis

Issue - State: closed - Opened by kaizu over 5 years ago - 1 comment
Labels: enhancement

#56 - Add a method to check units in a model

Pull Request - State: closed - Opened by kaizu over 5 years ago

#55 - Fix bugs

Pull Request - State: closed - Opened by kaizu over 5 years ago

#54 - can't load an sbml file

Issue - State: closed - Opened by ortega2247 over 5 years ago - 2 comments
Labels: bug

#53 - can't install ecell4 on Mac

Issue - State: closed - Opened by ortega2247 over 5 years ago - 2 comments
Labels: question

#52 - ax.set_aspect('equal') doesn't work in the latest matplotlib

Issue - State: closed - Opened by kaizu over 5 years ago - 1 comment
Labels: bug

#51 - installation problem

Issue - State: closed - Opened by KSimi7 over 5 years ago - 18 comments
Labels: question

#50 - Fix some bugs

Pull Request - State: closed - Opened by kaizu almost 6 years ago

#49 - Import data and fix some bugs

Pull Request - State: closed - Opened by kaizu almost 6 years ago

#48 - Avoid importing all from a module

Pull Request - State: closed - Opened by kaizu almost 6 years ago
Labels: bug

#47 - Contact map visualization with cytoscape.js

Issue - State: closed - Opened by kozo2 over 10 years ago - 3 comments
Labels: enhancement

#46 - Contact map visualization with cytoscape.js

Issue - State: closed - Opened by kozo2 about 6 years ago - 3 comments
Labels: enhancement

#45 - Garuda datasource support

Issue - State: open - Opened by kozo2 over 9 years ago

#44 - Prepare an example reproducing a model by Rodríguez2006

Issue - State: closed - Opened by kozo2 over 9 years ago - 1 comment
Labels: document

#43 - Jupyter notebook for metabolic profile visualization with Cytoscape

Issue - State: closed - Opened by kozo2 about 9 years ago - 2 comments
Labels: document

#42 - plotly.js support

Issue - State: closed - Opened by kozo2 about 9 years ago - 1 comment
Labels: enhancement

#41 - Provide Session class for encapsulating a single simulation

Issue - State: closed - Opened by kaizu about 9 years ago - 6 comments
Labels: enhancement, proposal

#40 - DataSource module for modeling in cooperation with databases

Issue - State: open - Opened by kaizu about 9 years ago - 2 comments
Labels: enhancement, proposal, working on

#39 - Mathematical functions in rate laws cannot be pre-defined

Issue - State: open - Opened by kaizu about 9 years ago - 1 comment
Labels: bug, invalid

#38 - Rule-based modeling for a Model with RateLaws

Issue - State: open - Opened by kaizu almost 9 years ago
Labels: enhancement

#37 - Refactor multiple plot functions

Issue - State: closed - Opened by kaizu almost 9 years ago - 1 comment
Labels: refactoring

#36 - Save species_attributes into a SBML file

Issue - State: open - Opened by kaizu almost 9 years ago
Labels: enhancement

#35 - Support ipywidgets

Issue - State: open - Opened by kaizu about 8 years ago

#34 - pytest for ecell4.datasource

Issue - State: open - Opened by kozo2 almost 8 years ago - 1 comment
Labels: deployment, proposal

#33 - Parameter optimization tools

Issue - State: open - Opened by kaizu almost 8 years ago - 1 comment
Labels: enhancement, proposal

#32 - Plot mean squre displacements with TrajectoryObserver

Issue - State: open - Opened by kaizu almost 8 years ago
Labels: enhancement

#31 - Simpler rule-based modeling

Issue - State: open - Opened by kaizu over 7 years ago - 1 comment
Labels: enhancement, proposal

#30 - Refactor Python samples

Issue - State: open - Opened by kaizu over 7 years ago - 3 comments
Labels: deployment, refactoring

#29 - Abbreviations

Issue - State: open - Opened by kaizu about 7 years ago - 1 comment
Labels: enhancement, proposal

#28 - Use ConfigParser to set parameters for ensemble

Issue - State: closed - Opened by kaizu about 7 years ago - 1 comment
Labels: enhancement, refactoring

#27 - Enable to use virtualenv or pyenv in ensemble

Issue - State: open - Opened by kaizu about 7 years ago - 1 comment
Labels: bug

#26 - Association with COBRApy

Issue - State: open - Opened by kaizu about 7 years ago
Labels: enhancement, proposal

#25 - ExcludeReactants

Issue - State: open - Opened by kaizu about 7 years ago - 1 comment
Labels: enhancement, proposal

#24 - Adding Species attribute LaTeX table generate function to latex.py

Issue - State: open - Opened by kozo2 almost 7 years ago - 1 comment
Labels: enhancement

#23 - An unit of the kinetic rate constant on surface

Issue - State: closed - Opened by kaizu over 6 years ago - 3 comments
Labels: invalid

#22 - Prepare an example using the ensemble feature

Issue - State: closed - Opened by kaizu over 6 years ago - 1 comment
Labels: document

#21 - Adding meda-data column to Species latex table

Issue - State: open - Opened by kozo2 over 6 years ago
Labels: enhancement

#20 - Pipe to scopyon

Issue - State: closed - Opened by kaizu over 6 years ago - 1 comment
Labels: enhancement, proposal

#19 - Enable to split species attribute definition

Issue - State: closed - Opened by kaizu over 6 years ago - 5 comments
Labels: enhancement, proposal, spec change

#18 - Refactor ensemble_simulations and run_* functions

Issue - State: closed - Opened by kaizu over 6 years ago - 1 comment
Labels: refactoring, spec change

#17 - Enable reducer in ensemble functions

Issue - State: open - Opened by kaizu over 6 years ago

#16 - Support PySB

Issue - State: open - Opened by kaizu over 6 years ago - 5 comments
Labels: enhancement

#15 - Enable to save an image in plot_world

Issue - State: open - Opened by kaizu over 6 years ago

#12 - azure_batch.py fails with pickle FileNotFoundError

Issue - State: closed - Opened by kozo2 about 6 years ago - 2 comments

#11 - Result object for run_simulation

Issue - State: closed - Opened by kaizu about 6 years ago - 1 comment
Labels: enhancement, proposal

#10 - Fix module names more

Pull Request - State: closed - Opened by kaizu about 6 years ago
Labels: bug

#9 - Fix the module name

Pull Request - State: closed - Opened by kaizu about 6 years ago

#8 - Prepare CIs

Issue - State: open - Opened by kaizu about 6 years ago
Labels: deployment

#7 - Version information is duplicated

Issue - State: closed - Opened by kaizu about 6 years ago

#6 - Update the warning message in unit

Issue - State: closed - Opened by kaizu about 6 years ago - 1 comment

#5 - Update README.md

Issue - State: closed - Opened by kaizu about 6 years ago
Labels: deployment, document

#4 - Rename modules

Pull Request - State: closed - Opened by kaizu about 6 years ago

#3 - Use ecell4_base

Issue - State: closed - Opened by kaizu about 6 years ago
Labels: bug

#2 - SpatiocyteWorld.actual_volume changed its meaning

Issue - State: open - Opened by kaizu about 6 years ago
Labels: bug

#1 - Add integration tests for spatiocyte

Issue - State: open - Opened by 0ncorhynchus about 6 years ago