tvb - Release 2.10.0

Ensure compatibility with numpy 2, python 3.13 and siibra latest

Tasks:

EBR-75 numpy 2.0 compatibility VT-123 tvb-root vs siibra latest TVB-3126 Installation of tvb-framework is missing a library for Python 3.13 environments TVB-3132 Error when importing Connectivity VEP TVB-3134 Create Github Actions for build and release

- Jupyter Notebook
Published by popaula937 6 months ago

tvb - Release 2.9.2

Release tvb-library on Pypi for compatibility with scipy ~1.14 or 1.15

- Jupyter Notebook
Published by liadomide 11 months ago

tvb - Release 2.9.1

Release 2.9.1

Release for tvb-library and tvb-contrib on Pipy

Bug

EBR-63 Problem in remake_figure_WilsonCowan.ipynb

Task

EBR-53 Move rateML module from under tvb-library into tvb-contrib

EBR-54 Update copyright year and Authors on tvb-root repo

EBR-81 scipy compatibility with 1.14

EBR-82 compatibility with siibra 1.0a14

- Jupyter Notebook
Published by 915-Misan-Teodora over 1 year ago

tvb - Release 2.9.0

Maintenance release
* compatibility with py3.11 and py3.12 * adjust to siibra 1.0 * migrate from OKD to Kubernetes * fix Phase Plane dependency towards old contour implementation in matplotlib * improve first time setting validation

- Jupyter Notebook
Published by liadomide over 1 year ago

tvb - Release 2.8.2

Release for tvb-framework on Pipy - Cleanup after tvb-data changed (by removing personal data in release 2.8 on Zenodo). - fix bug in tvb-library https://req.thevirtualbrain.org/browse/TVB-3089

- Jupyter Notebook
Published by liadomide over 2 years ago

tvb - Release 2.8.1

Changes in Models - The AdEx (ZerlautSecondOrder) model was consolidated with other external implementations, has changed number of variables (adding an external input) and has now examples replicating some of the figures from papers - K ION Exchange model was added

Bug - [TVB-2380] - SQLite refuses DB path with Greek letters - [TVB-3062] - EpileptorT default attribute not among choices - [TVB-3063] - KuramotoT model not working inside the Simulator - [TVB-3072] - Investigate and fix testnodecomplexcoherenceadapter - [TVB-3074] - tvb-web refuses to launch when tvb-data is installed from Pypi - [TVB-3077] - Fix dfun eq for some models in MatJax - PhasePlane web page - [TVB-3081] - Deepcopy of a simulator obj handles incorrectly the sim.monitors list

Task - [TVB-2118] - Make getting more logging info easier for ipython user - [TVB-3069] - Adapt tvb-framework to the latest siibra release 0.4* - [TVB-3073] - Release 2.8.1 on OKD - [TVB-3078] - Deal with "tvb" namespace on Pypi - [TVB-3080] - Run siibra notebooks as part of a github action

Improvement - [TVB-3075] - When parsing .tvb.configuration value, strip spaces

- Jupyter Notebook
Published by liadomide over 2 years ago

tvb - Release 2.8

Release for tvb-library. It included enhanced HTML representation for HasTraits objects from tvb. This means in particular usages in JupyterLab. It also included few bug-fixes (TVB-3067 and TVB-3071 )

- Jupyter Notebook
Published by liadomide almost 3 years ago

tvb - Release 2.7.3

Fix package tvb-framework (2.7.3 and 2.7.3.3) not to include bids_monitor package
Change signature Connectivity.from_bytes_stream(cls, bytes_stream, content_type='.zip') by adding the second param
- same for Surface, Sensors and TimeSeries

- Jupyter Notebook
Published by liadomide almost 3 years ago

tvb - Release 2.7.2

Update copyright text Convert Tumor import button into a proper Importer with user-given data. Change default param values in SigmoidalJansenRit

- Jupyter Notebook
Published by liadomide almost 3 years ago

tvb - Release 2.7.1

Enable siibra after 3rd party fix. Project sharing changes. Visual effect on button pressed

