vivarium-collective/vivarium-core issues and pull requests

#240 - fix Quantity import

Pull Request - State: closed - Opened by eagmon 7 months ago

#239 - python 3.12

Pull Request - State: closed - Opened by eagmon 7 months ago

#238 - correct emit_time for the global_time_precision

Pull Request - State: closed - Opened by eagmon 9 months ago

#237 - Add tests for MongoDB and fix bugs

Pull Request - State: closed - Opened by thalassemia 10 months ago - 1 comment

#236 - Add data key to breakdown documents if missing

Pull Request - State: closed - Opened by thalassemia 10 months ago - 3 comments

#235 - Publish v1.6.1

Issue - State: closed - Opened by thalassemia 12 months ago - 1 comment

#234 - Recursively compare schemas during validation

Pull Request - State: closed - Opened by thalassemia about 1 year ago

#233 - Emitter bug fixes

Pull Request - State: closed - Opened by thalassemia about 1 year ago

#232 - v1.6.0

Pull Request - State: closed - Opened by thalassemia about 1 year ago - 1 comment

#231 - Update networkx error msg for already deleted Step

Pull Request - State: closed - Opened by thalassemia about 1 year ago

#230 - expanded _move target to support tuples going through port to sub-store

Pull Request - State: closed - Opened by eagmon about 1 year ago

#229 - Move update allows state updates

Pull Request - State: closed - Opened by eagmon over 1 year ago

#228 - Schema validation fails with Numpy arrays

Issue - State: closed - Opened by thalassemia over 1 year ago

#227 - Make Process.default_state recursive

Pull Request - State: closed - Opened by thalassemia over 1 year ago - 1 comment

#226 - support python 3.11

Pull Request - State: closed - Opened by eagmon over 1 year ago - 10 comments

#225 - import registries from registry module to fix bug

Pull Request - State: closed - Opened by eagmon over 1 year ago

#224 - Hierarchy division test

Pull Request - State: closed - Opened by eagmon almost 2 years ago

#223 - update pint imports for 0.20.1

Pull Request - State: closed - Opened by eagmon about 2 years ago

#222 - Breakdown fixes

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#221 - Allow breakdown document to lack data key

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#220 - Recalculate hashes for comparison of Units

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#219 - Parallel queries

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#218 - Create new MongoClient per OS process

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#217 - Create Mongo index for simulation time

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#216 - Add orjson to install requirements

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#215 - Serialization fixes

Pull Request - State: closed - Opened by thalassemia about 2 years ago - 2 comments

#214 - Optimize dictionary key removal

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#213 - Clean up documentation

Pull Request - State: closed - Opened by thalassemia about 2 years ago

#212 - Make TimelineProcess a Step

Pull Request - State: closed - Opened by thalassemia about 2 years ago - 1 comment

#211 - Fix memory leak and parallel process division

Pull Request - State: closed - Opened by thalassemia about 2 years ago - 1 comment

#210 - External Controls for Dealing with Conflicting Updaters

Issue - State: open - Opened by WilliamIX about 2 years ago

#209 - Handling Multi-Updates

Issue - State: open - Opened by thalassemia over 2 years ago

#208 - Update CHANGELOG.md

Pull Request - State: closed - Opened by thalassemia over 2 years ago

#207 - Handle lists of Quantities in `Store.apply_update`

Pull Request - State: closed - Opened by U8NWXD over 2 years ago - 1 comment

#206 - Support multiple emits for the same timestep

Pull Request - State: closed - Opened by U8NWXD over 2 years ago - 1 comment

#205 - Prevent multi-updates in initial_state

Pull Request - State: closed - Opened by thalassemia over 2 years ago

#204 - Optimize Serialization Using BSON C Extensions

Pull Request - State: closed - Opened by thalassemia over 2 years ago - 4 comments

#203 - More comprehensive Store.sources

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#202 - Allow passing additional filters to data_from_database

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#201 - Add initial_state to composition.py Engine keys

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#200 - Deterministic step execution order within layers

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#199 - Removing dtypes from serialize.py that are not available on several platforms

Pull Request - State: closed - Opened by cyrus-bio over 2 years ago - 2 comments

#198 - Process Commands

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#197 - Proposal: Improved Handling of Parallel Processes

Issue - State: open - Opened by U8NWXD over 2 years ago - 3 comments

#196 - serialize.py: np.float128 and np.complex256 are not implemented on some platforms

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

#195 - Replace GoReleaser for Installing Vale

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#194 - Proposal: Multiple Production Branches

Issue - State: open - Opened by U8NWXD over 2 years ago

#193 - Engine(Process)

Pull Request - State: closed - Opened by prismofeverything over 2 years ago - 6 comments

