diff --git a/conda.yml b/conda.yml index 157a4bc7..4a5bccc7 100644 --- a/conda.yml +++ b/conda.yml @@ -10,7 +10,7 @@ dependencies: - docutils - recommonmark - requests - - sphinx + - sphinx>=7.1 - sphinx-autobuild - sphinx-markdown-tables - sphinx-argparse diff --git a/src/conf.py b/src/conf.py index 15b73f5f..6cc05ab7 100644 --- a/src/conf.py +++ b/src/conf.py @@ -85,3 +85,23 @@ 'nextclade': ('https://docs.nextstrain.org/projects/nextclade/page/', None), 'ncov': ('https://docs.nextstrain.org/projects/ncov/page/', None) } + + +# -- Linkchecking ------------------------------------------------------------ +linkcheck_ignore = [ + # we have links to localhost for explanatory purposes; obviously + # they will never work in the linkchecker + r'http://127.0.0.1:\d+', + r'http://localhost:\d+', + # these URLs block the client the linkchecker uses + r'https://www.pnas.org/doi/10.1073/pnas.1507071112', + r'https://www.ncbi.nlm.nih.gov/books/NBK25501', + # we specifically use this as an example of a link that _won't_ work + r'https://nextstrain.org/ncov/gisaid/21L/global/6m/2024-01-10', +] +linkcheck_anchors_ignore_for_url = [ + # Github uses anchor-looking links for highlighting lines but + # handles the actual resolution with Javascript, so skip anchor + # checks for Github URLs: + r'https?://github.com', +] diff --git a/src/guides/share/groups/migrate-from-s3.rst b/src/guides/share/groups/migrate-from-s3.rst index 40397f0c..b4eb15ef 100644 --- a/src/guides/share/groups/migrate-from-s3.rst +++ b/src/guides/share/groups/migrate-from-s3.rst @@ -213,8 +213,8 @@ to inform them of these changes. A copy of the email is below. Thank you for being an early adopter of Nextstrain Groups! We're excited to keep improving the functionality of Groups. If you have any feedback, - please don't hesitate to `email us`_ or post to `discussions.nextstrain.org - `__. + please don't hesitate to `email us`_ or post to `discussion.nextstrain.org + `__. —the Nextstrain team @@ -248,8 +248,8 @@ migrated. Thank you for being an early adopter of Nextstrain Groups! We're excited to keep improving the functionality of Groups. If you have any feedback, - please don't hesitate to `email us`_ or post to `discussions.nextstrain.org - `__. + please don't hesitate to `email us`_ or post to `discussion.nextstrain.org + `__. —the Nextstrain team diff --git a/src/guides/snapshots.rst b/src/guides/snapshots.rst index 5b270f8c..56a62e4f 100644 --- a/src/guides/snapshots.rst +++ b/src/guides/snapshots.rst @@ -38,7 +38,7 @@ Viewing all available (core) resources and their snapshots available core datasets grouped by pathogen, as well as exposing all the known snapshots for each resource. Next to each resource you'll see the total number of available snapshots as well as an indication of how frequently the dataset is -updated, for instance at the time of writing `nextstrain.org/rsv/A/G `__ +updated, for instance at the time of writing `nextstrain.org/rsv/a/G `__ had 82 snapshots and was being updated weekly: .. image:: ../images/snapshots-listing-ui-hover.jpg diff --git a/src/learn/augur-to-auspice.rst b/src/learn/augur-to-auspice.rst index d5a528b3..18e68660 100644 --- a/src/learn/augur-to-auspice.rst +++ b/src/learn/augur-to-auspice.rst @@ -403,7 +403,7 @@ to see the available options here. The most comprehensive description of this file is via `its schema `__, however to introduce this file here's a snippet of the `Auspice config JSON for the -measles dataset presented above `__: +measles dataset presented above `__: .. code-block:: json @@ -535,7 +535,7 @@ A colors TSV file may be provided to ``augur export v2`` which is the most common way to associate (discrete) values with actual colors. Such a file has 3 tab-separated columns: the coloring key, the metadata value, and the color hex; no headers are necessary. As an example, `here -are (some of) the colors TSV `__ +are (some of) the colors TSV `__ used in the measles build: .. code-block:: text @@ -757,7 +757,7 @@ The **maintainers** (array of dictionaries) is used in the Auspice header to identify who created or maintains the dataset. As an example, here's how the `measles auspice-config uses these -keys `__ +keys `__ and you can `see here `__ how Auspice renders these: diff --git a/src/reference/documentation-style-guide.rst b/src/reference/documentation-style-guide.rst index d025f6b6..1a324457 100644 --- a/src/reference/documentation-style-guide.rst +++ b/src/reference/documentation-style-guide.rst @@ -57,4 +57,4 @@ Do not use:: This is particularly important for unversioned subprojects (e.g. using ``latest``) which we might start versioning later. -.. _default version redirect: https://docs.readthedocs.io/en/stable/automatic-redirects.html#redirecting-to-a-page +.. _default version redirect: https://docs.readthedocs.io/en/stable/user-defined-redirects.html#page-redirects-at-page diff --git a/src/reference/faq.rst b/src/reference/faq.rst index fa6292bf..03d5cf14 100644 --- a/src/reference/faq.rst +++ b/src/reference/faq.rst @@ -128,7 +128,7 @@ There are two ways to work around this: This provides easy compatibility with a broader set of bioinformatics packages, but comes at the cost of relatively longer run times for packages that have native ARM64 support. -2. Create a custom Conda environment that installs and runs packages under `Intel emulation `__. Run this after setting up an **empty** Conda environment and before installing any packages to it: +2. Create a custom Conda environment that installs and runs packages under `Intel emulation `__. Run this after setting up an **empty** Conda environment and before installing any packages to it: .. code-block:: bash diff --git a/src/tutorials/creating-a-bacterial-phylogenetic-workflow.rst b/src/tutorials/creating-a-bacterial-phylogenetic-workflow.rst index 21806b57..0952c3d3 100644 --- a/src/tutorials/creating-a-bacterial-phylogenetic-workflow.rst +++ b/src/tutorials/creating-a-bacterial-phylogenetic-workflow.rst @@ -26,7 +26,7 @@ Setup .. note:: - The data in this tutorial is public and is a subset of the data from Lee et al.'s 2015 paper `Population genomics of Mycobacterium tuberculosis in the Inuit `_. As location was anonymized in the paper, location data provided here was randomly chosen from the region for illustrative purposes. + The data in this tutorial is public and is a subset of the data from Lee et al.'s 2015 paper `Population genomics of Mycobacterium tuberculosis in the Inuit `_. As location was anonymized in the paper, location data provided here was randomly chosen from the region for illustrative purposes. Create the Nextstrain Build =========================== @@ -307,7 +307,7 @@ Reconstruct Ancestral Traits Identify Specified Clades ~~~~~~~~~~~~~~~~~~~~~~~~~ -In the `original paper `_, the authors identified 'sublineages' within the dataset. We can add these to our dataset as 'clades' by defining the sublineages with amino-acid or nucleotide mutations specific to that sublineage, given here in the file ``config/clades.tsv``. Open it up in a text editor to have a look at the format. +In the `original paper `_, the authors identified 'sublineages' within the dataset. We can add these to our dataset as 'clades' by defining the sublineages with amino-acid or nucleotide mutations specific to that sublineage, given here in the file ``config/clades.tsv``. Open it up in a text editor to have a look at the format. The ``clades.tsv`` file must be tab-delimited with four columns: clade, gene, site, and alt. The 'clade' column gives the name of the clade being defined - you can have more than one row per clade - it will only be defined from the branch where all criteria are met. The 'gene' and 'site' columns specify the gene (or ``nuc`` for nucleotide) and location (by AA position in the gene, or nucleotide position in the genome) where the branch must have the 'alt' (4th column) value to be considered this clade. diff --git a/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst b/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst index d909dfb2..6cad602b 100644 --- a/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst +++ b/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst @@ -414,7 +414,7 @@ If you write a custom script that follows the same pattern, you can add your scr curation pipeline before the final ``augur curate apply-record-annotations`` command. A typical pathogen-specific step for curation is the standardization of strain names since pathogens usually have different naming conventions -(e.g. `influenza `_ vs `measles `_). +(e.g. `influenza `_ vs `measles `_). For example, we've added a step in the curation pipeline to normalize the strain names for the `Zika ingest workflow `_. 1. We added a `custom Python script `_