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fix documentation building #56

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Jan 18, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.rst
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ Update Roussel et al.'s pipeline to match implementation from the paper (#12)
* Update Roussel et al.'s pipeline to match the implementation from the paper. Htr3a is now split into vip and lamp5.
* Added a warning for the user in case the thresholding causes the dataset to be entirely null.
* A threshold can be applied to the Nissl and raw ISH datasets to remove a part of the background expression.
If the expression outside the test datasets is too high then the thresholding process will set the whole dataset to 0. Some tests will therefore randomly fail when this event happen.
If the expression outside the test datasets is too high then the thresholding process will set the whole dataset to 0. Some tests will therefore randomly fail when this event happen.

add examples to README.rst (#6)
* Add references to Rodarie's and Roussel's and Kim's paper.
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16 changes: 10 additions & 6 deletions README.rst
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
.. image:: atlas-densities.jpg
|banner|

Overview
=========
Expand Down Expand Up @@ -343,17 +343,17 @@ mapping csv file (see also `mtypes_probability_map_config.yaml`_).
--n-jobs 8 \
--output-dir=data/ccfv2/me-types/

The molecular density of approx_lamp5 was calculated from the other molecular densities as
The molecular density of approx_lamp5 was calculated from the other molecular densities as

.. code-block:: math
.. math::

approx_lamp5 = gad67 - vip - sst - pv

which approximates the molecular density of lamp5.

The command outputs the density files in the output-dir and a metadata json file:

.. code-block:: json
.. code-block:: javascript

{
"SLAC": {
Expand All @@ -363,9 +363,9 @@ The command outputs the density files in the output-dir and a metadata json file
},
"NGC-SA": {
"cNAC": "data/ccfv2/test_regions_me-types/NGC-SA|cNAC_densities.nrrd",
...
// ...
},
...
// ...
}

Subdivide excitatory files into pyramidal subtypes
Expand Down Expand Up @@ -429,3 +429,7 @@ Copyright © 2022 Blue Brain Project/EPFL
.. _`mmc3.xlsx`: https://github.com/BlueBrain/atlas-densities/blob/main/atlas_densities/app/data/measurements/mmc3.xlsx
.. _`gaba_papers.xlsx`: https://github.com/BlueBrain/atlas-densities/blob/main/atlas_densities/app/data/measurements/gaba_papers.xlsx
.. _`mtypes_probability_map_config.yaml`: https://github.com/BlueBrain/atlas-densities/blob/main/atlas_densities/app/data/mtypes/mtypes_probability_map_config.yaml

.. substitutions

.. |banner| image:: doc/source/static/atlas-densities.jpg
3 changes: 3 additions & 0 deletions doc/source/readme.rst
Original file line number Diff line number Diff line change
@@ -1 +1,4 @@
.. include:: ../../README.rst
:end-before: .. substitutions

.. |banner| image:: static/atlas-densities.jpg
File renamed without changes
2 changes: 1 addition & 1 deletion tox.ini
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ deps =
sphinx-bluebrain-theme
sphinx-click
commands = make html SPHINXOPTS=-W
whitelist_externals = make
allowlist_externals = make

[testenv:check-packaging]
deps =
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