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Add git submodule for tutorials (#852)
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* turn off warn as error so we can look at docs while changing

* add submodule for notebooks

* Add submodule commands to readthedocs

* Change theme?

* Revert "Change theme?"

This reverts commit ec87af2.

* Fix syntax highlighting in notebooks

* Capitalization?

* Add extension, ignore other files from tutorial repo

* Remove github links custom extension

* Turn warningiserror back on

* Fix up text on tutorials landing page
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ivirshup authored Dec 2, 2022
1 parent 57a602d commit 385bb5a
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3 changes: 3 additions & 0 deletions .gitmodules
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[submodule "docs/tutorials/notebooks"]
path = docs/tutorials/notebooks
url = https://github.com/scverse/anndata-tutorials
4 changes: 4 additions & 0 deletions .readthedocs.yml
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Expand Up @@ -11,3 +11,7 @@ python:
path: .
extra_requirements:
- doc
submodules:
include:
- "docs/tutorials/notebooks"
recursive: true
12 changes: 10 additions & 2 deletions docs/conf.py
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Expand Up @@ -34,7 +34,13 @@
source_suffix = ".rst"
master_doc = "index"
default_role = "literal"
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
exclude_patterns = [
"_build",
"Thumbs.db",
".DS_Store",
"**.ipynb_checkpoints",
"tutorials/notebooks/*.rst",
]
pygments_style = "sphinx"

extensions = [
Expand All @@ -46,14 +52,16 @@
"sphinx.ext.napoleon",
"sphinx.ext.autosummary",
"sphinx_autodoc_typehints", # needs to be after napoleon
"sphinx_issues",
"scanpydoc",
"nbsphinx",
*[p.stem for p in (HERE / "extensions").glob("*.py")],
"IPython.sphinxext.ipython_console_highlighting",
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
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50 changes: 0 additions & 50 deletions docs/extensions/github_links.py

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2 changes: 1 addition & 1 deletion docs/index.rst
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Expand Up @@ -25,7 +25,7 @@ Latest additions
:maxdepth: 1
:hidden:

tutorials
tutorials/index
api
concatenation
fileformat-prose
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22 changes: 11 additions & 11 deletions docs/release-notes/0.6.0.rst
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Expand Up @@ -2,27 +2,27 @@
~~~~~~~~~~~~~~~~~~~~~~~~~

- better support for aligned mappings (obsm, varm, layers)
:noteversion:`0.6.22` :pr:`155` :smaller:`I Virshup`
`0.6.22` :pr:`155` :smaller:`I Virshup`
- convenience accesors :func:`~anndata.AnnData.obs_vector`, :func:`~anndata.AnnData.var_vector` for 1d arrays.
:noteversion:`0.6.21` :pr:`144` :smaller:`I Virshup`
`0.6.21` :pr:`144` :smaller:`I Virshup`
- compatibility with Scipy >=1.3 by removing `IndexMixin` dependency.
:noteversion:`0.6.20` :pr:`151` :smaller:`P Angerer`
`0.6.20` :pr:`151` :smaller:`P Angerer`
- bug fix for second-indexing into views.
:noteversion:`0.6.19` :smaller:`P Angerer`
`0.6.19` :smaller:`P Angerer`
- bug fix for reading excel files.
:noteversion:`0.6.19` :smaller:`A Wolf`
`0.6.19` :smaller:`A Wolf`
- changed default compression to `None` in :func:`~anndata.AnnData.write_h5ad` to speed up read and write, disk space use is usually less critical.
:noteversion:`0.6.16` :smaller:`A Wolf`
`0.6.16` :smaller:`A Wolf`
- maintain dtype upon copy.
:noteversion:`0.6.13` :smaller:`A Wolf`
`0.6.13` :smaller:`A Wolf`
- :attr:`~anndata.AnnData.layers` inspired by `.loom <https://loompy.org>`_ files allows their information lossless reading via :func:`~anndata.read_loom`.
:noteversion:`0.6.7`–:noteversion:`0.6.9` :pr:`46` & :pr:`48` :smaller:`S Rybakov`
`0.6.7`–`0.6.9` :pr:`46` & :pr:`48` :smaller:`S Rybakov`
- support for reading zarr files: :func:`~anndata.read_zarr`
:noteversion:`0.6.7` :pr:`38` :smaller:`T White`
`0.6.7` :pr:`38` :smaller:`T White`
- initialization from pandas DataFrames
:noteversion:`0.6.` :smaller:`A Wolf`
`0.6.` :smaller:`A Wolf`
- iteration over chunks :func:`~anndata.AnnData.chunked_X` and :func:`~anndata.AnnData.chunk_X`
:noteversion:`0.6.1` :pr:`20` :smaller:`S Rybakov`
`0.6.1` :pr:`20` :smaller:`S Rybakov`

0.6.0 :small:`1 May, 2018`
~~~~~~~~~~~~~~~~~~~~~~~~~~
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2 changes: 1 addition & 1 deletion docs/release-notes/0.9.0.rst
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Expand Up @@ -20,4 +20,4 @@
.. rubric:: Deprecations

* :meth:`AnnData.concatenate() <anndata.AnnData.concatenate>` is now deprecated in favour of :func:`anndata.concat` :pr:`845` :smaller:`ivirshup`
* Previously deprecated `force_dense` arugment :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` has been removed.:pr:`855` :smaller:`ivirshup`
* Previously deprecated `force_dense` arugment :meth:`AnnData.write_h5ad() <anndata.AnnData.write_h5ad>` has been removed. :pr:`855` :smaller:`ivirshup`
10 changes: 0 additions & 10 deletions docs/tutorials.rst

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14 changes: 14 additions & 0 deletions docs/tutorials/index.rst
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Tutorials
=========

For a quick introduction to `AnnData`, check out :doc:`Getting Started with AnnData <notebooks/getting-started>`.

For working with the experimental data loaders also see :ref:`experimental_api`.

.. toctree::
:maxdepth: 1

notebooks/getting-started
notebooks/annloader
notebooks/anncollection
notebooks/anncollection-annloader
1 change: 1 addition & 0 deletions docs/tutorials/notebooks
Submodule notebooks added at 6778cf
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -71,6 +71,7 @@ doc = [
"nbsphinx",
"scanpydoc>=0.7.7",
"zarr",
"IPython", # For syntax highlighting in notebooks
]
test = [
"loompy>=3.0.5",
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