#192 - remove composition.py

Pull Request - State: closed - Opened by eagmon over 2 years ago - 4 comments

#191 - don't use timestep for quiet paths

Pull Request - State: closed - Opened by prismofeverything over 2 years ago

#190 - make global_time_precision an Engine parameter

Pull Request - State: closed - Opened by eagmon over 2 years ago

#189 - track composite updates in engine

Pull Request - State: closed - Opened by eagmon over 2 years ago

#188 - RAMEmitter only returns query if data exists

Pull Request - State: closed - Opened by eagmon over 2 years ago

#187 - changes to get notebook running all the way through

Pull Request - State: closed - Opened by eagmon over 2 years ago

#186 - Apply function to data from emitter

Pull Request - State: closed - Opened by thalassemia over 2 years ago

#185 - timestep instead of time_step

Pull Request - State: closed - Opened by eagmon over 2 years ago

#184 - Prototype of logging updates

Pull Request - State: closed - Opened by U8NWXD over 2 years ago - 1 comment

#183 - floating-point timestep precision

Pull Request - State: closed - Opened by eagmon over 2 years ago

#182 - add pytest to setup

Pull Request - State: closed - Opened by eagmon over 2 years ago

#181 - vivarium-core requires pytest

Issue - State: closed - Opened by eagmon over 2 years ago - 1 comment

#180 - Handle nan in units serializer

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#179 - Register the Injector process

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#178 - remove compose_experiment from composition.py

Pull Request - State: closed - Opened by eagmon over 2 years ago

#177 - Process keywords

Pull Request - State: closed - Opened by eagmon over 2 years ago

#176 - Fix units serializer to correctly handle lists and tuples

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#175 - override schema directly in Engine

Pull Request - State: closed - Opened by eagmon over 2 years ago - 3 comments

#174 - make PyPI name more prominent in readme

Pull Request - State: closed - Opened by eagmon over 2 years ago

#173 - Pull Schema, Topology, and Hierarchy Utilities into Separate Library

Issue - State: open - Opened by U8NWXD over 2 years ago

#172 - project assembly_id when querying db

Pull Request - State: closed - Opened by eagmon over 2 years ago

#171 - Improve Handling of Process Parameters and Defaults

Issue - State: open - Opened by U8NWXD over 2 years ago - 2 comments

#170 - Set emits on/off in Store

Pull Request - State: closed - Opened by eagmon over 2 years ago

#169 - `get_history_data_db` remove time key requirement

Pull Request - State: closed - Opened by eagmon over 2 years ago

#168 - More flexible topology rewiring for glob schemas

Issue - State: open - Opened by U8NWXD over 2 years ago - 5 comments
Labels: enhancement

#167 - Make Serializers Robust and Structured

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#166 - Stop adding units to emitted data keys

Issue - State: open - Opened by U8NWXD over 2 years ago
Labels: enhancement

#165 - Store initial_state

Pull Request - State: closed - Opened by eagmon over 2 years ago

#164 - Add _no_original_parameters config to Process

Pull Request - State: closed - Opened by U8NWXD over 2 years ago

#163 - Fix divider and flow bugs

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago

#162 - add vivarium reference to docs

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#161 - initial_state added to Composite

Pull Request - State: closed - Opened by eagmon almost 3 years ago - 2 comments

#160 - Support serialization with original parameters from subclasses

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago - 1 comment

#159 - Process Serialization with Inheritance

Issue - State: closed - Opened by U8NWXD almost 3 years ago - 3 comments

#158 - Composite API

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#157 - Composite.generate_store flows and steps

Pull Request - State: closed - Opened by eagmon almost 3 years ago - 2 comments

#156 - minor fixes

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#155 - Add error messages for flows with extra steps and unknown dividers

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago

#154 - Interrupts for Engine

Issue - State: open - Opened by eagmon almost 3 years ago - 2 comments

#153 - resize tutorial figures

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#152 - Post-v1.0.0 Documentation Updates

Issue - State: open - Opened by U8NWXD almost 3 years ago

#151 - make Engine.run_steps public again

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#150 - Update docs

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago

#149 - Add Mattheus, Sean, Michael, and William to AUTHORS.md

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago - 1 comment

#148 - Bump version to 1.0.0

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago

#147 - Pass Parameters Positionally in setstate

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago

#146 - Update Documentation

Issue - State: closed - Opened by U8NWXD almost 3 years ago - 1 comment

#145 - Name workflows and create codeowners for permissions

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago - 3 comments

#144 - Readme

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#143 - make methods private

Pull Request - State: closed - Opened by eagmon almost 3 years ago

#142 - Permissions and Responsibilities Structure

Issue - State: closed - Opened by U8NWXD almost 3 years ago - 1 comment

#141 - Add community health files

Pull Request - State: closed - Opened by U8NWXD almost 3 years ago - 1 comment

GitHub / vivarium-collective/vivarium-core issues and pull requests