[MRG] fix docs build

.readthedocs.yml

@@ -12,7 +12,7 @@ conda:
   environment: doc/environment.yml
 
 python:
-  version: 3.7
+  version: 3.8
   install:
     - method: pip
       path: .

doc/classifying-signatures.md

@@ -57,7 +57,7 @@ genomes based on greedy partitioning. Essentially, it takes a query
 metagenome and searches the database for the most highly contained
 genome; it then subtracts that match from the metagenome, and repeats.
 At the end it reports how much of the metagenome remains unknown.  The
-[basic sourmash tutorial](tutorial-basic.md#what-s-in-my-metagenome)
+[basic sourmash tutorial](tutorial-basic.md#whats-in-my-metagenome)
 has some sample output from using gather with GenBank.  See Appendix A at
 the bottom of this page for more technical details.
 

doc/conf.py

@@ -37,7 +37,7 @@
     'sphinx.ext.doctest',
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
-    'sphinxcontrib.napoleon',
+    'sphinx.ext.napoleon',
     'nbsphinx',
     'IPython.sphinxext.ipython_console_highlighting',
     'myst_parser'
@@ -302,3 +302,4 @@
 #texinfo_no_detailmenu = False
 
 autodoc_mock_imports = ["sourmash.minhash"]
+myst_heading_anchors = 3

doc/index.md

@@ -28,7 +28,7 @@ background information on how and why MinHash works.
 
 **Want to migrate to sourmash v4?** sourmash v4 is now available, and
 has a number of incompatibilites with v2 and v3. Please see 
-[our migration guide](support.md#migrating-from-sourmash-v3-x-to-sourmash-v4-x)!
+[our migration guide](support.md#migrating-from-sourmash-v3x-to-sourmash-v4x)!
 
 ----
 

doc/release-notes/sourmash-2.0.md

@@ -19,11 +19,11 @@ in the
 This is a list of substantial new features and functionality in sourmash 2.0.
 
 * Added Sequence Bloom Tree search to enable similarity and containment queries on very large collections of signatures in low memory; see `sourmash index`, `sourmash search`, and `sourmash gather` in [the command line documentation](../command-line.md).
-* Added "LCA databases" for fast searching of large databases in not-so-low memory; see [`sourmash lca index` in command-line docs](../command-line.md#sourmash-lca-subcommands-for-taxonomic-classification).
+* Added "LCA databases" for fast searching of large databases in not-so-low memory; see [`sourmash lca index` in command-line docs](../command-line.md#sourmash-lca-subcommands-for-in-memory-taxonomy-integration).
 * Created [precomputed databases](../databases.md) for most of GenBank genomes.
-* Added taxonomic reporting functionality in the `sourmash lca` submodule - [see command-line docs](../command-line.md#sourmash-lca-subcommands-for-taxonomic-classification).
+* Added taxonomic reporting functionality in the `sourmash lca` submodule - [see command-line docs](../command-line.md#sourmash-lca-subcommands-for-in-memory-taxonomy-integration).
 * Added signature manipulation utilities in the `sourmash signature` submodule - [see command-line docs](../command-line.md#sourmash-signature-subcommands-for-signature-manipulation)
-* Introduced new modulo hash or "scaled" signatures for containment analysis; see [Using sourmash: a practical guide](../using-sourmash-a-guide.md#what-resolution-should-my-signatures-be-how-should-i-create-them) and [more details in the Python API examples](../api-example.md#advanced-features-of-sourmash-minhash-objects-scaled-and-num).
+* Introduced new modulo hash or "scaled" signatures for containment analysis; see [Using sourmash: a practical guide](../using-sourmash-a-guide.md#what-resolution-should-my-signatures-be--how-should-i-create-them) and [more details in the Python API examples](../api-example.md#advanced-features-of-sourmash-minhash-objects---scaled-and-num).
 * Switched to using JSON instead of YAML for signatures.
 * Many performance optimizations!
 * Many more tests!

doc/release-notes/sourmash-4.0.md

@@ -9,7 +9,7 @@ contains many feature improvements and new functionality, as well as
 many breaking changes with sourmash 2.x and 3.x.
 
 Please see
-[our migration guide](../support.md#migrating-from-sourmash-v3-x-to-sourmash-v4-x)
+[our migration guide](../support.md#migrating-from-sourmash-v3x-to-sourmash-v4x)
 for guidance on updating to sourmash v4, and post questions about
 migrating to sourmash 4.0 in the
 [sourmash issue tracker](https://github.com/dib-lab/sourmash/issues/new).

doc/sourmash-sketch.md

@@ -109,8 +109,8 @@ The `-p` argument to `sourmash sketch` provides parameter strings to sourmash, a
 
