Add Makefile and config file for Sphinx, nbsphinx (Add Sphinx docs - Part 3) #97
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chmreid
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chmreid
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* udpate install-hca nb * update install-hca readme * update text of intro nb cell in install-hca * update index.rst to avoid conflict
* update find-cell-type-count nb * update cell counts (WIP) * add proper cell counts to find-cell-type-count nb * update readme for find cell type count * update index.rst to avoid conflict
* update explore-scanpy-may-2019 * update explore-scanpy nb with prod run * replace 2 explore-hca-dataset-scanpy nbs with 1 * update readme and rename explore-hca-scanpy nb * update index.rst to avoid conflict
* add new elasticsearch-queries notebook * update elasticsearch-queries nb with prod results * add a readme
* update download-smartseq2-matrix nb * update smartseq2-matrix nb with prod results * update readme * update index.rst to avoid conflict
* update download-any-bam-file nb * update download any bam file to use functions * fix wording * fix typo * update readme description and link * update index.rst to avoid conflict
* update download-all-fastq-files * refactor functions in download-all-fastq-files nb * fix a function * update readme * update index.rst to avoid conflict
* mv download-10x-seq-tcell to download-10x-liver * update name of 10x-liver nb in index * add examples of downloading 10x-liver data * remove old 10x-seq-tcell nb dir * add 10x-liver readme * update index.rst to avoid conflict
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CI/CD system is failing on running treon tests on the explore scanpy notebook. The failure is caused by a typing system issue when using scanpy to create a tSNE plot. This type error is an artifact of changes to typing system in Python. The treon tests pass using Python 3.6.3 but do not pass using Python 3.6.9 or 3.7+. Looking into a fix now... |
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Fix was to pin scanpy version to be 1.3.* |
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Add files for building Sphinx docs. Incorporate
nbsphinxinto the Sphinx Makefile.Closes #98