~tfardet

https://tfardet.srht.site

I'm a postdoctoral researcher working on complex systems and networks, notably in neuroscience.

My projects include mostly graph-related libraries in Python and C++. https://git.sr.ht/~tfardet https://codeberg.org/tfardet

You can follow me on the Fediverse: https://fediscience.org/@tfardet https://scicomm.xyz/@tfardet

~tfardet/nngt-developers

Last active 18 days ago

~tfardet/nngt-users

Last active 9 months ago
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Recent activity

Re: Collecting topics for the next Mumble meeting 12 days ago

From Tanguy Fardet to ~sircmpwn/sr.ht-discuss

I would be curious to have the opinion of the SourceHut community on
ForgeFriends [1] (formerly FedeProxy) and potential interactions.

[1]: https://forgefriends.org

[PATCH NNGT v1] I/O - Full GraphML support and NN/GML improvements 5 months ago

From Tanguy Fardet to ~tfardet/nngt-developers

Library independent support for GraphML format (read/write).
Bugfix for GML in corner cases with 0 nodes or edges.
Correction of neighbor list for undirected graphs.
Improved checks for edges attributes.
---
 README.md                        |  12 +-
 nngt/analysis/nngt_functions.py  |  13 +-
 nngt/core/graph.py               |   4 +-
 nngt/core/gt_graph.py            |   4 +
 nngt/core/ig_graph.py            |   7 +-
 nngt/core/nngt_graph.py          |   4 +
 nngt/core/nx_graph.py            |   7 +-
 nngt/generation/connectors.py    |   8 +-
 nngt/io/graph_loading.py         |  17 ++-
[message trimmed]

[PATCH NNGT v1] Core - More efficient edge attribute access 5 months ago

From Tanguy Fardet to ~tfardet/nngt-developers

Make access to a subset of edge attributes faster by using the underlying library's methods rather than generating the array for all edges every time.
This also reduces the memory footprint.
---
 doc/developer/library_shipping.rst |  2 +-
 nngt/core/graph.py                 | 40 ++++++-------
 nngt/core/gt_graph.py              | 76 ++++++++++++------------
 nngt/core/ig_graph.py              | 62 ++++++++++++-------
 nngt/core/nngt_graph.py            | 36 +++++++++++
 nngt/core/nx_graph.py              | 95 +++++++++++++++---------------
 nngt/io/saving_helpers.py          |  9 ++-
 nngt/lib/connect_tools.py          | 13 +++-
 nngt/lib/graph_helpers.py          |  2 +-
 nngt/lib/rng_tools.py              |  6 +-
 testing/test_attributes.py         | 18 +++---
[message trimmed]

[PATCH NNGT v1] Version 2.4.0 - Core - Make default NeuralGroup excitatory and fix Structure.create_neta_group 5 months ago

From tfardet to ~tfardet/nngt-developers

---
 nngt/__init__.py              |  2 +-
 nngt/core/graph.py            |  3 ---
 nngt/core/group_structure.py  |  4 ++--
 nngt/core/neural_pop_group.py |  4 ++--
 nngt/generation/connectors.py |  2 ++
 testing/base_test.py          |  1 -
 testing/test_group_pop.py     |  7 +++++++
 testing/test_nest.py          | 13 +++++++++++--
 8 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/nngt/__init__.py b/nngt/__init__.py
index 3252b42..ede5108 100644
--- a/nngt/__init__.py
[message trimmed]

[PATCH NNGT v1] Core - Check Graph **kwargs, automatic class 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch checks that all keyword arguments passed to the Graph classes
are eventually used or raises a warning if not.
It also introduces a
custom __new__ method for Graph that automatically converts new Graphs
to Networks or SpatialGraphs if a population or shape argument is
detected.
---
 nngt/core/graph.py                    | 41 +++++++++++++++++++-
 nngt/core/gt_graph.py                 |  4 +-
 nngt/core/ig_graph.py                 |  2 +-
 nngt/core/networks.py                 | 54 +++++++++++++++++++--------
 nngt/core/nngt_graph.py               |  4 +-
 nngt/core/nx_graph.py                 |  4 +-
 nngt/core/spatial_graph.py            | 11 +++---
[message trimmed]