- Jupyter Notebook
Published by liadomide about 3 years ago

tvb - Release 2.7

Bug fixes (e.g. Wavelet adapter, allenSDK compatibility, mutable neotraits, neocom.DirLoader)
BCT analyzers - switch to bctpy library
Siibra integration - temporarily disabled from TVB-Distribution web GUI due to a KG query - siibra issue
BIDS monitoring module
add deepcopy implementation on HasTraits
Projects can be marked as read-only (useful for shared projects like DefaultProject on OKD EBRAINS)

- Jupyter Notebook
Published by liadomide about 3 years ago

tvb - Release 2.6

Release on Pypi.

* [TVB-2827] - Support h5py>3
* [TVB-3014] - Generate a BIDS demo dataset
* [TVB-3015] - EEG monitor drops data on H5 export
* [TVB-2900] - TVB-BIDS derivatives compatibility
* [TVB-3009] - Rename scientific_library into tvb_library and framework
* [TVB-3011] - Review and merge PR from GSOC on plotting tools
* [TVB-3006] - Integrate Sonar with tvb code

- Jupyter Notebook
Published by liadomide over 3 years ago

tvb - Release 2.5

Release on Pypi

The Datatypes got few new methods.

Jira tasks on this version:

* [TVB-2986] - Import data Lesion2TVB
* [TVB-2122] - Parallelize test suite run
* [TVB-2219] - Project monitor incorrectly pads gain matrix
* [TVB-2634] - Ordering of cortical and subcortical gain rows not respected
* [TVB-2799] - History shape mismatch surface simulation 
* [TVB-2902] - Region mapping viewer displays empty navigator windows
* [TVB-2962] - neotraits test fails after numpy upgrade
* [TVB-2990] - default cortex
* [TVB-2991] - Connectivity needs to be transposed for allen_creator.py adaptor and related notebook
* [TVB-3007] - User tab from footer not active on user page
* [TVB-2981] - Review range parameters
* [TVB-2982] - Work on D6.4 report
* [TVB-2983] - VRE integration 
* [TVB-2988] - Add comments and review code about Keycloak and OpenShift
* [TVB-2989] - Support context path 
* [TVB-2996] - Reporting Period 2
* [TVB-3008] - Prepare, test and do release 2.5
* [TVB-2977] - Some simulation related params should be displayed as symbols in Web GUI
* [TVB-3006] - Integrate Sonar with tvb code

- Jupyter Notebook
Published by liadomide over 3 years ago

tvb - Release 2.4.1 for TVB_Distribution

Fix Jupyter kernel for Windows/Linux distributions.

Bug

[TVB-2984] - Jupyther kernel not starting from tvb Dockerfiles

- Jupyter Notebook
Published by popaula937 about 4 years ago

tvb - Release 2.4

Released packages:

On Pypi
- tvb-library
- tvb-framework
- tvb-storage
- tvb-rest-client
- tvb-contrib

Release notes:

Bug fixing
Extend encryption support to data export features
Improve mechanism to delete projects with links
Add EnumAttr to tvb-library neotraits
Code reviews related to tvb-storage module
Support Spack packaging for tvb-library, tvb-data, tvb-storage and tvb-framework

Involved Jira tasks in 2.4

Bug

* [TVB-2808] - shape mismatch in SpatialAverage monitors default spatial mask
* [TVB-2924] - Mock error using Python 3.8 environment
* [TVB-2927] - Cannot visualize TimeSeriesSurface with BOLD ROI monitor
* [TVB-2930] - Can't delete project containing links with Postgres
* [TVB-2931] - Review deleting projects with links
* [TVB-2940] - Cannot select the default mask for spatial monitor
* [TVB-2949] - Ensure tests are copied to the final tvb-storage package
* [TVB-2960] - Brain Activity Visualizer doesn't work for surface simulation with Bold ROI monitor
* [TVB-2969] - BOLD ROI monitor is not working
* [TVB-2970] - BOLD ROI monitor is not working for conn with subcortical regions
* [TVB-2972] - Fix Tumor Dataset importer
* [TVB-2973] - Fix tests related to REST that are failling in Jenkins

