Remove force indexing of microscopy and update ct

[mariehbourget]

Checklist

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PR contents

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• I've added relevant tests for my contribution
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Description

This PR aims to:

• Remove the force indexing of microsocpy files no longer required since microscopy was integrated in the bids-validator v1.9.0 and in pybids v0.15.2.
• Update the config_bids.json file to the latest version from pybids 0.15.5 with the addition of custom ct datatype.
• Update the comments in the bids_dataframe.py file regarding ct-scan force indexing for clarity (related to Confusing variable name #1026).
• Update CI tests and microscopy tutorial accordingly.

Notes:

• The PR is still a draft since we have issues/investigations in-progress that I would like to check in parallel before merging (BIDS derived datasets file naming #860, Update our definition of labels to comply with BIDS #1202 and ADS #605). EDIT: After verification, these issues are not in conflict with the implementation from this PR.
• As a reference, this PR was tested with pybids version 0.15.4 and 0.15.5.

Linked issues

Fixes #1026

[coveralls]

Pull Request Test Coverage Report for Build 3515689391

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

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Details

• 3 of 3 (100.0%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.2%) to 69.146%

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Totals
Change from base Build 3515543572:	0.2%
Covered Lines:	4305
Relevant Lines:	6226

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💛 - Coveralls

[mariehbourget]

Note to the reviewer:
This file was use as a "custom" pybids config to index microscopy & ct-scan files while they were not BIDS compliant. It is a copy of the pybids config file with the addition of "custom" field needed for micr & ct.

With this PR, we won't need the "custom" pybids config anymore for micr, but will still need it for ct.
As such, the only difference between this custom file and the official pybids config from here is the addition of ct on this line.

[jcohenadad]

i only gave it a quick glance, thank you @mariehbourget !