PR: merge Rootstock updates on 2020-02-28 #991

dhimmel · 2020-02-28T19:34:41Z

No description provided.

merges manubot/rootstock#286 closes manubot/rootstock#284 - removes table scroll plugin - relies on pandoc-tablenos to wrap `<table>` elements in `<div>`s that can be scrolled - updates CSS such that breaks are forced when printing or when a table isn't given an id (and thus isn't wrapped with a `<div>` - simplifies plugins a bit as a result of pandoc-tablenos and pandoc-fignos changes - adds tolerance to scroll-out-of-bounds feature - adds support for equations in anchors plugin

Merges manubot/rootstock#289 * Update metadata.yaml to use 'authors' * Mention delete-me.md in USAGE

merges manubot/rootstock#298

merges manubot/rootstock#290 The options for the pandoc commands in build/build.sh are now configured in YAML files that are passed to Pandoc using --defaults. export PANDOC_DEFAULTS_DIR to override the directory with pandoc --defaults files

merges manubot/rootstock#300

merges manubot/rootstock#301

merges manubot/rootstock#297

merges manubot/rootstock#302 GitHub Actions: do not run deploy.sh if secrets.MANUBOT_SSH_PRIVATE_KEY is not set resulting in `env: MANUBOT_SSH_PRIVATE_KEY: ""` https://github.saobby.my.eu.orgmunity/t5/GitHub-Actions/If-expression-with-context-variable/m-p/34560/highlight/true#M1959 Travis CI: condition deploy on MANUBOT_SSH_PRIVATE_KEY being set or variable name expansion for encrypted_*. https://unix.stackexchange.com/a/290296/294987 https://wiki.bash-hackers.org/syntax/pe#variable_name_expansion

https://travis-ci.com/manubot/rootstock/builds/145087566#L2163 travis_run_after_success: command not found

merges manubot/rootstock#303 SETUP manubot upgrade instructions. add --no-rebase to git pull Upgrade Manubot to fix get_rootstock_commit GitHub Actions: fetch entire commit history to support get_rootstock_commit

merges manubot/rootstock#305 Create artifacts that are named like manuscript-32632624-d1c4caf and contain the GitHub Actions run-id as well as the head of the triggering commit hash. Note that on a pull request, this is the commit that was added to the PR and not the auto-generated merge commit that the action is actually evaluating.

Rename environment variables for deployment to: $CI_BUILD_WEB_URL $CI_JOB_WEB_URL Fix bug with $CI_JOB_WEB_URL on GitHub Actions

merges manubot/rootstock#304 autogenerated by https://ecotrust-canada.github.io/markdown-toc/

merges manubot/rootstock#309 closes manubot/rootstock#308

merges manubot/rootstock#311 Includes manubot update with yamllint output for invalid metadata.yaml files.

merges manubot/rootstock#310 Previously secrets.GITHUB_TOKEN did not work for deployment because the commits it pushed to `gh-pages` were unable to trigger a GitHub Pages build on public repositories. However, this issue seems to have been quietly resolved. There has been no official GitHub announcement about the change, so there is a risk that it will be temporary. Deployment now uses MANUBOT_SSH_PRIVATE_KEY over MANUBOT_ACCESS_TOKEN when both are set. The idea is that if GitHub's support for GITHUB_TOKEN is temporary (since no official commitment yet), then users who have configured MANUBOT_ACCESS_TOKEN will not be affected. Only users who did not set up MANUBOT_SSH_PRIVATE_KEY will be affected, but they could then set up MANUBOT_SSH_PRIVATE_KEY without having to upgrade Manubot Rootstock to get deployment to work.