Task

* [TVB-2755] - Add EnumAttr in neotraits
* [TVB-2849] - Export/Import of DatatypeGroup with related entities
* [TVB-2879] - Review SelectField in forms
* [TVB-2889] - Eliminate numerical runtime warnings from test suite
* [TVB-2941] - Review importing of projects having older versions
* [TVB-2950] - Project planning and discussions VBC
* [TVB-2961] - Delete unnecessary code related to remove methods
* [TVB-2968] - Surface Sim in TVB v2.* no longer has possibility to range Cortex.local_coupling_strength
* [TVB-2971] - Limit number of launched PSE operations
* [TVB-2974] - Testing before release 2.4
* [TVB-2976] - Fix Jenkins builds
* [TVB-2978] - Prepare release 2.4
* [TVB-2979] - Replace infinite values with float max in Matrix Viewer

Improvement

* [TVB-2916] - Remove dependency with typing package for python>3.5
* [TVB-2932] - Refactor storage encryption to support multi-pod deploy
* [TVB-2933] - More functionality from exporters could move to tvb-storage
* [TVB-2934] - Review HPC encryption exposed in the StorageInterface
* [TVB-2945] - Keep configuration of monitors throughout simulator page
* [TVB-2947] - Disable editing of monitored variables at simulation branch
* [TVB-2948] - Hide the Tumor Dataset importer from importers list
* [TVB-2964] - Provide option to generate TS file through the console interface

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 over 4 years ago

tvb - Release 2.3

Released packages:

On Pypi
- tvb-library
- tvb-framework
- tvb-storage
- tvb-rest-client
- tvb-contrib

tvb-framework

optimizations related to: simulation run flow, Operations and Data structure page load
start support for BIDS data: new button on Data structure page to import the Brain Tumor dataset from EBRAINS
improve mechanism to cancel/delete PSE operations
separate code related to storage into a new package called tvb-storage
bug fixing

tvb-storage

first version of the tvb-storage released as a separate package

tvb-rest-client

adjustments to new architecture

tvb-contrib

correct models and adjust their code to neotraits API

Involved Jira tasks in 2.3

Sub-task

* [TVB-2907] - Study BIDS specification
* [TVB-2911] - Implement a BIDS importer for Tumor dataset
* [TVB-2912] - Analyze API to download data from EBRAINS
* [TVB-2942] - Review description for importers/exporters

Bug

* [TVB-2356] - Update Tutorial 0 on docs site
* [TVB-2836] - Fix 'edit simulation' popup window in the simulator page
* [TVB-2846] - SQLAlchemy raises exceptions during framework tests
* [TVB-2867] - Models under tvb_contrib are not working
* [TVB-2935] - Jupyter fails to start from linux distribution
* [TVB-2943] - Cannot delete PSE simulations
* [TVB-2944] - miss dependence : package requests

Task

* [TVB-2528] - Optimize run_simulation in version 2.*
* [TVB-2868] - Update license text
* [TVB-2900] - TVB-BIDS compatibility
* [TVB-2909] - Fix wrongly loaded Simulator fragments when clicking Back
* [TVB-2913] - Separate the storage handling in a different module  
* [TVB-2915] - Project planning and discussions VBC
* [TVB-2936] - Remove portlets module
* [TVB-2937] - Optimize Data Structure page
* [TVB-2938] - Prepare release 2.3
* [TVB-2939] - Testing before release 2.3

Improvement

* [TVB-2883] - Branch button should be active only if simulation is finished
* [TVB-2908] - Ensure all operations of PSE are cancelled
* [TVB-2923] - Optimise operations page

