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WIP: update developer instructions #2811

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77e4f49
first try at revised index
ctb Aug 6, 2022
9f9f046
Merge branch 'latest' into update_doc_structure
ctb Aug 15, 2022
33eeb06
lots of details
ctb Aug 16, 2022
68fe6d7
much docs, so wow
ctb Aug 16, 2022
0bf170d
even more docs
ctb Aug 16, 2022
f3ccf11
even more docs
ctb Aug 16, 2022
4c60cd7
mo'
ctb Aug 16, 2022
471ddf4
add issue links
ctb Aug 16, 2022
419e433
fix more links
ctb Aug 16, 2022
8e9248f
notes
ctb Aug 17, 2022
91fbf7c
update text
ctb Aug 17, 2022
b67d38f
Apply suggestions from code review
ctb Aug 18, 2022
fbbcee5
address many of @ccbaumler suggestions
ctb Aug 18, 2022
87ab0dc
Update doc/sourmash-internals.md
ctb Aug 18, 2022
ee17cf3
misc changes
ctb Aug 18, 2022
bb4a89d
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Aug 19, 2022
6d4a397
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Aug 20, 2022
8fce224
whups, add faq.md
ctb Aug 20, 2022
9e1fbfc
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Aug 21, 2022
df8d0e2
Merge branch 'latest' into update_doc_structure
ctb Aug 22, 2022
a967534
Merge branch 'latest' into update_doc_structure
ctb Aug 26, 2022
a1ec24b
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Aug 30, 2022
2b6e3df
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Aug 31, 2022
e468205
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Sep 23, 2023
2f1eb4b
update some text
ctb Sep 23, 2023
6576d07
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Sep 26, 2023
87ae6a2
more FAQ
ctb Sep 26, 2023
1d5b754
update / add verify notes
ctb Sep 26, 2023
7a254ee
more writing
ctb Sep 26, 2023
651ca6e
more
ctb Sep 26, 2023
01ed183
more
ctb Sep 27, 2023
8b2fac3
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Sep 27, 2023
d99d7c9
fix links etc
ctb Sep 27, 2023
c60da96
add faq
ctb Sep 27, 2023
0120b78
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Sep 28, 2023
47aa759
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Sep 29, 2023
b21282e
add funding acks
ctb Sep 29, 2023
de2b5a4
detailed gather output
ctb Sep 30, 2023
b789b73
minor updates
ctb Sep 30, 2023
fb45b6c
add information about save formats and memory usage
ctb Sep 30, 2023
69dfbc0
add section on choosing a reference for read mapping
ctb Sep 30, 2023
e828ff9
add section on retrieving reads to FAQ
ctb Sep 30, 2023
4d2a91b
collection load order
ctb Sep 30, 2023
4e97e8e
update author/copyright
ctb Sep 30, 2023
571c865
minor corrections
ctb Sep 30, 2023
c6251d3
close to done with a first pass
ctb Oct 1, 2023
1d1e460
finish off internals
ctb Oct 1, 2023
4ed0367
finish things off?
ctb Oct 1, 2023
a4c1244
clean up missing refs
ctb Oct 3, 2023
3967b15
add publications
ctb Oct 3, 2023
30ed122
Merge branch 'latest' into update_doc_structure
ctb Oct 3, 2023
362a48f
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Oct 13, 2023
1f44043
Merge branch 'update_doc_structure' of https://github.com/sourmash-bi…
ctb Oct 13, 2023
535d7eb
update new -> index
ctb Oct 13, 2023
6026ecb
Apply suggestions from code review
ctb Oct 13, 2023
247d4e4
Merge branch 'update_doc_structure' into update_doc_structure_index
ctb Oct 14, 2023
82aa9ed
update
ctb Oct 14, 2023
14e9a51
add global toc
ctb Oct 14, 2023
c30aea6
remove ToC at top
ctb Oct 14, 2023
a08a36f
try unhiding
ctb Oct 14, 2023
d128c65
add sidebar
ctb Oct 14, 2023
13fde86
add TOC to sidebar
ctb Oct 14, 2023
8144c3c
upd sidebar
ctb Oct 14, 2023
6a5bb1a
rename internals page
ctb Oct 14, 2023
817092f
clean up
ctb Oct 14, 2023
2aea751
add developer quickstart
ctb Oct 15, 2023
b944b69
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Oct 15, 2023
8441727
Merge branch 'update_doc_structure' into update_doc_add_dev_and_install
ctb Oct 15, 2023
32ecc0d
clean up dev instructions a bit
ctb Oct 15, 2023
16bf8b5
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Oct 15, 2023
499e172
Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
ctb Oct 16, 2023
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add sidebar
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ctb committed Oct 14, 2023

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This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
commit d128c6521977106b3b4135fe06beea683e777ac2
4 changes: 3 additions & 1 deletion doc/index.md
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@@ -65,6 +65,8 @@ supported by further funding from the NIH and NSF. Please see

## Using sourmash

<!-- Please remember to add things to sidebar.md ;) -->

### Tutorials and examples

These tutorials are command line tutorials that should work on Mac OS
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maxdepth: 3
---

index.md
sidebar
```

# Indices and tables
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## Tutorials and examples

These tutorials are command line tutorials that should work on Mac OS
X and Linux. They require about 5 GB of disk space and 5 GB of RAM.

* [The first sourmash tutorial - making signatures, comparing, and searching](tutorial-basic.md)

* [Using sourmash LCA to do taxonomic classification](tutorials-lca.md)

* [Analyzing the genomic and taxonomic composition of an environmental genome using GTDB and sample-specific MAGs with sourmash](tutorial-lemonade.md)

* [Some sourmash command line examples!](sourmash-examples.ipynb)

## How-To Guides

* Installing sourmash

* [Classifying genome sketches](classifying-signatures.md)

* [Working with private collections of genome sketches](sourmash-collections.ipynb)

* [Using the `LCA_Database` API](using-LCA-database-API.ipynb)

* [Building plots from `sourmash compare` output](plotting-compare.ipynb).

* [A short guide to using sourmash output with R](other-languages.md).

## How sourmash works under the hood

* [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.ipynb)
* [Support, versioning, and migration between versions](support.md)

## Reference material

* [Full table of contents for all docs](toc.md)
* [UNIX command-line documentation](command-line.md)
* [Genbank and GTDB databases and taxonomy files](databases.md)
* [Python examples using the API](api-example.md)
* [Publications about sourmash](publications.md)
* [A guide to the internals of sourmash](sourmash-internals.md)
* [Funding acknowledgements](funding.md)

## Developing and extending sourmash

* [Releasing a new version of sourmash](release.md)