Fix: pull changes from Rootstock 2020-11-12 #18
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merges manubot/rootstock#366 clarifies that 1. OWNER can be an organization! 2. no additional configuration is needed for github actions.
merges manubot/rootstock#374 From https://github.com/manubot/rootstock/runs/1212860980#step:2:10: > Warning: The `set-env` command is deprecated and will be disabled soon. > Please upgrade to using Environment Files. > For more information see: > https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/ https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable
merges manubot/rootstock#375 supersedes manubot/rootstock#373 By default, these plugins are disabled. Enable in `build/pandoc/defaults/html.yaml`. Co-authored-by: Matthew Turk <[email protected]>
merges manubot/rootstock#383 pandoc-eqnos upgrade addresses the following error: UnboundLocalError: local variable 'ret' referenced before assignment tomduck/pandoc-eqnos#43 Hold back pandoc due to the lack of panflute support. Switch commands in build/README.md to be relative to the repo root.
merges manubot/rootstock#385 Pin panflute dependency We use panflute to build custom pandoc filters. Panflute versions only work with specific versions of the Pandoc AST. We need to pin pandoc/panflute to a version pair that is known to work together. Pin versions of additional explicit manubot dependencies, as of https://github.com/manubot/manubot/blob/01d69f066eaf6554111e6bcf197f7ee1fcfb240b/setup.py#L65-L80 CI: use conda-incubator/setup-miniconda on GH actions https://github.com/conda-incubator/setup-miniconda appears to have replaced https://github.com/goanpeca/setup-miniconda. The later is currently 31 commits behind.
merges manubot/rootstock#389 closes manubot/rootstock#388 > The `set-env` command is deprecated and will be disabled on November 16th. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/
…otstock-2020-11-12
dcsoto
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Nov 12, 2020
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[ci skip] This build is based on f5ca2a3. This commit was created by the following CI build and job: https://github.com/computer-aided-biotech/better-cb/commit/f5ca2a3aea7fe8148ced27153c03eb8cd1fae270/checks https://github.com/computer-aided-biotech/better-cb/runs/360145178
github-actions bot
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Nov 12, 2020
[ci skip] This build is based on f5ca2a3. This commit was created by the following CI build and job: https://github.com/computer-aided-biotech/better-cb/commit/f5ca2a3aea7fe8148ced27153c03eb8cd1fae270/checks https://github.com/computer-aided-biotech/better-cb/runs/360145178
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The CI started erroring due to an update in Github Actions, so I pulled from the original repo all the changes since we did the fork in July. @dcsoto this maybe is a sign that we should not remove the history as discussed in #7?
The CI is now working fine, once this is merged to master I can merge in turn to the other open PRs (#16 and #17).