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 over 4 years ago

tvb - Release 2.2.2 for TVB_Distribution

Release notes

Fix migration of H5 files to work in case truncated files are present

Involved Jira tasks in 2.2.2

Bug

* [TVB-2925] - Solve truncated H5 files migration related bugs

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 over 4 years ago

tvb - Release 2.2.1 for TVB_Distribution

Release notes

Fix second startup with SQLite after migrating data from 1.5.8
Fix second startup with PostgreSQL with clean storage

Involved Jira tasks in 2.2.1

Bug

* [TVB-2917] - TVB with Postgres startup fails at the second attempt
* [TVB-2921] - TVB with Sqlite and migration does not start at second attempt

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 almost 5 years ago

tvb - Release 2.2 for TVB_Distribution

Release Notes

Make code compatible with Python 3
Neotraits (splitting the aspects of: datatypes, storage, indexing, web forms)
Add a REST API
Support authentication in web with a Keycloak server
Added encryption mechanism for the TVB storage
Added encryption mechanism for uploaded data
Support an HPC backend to run heavy simulations with secured data
Change the Simulator configuration page towards a wizard structure
The command API has been improved and can be used individually from the web GUI now
Use Jinja instead of Genshi for tvb web GUI
CFF importer was removed
New export button on datatypes to allow exporting a datatype together with its references.
Data migration from version 1.5.8 is supported. For data generated with older versions, users should first install 1.5.8 to update their data, and then install 2.2

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 almost 5 years ago

tvb - Release 2.2

Released packages:

On Pypi
- tvb-library
- tvb-framework
- tvb-rest-client
- tvb-contrib

tvb-library

review API to merge serial and parallel co-simulations

tvb-framework

tvb data stoage encription and decryption when a project is used

tvb-rest-client

Code refactor

tvb-contrib

review API to merge serial and parallel simulations

Involved Jira tasks in 2.2

Bug

* [TVB-2714] - Running all FRW unit-tests on Windows fails worse than on Unix
* [TVB-2858] - Importing TS with links in empty project fails
* [TVB-2859] - Fix surface visualizer with region boundaries
* [TVB-2862] - Clean files sent via REST uploaders after the operation is complete
* [TVB-2864] - Analyze simulator errors
* [TVB-2869] - Review the usage of boolean values as filter parameters
* [TVB-2876] - Fix integrator choice in PhasePlane
* [TVB-2881] - Removing a PSE burst throws exception
* [TVB-2886] - Fix surface visualizer for large surfaces
* [TVB-2887] - Fix TimeSeriesVolumeVisualiser 
* [TVB-2910] - Fix Brain Viewer for TimeSeriesSurface
* [TVB-2914] - Jupyther Notebook not starting from TVB_Distribution

Story

* [TVB-2733] - Review Simulator Page Flow
* [HBP-90] - TVB with HCP backend and Security

Task

* [TVB-2664] - Review and clean the fire operation flow
* [TVB-2704] - Review Jenkins builds on versions 2.*
* [TVB-2849] - Export/Import of DatatypeGroup with related entities
* [TVB-2855] - Migrate Tracts importers to neoforms and fix the Tracts Visualizer
* [TVB-2857] - Project planning and discussions VBC
* [TVB-2861] - Operation overlay does not display inputs for all operations
* [TVB-2865] - Prepare for meetings
* [TVB-2871] - Review usages of load_h5_of_gid method in viewers
* [TVB-2875] - Define a Jenkins job to test migration from 1.5.8
* [TVB-2901] - Testing before end of sprint
* [TVB-2904] - Prepare release 2.2
* [TVB-2906] - Prepare video of TVB on JupyterHub VRE

Improvement

* [TVB-2880] - Export only view model H5 in simulation ZIP

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)

Schirner M, Domide L, Perdikis D, Triebkorn P, Stefanovski L, Pai R, Prodan P, Valean B, Palmer J, Langford C, Blickensdörfer A, van der Vlag M, Diaz-Pier S, Peyser A, Woodman M, Zehl L, Fousek J, Petkoski S, Kusch L, Hashemi M, Marinazzo D, Mangin JF, Flöel A, Akintoye S, Stahl C, Deco G, McIntosh, Hilgetag C, Morgan M, Schuller B, Upton A, McMurtrie C, Dickscheid T, Bjaalie J, Amunts K, Mersmann J, Jirsa V, Ritter P. https://arxiv.org/abs/2102.05888 Brain simulation as a Service: The Virtual Brain on the European Research Platform EBRAINS.

