We ask that third parties who build upon the codebase to do so from a versioned release. This will help them determine when bug fixes apply and generally make it easier to collaborate. If more intensive modifications happen then we request that the repository is forked, again preferably from a version tag.
make should build everything, including tests and "development" code.
Still in the works, but read this.
Make a branch on dib-lab (preferred so others can contribute) or fork the repository and make a branch there.
Each piece or fix you are working on should have its own branch; make a pull- request to dib-lab/master to aid in code review, testing, and feedback.
If you want your code integrated then it needs to be mergable
Example pull request update using the command line:
- Clone the source of the pull request (if needed)
git clone git@github.com:mr-c/khmer.git
- Checkout the source branch of the pull request
git checkout my-pull-request
- Pull in the destination of the pull request and resolve any conflicts
git pull git@github.com:dib-lab/khmer.git masterPush your update to the source of the pull request
git pushJenkins will automatically attempt to build and test your pull requests.
Jenkins calculates code coverage for every build. Navigate to the results from the master node first to view the coverage information.
Code coverage should never go down and new functionality needs to be tested.
All khmer scripts used by a published recommended analysis pipeline must be
included in scripts/ and meet the standards therein implied.
Python command-line scripts should use '-' instead of '_' in the name. (Only filenames containing code for import should use _.)
Please follow the command-line conventions used under scripts/. This includes most especially standardization of '-x' to be hash table size, '-N' to be number of hash tables, and '-k' to always refer to the k-mer size.
Command line thoughts:
If a filename is required, typically UNIX commands don't use a flag to specify it.
Also, positional arguments typically aren't used with multiple files.
CTB's overall philosophy is that new files, with new names, should be created as the result of filtering etc.; this allows easy chaining of commands. We're thinking about how best to allow override of this, e.g.
filter-abund.py <ct file> <filename> [ -o <filename.keep> ]
All code in scripts/ must have automated tests; see
tests/test_scripts.py. Otherwise it belongs in sandbox/.
When files are overwritten, they should only be opened to be overwritten after the input files have been shown to exist. That prevents stupid command line mistakes from trashing important files.
A general error should be signaled by exit code 1 and success by 0. Linux supports exit codes from 0 to 255 where the value 1 means a general error. An exit code of -1 will get converted to 255.
CLI reading:
The Python extension that wraps the C++ core of khmer lives in
khmer/_khmer.cc
This wrapper code is tedious and annoying so we use a static analysis tool to check for correctness.
https://gcc-python-plugin.readthedocs.io/en/latest/cpychecker.html
Developers using Ubuntu Precise will want to install the gcc-4.6-plugin-dev package
Example usage:
CC="/home/mcrusoe/src/gcc-plugin-python/gcc-python-plugin/gcc-with-cpychecker
--maxtrans=512" python setup.py build_ext 2>&1 | less
False positives abound: ignore errors about the C++ standard library. This tool is primarily useful for reference count checking, error-handling checking, and format string checking.
Errors to ignore: "Unhandled Python exception raised calling 'execute' method", "AttributeError: 'NoneType' object has no attribute 'file'"
Warnings to address:
khmer/_khmer.cc:3109:1: note: this function is too complicated
for the reference-count checker to fully analyze: not all paths were
analyzed
Adjust --maxtrans and re-run.
khmer/_khmer.cc:2191:61: warning: Mismatching type in call to
Py_BuildValue with format code "i" [enabled by default]
argument 2 ("D.68937") had type
"long long unsigned int"
but was expecting
"int"
for format code "i"
See below for a format string cheat sheet One also benefits by matching C type with the function signature used later.
"I" for unsigned int "K" for unsigned long long a.k.a khmer::HashIntoType.
Several bugs have gone unnoticed due to inconsistencies in read handling.
On the C++ side, there are an abundance of consume functions for loading
Fasta/Fastq sequences. On the Python side, read handling is sometimes delegated
to the C++ library, and sometimes handled in Python using screed.
In an attempt to normalize read handling in Python, the functions in
khmer/utils.py should be used whenever possible. Here,
broken_paired_reader in khmer/utils.py should be used to do all
paired-end sequence handling, and sequence loading should
go through khmer.utils.clean_input_reads(iter); this is a
generator that wraps the iterator produced by screed.open, and it
adds a cleaned_seq attribute to screed Record objects. This
attribute should be used for any k-mer or graph operations, while
the normal sequence attribute is what should be written out.
write_record and write_record_pair should be used to output
records. All of these functions are aware of FASTA and FASTQ records,
too.
For applying operations to collections of reads, the ReadBundle class is
available. This is used to wrap a collection of reads for examination and
processing in situations where (for example) something should be done to
either both reads in a pair, or neither.
Some basic rules of sequence handling in khmer are:
khmer.utils.broken_paired_reader.khmer.utils.ReadBundle(...).record.cleaned_seq. See
khmer.utils.clean_input_read(...).