fix links with html extensions

Makefile

@@ -23,7 +23,7 @@ test: all
 	$(PYTHON) -m pytest
 	cargo test
 
-doc: .PHONY
+doc: build
 	cd doc && make html
 
 include/sourmash.h: src/core/src/lib.rs \

doc/classifying-signatures.md

@@ -28,8 +28,7 @@ a plasmid as a query, you would use `--containment` to find genomes
 that contained that plasmid.  `gather` (discussed below) uses containment
 analysis only.
 
-See [the main sourmash
-tutorial](http://sourmash.readthedocs.io/en/latest/tutorials.html#make-and-search-a-database-quickly)
+See [the main sourmash tutorial](tutorial-basic.md#make-and-search-a-database-quickly)
 for information on using `search` with and without `--containment`.
 
 ## Breaking down metagenomic samples with `gather` and `lca`
@@ -49,7 +48,7 @@ k-mers. (This is the approach pioneered by
 [Kraken](https://ccb.jhu.edu/software/kraken/) and used by many other tools.)
 `sourmash lca` can be used to classify individual genome bins with
 `classify`, or summarize metagenome taxonomy with `summarize`.  The
-[sourmash lca tutorial](http://sourmash.readthedocs.io/en/latest/tutorials-lca.html)
+[sourmash lca tutorial](tutorials-lca.md)
 shows how to use the `lca classify` and `lca summarize` commands, and also
 provides guidance on building your own database.
 
@@ -58,8 +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](http://sourmash.readthedocs.io/en/latest/tutorials.html#what-s-in-my-metagenome)
+[basic sourmash tutorial](tutorial-basic.md#what-s-in-my-metagenome)
 has some sample output from using gather with GenBank.  See the appendix at
 the bottom of this page for more technical details.
 

doc/command-line.md

@@ -57,7 +57,7 @@ Matrix:
 To get a list of subcommands, run `sourmash` without any arguments.
 
 There are five main subcommands: `compute`, `compare`, `plot`,
-`search`, and `gather`.  See [the tutorial](tutorials.html) for a
+`search`, and `gather`.  See [the tutorial](tutorials.md) for a
 walkthrough of these commands.
 
 * `compute` creates signatures.
@@ -68,7 +68,7 @@ walkthrough of these commands.
 
 There are also a number of commands that work with taxonomic
 information; these are grouped under the `sourmash lca`
-subcommand. See [the LCA tutorial](tutorials-lca.html) for a
+subcommand. See [the LCA tutorial](tutorials-lca.md) for a
 walkthrough of these commands.
 
 * `lca classify` classifies many signatures against an LCA database.
@@ -185,7 +185,7 @@ containing the matches.
 be slow and somewhat memory intensive for large collections.  You can
 use `sourmash index` to create a Sequence Bloom Tree (SBT) that can
 be quickly searched on disk; this is [the same format in which we provide
-GenBank and other databases](databases.html).
+GenBank and other databases](databases.md).
 
 Usage:
 ```
@@ -210,7 +210,7 @@ similarity   match
 
 The `gather` subcommand finds all non-overlapping matches to the
 query.  This is specifically meant for metagenome and genome bin
-analysis.  (See [Classifying Signatures](classifying-signatures.html)
+analysis.  (See [Classifying Signatures](classifying-signatures.md)
 for more information on the different approaches that can be used
 here.)
 
@@ -222,7 +222,7 @@ matches.
 `gather`, like `search`, will load all of provided signatures into
 memory.  You can use `sourmash index` to create a Sequence Bloom Tree
 (SBT) that can be quickly searched on disk; this is
-[the same format in which we provide GenBank and other databases](databases.html).
+[the same format in which we provide GenBank and other databases](databases.md).
 
 Usage:
 ```
@@ -243,7 +243,7 @@ overlap     p_query p_match
 The command line option `--threshold-bp` sets the threshold below
 which matches are no longer reported; by default, this is set to
 50kb. see the Appendix in
-[Classifying Signatures](classifying-signatures.html) for details.
+[Classifying Signatures](classifying-signatures.md) for details.
 
 Note:
 
@@ -256,7 +256,7 @@ using a collection of genomes with taxonomic information.
 