- Jupyter Notebook
Published by popaula937 almost 5 years ago

tvb - Release 2.1

Release for: - tvb-library - tvb-framework - tvb-rest-client - tvb-contrib

Release Notes

Sub-task

* [TVB-2845] - Remove dependency of project from forms

Bug

* [TVB-2710] - Web Page TVB - Project - Data does not populate the tree
* [TVB-2749] - Wrong status on a BurstConfiguration PSE sometimes
* [TVB-2848] - Clean temporary files after import
* [TVB-2853] - Fix import of datatype groups

Task

* [TVB-2538] - Enhance Branch simulation use-case
* [TVB-2705] - Decouple form fields from TVB backend
* [TVB-2729] - Update sqlalchemy version
* [TVB-2738] - Refactor analyzers
* [TVB-2761] - Export/Import of DT with related entities
* [TVB-2786] - Review metadata of Timeseries generated from PSE
* [TVB-2795] - Review the execution of operations in PSE Simulation 
* [TVB-2811] - Display theta models in GUI
* [TVB-2835] - Create tests for forms
* [TVB-2843] - Delete project fails in case of incomplete PSE 
* [TVB-2844] - PSE Discrete viewer throws error on intermediary results
* [TVB-2850] - Test latest code before end of sprint
* [TVB-2851] - REST server should start only if the keycloak setting is filled 
* [TVB-2856] - Prepare release 2.1

Improvement

* [TVB-2792] - PSE Isocline is empty if single Connectivity in project

- Jupyter Notebook
Published by popaula937 about 5 years ago

tvb - Release 2.0.10

Released packages: - tvb-library - tvb-framework - tvb-rest-client - tvb-contrib

Release notes

tvb-library

Added implementations of models from a family of exact mean field models of theta neurons ## tvb-framework
Allow COMMAND_PROFILE to be independent of the GUI and do its own configuration and storage initialization. This would allow the tvb-framework to be usable from a jupyter lab instance.
First version of migrating the data storage from version 4 (1.5.8) to version 5 (2.0.10).
Improve export/import functionalities.
Bug fixes in the viewers.

Sub-task

* [TVB-2797] - Installing tvb-gdist from source faills in jupyterhub
* [TVB-2798] - COMMAND_PROFILE should work independently of GUI
* [TVB-2810] - Investigate errors happening on different environments
* [TVB-2812] - Test migration script also with PostgreSQL
* [TVB-2813] - Correct VM create date to fix the import in PostgreSQL
* [TVB-2814] - Publish updated tvb-data package on Zenodo
* [TVB-2816] - Adjust migration to newly added fields
* [TVB-2818] - PSE datatypes and operations are not migrated in case of Datatype range

Bug

* [TVB-2522] - Nbviewer fails with 503
* [TVB-2642] - When running simulations, sampling period should not be more  than the simulation length
* [TVB-2745] - TVB_Distribution should not remove existing data under TVB_DATA folder
* [TVB-2754] - Topograpic Viewer: ears/nose positions are wrong positioned for the default conn_76
* [TVB-2780] - Possible error in Analyzer BalloonModel
* [TVB-2781] - Don't allow to upload H5 files for which TVB doesn't have the dependent datatypes in DB
* [TVB-2787] - Fix loading a newly created connectivity in Connectivity viewer
* [TVB-2788] - Region stimulus - click on a cube should toggle the corresponding checkbox
* [TVB-2794] - Green question marks offering extra help to the user are missing from several places
* [TVB-2806] - Unable to subclass stimulus in neotraits
* [TVB-2819] - Fix delete project on postgresql

