Merge pull request #1570 from nextstrain/fix-broken-links-1569

Fix broken links [#1569]

Author: genehack

docs/conf.py

@@ -148,3 +148,18 @@ def prose_list(items):
     'pandas': ('https://pandas.pydata.org/docs', None),
     'treetime': ('https://treetime.readthedocs.io/en/stable/', None),
 }
+
+# -- Linkchecking ------------------------------------------------------------
+
+## NOTE: for both sets of regular expressions that follow, the
+## underlying linkchecker code uses `re.match()` to apply them to URLs
+## — so there's already an implicit "only at the beginning of a
+## string" matching happening, and something like a plain `r'google'`
+## regular expression will _NOT_ match all google.com URLs.
+linkcheck_ignore = []
+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',
+]

docs/faq/metadata.rst

@@ -81,8 +81,7 @@ locations ('new_zealand' became 'New Zealand').
 
 Auspice will still do this if you are exporting 'V1' type JSON files
 (from augur v5 or augur v6 using ``export v1``), but will not do this if
-you are using ``export v2`` (`read
-more <../releases/migrating-v5-v6.html#prettifying-metadata-fields>`__).
+you are using ``export v2`` (:ref:`read more <prettifying-metadata-fields>`).
 Instead, you should update your metadata files so that traits look the
 same as you'd like them to display in Auspice (change 'new_zealand' to
 'New Zealand' in your metadata, and in any additional latitude-longitude

docs/faq/what-is-a-build.md

@@ -11,7 +11,7 @@ These steps, taken together, are what we refer to as a "build".
 
 ### Example build
 
-The [Zika virus tutorial](https://docs.nextstrain.org/en/latest/tutorials/zika.html#build-steps) describes a build which contains the following steps:
+The [Zika virus tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html#run-a-nextstrain-build) describes a build which contains the following steps:
 
 1. Prepare pathogen sequences and metadata
 2. Align sequences
@@ -28,5 +28,5 @@ If you look at the [other tutorials](https://docs.nextstrain.org/en/latest/tutor
 While it is possible to run a build by running each of the individual steps, we typically group these together into a make-type file.
 [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) is "a tool to create reproducible and scalable data analyses... via a human-readable, Python-based language."
 
-> Snakemake is installed as part of the [conda environment](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html#install-augur-auspice-with-conda) or the [docker container](https://docs.nextstrain.org/en/latest/guides/install/cli-install.html).
+> Snakemake is installed as part of the [conda environment](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html) or the [docker container](https://docs.nextstrain.org/en/latest/guides/install/cli-install.html).
 If you ever see a build which has a "Snakefile" then you can run this by typing `snakemake --cores 1` or `nextstrain build --cpus 1 .`, respectively.

docs/installation/non-python-dependencies.rst

@@ -5,7 +5,7 @@ Augur uses some external bioinformatics programs that are not available on PyPI:
 - ``augur tree`` requires at least one of:
 
    - `IQ-TREE <http://www.iqtree.org/>`__ (used by default)
-   - `RAxML <https://sco.h-its.org/exelixis/web/software/raxml/>`__ (optional alternative)
+   - `RAxML <https://cme.h-its.org/exelixis/web/software/raxml/>`__ (optional alternative)
    - `FastTree <http://www.microbesonline.org/fasttree/>`__ (optional alternative)
 
 - ``augur merge`` requires ``sqlite3``, the `SQLite <https://sqlite.org>`__ CLI (version ≥3.39).