Minimal export (no node-data files needed) #1299

These properties were never actually used (neither exported from augur export v2 nor consumed by auspice) Closes #867 <#867>

A number of parts of the auspice-config have identical (or almost-identical) shape to those in the resulting dataset JSON, although the actual data may be modified as it passes through `augur export v2`. Rather than referencing the entire auspice-config schema and pruning down properties, which I don't actually think is possible in jsonschema, I chose to use $refs at a more fine grained level which I find easier to read. The actual schema definitions should be unchanged by this commit, although comments / descriptions have been improved.

Auspice can already set the tip label via URL state (`?tl=...`) and will shortly be able to parse the display_default added here. Closes #1115 <#1115>

These work fine in Auspice. While the 'colorings' property is optional, `augur export v2` will always set a (possibly empty) array. I also chose to allow the auspice config file to have an empty colorings definition, which in practice behaves the same as leaving it out. Addresses comment in #273 <#273 (comment)>

Removes previously valid string patterns which were never used within augur and would result in unexpected behaviour in auspice. Also updates the patternProperties of CDSs to match that used in the genome_annotations (schema-annotations.json)

Trees could currently be produced with neither "div" nor "num_date" information. Arguably Auspice could interpret these as cladograms but as it stands these datasets aren't rendered by Auspice. Datasets without this information are easy to create but rare in practice: If the node-data files don't define "mutation_length" or "branch_length" then there's no "div" and if they don't define "num_date" then that's not there either. Note that what we really want to require is that "div" is present on all nodes and/or "num_date" is present on all nodes, but the schema doesn't let us do this.

Allows a minimal `augur export` using only a (newick) tree as input, functionality that we've wanted for over 4 years! To facilitate this we parse branch lengths¹ from the newick file if such data wasn't available in the node-data inputs (e.g. because there are none!). The code for deciding where to read divergence from has been refactored and in the process improved: the (rare? never encountered?) case where divergence was sometimes read from node-data keys 'mutation_length' and sometimes from 'branch_length' can non longer happen. If data is provided which doesn't define divergence or num_date (irregardless of whether node-data files were provided as inputs), then the resulting dataset will fail validation. Closes #273 <#273> ¹ I suppose these might represent time in certain cases, but I haven't seen such data in Newick files.

Adds a flag to the diff JSONs script to ignore numeric type changes when running DeepDiff [1]. Updates the export v2 minimal export test to use this new flag instead of creating an intermediate file with sed. [1] https://zepworks.com/deepdiff/current/ignore_types_or_values.html

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Minimal export (no node-data files needed) #1299

Minimal export (no node-data files needed) #1299

Commits on Sep 20, 2023