Task

* [TVB-2430] - Migration script from old to new storage version
* [TVB-2747] - Implement Import / Export of PSE
* [TVB-2751] - Review notebooks simulate_for_mouse and interacting_with_allen ipynb after recent tvb changes
* [TVB-2767] - Review flow for calculating and displaying the disk usage
* [TVB-2770] - Generate new images for MB and VJ
* [TVB-2778] - Update default project and tvb_data on Zenodo
* [TVB-2784] - Project planning and discussions VBC
* [TVB-2785] - PSE Discrete Viewer should link circles to corresponding Timeseries
* [TVB-2796] - Prepare tvb-framework for deploy in jupyterhub
* [TVB-2815] - Add a specific notification scheme for INDOC
* [TVB-2817] - Test latest code before release 2.0.10
* [TVB-2821] - Prepare release 2.0.10

Improvement

* [TVB-2553] - Allow integrator parameters configuration in Phase Plane
* [TVB-2791] - Some metadata is lost during export/import of project

- Jupyter Notebook
Published by popaula937 about 5 years ago

tvb - Release Candidate 1 2.0.10

This is small release candidate that enables CUDA GPU parallel parameter sweeps, using a specializing code generator based on a domain specific language. Release for

tvb-library

Release notes

* [TVB-1824] Specific GPU implementations

- Jupyter Notebook
Published by maedoc over 5 years ago

tvb - Release 2.0.9

Release for: - tvb-library, - tvb-framework, - tvb-rest-client and - tvb-contrib

Release Notes

Sub-task

* [TVB-2773] - On Operation replace column parameters with view_model_gid
* [TVB-2774] - Fix and add tests for Export/Import
* [TVB-2777] - Fix operation_dao queries or remove Project -Data Structure -Graph TAB
* [TVB-2779] - ResultFigure.op_gid reference cleanup

Bug

* [TVB-2376] - Improve tvb-framework unit-tests
* [TVB-2693] - Correct the upper-left corner overlay
* [TVB-2735] - BCT algorithms are failing to run on Jenkins with tvb-run docker image
* [TVB-2746] - Reload Simulation from web page Project-Operations
* [TVB-2753] - Connectivity Creator - after cut of nodes only from one hemisphere, the split by left/right is incorrect 
* [TVB-2758] - Preview Surface Stimulus in step 2  does not work
* [TVB-2762] - Complex Numbers and *Index inheriting from DataTypeMatrix are not working on PostgreSQL
* [TVB-2766] - Fix H5 importer in latest versions
* [TVB-2768] - Display of Inputs for any Uploader in Operation overlay fails
* [TVB-2769] - Change of DT metadata in overlay is not working
* [TVB-2771] - Clear SessionStoredSim on project delete (and not only)
* [TVB-2776] - Mistake in parameter labelling for WilsonCowan Model

Task

* [TVB-2511] - Make sure that the Simulation / Phase plane is 100% correct with all its equations and everything
* [TVB-2637] - Link on the top toc DLS documentation and demo
* [TVB-2661] - Fix Export/Import project
* [TVB-2748] - Remove Operation.xml files
* [TVB-2752] - Top-Right call-out should be filled with current loaded ViewModel
* [TVB-2763] - Launching further Analysers on a Simulation results should preserve the Simulation name
* [TVB-2765] - Refactor ABCAdapter
* [TVB-2772] - Display equations in Phase Plane for each Model with correct Matjax syntax
* [TVB-2775] - Review FilesHelper module
* [TVB-2782] - Test latest code before release 2.0.9
* [TVB-2783] - Release version 2.0.9

Improvement

* [TVB-2731] - Labels/info in Correlation/Wavelet/Other TimeSeries derived data

- Jupyter Notebook
Published by liadomide over 5 years ago

tvb - Release 2.0.8

Released packages: * tvb-library * tvb-rest-client * tvb-framework * tvb-contrib

! This is the first release (non-alpha) on Pypi for tvb-framework compatible with Py3 and with our neotraits internal mechanism in. It is almost the same web GUI functionality, changes have appeared in the Simulator launch part and behind the scenes in the way we launch an operation and we serialize configurations or results. A TVB REST server is also launched at the same time as tvb-web server launched in tvb-framework.

