Repository navigation
Rewrite the home page, Guide, installation, tutorials and protocol pages - #112
Merged
Merged
Conversation
The pages are written anew from their content, with the code blocks unchanged. PyPI installation commands use --pre, because the stable release on PyPI is 0.4.0. Download sizes follow the toolbox-assets release assets. The answer boxes of Tutorial 4 use dropdowns.
Documentation build overview
47 files changed ·
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The home page, the 23 Guide pages, the installation pages, the five legacy tutorials, the ten protocol pages,
yaml-format.md,data/README.mdandtuned-parameters.mdare written anew from their content. The code and output blocks are unchanged, except for the quick start of the home page and the PyPI installation commands.Statements corrected against the code and the releases:
pip install --pre raven-toolbox.setRavenSolver.toolbox-assetsreleases (49 MB KEGG core bundle, 135 MB and 155 MB HMM libraries), and bundles exist for Linux x86-64, macOS arm64 and Windows x86-64.parseTaskListrequires theIDcolumn and a header row that starts with an empty cell; the full set of columns is optional.getModelFromHomologykeeps a reaction with a missing subunit under the defaultcomplexPolicyflag.constrain_reversible_reactionshaseps=1e-10, andftinithas noepsparameter.reservedRxnsofsimplifyModelprotects against three of the flags.prepINITModelruns serially by default.yaml-format.mdstates that a round trip through cobrapy drops the RAVEN extensions.dropdownblocks, which this site renders; the previous???syntax rendered as plain text.yaml-format.mdpoints tosrc/io.