diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 521af38..37c263f 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -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. diff --git a/README.rst b/README.rst index 0982654..9b28f00 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,4 @@ -.. image:: atlas-densities.jpg +|banner| Overview ========= @@ -343,9 +343,9 @@ 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 @@ -353,7 +353,7 @@ 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": { @@ -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 @@ -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 diff --git a/doc/source/readme.rst b/doc/source/readme.rst index a6210d3..84da2e2 100644 --- a/doc/source/readme.rst +++ b/doc/source/readme.rst @@ -1 +1,4 @@ .. include:: ../../README.rst + :end-before: .. substitutions + +.. |banner| image:: static/atlas-densities.jpg diff --git a/atlas-densities.jpg b/doc/source/static/atlas-densities.jpg similarity index 100% rename from atlas-densities.jpg rename to doc/source/static/atlas-densities.jpg diff --git a/tox.ini b/tox.ini index c795446..d42f5f2 100644 --- a/tox.ini +++ b/tox.ini @@ -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 =