 These commands use LCA databases (created with `lca index`, below, or
 prepared databases such as
-[genbank-k31.lca.json.gz](databases.html)).
+[genbank-k31.lca.json.gz](databases.md)).
 
 ### `sourmash lca classify`
 
@@ -377,7 +377,7 @@ The same information is reported in a CSV file if `-o/--output` is used.
 The `sourmash lca gather` command finds all non-overlapping
 matches to the query, similar to the `sourmash gather` command.  This
 is specifically meant for metagenome and genome bin analysis.  (See
-[Classifying Signatures](classifying-signatures.html) for more
+[Classifying Signatures](classifying-signatures.md) for more
 information on the different approaches that can be used here.)
 
 If the input signature was computed with `--track-abundance`, output
@@ -412,7 +412,7 @@ a lineage spreadsheet and a collection of signatures.  This can be used
 to create LCA databases from private collections of genomes, and can
 also be used to create databases for e.g. subsets of GenBank.
 
-See [the `sourmash lca` tutorial](tutorials-lca.html) and the blog
+See [the `sourmash lca` tutorial](tutorials-lca.md) and the blog
 post
 [Why are taxonomic assignments so different for Tara bins?](http://ivory.idyll.org/blog/2017-taxonomic-disagreements-in-tara-mags.html)
 for some use cases.

doc/index.md

@@ -28,7 +28,7 @@ background information on how and why MinHash works.
 ----
 
 To use sourmash, you must be comfortable with the UNIX command line;
-programmers may find the [Python library and API](api.md) useful as well.
+programmers may find the [Python library and API](api.rst) useful as well.
 
 If you use sourmash, please cite us!
 
@@ -62,7 +62,7 @@ be stored, searched, explored, and taxonomically annotated.
 
 * `sourmash` also has a simple Python API for interacting with signatures,
   including support for online updating and querying of signatures
-  (see [the API docs](api.md)).
+  (see [the API docs](api.rst)).
 
 * `sourmash` relies on an underlying Rust core for performance.
 

doc/more-info.md

@@ -2,11 +2,11 @@
 
 ## Computational requirements
 
-Read more about the [compute requirements, here.](requirements.html)
+Read more about the [compute requirements, here.](requirements.md)
 
 ## Prepared search database
 
-We offer a number of [prepared search databases.](databases.html)
+We offer a number of [prepared search databases.](databases.md)
 
 ## Other MinHash implementations for DNA
 
@@ -138,5 +138,5 @@ Newer versions of matplotlib do not seem to have this problem.
 [21]:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
 [22]:http://joss.theoj.org/papers/3d793c6e7db683bee7c03377a4a7f3c9
 [23]:https://www.biorxiv.org/content/early/2017/09/04/184150
-[24]:developer.html
-[25]:release.html
+[24]:developer.md
+[25]:release.md

doc/other-languages.md

@@ -11,7 +11,7 @@ Below are some code snippets and links that might be useful.
 `sourmash compare` can output matrices in a CSV format, which can
 easily be read into R.  For example, if you download the Eschericia
 signature collection as in
-[the sourmash tutorial](https://sourmash.readthedocs.io/en/latest/tutorials.html#make-and-search-a-database-quickly),
+[the sourmash tutorial](tutorial-basic.md#make-and-search-a-database-quickly),
 then the shell command
 
 ```shell
@@ -32,7 +32,8 @@ sourmash_comp_matrix <- as.matrix(sourmash_comp_matrix)
 
 ```
 
-[See the output of plotting and clustering this matrix](_static/ecoli-cmp.html), produced by [this RMarkdown file](_static/ecoli-cmp.Rmd).
+[See the output of plotting and clustering this matrix](https://sourmash.readthedocs.io/en/latest/_static/ecoli-cmp.html),
+produced by [this RMarkdown file](https://sourmash.readthedocs.io/en/latest/_static/ecoli-cmp.Rmd).
 
