Development

This section is intended for developers seeking to extend the hgvs package. You should be familiar with the architecture, conventions, and basic functionality elsewhere in this documentation.

Get Cozy with make

The hgvs package includes a GNU Makefile that aids nearly all developer tasks. It subsumes much of the functionality in setup.py. While using the Makefile isn’t required to develop, it is the official way to invoke tools, tests, and other development features. Type make for hgvs-specific help.

Some of the key targets are:

develop:Prepare the directory for local development.
install:Install hgvs (as with python setup.py install).
test:Run the default test suite (~4 minutes).
test-quick:Run the quick test suite (~35s) of most functionality.
clean, cleaner, cleanest:
 Remove extraneous files, leaving a directory in various states of tidiness.
docs:Make the sphinx docs in doc/build/html/.
upload:Upload package to PyPI

Installation for Development

$ hg clone ssh://hg@bitbucket.org/biocommons/hgvs
$ cd hgvs
$ make develop

Variables

The following code variable conventions are used for most of the hgvs code base. They should be considered aspirations rather than reality or policy. Understanding these conventions will help uses and developers understand the code.

Note

A note on variable suffixes If a particular variant type is expected, a suffix is often added to variable names. e.g., var_c in a function argument list signifies that a SequenceVariant object with type=’c’ is expected.

hgvs*:a string representing an HGVS variant name.
var*:a hgvs.variant.SequenceVariant object
pos:
posedit:
hgvs_position:

Submitting Patches

Yes! We’ll be thrilled to have your contributions!

The preferred way to submit a patch is by forking the project on BitBucket, commiting your changes there, then sending a pull request.

If you have a really worthwhile patch, we’ll probably accept a diff-formatted patch, but that’ll make it harder for us and impossible for you to get credit.

Developing and Contributing to HGVS

(The Makefile in hgvs wraps functionality in setup.py, and also provides many useful utilitarian rules. Type make to see a list of targets.)

  • Code away, then commit and push

    $ hg commit -m ‘fixes #141: implements Formatter class’

    $ hg push

  • If you’d like to contribute back, submit a pull request on the hgvs web site.

Using a local/alternative UTA instance

  • Install UTA from a PostgreSQL as described at in the UTA README.
  • Specify an alternate UTA instance.

The easiest way to use a UTA instance other than the default is by setting UTA_DB_URL. The format is postgresql://<user>:<pass>@<host>/<db>/<schema>. For example:

postgresql://anonymous:anonymous@uta.biocommons.org/uta/uta_20140210

explicitly selects the public database, and

postgresql://localhost/uta/uta_20140210

selects a local instance. Developers can test connectivity like this:

$ UTA_DB_URL=postgresql://localhost/uta/uta_20140210 make test-quick

See hgvs/dataproviders/uta.py for current UTA database URLs.

Release Process

hgvs uses a home-grown tool, clogger, to generate change logs. This section documents the process. (Clogger will be released at some point, but it is currently really only executable by Reece.)

clogger‘s primary goal is to propose a preliminary changelog based on commit messages between specified release tags. That .clog file is a simple format like this:

clog format: 1; -*-outline-*-
* 0.4.1 (2015-09-14)
Changes since 0.4.0 (2015-09-09).
** Bug Fixes
*** fixes #274, #275: initialize normalizer with same alt_aln_method as EasyVariantMapper [43e174d6f8af]
*** fixes #276: raise error when user attempts to map to/from c. with non-coding transcript [3f7b659f4f02]

.clog files should be edited for readability during the release process and committed to the repo (in hgvs/doc/changelog/).

A Makefile in the same directory generates an .rst file from the .clog. This file must also be committed to the repo. This file becomes the release changelog.

Finally, releases are bundled by major.minor versions in a file like 0.4.rst (no patch level). That file must be edited to include the new release and committed to the repo.

Specific Example – 0.4.3 release

The 0.4.x branch has two recent changes for the 0.4.3 release. Here’s how the release was prepared:

hg up 0.4.x
hg tag 0.4.3cl

cd doc/changelog
make 0.4.3cl.clog
mv 0.4.3cl.clog 0.4.3.clog
#edit 0.4.3.clog for readability
make 0.4.3.rst
#edit 0.4.rst to add 0.4.3 to index

cd ../.. (hgvs top-level), then hg status should now look like:

M doc/changelog/0.4.rst
A doc/changelog/0.4.3.clog
A doc/changelog/0.4.3.rst

Check your work. Type make docs, then view build/sphinx/html/changelog/0.4.3.html.

Now we’re ready to finish up:

hg tag --remove 0.4.3cl
hg com -m 'added docs for 0.4.3 release'
hg tag 0.4.3
hg push
make upload # (builds distribution and uploads to pypi)