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Fix broken links in docs #1133

Closed
2 tasks done
genehack opened this issue Aug 6, 2024 · 0 comments · Fixed by #1137
Closed
2 tasks done

Fix broken links in docs #1133

genehack opened this issue Aug 6, 2024 · 0 comments · Fixed by #1137
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genehack commented Aug 6, 2024 •
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In order to implement automated link checking in RTD as part of CI, it is necessary to manually audit broken links in this repo first.

Remaining broken links:

Slack context for the above; created child issues so that I can link to them in FIXME comments in the config file, where I'm setting those two links to "ignore" temporarily, in order to get a clean doc build.
@genehack genehack added the bug Something isn't working label Aug 6, 2024
@genehack genehack self-assigned this Aug 6, 2024
@genehack genehack mentioned this issue Aug 6, 2024
Merged
5 tasks
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Add linkchecker configuration [#1133]
58ad27e 
Note: this contains 2 URLs in the `linkcheck_ignore` section that need
to be fixed; each has an associated FIXME comment linking to a Github
issue.

I'm ignoring those temporarily so that after this PR is merged, `make
linkcheck` will exit without error in this repo, which will unblock
activating linkchecking in _all_ the CI doc builds.
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Convert change_log.md to RST [#1133]
b455a5e
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove long anchor from wikipedia link [#1133]
391dce6 
I think this was supposed to highlight or focus some text, somehow?
But it wasn't doing anything, and the text in the anchor is already at
the top of the entry on wikipedia.

Removing it didn't change any behavior.
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Switch internal links to use :doc: [#1133]
d494d86
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Correct link to Nextstrain documentation [#1133]
e953e30
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Add anchors used in other files/links [#1133]
5558528
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove cross-reference to non-existent file [#1133]
9bdabbb
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix GISAID registration links [#1133]
6b7855a
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix link to Pybus review PDF [#1133]
11c0cbb
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix link to CDC gen-epi-toolkit [#1133]
2302224
@genehack genehack mentioned this issue Aug 9, 2024
Merged
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Convert change_log.md to RST [#1133]
3ab738b
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove long anchor from wikipedia link [#1133]
ec3f643 
I think this was supposed to highlight or focus some text, somehow?
But it wasn't doing anything, and the text in the anchor is already at
the top of the entry on wikipedia.

Removing it didn't change any behavior.
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Switch internal links to use :doc: [#1133]
0755cbb
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Correct link to Nextstrain documentation [#1133]
f3c2b5a
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Add anchors used in other files/links [#1133]
86acdac
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove cross-reference to non-existent file [#1133]
0f71604
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix GISAID registration links [#1133]
abc0f0a
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix link to Pybus review PDF [#1133]
f729dc7
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Fix link to CDC gen-epi-toolkit [#1133]
487e3a2
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Add linkchecker configuration [#1133]
d06461d 
Note: this contains 2 URLs in the `linkcheck_ignore` section that need
to be fixed; each has an associated FIXME comment linking to a Github
issue.

I'm ignoring those temporarily so that after this PR is merged, `make
linkcheck` will exit without error in this repo, which will unblock
activating linkchecking in _all_ the CI doc builds.
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Convert change_log.md to RST [#1133]
3132e88
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove long anchor from wikipedia link [#1133]
69599ce 
I think this was supposed to highlight or focus some text, somehow?
But it wasn't doing anything, and the text in the anchor is already at
the top of the entry on wikipedia.

Removing it didn't change any behavior.
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Switch internal links to use :doc: [#1133]
2a086a3
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Correct link to Nextstrain documentation [#1133]
2b13e33
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Add anchors used in other files/links [#1133]
08b15e6
genehack added a commit that referenced this issue Aug 9, 2024
@genehack
Remove cross-reference to non-existent file [#1133]
346f5ba
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Update GitHub URL [#1133]
3fd1204 
* switch `tree` to `blob`, because they 301 that way
* swap `master` for `-`, for future-proofing
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Exclude wikipedia link with text fragement anchor from anchor checks [#…
83f4316 
…1133]

The linkchecker doesn't recognize the text fragment thing as a real
anchor, so just exclude that from the full anchor check.
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Switch internal links to use :doc: [#1133]
814a4a7
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Correct link to Nextstrain documentation [#1133]
1a19d02
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Add anchors used in other files/links [#1133]
4ef9f03
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix non-existent file cross-reference to point to different file [#1133]
946c0e8
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix GISAID registration links [#1133]
43eb18f
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix link to Pybus review PDF [#1133]
6f7aac0
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix link to CDC gen-epi-toolkit [#1133]
95c115e
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Change relative internal anchor links to full URIs [#1133]
b695707
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Correct link to CDC variant info [#1133]
63211f9
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Remove done FIXME; exclude known-good URL [#1133]
d2a3e7b 
Known-good URL is failing for technical reasons related to how
nextstrain.org handles routing datasets without a default.

[Slack context](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1723571470133649)
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Change all www.gisaid.org to gisaid.org` [#1133]
c82f4aa 
GISAID is returning 301 on `www.gisaid.org` links, so let's respect it
and update our URLs.

Also correct some URLs to where they ultimately redirect.
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Update GitHub URL [#1133]
c9f7cfa 
* switch `tree` to `blob`, because they 301 that way
* swap `master` for `-`, for future-proofing
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Add linkchecker configuration [#1133]
1b01638 
Note: this contains 2 URLs in the `linkcheck_ignore` section that need
to be fixed; each has an associated FIXME comment linking to a Github
issue.

I'm ignoring those temporarily so that after this PR is merged, `make
linkcheck` will exit without error in this repo, which will unblock
activating linkchecking in _all_ the CI doc builds.
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Exclude wikipedia link with text fragement anchor from anchor checks [#…
e4060a3 
…1133]

The linkchecker doesn't recognize the text fragment thing as a real
anchor, so just exclude that from the full anchor check.
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Switch internal links to use :doc: [#1133]
3a583ff
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Correct link to Nextstrain documentation [#1133]
0739bbc
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Add anchors used in other files/links [#1133]
ecea383
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix non-existent file cross-reference to point to different file [#1133]
8888bf0
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix GISAID registration links [#1133]
da0112b
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix link to Pybus review PDF [#1133]
8bfc379
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Fix link to CDC gen-epi-toolkit [#1133]
31530dd
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Change relative internal anchor links to full URIs [#1133]
2ccf285
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Correct link to CDC variant info [#1133]
3032ab1
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Remove done FIXME; exclude known-good URL [#1133]
913f2ca 
Known-good URL is failing for technical reasons related to how
nextstrain.org handles routing datasets without a default.

[Slack context](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1723571470133649)
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Change all www.gisaid.org to gisaid.org` [#1133]
136675f 
GISAID is returning 301 on `www.gisaid.org` links, so let's respect it
and update our URLs.

Also correct some URLs to where they ultimately redirect.
genehack added a commit that referenced this issue Aug 13, 2024
@genehack
Update GitHub URL [#1133]
5810e0f 
* switch `tree` to `blob`, because they 301 that way
* swap `master` for `-`, for future-proofing
genehack added a commit that referenced this issue Aug 15, 2024
@genehack
Merge pull request #1137 from nextstrain/fix-broken-links-1133
8e33e22 
Fix broken links [#1133]
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Fix broken links [#1133] nextstrain/ncov
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