[PATCH NNGT v5] Simulation/Analysis - NEST3 support and bugfix for SWP 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch provides full support for NEST 3 as well as some fixes for
NEST 2 and tests for the simulation functions.
It also fixes an extra square that was missed in 223231a2.
---
 .build.yml                             |   4 +-
 doc/conf.py                            |  10 +-
 doc/examples/basic_nest_network.py     |  21 +++-
 doc/examples/introduction_to_groups.py |   4 +-
 doc/examples/nest_network.py           |  17 +++-
 doc/examples/random_balanced.py        |  41 ++++----
 doc/user/nest-interaction.rst          |   6 +-
 doc/user/neural-groups.rst             |  16 +--
 doc/user/tutorial.rst                  |   4 +-
 nngt/analysis/activity_analysis.py     |  40 +++++---
[message trimmed]

[PATCH NNGT v4] Simulation/Analysis - NEST3 support and bugfix for SWP 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch provides full support for NEST 3 as well as some fixes for
NEST 2 and tests for the simulation functions.
It also fixes an extra square that was missed in 223231a2.		
---
 .build.yml                             |   4 +-
 doc/conf.py                            |  10 +-
 doc/examples/basic_nest_network.py     |  21 ++++-
 doc/examples/introduction_to_groups.py |   4 +-
 doc/examples/nest_network.py           |  17 +++-
 doc/examples/random_balanced.py        |  41 ++++----
 doc/user/nest-interaction.rst          |   6 +-
 doc/user/neural-groups.rst             |  16 ++--
 doc/user/tutorial.rst                  |   4 +-
 nngt/analysis/activity_analysis.py     |  40 +++++---
[message trimmed]

[PATCH NNGT v3] Simulation/Analysis - NEST3 support and bugfix for SWP 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch provides full support for NEST 3 as well as some fixes for
NEST 2 and tests for the simulation functions.
It also fixes an extra square that was missed in 223231a2.
---
 .build.yml                             |   4 +-
 doc/conf.py                            |  10 +-
 doc/examples/basic_nest_network.py     |  21 ++++-
 doc/examples/introduction_to_groups.py |   4 +-
 doc/examples/nest_network.py           |  17 +++-
 doc/examples/random_balanced.py        |  41 ++++----
 doc/user/nest-interaction.rst          |   6 +-
 doc/user/neural-groups.rst             |  16 ++--
 doc/user/tutorial.rst                  |   4 +-
 nngt/analysis/activity_analysis.py     |  40 +++++---
[message trimmed]

[PATCH NNGT v1] Simulation/Analysis - NEST3 support and bugfix for SWP 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch provides full support for NEST 3 as well as some fixes for
NEST 2 and tests for the simulation functions.
It also fixes an extra square that was missed in 223231a2.
---
 .build.yml                             |   4 +-
 doc/conf.py                            |  10 +-
 doc/examples/basic_nest_network.py     |  21 ++++-
 doc/examples/introduction_to_groups.py |   4 +-
 doc/examples/nest_network.py           |  17 +++-
 doc/examples/random_balanced.py        |  41 ++++----
 doc/user/nest-interaction.rst          |   6 +-
 doc/user/neural-groups.rst             |  16 ++--
 doc/user/tutorial.rst                  |   4 +-
 nngt/analysis/activity_analysis.py     |  40 +++++---
[message trimmed]

[PATCH v1] Simulation/Analysis - NEST3 support and bugfix for SWP 5 months ago

From tfardet to ~tfardet/nngt-developers

This patch provides full support for NEST 3 as well as some fixes for
NEST 2 and tests for the simulation functions.
It also fixes an extra square that was missed in 223231a2.
---
 .build.yml                             |   4 +-
 doc/conf.py                            |  10 +-
 doc/examples/basic_nest_network.py     |  21 ++++-
 doc/examples/introduction_to_groups.py |   4 +-
 doc/examples/nest_network.py           |  17 +++-
 doc/examples/random_balanced.py        |  41 ++++----
 doc/user/nest-interaction.rst          |   6 +-
 doc/user/neural-groups.rst             |  16 ++--
 doc/user/tutorial.rst                  |   4 +-
 nngt/analysis/activity_analysis.py     |  40 +++++---
[message trimmed]