Releases: the-virtual-brain/tvb-root
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
Release 2.4.1 for TVB_Distribution
Fix Jupyter kernel for Windows/Linux distributions.
Bug
- [TVB-2984] - Jupyther kernel not starting from tvb Dockerfiles
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.
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.
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.
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.
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.
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.
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
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