[skip ci]

merges manubot/rootstock#313 Previously deployment was governed by the presence of MANUBOT_SSH_PRIVATE_KEY, but now that GITHUB_TOKEN is supported for deployment, forks with master branch commits attempted to deploy.

merges manubot/rootstock#314 * Simplify setup by creating branches later For a new manuscript, the first deploy event won't be able to fetch gh-pages and output because they were not pushed during setup. However, the deploy script now ignores the error on fetch and continues with the deployment, creating those branches at the first deployment. All subsequent deployments work as they did previously. * SETUP: Update with how to workaround GITHUB_TOKEN not triggering Pages builds.

merges manubot/rootstock#315 Update environment on 2020-02-27 USAGE: clarify citation key syntax

AppVeyorBot · 2020-02-28T19:36:47Z

AppVeyor build 1.0.26 for commit dfaf888 by @dhimmel failed.

reference_counts is no longer added to manuscript_stats because citation processing has been moved to pandoc-manubot-cite filter.

dhimmel · 2020-02-28T19:42:23Z

I think this PR has to be merged before GitHub actions will start running. However, once that's the case, we could remove Travis and use GitHub Actions + AppVeyor. @agitter?

content/citation-tags.tsv is now deprecated

dhimmel · 2020-02-28T20:07:03Z

builds for c822167 seem to be timing out. Not sure why. One possibility is that something wrote to stdout and has somehow caused pandoc to indefinitely wait on the pandoc-manubot-cite filter output

Ah I bet its https://github.com/manubot/manubot/blob/68ae7cfeb3928729228b5c9f0e11abbaceb7edb9/manubot/util.py#L128-L129

Actually it's looking like it's running just slowly. Looks like retrieving citation metadata is slow. Possibly due to datacite switch?

AppVeyorBot · 2020-02-28T20:14:54Z

AppVeyor build 1.0.27 for commit c822167 by @dhimmel is now complete. The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot · 2020-02-28T20:39:56Z

AppVeyor build 1.0.28 for commit d8c2b79 by @dhimmel is now complete. The rendered manuscript from this build is temporarily available for download at:

agitter

we could remove Travis and use GitHub Actions + AppVeyor

Yes, that switch works for me.

I wonder why the AppVeyor builds still work despite the Travis CI builds timing out? I made an initial pass over the changes, and they look good so far. I'd like to do a final check once the Travis timeouts are resolved. I haven't inspected the manuscript artifacts yet.

agitter · 2020-02-28T21:03:39Z

README.md

@@ -2,7 +2,8 @@

 [![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://greenelab.github.io/deep-review/)
 [![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://greenelab.github.io/deep-review/manuscript.pdf)
-[![Build Status](https://travis-ci.org/greenelab/deep-review.svg?branch=master)](https://travis-ci.org/greenelab/deep-review)
+[![GitHub Actions Status](https://github.com/greenelab/deep-review/workflows/Manubot/badge.svg)](https://github.com/greenelab/deep-review/actions)
+[![Travis Build Status](https://travis-ci.org/greenelab/deep-review.svg?branch=master)](https://travis-ci.org/greenelab/deep-review)


We can remove this if we switch to GitHub Actions+AppVeyor

dhimmel · 2020-02-28T21:15:00Z

I wonder why the AppVeyor builds still work despite the Travis CI builds timing out?

Travis (by default) times out after 10 minutes of inactivity in terms of log output. AppVeyor must be more patient.

AppVeyorBot · 2020-02-28T21:16:05Z

AppVeyor build 1.0.29 for commit 968c918 by @dhimmel is now complete. The rendered manuscript from this build is temporarily available for download at:

dhimmel · 2020-02-28T21:34:15Z

Okay I think the timeout was caused by the datacite DOI resolver being a bit slower than what we used previously combined with having to regenerate the cache for all DOIs. @agitter I think we can merge with the slowness.

One thing we should probably do is freeze the references. But possibly in a follow up PR

agitter

I didn't notice any problems in the PDF.

