Use a single markup syntax throughout

[david4096]

What are folks opinions on RST vs. markdown? I think they perform the same functions but I personally find markdown easier to write.

There is probably a way to edit it on the docker side, but you can see how the RST appears there. https://hub.docker.com/r/ga4gh/server/ . I think the docs would be easier to maintain in markdown but I don't have concrete numbers on its acceptance.

[dcolligan]

Unless we are willing to rewrite the docs, we should stick with RST. (Obviously we use markdown in a few places, mostly for GitHub-specific files, and those should stay as Markdown.)

[kozbo]

Then maybe we should change the the readme.md in ga4gh-client and compliance to readme.rst

[david4096]

I got that one @kozbo . https://github.com/ga4gh/ga4gh-client/pull/73

Github does a fine job with RST, so we could convert them all that way. Once they're all RST I'll probably issue a PR switching them all to markdown :).

Changed the title to reflect how to close.

[dcolligan]

This issue should by updated with the list of files that use Markdown in our codebase that we desire to convert.

Here are all the markdown files in five repos (found with git ls-files | grep '\.md$'):

ga4gh-server:

CONTRIBUTING.md
STYLE.md
oidc-provider/README.md
tests/datadriven/README.md
tests/faultydata/variants/duplicated_sampleid/README.md
tests/faultydata/variants/inconsist_meta/README.md
tests/faultydata/variants/inconsist_sampleid/README.md
tests/faultydata/variants/inconsist_sampleid2/README.md
tests/faultydata/variants/no_indexed_vcf/README.md
tests/faultydata/variants/overlapping_vcf/README.md

schemas:

doc/release-notes.md
scripts/release/README.md

common:

README.md

client: none

compliance:

CONTRIBUTING.md
README.md
docs/ArchitectureOverview.md
docs/ConfigTheCTK.md
docs/FutureSteps.md
docs/PredicatesAndConditions.md
docs/Quickstart.md
docs/RunningTests_CLI.md
docs/RunningTests_IDE.md
docs/RunningTests_maven.md
docs/StructureAndRationale.md
docs/TestArchAndConventions.md
docs/UpdatingTheSchemas.md
docs/WritingATest.md
test-data/README_COMPLIANCE_DATA.md

[david4096]

As long as we choose one it's pretty easy to use pandoc to go back and forth between them.

pandoc doc/release-notes.md --to=rst --from=markdown --output=changelog.rst