Rc 0.7.0 beta

[bgmeulem]

This is a relatively large refactor to address many reviewer comments, and to make ISF more generally applicable.

swc support

We now support swc. ISF pipelines are agnostic to whether a morphology file is hoc or swc. Reading in and building the morphology is simply handled by single_cell_parser.io.morphology.read_morphology. Big thanks to @su-saka and @fkkastrinakis for writing the initial converters, that save me a bunch of time for further integration.

We have converters from swc to hoc and hoc to swc. Converting hoc to swc can slightly change connectivity of some sections to the soma, but this is of no impact in ISF as we connect them by default at
x=0.5.

Simulations on both yield almost identical results. I implemented a test for this. variable time step simulations are not fully identical, fixed timesteps simulations are. I am not sure yet why this is the case. Variable time step simulations for hoc vs swc are virtually indistinguishable, but the time steps are ever so slightly different.

#482 and #476

Network mapping generalizibility

I changed the network mapping procedure so it does not depend anymore on any particular label (e.g. "apical"). Instead, labels are inferred from the morphology file. Additional empirical data should then match these labels (e.g. connections spreadsheet) case-insensitively #478 #467

singlecell_input_mapper has been refactored extensively. It now uses a builder pattern to add network parameters. this makes it way easier to modularize and understand which data is being added, and how (see #465). In addition, the default network embedding strategy can now be configured on a user-level (see #466 )

I extended the network parameters with a NetworkParamBuilder class that makes it way more convenient to build network parameters, and makes it explicit which data you add, when, and where. This is explored
extensively in the tutorials. #465

Network mapping does not rely anymore on a NrOfConnections.csv. This used to be default output of our network mapper. However, the same information is contained in a .con file. We now parse it from a .con file. This way, ISF is fully independent of any particular network mapping procedure, and simply relies on a syn and con file.

I augmented our dataset for activity data. The correct activity data file + key used to be inferred at runtime, i.e. depending on your recording site and stimulus, it would redirect you to the correct activity data file on the fly. This was very barrel cortex specific. I augmented the activity data by simply generating datasets for all stimuli. The augmentation method is saved as a notebook in getting_started/functional_constraints/evoked_activity/empirical_recordings. Now, the key you pass under "whisker" is instead interpreted as a globstring that fetches the correct data file in a preconfigured data directory. The NetworkParamBuilder of course also allows you to directly add activity data, independent of any directory configuration. #465

A tutorial now explores all the data requirements for Udvary 2022 #480

The network mapper used in ISF is Udvary 2022, but it should be clear that ISF does not rely on this particular network mapping. I refactored the top-level pipeline so it infers a specific network mapping procedure, and refactored Udvary 2022 as a separate subpackage in singlecell_input_mapper. #466

L5PT mentions

I removed all mentions of "L5PT" in the code, except for those methods that are actually specific to L5PTs. In the latter case, it should be clear that this methods provides an example, and should not live in top-level pipelines or modules #469

Tutorials

Updated the intro tutorial so be more targeted at exactly what ISF does. Removed configuration setup. Added more headings, intro and explanation on what we do, how, and why. #484

Updated network mapping tutorial to add API for the SynapseMapper and visualizations. Added auxiliary tutorials. They are hidden from direct view in the webpage, but reflinks work. This is e.g. used in tutorial 2.1 #485

Config

Added config for morphology labels. You can extend a map so labels identified in morphology files are renamed to something else. This is useful for having a consistent internal representation. I had to do this to rename "BasalDendrite" (in network mapping methods) to "Dendrite"

Added mechanisms to user config, since the mechanisms are user-specific,
technically.

Docs

Added documentation on swc and mod files. Wrote a custom lexer for
NMODL :)
Extended installation instructions for more info on how ISF handles environments and env variables.
Extended documentation on file formats, added data sources to paramfile overview
Extended tutorials