Merge pull request #218 from nextstrain/fix-broken-links-14

Fix broken links [#14]

conda.yml

@@ -10,7 +10,7 @@ dependencies:
     - docutils
     - recommonmark
     - requests
-    - sphinx
+    - sphinx>=7.1
     - sphinx-autobuild
     - sphinx-markdown-tables
     - sphinx-argparse

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',
+]

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
-    <https://discussions.nextstrain.org>`__.
+    please don't hesitate to `email us`_ or post to `discussion.nextstrain.org
+    <https://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
-    <https://discussions.nextstrain.org>`__.
+    please don't hesitate to `email us`_ or post to `discussion.nextstrain.org
+    <https://discussion.nextstrain.org>`__.
 
     —the Nextstrain team
 

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 <https://nextstrain.org/rsv/A/G>`__
+updated, for instance at the time of writing `nextstrain.org/rsv/a/G <https://nextstrain.org/rsv/a/G>`__
 had 82 snapshots and was being updated weekly:
 
 .. image:: ../images/snapshots-listing-ui-hover.jpg

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 <https://nextstrain.org/schemas/auspice/config/v2>`__, however to
 introduce this file here's a snippet of the `Auspice config JSON for the
-measles dataset presented above <https://github.com/nextstrain/measles/blob/main/config/auspice_config.json>`__:
+measles dataset presented above <https://github.com/nextstrain/measles/blob/main/phylogenetic/defaults/auspice_config.json>`__:
 
 .. 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 <https://github.com/nextstrain/measles/blob/main/config/colors.tsv>`__
+are (some of) the colors TSV <https://github.com/nextstrain/measles/blob/main/phylogenetic/defaults/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 <https://github.com/nextstrain/measles/blob/main/config/auspice_config.json>`__
+keys <https://github.com/nextstrain/measles/blob/main/phylogenetic/defaults/auspice_config.json>`__
 and you can `see here <https://nextstrain.org/measles>`__ how Auspice
 renders these:
 

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

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 <https://conda-forge.org/docs/user/tipsandtricks.html#installing-apple-intel-packages-on-apple-silicon>`__. 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 <https://conda-forge.org/docs/user/tipsandtricks/#installing-apple-intel-packages-on-apple-silicon>`__. Run this after setting up an **empty** Conda environment and before installing any packages to it:
 
    .. code-block:: bash
 

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 <http://www.pnas.org/content/112/44/13609>`_. 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 <https://www.pnas.org/doi/10.1073/pnas.1507071112>`_. 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 <http://www.pnas.org/content/112/44/13609>`_, 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 <https://www.pnas.org/doi/10.1073/pnas.1507071112>`_, 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.
 

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 <https://www.cdc.gov/flu/about/viruses/types.htm#naming-influenza-viruses>`_ vs `measles <https://www.cdc.gov/measles/lab-tools/genetic-analysis.html#guide>`_).
+(e.g. `influenza <https://www.cdc.gov/flu/about/viruses/types.htm>`_ vs `measles <https://www.cdc.gov/measles/php/laboratories/genetic-analysis.html#cdc_generic_section_3-guidelines-for-naming-measles-strains-or-sequences>`_).
 For example, we've added a step in the curation pipeline to normalize the strain names for the `Zika ingest workflow <https://github.com/nextstrain/zika/tree/main/ingest>`_.
 
 1. We added a `custom Python script <https://github.com/nextstrain/zika/blob/a91e575bff38f154390c9eb11a44a89abf95a55b/ingest/bin/fix-zika-strain-names.py>`_