Merge pull request #1808 from nextstrain/fix-broken-links-1807

Fix broken links [#1807]

CHANGELOG.md

@@ -1217,7 +1217,7 @@ This also fixed potential issues related to loading datasets where the URL queri
 * Disable Untangling
 
 ## version 1.21.1 - 2018/06/04
-* Narratives are now sourced from [the static github repo](https://github.com/nextstrain/static/tree/master/narratives)
+* Narratives are now sourced from [the static github repo](https://github.com/nextstrain/static/tree/eea71fc22299c1d7febd25ea0ec1b00dcd286a3a~/narratives)
 
 ## version 1.21.0 - 2018/06/01
 * Untangling via a simple algorithm upon 2nd tree load
@@ -1396,7 +1396,7 @@ This also fixed potential issues related to loading datasets where the URL queri
 ## version 1.14.0 - 2018/02/27
 
 ### Features
-* Strain search (using [awesomplete](https://leaverou.github.io/awesomplete/)).
+* Strain search (using [awesomplete](https://projects.verou.me/awesomplete/)).
 This highlights the path to a single tip and increases the tip radius.
 Strain is stored in the URL query (`s=...`) and can be restored via URL.
 Selected strain also appears in the info panel (top of screen).

docs/conf.py

@@ -66,3 +66,23 @@
 intersphinx_mapping = {
     'docs.nextstrain.org': ('https://docs.nextstrain.org/en/latest/', 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 = [
+     # we have links to localhost for explanatory purposes; obviously
+     # they will never work in the linkchecker
+     r'^http://localhost:\d+',
+]
+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/customise-client/overview.rst

@@ -3,7 +3,7 @@ Overview (Client)
 ======================================
 
 
-Auspice allows you to customise the appearance and functionality of Auspice `when the client is built <../introduction/how-to-run.html#auspice-build>`_.
+Auspice allows you to customise the appearance and functionality of Auspice :ref:`when the client is built <auspice-build>`.
 This is how Auspice running locally and nextstrain.org look different, despite both using "Auspice".
 
 .. image:: ../assets/auspice-vs-nextstrain.png
@@ -21,7 +21,7 @@ This is achieved by providing a JSON at build time to Auspice which defines the
 `Here's <https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json>`_ the file used by nextstrain.org to change the appearance of Auspice in the above image.
 
 
-See the `client customisation API <api.html>`_ for the available options.
+See the :doc:`client customisation API <./api>` for the available options.
 
 AGPL Source Code Requirement
 ============================

docs/customise-client/requests.rst

@@ -1,7 +1,7 @@
 Requests Made from the Client
 =============================
 
-The Auspice client will make a number of requests to various endpoints, which this document aims to provide an overview of. Some of these are dependent on the `build-time customisations <./api>`__ in use, and we plan to allow more flexibility here using this mechanism.
+The Auspice client will make a number of requests to various endpoints, which this document aims to provide an overview of. Some of these are dependent on the :doc:`build-time customisations <./api>` in use, and we plan to allow more flexibility here using this mechanism.
 
 Requests to the Auspice Server
 ------------------------------
@@ -36,15 +36,10 @@ The initial Auspice page (i.e. the one which displays a listing of available dat
 External Requests
 -----------------
 
-Fonts
-~~~~~
-
-Two initial requests for fonts are made, for `Google-hosted Lato fonts (CSS) <https://fonts.googleapis.com/css?family=Lato:100,200,300,400,500,700>`__ and `font-awesome (CSS) <https://maxcdn.bootstrapcdn.com/font-awesome/4.4.0/css/font-awesome.min.css%22%3E>`__. These in turn make a number of subsequent requests for the individual font files etc.
-
 Leaflet
 ~~~~~~~
 
-We use `Leaflet <https://leafletjs.com/>`__ to display the map tiles. There is one `initial CSS request <https://unpkg.com/[email protected]/dist/leaflet.css>`__ which is always made, regardless of whether a map is displayed.
+We use `Leaflet <https://leafletjs.com/>`__ to display the map tiles.
 
 If a map is displayed by Auspice the individual tiles are requested from api.mapbox.com. Panning and zooming of the map result in futher requests for tiles. These are requested using our hardcoded access key, however this may change to a build-time-customisation in the future.
 

docs/index.rst

@@ -42,7 +42,7 @@ License and Copyright
 
 Copyright © 2014-2020 Trevor Bedford and Richard Neher.
 
-Source code to Nextstrain is made available under the terms of the `GNU Affero General Public License <LICENSE.txt>`_ (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.
+Source code to Nextstrain is made available under the terms of the `GNU Affero General Public License <https://github.com/nextstrain/auspice/blob/-/LICENSE.txt>`_ (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.
 
 
 .. toctree::

docs/introduction/how-to-run.rst

@@ -43,6 +43,8 @@ This is the main command we'll run Auspice with, as it makes Auspice available i
 
 For more complicated setups, where you define your own server handlers, see :ref:`supplying custom handlers to the Auspice server <server-api-supplying-custom-handlers>`.
 
+.. _auspice-build:
+
 ``auspice build``
 -----------------
 

docs/releases/v2.rst

@@ -114,7 +114,7 @@ We've made more things available when you hover over the tree or click on a tree
 Display of second trees
 -----------------------
 
-Auspice has had the ability to display two trees side-by-side for a while now (and `finally documented <../advanced-functionality/second-trees.md>`__). If you wanted to, say, compare influenza HA & NA trees, the URL used to look like "flu/seasonal/h3n2/ha:na/2y". This turned out to be problematic when coming up with suitable candidates for potential second-trees, and also made it impossible to compare, for instance, "ha/2y" with "na/3y"
+Auspice has had the ability to display two trees side-by-side for a while now (and :doc:`finally documented <../../advanced-functionality/second-trees>`). If you wanted to, say, compare influenza HA & NA trees, the URL used to look like "flu/seasonal/h3n2/ha:na/2y". This turned out to be problematic when coming up with suitable candidates for potential second-trees, and also made it impossible to compare, for instance, "ha/2y" with "na/3y"
 
 We now use a more verbose syntax to define the display of multiple trees, specifying the entire pathname for both datasets. The above example is now "flu/seasonal/h3n2/ha/2y:flu/seasonal/h3n2/na/2y". Any available datasets can be compared using this URL syntax, even if the result is rather nonsensical. The old syntax will continue to work and will automatically correct to the new syntax (and show you a warning).
 

docs/server/overview.rst

@@ -27,7 +27,7 @@ Currently the client is able to make three requests:
 For instance, when you're running ``auspice view`` if you go to `localhost:4000/charon/getAvailable <http://localhost:4000/charon/getAvailable>`_ you'll see a list of the available datasets and narratives known to the server.
 Similarly, nextstrain.org is a server which has handlers for these three API endpoints, so if you visit `nextstrain.org/charon/getAvailable <https://nextstrain.org/charon/getAvailable>`_ you'll see Nextstrain's available datasets.
 
-See `the server API <../server/api.html>`_ for details about each of these requests.
+See :doc:`the server API <./api>` for details about each of these requests.
 
 .. note::
    Note that "/charon" can be changed to any address you wish by customising the client at build time.
@@ -45,7 +45,7 @@ Customising the Default Auspice Server
 ======================================
 
 You can customise the default Auspice server by supplying your own handlers for each of the three GET requests.
-See `the API documentation <../server/api.html#supplying-custom-handlers-to-the-auspice-server>`_ for how to define these and provide them to `auspice view`.
+See :ref:`the API documentation <server-api-supplying-custom-handlers>` for how to define these and provide them to `auspice view`.
 
 
 AGPL Source Code Requirement