One thing we should probably do is freeze the references. But possibly in a follow up PR

Yes, let's save this for a follow up PR.

agitter · 2020-02-28T22:04:21Z

content/90.back-matter.md

+[@tag:Gulshan2016_dt]: doi:10.1001/jama.2016.17216
+[@tag:Gupta2015_exprs_yeast]: doi:10.1101/031906
+[@tag:Gupta2015_prec]: arxiv:1502.02551
+[@tag:Guetterman]: url:http://www.fasebj.org/content/30/1_Supplement/406.3


If we freeze references post-merge, we need to add a manual reference for this first. We're adding a broken DOI link https://doi.org/10.1096/fasebj.30.1_supplement.406.3

[ci skip] This build is based on 0b92301. This commit was created by the following CI build and job: https://github.com/greenelab/deep-review/commit/0b923010707347c447c4dafb66fe95b0d34061fa/checks https://github.com/greenelab/deep-review/runs/46994285

vincerubinetti and others added 23 commits December 13, 2019 15:12

Update metadata.authors & USAGE

37b3378

Merges manubot/rootstock#289 * Update metadata.yaml to use 'authors' * Mention delete-me.md in USAGE

SETUP: better manubot update instructions

b5c196f

merges manubot/rootstock#298

Process citations / references with pandoc-manubot-cite filter

6636b91

merges manubot/rootstock#300

Minor environment updates on 2020-01-14

52211e1

merges manubot/rootstock#301

GitHub Actions workflow for building and deployment

f072e93

merges manubot/rootstock#297

Tweaks following up GitHub Actions

af52dea

Attempt to fix .travis.yml syntax error

f6b6231

https://travis-ci.com/manubot/rootstock/builds/145087566#L2163 travis_run_after_success: command not found

Fix get_rootstock_commit on CI

42669ce

merges manubot/rootstock#303 SETUP manubot upgrade instructions. add --no-rebase to git pull Upgrade Manubot to fix get_rootstock_commit GitHub Actions: fetch entire commit history to support get_rootstock_commit

CI deployment: update env vars

8924d7d

Rename environment variables for deployment to: $CI_BUILD_WEB_URL $CI_JOB_WEB_URL Fix bug with $CI_JOB_WEB_URL on GitHub Actions

SETUP.md: add table of contents

40b0e5b

merges manubot/rootstock#304 autogenerated by https://ecotrust-canada.github.io/markdown-toc/

.appveyor.yml: note about skipping branches with PR

7412f76

merges manubot/rootstock#309 closes manubot/rootstock#308

Update environment on 2020-02-17

7545592

merges manubot/rootstock#311 Includes manubot update with yamllint output for invalid metadata.yaml files.

SETUP.md: fix double negative typo

d14dd7d

[skip ci]

GH Actions: skip deployment on forks

9bdf4c1

merges manubot/rootstock#313 Previously deployment was governed by the presence of MANUBOT_SSH_PRIVATE_KEY, but now that GITHUB_TOKEN is supported for deployment, forks with master branch commits attempted to deploy.

fixup! GH Actions: skip deployment on forks

cd8ce12

Update environment 2020-02-27 & citations usage

cde7fa2

merges manubot/rootstock#315 Update environment on 2020-02-27 USAGE: clarify citation key syntax

Merge Rootstock updates on 2020-02-28

dfaf888

Remove {{manubot.manuscript_stats.reference_counts}}

c822167

reference_counts is no longer added to manuscript_stats because citation processing has been moved to pandoc-manubot-cite filter.

Move citation tags in backmatter

d8c2b79

content/citation-tags.tsv is now deprecated

dhimmel mentioned this pull request Feb 28, 2020

Prevent subprocess calls from writing to stdout manubot/manubot#212

Merged

agitter reviewed Feb 28, 2020

View reviewed changes

dhimmel force-pushed the rootstock-2020-02-28 branch from 968c918 to d8c2b79 Compare February 28, 2020 22:02

agitter approved these changes Feb 28, 2020

View reviewed changes

dhimmel merged commit 0b92301 into greenelab:master Feb 28, 2020

dhimmel deleted the rootstock-2020-02-28 branch February 28, 2020 22:13

dhimmel mentioned this pull request Feb 28, 2020

Follow up tweaks after switching to GitHub actions #992

Merged

2 tasks

agitter mentioned this pull request Mar 16, 2020

add discussion in interpretability section and updates to molecular design section and discussion sections (issues with previous PR fixed) #988

Merged

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PR: merge Rootstock updates on 2020-02-28 #991

PR: merge Rootstock updates on 2020-02-28 #991

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PR: merge Rootstock updates on 2020-02-28 #991

PR: merge Rootstock updates on 2020-02-28 #991

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