ecell/ecell4_base issues and pull requests

#496 - update the referencing revision of pybind11

Pull Request - State: open - Opened by YukiSakamoto 11 months ago

#495 - Known vulnerabilities in the C library which ecell4-base depends on.Can you help upgrade to patch versions?

Issue - State: open - Opened by andy201709 almost 3 years ago

#494 - Add cp39-cp39

Pull Request - State: closed - Opened by kozo2 almost 4 years ago

#493 - :green_heart: untap openssl and python2 from brew

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

#492 - :green_heart: include <array> explicitly

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

#491 - :heavy_minus_sign: drop python 3.5 support

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

#490 - :arrow_up: update pybind11 from 2.3.0 to 2.6.0

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

#489 - Attributes of ReactionRules are not inherited in `expand`

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

#488 - Fix and speedup distance_point_to_Triangle under PBC

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

#487 - :recycle: ParticleSpaceRTreeImpl

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

#486 - :recycle: remove template from VolumeClearer

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

#485 - Use PeriodicRTree to store triangles in Polygon

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

#484 - Bump version to 2.1.0b2

Pull Request - State: closed - Opened by kozo2 over 4 years ago

#483 - Bump version to 2.1.0.b2

Pull Request - State: closed - Opened by kozo2 over 4 years ago

#482 - ODESimulator only accepts NetworkModel

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

#481 - :recycle: refactoring eGFRD

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment

#480 - replace boost::array by std::array

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

#479 - Enable to pickle observers #250

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

#478 - :green_heart: fix appveyor build

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

#477 - :rotating_light: Suppress warnings

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

#476 - ecell4_base version 2.1.0b1

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

#475 - Update count_species_matches

Pull Request - State: closed - Opened by kaizu almost 5 years ago - 1 comment

#474 - :bento: update position of sphere.stl

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

#473 - Add get_faces_within_radius to Polygon

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

#472 - :fire: remove needless undef

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

#471 - Boost to c++11

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: refactoring

#470 - :heavy_minus_sign: Use std::shared_ptr instead of boost::shared_ptr

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: refactoring

#469 - Fix CI

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

#468 - :green_heart: fix github action; cmake is already installed

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment

#467 - :green_heart: use boost::mpl::list for boost < 1.68

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment

#466 - :recycle: remove macro, it's always C++11

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: refactoring

#465 - :green_heart: update OS X on Azure

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: azure

#464 - :alembic: add Boundary condition classes

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: proposal

#463 - :recycle: Wrap egfrd in namespace ecell4::egfrd

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 3 comments
Labels: refactoring

#462 - :alembic: generalize periodic R-Tree

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: enhancement, proposal

#461 - :recycle: add throw_exception

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: proposal

#460 - :fire: remove unused code in egfrd module

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment
Labels: refactoring

#459 - :fire: remove core linear algebra

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: refactoring

#458 - :fire: remove global constants

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago
Labels: proposal, refactoring

#457 - :recycle: Remove blit_swap

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment
Labels: refactoring

#456 - :recycle: always use std::unordered_map

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment
Labels: refactoring

#455 - :recycle: replace boost::scoped_ptr by std::unique_ptr

Pull Request - State: closed - Opened by ToruNiina almost 5 years ago - 1 comment
Labels: proposal, refactoring

#454 - Add Python wrapper for UnitSpecies APIs

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

#453 - OffLattice support

Pull Request - State: closed - Opened by 0ncorhynchus about 5 years ago - 2 comments

#452 - :arrow_up: Update ubuntu and hdf5 version

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

#451 - Locking hdf5 version

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

#450 - #250 Make observers picklable

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

#449 - :children_crossing: Add a custom option for the parallel build

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

#448 - Fix the process on CircleCI

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

#447 - Add tests for proceed

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

#446 - Proceed

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

#445 - Fix get_neighbor* and Reactions related to OffLatticeSpace

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

#444 - A new reserved word in species_attributes

Issue - State: closed - Opened by kaizu about 5 years ago - 1 comment
Labels: proposal

#443 - :package: Add manylinux wheel for Python3.8

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

#442 - :zap: Don't repeat cmake, gsl, hdf5 building in CircleCI

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

#441 - :bookmark: Bump version

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

#440 - Add a new CI system for the automatic release

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

#439 - :green_heart: Enforce to run 'brew upgrade' on Github Actions

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

#438 - Automation of archive and release with greens_functions

Issue - State: closed - Opened by 0ncorhynchus about 5 years ago

#437 - :green_heart: Enable to use system-installed pybind11

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

#436 - Speeding up manylinux wheel build

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

#435 - Remove particle voxel

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

#434 - Refactor spatiocyte

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

#433 - GitHub actions

Pull Request - State: closed - Opened by 0ncorhynchus about 5 years ago - 1 comment

#432 - bug fixes and stability improvements in sGFRD

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

#431 - Add Python API for OffLattice

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

#430 - Tasks for OffLattice

Issue - State: open - Opened by 0ncorhynchus about 5 years ago

#429 - Clean up the configuration file of conda-build

Pull Request - State: closed - Opened by 0ncorhynchus over 5 years ago - 1 comment
Labels: deployment

#428 - :bug: never assume Species has attributes

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

#427 - :green_heart: Stop adding conda-forge channel

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

#426 - :green_heart: Fix for conda37 in appveyor

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

#425 - :bug: check bound model before adding molecules

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

#424 - :checkered_flag: set WITH_HDF5 flag on Windows

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

#423 - Release note for version2.*

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

#422 - :sparkles: enable to get a triangle on which a particle locates

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

#421 - :bug: fix name lookup in egfrd/StlFileReader

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

#420 - Project metrics measurement

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

#419 - Having contribution / coding guidelines

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

#418 - Having a community engagement

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

#417 - Adding a code of conduct

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

#416 - Update base code to the current master

Pull Request - State: closed - Opened by kozo2 over 5 years ago - 1 comment

#415 - 🔖 Bump version to 2.0.1

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

#414 - Moving E-Cell4 license from GPLv2 to GPLv3

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

#413 - :truck: Move github pages to ecell/ecell4

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

#412 - :pencil: Add notes about Python2 and pip install

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

#411 - :pencil: Update README for version 2.0.0

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

#410 - :package: Install dependent packages from conda-forge

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

#409 - :construction_worker: use both conda 36 and 37 on appveyor

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

#408 - :bookmark: Bump version to 2.0.0b3

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

#406 - :rotating_light: suppress warnings while compilation

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

#402 - Library not loaded: @rpath/libgsl.23.dylib on OSX Conda Py37

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

#396 - Re-sending pull request to conda-forge

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

#395 - Releasing 2.0.0b3

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

#356 - A reaction between a 3d-diffusing molecle and 3d structure has the wrong dimensionality

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

#343 - Reconsider Structure and Vacant

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

#330 - Add references for algorithms in docstring

Issue - State: open - Opened by kaizu about 6 years ago - 3 comments
Labels: document

#311 - Wrap egfrd in the namespace

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

#310 - Enable Quantity in Model

Pull Request - State: closed - Opened by kaizu over 6 years ago
Labels: spec change

#250 - Observers are NOT picklable

Issue - State: closed - Opened by kaizu almost 7 years ago
Labels: proposal

#143 - init.py is generated in the source directory

Issue - State: closed - Opened by kaizu over 8 years ago - 1 comment
Labels: deployment

GitHub / ecell/ecell4_base issues and pull requests