{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1620","repository_url":"https://api.github.com/repos/cBioPortal/cbioportal","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1620/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1620/comments","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1620/events","html_url":"https://github.com/cBioPortal/cbioportal/issues/1620","id":173167531,"number":1620,"title":"Markup errors in ReadtheDocs documentation","user":{"login":"fedde-s","id":4929431,"avatar_url":"https://avatars.githubusercontent.com/u/4929431?v=3","gravatar_id":"","url":"https://api.github.com/users/fedde-s","html_url":"https://github.com/fedde-s","followers_url":"https://api.github.com/users/fedde-s/followers","following_url":"https://api.github.com/users/fedde-s/following{/other_user}","gists_url":"https://api.github.com/users/fedde-s/gists{/gist_id}","starred_url":"https://api.github.com/users/fedde-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fedde-s/subscriptions","organizations_url":"https://api.github.com/users/fedde-s/orgs","repos_url":"https://api.github.com/users/fedde-s/repos","events_url":"https://api.github.com/users/fedde-s/events{/privacy}","received_events_url":"https://api.github.com/users/fedde-s/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/documentation","name":"documentation","color":"0052cc"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-08-25T10:26:12Z","updated_at":"2016-09-07T16:30:23Z","closed_at":null,"body":"The markup on https://cbioportal.readthedocs.io/en/hotfix/File-Formats.html was written for GitHub, and copied to ReadtheDocs without adjustments in pull request #1546. This has caused several syntax elements to show up verbatim in the document rather than being typeset:\r\n\r\n- [ ] HTML escape sequences in the explanation of the `data_filename` fields of most metadata files   \r\n![screen shot 2016-08-25 at 12 22 42](https://cloud.githubusercontent.com/assets/4929431/17965814/c40a3266-6abe-11e6-97ca-1e38ad099660.png)\r\n\r\n- [ ] level-five headers under [Clinical Data → Data Files](https://cbioportal.readthedocs.io/en/hotfix/File-Formats.html#data-files)   \r\n![screen shot 2016-08-25 at 12 24 17](https://cloud.githubusercontent.com/assets/4929431/17965835/ebf3867e-6abe-11e6-9536-6eee53611241.png)\r\n\r\n- [ ] the table under [Expression Data → Supported stable_id values for MRNA_EXPRESSION](https://cbioportal.readthedocs.io/en/hotfix/File-Formats.html#supported-stable-id-values-for-mrna-expression)   \r\n![screen shot 2016-08-25 at 12 25 40](https://cloud.githubusercontent.com/assets/4929431/17965875/1323e6bc-6abf-11e6-84e1-fd6681ca7a18.png)\r\n\r\n- [ ] the emoji escape sequences `:warning:`, `:information_source`, `:arrow_up:` and `:arrow_down:` in various places\r\n![screen shot 2016-08-25 at 12 31 51](https://cloud.githubusercontent.com/assets/4929431/17966056/f349daee-6abf-11e6-8848-0595bfef4f46.png)\r\n\r\n- [ ] a hyperlink in the description of patient attribute files\r\n![screen shot 2016-08-25 at 12 46 36](https://cloud.githubusercontent.com/assets/4929431/17966489/17d06fde-6ac2-11e6-853f-700b79afe7c4.png)\r\n\r\n- [ ] and finally, an internal link in the description of the `groups` metadatum of studies, which was probably already broken when we moved away from GitHub’s wiki feature   \r\n![screen shot 2016-08-25 at 12 51 28](https://cloud.githubusercontent.com/assets/4929431/17966596/b2f0cc98-6ac2-11e6-85dd-1c63fc9ecf95.png)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments/245339032","html_url":"https://github.com/cBioPortal/cbioportal/issues/1620#issuecomment-245339032","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1620","id":245339032,"user":{"login":"fedde-s","id":4929431,"avatar_url":"https://avatars.githubusercontent.com/u/4929431?v=3","gravatar_id":"","url":"https://api.github.com/users/fedde-s","html_url":"https://github.com/fedde-s","followers_url":"https://api.github.com/users/fedde-s/followers","following_url":"https://api.github.com/users/fedde-s/following{/other_user}","gists_url":"https://api.github.com/users/fedde-s/gists{/gist_id}","starred_url":"https://api.github.com/users/fedde-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fedde-s/subscriptions","organizations_url":"https://api.github.com/users/fedde-s/orgs","repos_url":"https://api.github.com/users/fedde-s/repos","events_url":"https://api.github.com/users/fedde-s/events{/privacy}","received_events_url":"https://api.github.com/users/fedde-s/received_events","type":"User","site_admin":false},"created_at":"2016-09-07T16:30:22Z","updated_at":"2016-09-07T16:30:22Z","body":"@inodb I see, thanks for the info! As I understand the documentation, the way to include tables with the Markdown dialect used by recommonmark is using [HTML blocks](http://spec.commonmark.org/0.26/#html-blocks). And the problem with that particular level 5 header is probably this requirement in [the paragraph on ATX headings](http://spec.commonmark.org/0.26/#atx-headings): “The opening sequence of # characters must be followed by a space or by the end of line.”. So it might be trivial after all!"}}
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