czi-seed-rfa missing root-level gh-pages files

[dhimmel]

@cgreene alerted me to a potential Manubot malfunction where index.html and manuscript.pdf are missing from the gh-pages branch of greenelab/czi-seed-rfa, a manubot manuscript repo. See for example here. The versioned gh-pages directories still seem to be getting created properly, so a temporary user-facing workaround is to access the latest version with the URL https://greenelab.github.io/czi-seed-rfa/v/latest/.

[dhimmel]

The commit where these files first disappeared seems to be greenelab/czi-seed-rfa@f5fef7f, which was the gh-pages deployment commit triggered by greenelab/czi-seed-rfa@9dff46f. All greenelab/czi-seed-rfa@9dff46f did was add a line to .gitignore, which at quick glance does not seem problematic.

Here is the build deployment log:

Switched to branch 'master'
M	webpage/README.md
Your branch is up to date with 'origin/master'.
Agent pid 3702
Identity added: ci/deploy.key (ci/deploy.key)
Warning: Permanently added the RSA host key for IP address '192.30.253.112' to the list of known hosts.
From github.com:greenelab/czi-seed-rfa
 * [new branch]      gh-pages   -> gh-pages
 * [new branch]      output     -> output
 * [new branch]      gh-pages   -> origin/gh-pages
 * [new branch]      output     -> origin/output
Attempting checkout with the following command:
git --work-tree=webpage checkout gh-pages -- v
Namespace(checkout='gh-pages', freeze_directory=PosixPath('webpage/v/freeze'), latest_directory=PosixPath('webpage/v/latest'), output_directory=PosixPath('output'), version='9dff46fcbc4e5c70fb070a734d2bbe6b0a45bf86', version_directory=PosixPath('webpage/v/9dff46fcbc4e5c70fb070a734d2bbe6b0a45bf86'), versions_directory=PosixPath('webpage/v'), webpage_directory=PosixPath('webpage'))
['038e2ef17d27103ea5850ec9b45d14294f965e56', '0482082a45c04d0885ec51aab3135ce0d6043191', '0c0ce8122be0382b1dd0b6145a30523b16c2570f', '1d1435f4dd04c1c3cebac5aee3a80a2443f89660', '269b0e89d12a3614406aa99cbe4200e9675dc3d2', '2e95f7368c98dead7bc39f02d4e690f0a8795268', '32c307590deb76c18541b22c2923df9316d91152', '348e01f786f7e6cdcf6ad7cb8d69ba1a9cbadbcf', '375f6105876fe6e7784c11dfd254b50f2376db9a', '4add3aaa9bb3c91c6a15096d77cc46c6b020bdaa', '4ce288644548c703b0ce07d3728894d27c252d4c', '4d82cd8643fa00f268751626e463df8ca9b59a0d', '6870fecefdd25f17d5b3ab4402bf6a9ecf0a0860', '6d5bb32536cf44a47468429727154421de405a22', '89740a3d3322714a8d2e2a38d5eb403b0b373da9', '971138053f9af22175da0ce8328961f1a09d3ff9', '9d143acf90b9afb4342a432b1fa7f495cc2063dc', '9dff46fcbc4e5c70fb070a734d2bbe6b0a45bf86', 'a1ea9c08d728c589803ec90421ab3eceea7cda36', 'a31d628eef3078e81f3c4960168f0307f03abc0b', 'aca481b6e0efe6295937947886e1ac7d373b5b5a', 'b91109bdd5f8e61dd878326df3dd57bda592bbec', 'c206f3c3f513087afb23fd5fab63fd7387440694', 'c49556f2dd2e5d5d7679f1753294bfb6ef3476f7', 'c97109d9aa0c82f6ce113ab47a35af277a7ccbc0', 'd5348c269307cdb34b912826e72ca6d0ccdc93e5', 'd53fc877c753dd5315987ceff0fd5f5920611dfb', 'def30c11bc4b26a0bdd12d07093b2e240c15825b', 'ea7858dab28e56f26e689cb891951bdc86c20c7b', 'ee42334c754db729fc94f5fa3a23a57ce1889a46', 'f97307b9a724825552ea619948ac848f9ab12c72']
Submitting to remote calendar https://a.pool.opentimestamps.org
Submitting to remote calendar https://b.pool.opentimestamps.org
Submitting to remote calendar https://a.pool.eternitywall.com
Submitting to remote calendar https://ots.btc.catallaxy.com
Warning: Permanently added the RSA host key for IP address '192.30.253.113' to the list of known hosts.
To github.com:greenelab/czi-seed-rfa.git
   baee5d3..69680c4  output -> output
To github.com:greenelab/czi-seed-rfa.git
   0e19194..f5fef7f  gh-pages -> gh-pages
unset SSH_AUTH_SOCK;
unset SSH_AGENT_PID;
echo Agent pid 3702 killed;

[dhimmel]

Unrelated but wanted to note, the Travis CI - Branch build is attempting to run the deployment and failing.
See https://travis-ci.com/greenelab/czi-seed-rfa/builds/90217844#L750:

$ test $TRAVIS_BRANCH = "master" && test $TRAVIS_PULL_REQUEST = "false" && sh ci/deploy.sh
M	webpage/README.md
Switched to branch 'master'
Your branch is up to date with 'origin/master'.
iv undefined

The push build is okay. I need to look into why there are two builds here.

[dhimmel]

Ah I think I see what happened. greenelab/czi-seed-rfa@ec018b7 deleted three symbolic links from the master branch: webpage/images, webpage/index.html, and webpage/manuscript.pdf. These symlinks are required.

I think the following could work to revert the unwanted changes:

# https://stackoverflow.com/a/4796144/4651668
git revert --no-commit ec018b74379ab95772c8d536e90ce8c04196ef32
git reset HEAD .
git add webpage
git commit

[dhimmel]

I opened a PR at greenelab/czi-seed-rfa#3 that should resolve the issue.

@Loyale do you remember why you deleted the symlinks in the webpage directory in greenelab/czi-seed-rfa@ec018b7? I am guessing it was because you thought they were junk (since you also removed .DS_Store files in this commit). Perhaps there is a way we can improve the documentation so other users don't do this (unintentionally) in the future.

[agitter]

@dhimmel could we make the Travis CI build fail if these or any other essential files or symlinks are missing?

[Loyale]

Did I do this through the .gitignore? I don’t remember removing symlinks explicitly, although I wouldn’t put it past myself... Cheers, Loyal

…

________________________________________ Loyal A. Goff, Ph.D. Assistant Professor Institute of Genetic Medicine Johns Hopkins School of Medicine MRB 449 733 N Broadway Baltimore, MD 21205 loyalgoff@jhmi.edu

________________________________________

On Nov 5, 2018, 5:37 PM -0500, Anthony Gitter ***@***.***>, wrote: @dhimmel could we make the Travis CI build fail if these or any other essential files or symlinks are missing? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[Loyale]

So actually looking at the commit, I have no recollection of doing those deletions. So yeah, my bad. Thanks for the fix. Cheers, Loyal

…

________________________________________ Loyal A. Goff, Ph.D. Assistant Professor Institute of Genetic Medicine Johns Hopkins School of Medicine MRB 449 733 N Broadway Baltimore, MD 21205 loyalgoff@jhmi.edu

________________________________________

On Nov 5, 2018, 5:37 PM -0500, Anthony Gitter ***@***.***>, wrote: @dhimmel could we make the Travis CI build fail if these or any other essential files or symlinks are missing? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.