Added
New common_sub_strings function. The previous version was implemented in pure python that was quite fast, but still a bottleneck in the code.
Thanks to louisabraham, we now have code based on [pydivsufsort](https://github.com/louisabraham/pydivsufsort) which provide
bindings to libdivsufsort, a very fast suffix array construction algorithm written in c. As a consequence, the Assembly code is now much faster.
Poetry is now used for building pydna. I have removed the setup.py file. I also do not build
Anaconda packages anymore, as conda-build got too slow to work with. I have plans to update the Bioconda recipe for the new version. As pydna is pure Python, anyone can make a conda package using [grayskull](https://github.com/marcelotrevisani/grayskull) for example.
Changed
Dseq and Dseqrecord now only take a `circular` argument (True or False) to indicate topology. Previously, `linear` was also
accepted. This was a little used feature (by me) that made the __init__ methods of both classes slow and complex. As this
was a violation of zen13 ("There should be one-- and preferably only one...") This change could break code,
hence the bump of major version number.
Code formatting with Black (also suggested by louisabraham). I now use a git pre-commit hook for this, so formatting should be more standardized.
Removed cache for all but download and genbank. Several functions and methods could previously be cached, something that saw very little use. The cache for genbank and download remain as this reduces the load on Genbank servers and also speed things up.
Environment variable `pydna_assembly_limit` sets the execution time in seconds (default 10) for
the assemble_linear and assemble_circular methods. There might be a better way to find out if an assembly is likely to take long, usually when there are many paths through the assembly graph.
17:01 $ git log --oneline --graph v5.2.0..a03c2a06a20afef95415f5f1786df2f71e921fd0
* a03c2a06a2 (HEAD -> dev_bjorn, origin/dev_bjorn) only build on master
* c7ce8582fa uppd action
* ca4c969c28 fix tests and commented out unneeded code
* 6539a1f076 added this as probably needed for a future bioconda package
* c933ca5a7b added this as probably needed for a future bioconda package
* c32fc5c9be fastes dseq init in dsecrecord init
* 70ced77d24 added min_rotation from pydivsufsort
* 2cc4edbc68 (origin/black, black) ws
* 4888db36f3 all black
* 0bf9fbd993 formatted with black precommit hook
* 74e3e1c229 fromatted with black
* f78dcb2fdd uppd poetry.lock
* 769dc98d89 (mergeexp) merge
|\
| * d242459fc5 (speed_up_Dseqrecord) try to ignore prof dir
| * bef4f6800c (origin/speed_up_Dseqrecord) edit
| * e29ac49f8e prep for adding new dundermethods
| * 2acbc5033c prep for implementing __copy__ and __deepcopy__ methods
| * 9916a62c93 added pstats script
| * 0b41671c1c mod tests
| * 9f060a0dea ignore
| * cbd4773605 added back test for iterable
| * 9b93d8988c removed linear property
| * 798899569a profiling
| * 9b5e7a6c13 added back prof
| * b1a8771323 add back profilig dir
| * ae93cb340f added dep pydivsufsort
| * 6f3f39398a Remover 'linear' method for Dseq and Dseqrecord - passes modified tests
| * 694ea1b5d5 (smallest_rot) new faster common_sub_strings
* | c57f5cb3c5 try fix profining error
* | f82a5676d6 fix test
* | 9d18ed4c03 gitignore
|/
* 28d8e98fd8 separated doctests
* dacf9e1f3b whitespace
* 6513a0bf85 removed cruft
* c4a0265a12 removed profiling
* 3c11115871 try ignore
* 01999514c2 do not track profiling files
* 6eb2154fff reformatted code
* 4e08cb910d switched to array in smallest_rotation function and fixed a docstring
* 014b40e20d reorganized common_sub_strings
* 190541a51e fix pyproject.toml
* 4c9d27042f added pytest-profiling to env
* 733d83782a added profiling to run_test
* 1db40a1bc7 added experiment files
* 9ac4f4c6f2 added prof
* b867cd2039 removed old file
* 35f8eb03d1 added profiling
* 4b4bafb272 changed badge
* f496be825b url
* a16e7a004d uppdate
* 5190177811 removed python 2 code
* 76a5930791 set timeout from env var pydna_assembly_limit
* 3cf0bba9bc added assembly limit to default env vars
* cd76b4a123 added urls
* f4ef97dbc0 uppdated cheat sheet
* c0f111c67a changed target branch for pull req
* f0385b7981 New timeout for assembly
* 5252df3cf4 switched from wrapt-timeout-decorator
* 5d46b153e6 upd poetry deps
* 436ae27381 removed cython notebook
* ce9a919e15 fix dep
* 2ce61667de fix deps
* 8be47b5463 stuff
* 75ea5dbee1 Merge branch 'dev_bjorn' of https://github.com/BjornFJohansson/pydna into dev_bjorn
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| * 5c2ec77539 Merge pull request 106 from BjornFJohansson/dependabot/pip/coverage-7.2.2
| |\
| | * b15fd0cbb4 Bump coverage from 7.2.1 to 7.2.2
* | | 8e529ff1c7 remove cashing for some functions
|/ /
* / 8dd2ca19a0 bugfix: hardcoded strand set to 1
|/
* dacb024944 updated poetry.lock
* a3c3791917 fix
* 74d3850352 Merge pull request 94 from BjornFJohansson/dependabot/pip/ipython-8.10.0
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| * 66f20aa195 (origin/dependabot/pip/ipython-8.10.0) Bump ipython from 8.9.0 to 8.10.0
* | 30d109bbb2 Merge pull request 95 from BjornFJohansson/dependabot/pip/biopython-1.81
|\ \
| * | bd0ef21a96 Bump biopython from 1.80 to 1.81
| |/
* | 879c81ccf7 Merge pull request 96 from BjornFJohansson/dependabot/pip/pyqt5-5.15.9
|\ \
| * | 5482b0788f Bump pyqt5 from 5.15.8 to 5.15.9
| |/
* | 813ac07394 fix gel image test
* | 63de396a5f fix gel examples
* | 1eb18bc709 new example w gel
|/
* c6d1fbda8c fix link
* ffda81e24e Merge branch 'master' of https://github.com/BjornFJohansson/pydna
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| * f8896ab27f Update README.md
* | 546f357997 Merge branch 'dev_bjorn'
|\ \
| |/
|/|
| * 98b6eaa55f improve example
| * 186dbff025 bugfix for slicing genbankrecords
| * 10e79ccaba fix table
* | c45913bee0 Merge branch 'dev_bjorn'
|\|
| * 593b1f4dfb simplify readme
| * 9800fdf2bb whitespace
| * 9276a054fa start to make a better figure for amplicon
| * 0cb741bf84 better example with pcr
* | a6fda7a276 Merge branch 'dev_bjorn'
|\|
| * c1ec911a22 fix example
| * 5b53ffc9ff fix raw link
* | 77f2121d76 Merge branch 'dev_bjorn'
|/
* fbcdb0bea4 fix link
* b9ada45f20 (origin/poetry, LouisAbraham/poetry, poetry) new readme