Peyotl can be a bit intimidating because of the large number of subpackages. However, we do try to keep these packages from being intertangled with dependencies from any part to any other part.

As you can see from the simplified dependency graph below, there are low-level and high-level parts of peyotl. From “lowest” to highest their goals are:

Low level:

• utility provides helper functions for common string, and input/output opertions - no phylogenetics in here.
• phylo is a nascent package of phylogenetic data structures that are not based on the NexSON data model, but allow more efficient operations. It will not depend on any part of peyotl other than utility

Mid-level:

• nexson_syntax provides operations for transforming the various syntactic forms of NexSON into each other and into NeXML (which is a purely syntactic operation)
• nexson_validation provides support for validating the content of a NexSON and issuing errors/warnings if expected elements are not present
• phylesystem provides support treating a directory containing muliple git repositories (each with a study directory) as database of NexSON file. This performs the backend of the phylesystem-api operations used in open tree.
• manip is currently quite small. It is intended to help you write operations over the data model of NexSON. For instance, you can use functions in the subpackage to iterate over each tree in a NexSON.

High level:

• api: wrappers around Open Tree of Life web services
• sugar provides wrappers to make it easier to refer to parts of peyotl as tersely as possible.
• ott routines for reading the OTT taxonomy files and performing operations on the taxonomy. Currently just writes caches of smaller slices of information to enable limited operations in a more efficient manner

Experimental higher level modules:

• external is intended to handles conversion to external resources (Treebase import is supported now).
• string (may be renamed). It is not currently used, but provides some more exotic regular expressions intended to help parse taxonomic names.
• gcmdr a proof of concept reimplementation of parts of the gcmdr tool.

Open Tree maintainer modules (probably not of interest to other developers):

• [phylografter] contains code for dealing with synchronizing the phylesystem repositories with phylografter. This was used in the import of the data, but does not yet support continued syncing. It is fairly dormant.

dependency structure

The simplified graph of dependencies is:

The complete graph of dependencies:

The simplified dependency graph the python portion of other open tree tools shown in blue is below. Note that, for a tool like the curator, the user interacts with a javascript app that talks to both the phylesystem-api and the python curator backend. So the curator user app has the union of the dependencies of those two python code-bases:

building the graphs

The simplified graph can be produced by running:

python dev/detect_intra_peyotl_dependencies.py -d -s  > simple.dot
dot -Tsvg -osimple.svg simple.dot

The full graph is produced by omitting the -s flag from the first command above.

The graph with the external tools uses some hacks that rely on you having all of the open tree repos “sister” to each other on the filesystem. If that is the case then (from the peyotl directory) you can run:

bash dev/find_external_peyotl_imports.sh > dev/external_deps.txt

and then using -edev/external_deps.txt in the detect_intra_peyotl_dependencies.py script