-You can download the `ecoli.cmp.csv` file itself [here](_static/ecoli.cmp.csv).
+You can download the `ecoli.cmp.csv` file itself [here](https://sourmash.readthedocs.io/en/latest/_static/ecoli.cmp.csv).
 

doc/release-notes/sourmash-2.0.md

@@ -18,16 +18,16 @@ 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.html).
-* Added "LCA databases" for fast searching of large databases in not-so-low memory; see [`sourmash lca index` in command-line docs](../command-line.html#sourmash-lca-subcommands-for-taxonomic-classification).
-* Created [precomputed databases](../databases.html) for most of GenBank genomes.
-* Added taxonomic reporting functionality in the `sourmash lca` submodule - [see command-line docs](../command-line.html#sourmash-lca-subcommands-for-taxonomic-classification).
-* Added signature manipulation utilities in the `sourmash signature` submodule - [see command-line docs](../command-line.html#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.html#what-resolution-should-my-signatures-be-how-should-i-compute-them) and [more details in the Python API examples](../api-example.html#sourmash-minhash-objects-and-manipulations).
+* 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).
+* 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 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-compute-them) and [more details in the Python API examples](../api-example.md#sourmash-minhash-objects-and-manipulations).
 * Switched to using JSON instead of YAML for signatures.
 * Many performance optimizations!
 * Many more tests!
-* A much cleaner and more robust [Python API](../api-example.html).
+* A much cleaner and more robust [Python API](../api-example.md).
 * Installation via bioconda is now recommended (and actively maintained :)
 * Support for building signatures from BAM files.
 

doc/tutorial-basic.md

@@ -300,8 +300,8 @@ and `gather`; see `sourmash index`, above, [the LCA tutorial][4], or
 [Return to index][3]
 
 [0]:http://ivory.idyll.org/blog/2016-sourmash-sbt-more.html
-[1]:databases.html
+[1]:databases.md
 [2]:https://www.ncbi.nlm.nih.gov/pubmed/233877
-[3]:index.html
-[4]:tutorials-lca.html
-[5]:sourmash-collections.html
+[3]:index.md
+[4]:tutorials-lca.md
+[5]:sourmash-collections.md

doc/tutorials-lca.md

@@ -194,6 +194,6 @@ for an example format.
 [Return to index][3]
 
 [0]:http://ivory.idyll.org/blog/2016-sourmash-sbt-more.html
-[1]:databases.html
+[1]:databases.md
 [2]:https://www.ncbi.nlm.nih.gov/pubmed/233877
-[3]:index.html
+[3]:index.md

doc/tutorials.md

@@ -5,24 +5,24 @@
 These tutorials are both 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.html)
+* [The first sourmash tutorial - making signatures, comparing, and searching](tutorial-basic.md)
 
-* [Using sourmash LCA to do taxonomic classification](tutorials-lca.html)
+* [Using sourmash LCA to do taxonomic classification](tutorials-lca.md)
 
 ## Background and details
 
 These next three tutorials are all notebooks that you can view, run
 yourself, or run interactively online via the
 [binder](http://mybinder.org) service.
 
-* [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.html)
+* [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.md)
 
-* [Some sourmash command line examples!](sourmash-examples.html)
+* [Some sourmash command line examples!](sourmash-examples.md)
 
-* [Working with private collections of signatures.](sourmash-collections.html)
+* [Working with private collections of signatures.](sourmash-collections.md)
 
 ## More information
 
-If you are a Python programmer, you might also be interested in our [API examples](api-example.html) as well as a short guide to [Using the `LCA_Database` API.](using-LCA-database-API.html)
+If you are a Python programmer, you might also be interested in our [API examples](api-example.md) as well as a short guide to [Using the `LCA_Database` API.](using-LCA-database-API.ipynb)
 
-If you prefer R, we have [a short guide to using sourmash output with R](other-languages.html).
+If you prefer R, we have [a short guide to using sourmash output with R](other-languages.md).

doc/using-sourmash-a-guide.md

@@ -24,7 +24,7 @@ k=51.  The general rule is that longer k-mer sizes are less prone to
 false positives. But you can pick your own parameters.
 
 One additional wrinkle is that we provide a number of
-[precomputed databases](databases.html) at k=21, k=31, and k=51.
+[precomputed databases](databases.md) at k=21, k=31, and k=51.
 It is often convenient to calculate signatures at these sizes so that
 you can use these databases.