Changes: * Introduce/review enums in tvb-library and tvb-contrib for Sensors and Projection types * Fix bug in SpatialAverageMonitor (both for tvb-library and framework) * Improve MatrixViewers in web gui * Improve Simulation - Copy use-case in web gui

- Jupyter Notebook
Published by popaula937 over 5 years ago

tvb - Release 2.0.7

It contains refactor of H5 storage procedure and small bugs fixed.

Released packages: - tvb-library - tvb-rest-client

Relevant changes: - Fix bug in ICA analyzer - Fix bug on Epileptor 3 Codim + Larter Breakspear models - Improve serialization mechanism for ViewModels into H5 (affecting internal mechanism for tvb-rest-client)

- Jupyter Notebook
Published by liadomide over 5 years ago

tvb - Release 2.0.6

Released packages:

tvb-library 2.0.6 - Add method in the internal Sensors to group by electrode. Add missing lems init.py
tvb-framework 2.0.6a1 - POC with HPC secure run of simulations, few bug fixes in GUI -- it is still an alpha release
tvb-rest-client 2.0.6 - Small internal review

- Jupyter Notebook
Published by liadomide over 5 years ago

tvb - Release 2.0.5

Releases: - tvb-library 2.0.5 after tvb.simulator.plot changed and tvb.analyzers.info was restored - tvb-framework 2.0.5a1 after bug fixes in GUI and DB enhancements, but it is still an alpha release - tvb-rest-client 2.0.5 after enhancements (project permissions and pagination when getting users list) - tvb-contrib 2.0.5 is the first release of this package

- Jupyter Notebook
Published by popaula937 over 5 years ago

tvb - Release 2.0.3 of tvb-library

Small adjustments in the core part needed for the REST API settings

- Jupyter Notebook
Published by liadomide over 5 years ago

tvb - Release 2.0.2 tvb-library

Release tvb-library after some bug fixes with neotraits

- Jupyter Notebook
Published by liadomide over 5 years ago

tvb - Stable 1.5.10

Tag tvb-root before version 2.0 big changes

- Jupyter Notebook
Published by liadomide about 6 years ago

Recent Releases of tvb

tvb - Release 2.10.0

tvb - Release 2.9.2

tvb - Release 2.9.1

Release 2.9.1

Bug

Task

tvb - Release 2.9.0

tvb - Release 2.8.2

tvb - Release 2.8.1

tvb - Release 2.8

tvb - Release 2.7.3

tvb - Release 2.7.2

tvb - Release 2.7.1

tvb - Release 2.7

tvb - Release 2.6

tvb - Release 2.5

Release on Pypi

tvb - Release 2.4.1 for TVB_Distribution

Bug

tvb - Release 2.4

Released packages:

Release notes:

Involved Jira tasks in 2.4

Bug

Task

Improvement

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.3

Released packages:

tvb-framework

tvb-storage

tvb-rest-client

tvb-contrib

Involved Jira tasks in 2.3

Sub-task

Bug

Task

Improvement

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.2.2 for TVB_Distribution

Release notes

Involved Jira tasks in 2.2.2

Bug

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.2.1 for TVB_Distribution

Release notes

Involved Jira tasks in 2.2.1

Bug

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.2 for TVB_Distribution

Release Notes

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.2

Released packages:

tvb-library

tvb-framework

tvb-rest-client

tvb-contrib

Involved Jira tasks in 2.2

Bug

Story

Task

Improvement

Citation

When using TVB 2.2 or higher, for scientific publications, please cite it as follows:

tvb - Release 2.1

Release Notes

Sub-task

Bug

Task

Improvement

tvb - Release 2.0.10

Release notes

tvb-library