 A parameter string is a space-delimited collection that can contain one or more fields, comma-separated.
 * `k=<ksize>` - create a sketch at this k-mer size; can provide more than one time in a parameter string. Typically `ksize` is between 4 and 100.
-* `scaled=<int>` - create a scaled MinHash with k-mers sampled deterministically at 1 per `<scaled>` value. This controls sketch compression rates and resolution; for example, a 5 Mbp genome sketched with a scaled of 1000 would yield approximately 5,000 k-mers. `scaled` is incompatible with `num`. See [our guide to signature resolution](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be-how-should-i-create-them) for more information.
-* `num=<int>` - create a standard MinHash with no more than `<num>` k-mers kept. This will produce sketches identical to [mash sketches](https://mash.readthedocs.io/en/latest/). `num` is incompatible with `scaled`. See [our guide to signature resolution](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be-how-should-i-create-them) for more information.
+* `scaled=<int>` - create a scaled MinHash with k-mers sampled deterministically at 1 per `<scaled>` value. This controls sketch compression rates and resolution; for example, a 5 Mbp genome sketched with a scaled of 1000 would yield approximately 5,000 k-mers. `scaled` is incompatible with `num`. See [our guide to signature resolution](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be--how-should-i-create-them) for more information.
+* `num=<int>` - create a standard MinHash with no more than `<num>` k-mers kept. This will produce sketches identical to [mash sketches](https://mash.readthedocs.io/en/latest/). `num` is incompatible with `scaled`. See [our guide to signature resolution](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be--how-should-i-create-them) for more information.
 * `abund` / `noabund` - create abundance-weighted (or not) sketches. See [Classify signatures: Abundance Weighting](classifying-signatures.md#abundance-weighting) for details of how this works.
 * `dna`, `protein`, `dayhoff`, `hp` - create this kind of sketch. Note that `sourmash sketch dna -p protein` and `sourmash sketch protein -p dna` are invalid; please use `sourmash sketch translate` for the former.
 

doc/support.md

@@ -29,7 +29,7 @@ that depend on sourmash, e.g. specifying `sourmash >=3,<4` for
 software that is tested with sourmash 3.x. Read on for details!
 
 Upgrading major versions (to sourmash 4.0, for example) will often involve
-more work; see the [next section](#upgrading-versions) for more
+more work; see the [next section](#upgrading-major-versions) for more
 our suggested process.
 
 ### Semantic versioning
@@ -148,7 +148,7 @@ If you use sourmash from the command line, there are a few major changes in 4.0
 
 First, **`sourmash compute` is deprecated in favor of [`sourmash sketch`](sourmash-sketch.md)**, which provides quite a bit more flexibility in creating signatures.
 
-Second, **`sourmash index` will now save databases in the Zip format (`.sbt.zip`) instead of the old JSON+subdirectory format** (see [updated docs](command-line.md#sourmash-index-build-an-sbt-index-of-signatures)). You can revert to the old behavior by explicitly specifying the `.sbt.json` filename for output when running `sourmash index`.
+Second, **`sourmash index` will now save databases in the Zip format (`.sbt.zip`) instead of the old JSON+subdirectory format** (see [updated docs](command-line.md#sourmash-index---build-an-sbt-index-of-signatures)). You can revert to the old behavior by explicitly specifying the `.sbt.json` filename for output when running `sourmash index`.
 
 Third, all sourmash commands that operate on signatures should now be able to directly read from lists of signatures in signature files, SBT databases, LCA databases, directories, and files containing lists of filenames (see [updated docs](command-line.md#advanced-command-line-usage)).
 

doc/tutorials.md

@@ -13,7 +13,7 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM.
 
 These next three tutorials are all notebooks that you can view, run
 yourself, or run interactively online via the
-[binder](http://mybinder.org) service.
+[binder](https://mybinder.org) service.
 
 * [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.md)
 

doc/using-sourmash-a-guide.md

@@ -189,7 +189,7 @@ built and searched directly from the command line.
 
 Reverse indexed or LCA databases are *in-memory* databases that, once
 loaded from disk, support fast search and gather across 10s of thousands
-of signatures.  They can be created using `sourmash lca index` ([docs](command-line.md#sourmash-lca-index-build-an-lca-database))
+of signatures.  They can be created using `sourmash lca index` ([docs](command-line.md#sourmash-lca-index---build-an-lca-database))
 
 LCA databases are currently stored in JSON files (that can be gzipped).
 As these files get larger, the time required to load them from disk
@@ -198,7 +198,7 @@ can be substantial.
 LCA databases are also currently (sourmash 2.0-4.0) the only databases
 that support the inclusion of taxonomic information in the database,
 and there is an associated collection of commands
-[under `sourmash lca`](command.md#sourmash-lca-subcommands-for-taxonomic-classification).
+[under `sourmash lca`](command-line.md#sourmash-lca-subcommands-for-in-memory-taxonomy-integration).
 However, they can also be used as regular indexed databases for search
 and gather as above.
 

setup.cfg

@@ -64,13 +64,14 @@ demo =
     jupyter_client
     ipython
 doc =
-    sphinx
-    myst-parser>=0.13.7,<0.15.0
+    sphinx>=4.4.0,<5
+    myst-parser==0.17.0
+    Jinja2==3.0.3
     alabaster
     sphinxcontrib-napoleon
     nbsphinx
     ipython
-    docutils>=0.17.1
+    docutils>=0.17.1,<0.18.0
 storage =
     ipfshttpclient>=0.4.13
     redis