diff options
| -rw-r--r-- | .SRCINFO | 34 | ||||
| -rw-r--r-- | CHANGELOG.md | 575 | ||||
| -rw-r--r-- | PKGBUILD | 74 |
3 files changed, 45 insertions, 638 deletions
@@ -1,34 +1,30 @@ pkgbase = python-pydna - pkgdesc = Data structures for double-stranded DNA & simulation of homologous recombination - pkgver = 4.0.7 - pkgrel = 2 + pkgdesc = Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules + pkgver = 5.2.0 + pkgrel = 1 url = https://github.com/bjornfjohansson/pydna - changelog = CHANGELOG.md arch = any - license = BSD + license = custom:BSD-3-clause + checkdepends = python-pytest checkdepends = python-requests-mock checkdepends = ipython - checkdepends = python-codon-adaptation-index - makedepends = git makedepends = python-build makedepends = python-installer + makedepends = python-poetry-dynamic-versioning makedepends = python-wheel - makedepends = python-sphinx - makedepends = python-setuptools - makedepends = python-setuptools-scm - makedepends = python-pytest-runner + makedepends = git depends = python-appdirs depends = python-biopython depends = python-networkx depends = python-prettytable - depends = python-pyparsing - depends = python-requests - optdepends = python-matplotlib: gel simulation - optdepends = python-mpldatacursor: gel simulation - optdepends = python-numpy: gel simulation - optdepends = python-pint: gel simulation + depends = python-pyperclip + depends = python-pyfiglet optdepends = python-scipy: gel simulation - source = python-pydna::git+https://github.com/bjornfjohansson/pydna#tag=4.0.7 - sha256sums = SKIP + optdepends = python-matplotlib: gel simulation + optdepends = python-pyparsing: download + optdepends = python-requests: download + optdepends = python-cai2: express + source = git+https://github.com/bjornfjohansson/pydna.git?#tag=v5.2.0 + sha512sums = SKIP pkgname = python-pydna diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index 96b3a997801d..000000000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,575 +0,0 @@ -# Changelog - -All notable changes to this project will be documented in this file. - -The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), -and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - -## [Unreleased] -### Added -### Changed - -## [4.0.0] - 2020-10-10 - -### Added - -- New gel module -- New module myprimers_gdoc for storing primers in a google doc -- New module fakeseq for making DNA ladders. -- New module ladders containing DNA molecular weight markers. - -### Changed - -- Changes to myprimer module. - -## [3.1.3] - 2020-10-10 - -### Added - -- added .sorted_features method for SeqRecord -- added a new lcs (*l*ongest *c*ommon *s*ubstring) method for SeqRecord and DseqRecord - -### Changed - -- changed format for changelog -- biopython 1.78 in requirements.txt -- fix to scripts/check_my_primers.py - -## [3.1.2] - 2020-09-28 - -### Changed - --Bugfix release. There was a bug in stamping genbank files with cSEGUID. - -## [3.1.1] - 2020-09-25 - -### Changed - --Bugfix release. There was a bug in locating features in certain circular assemblies. --Added a test: "test_marker_replacement_on_plasmid" in test_module_assembly.py to test for this. - -## [3.1.0] - 2020-09-16 - -### Changed - --Changed to src layout for the package. Changed how melting temperature is calculated. --Changes to tests, added a conftest.py. Updated for comatibility with biopython 1.7.8. --Removed mysequences.py --Reformatted code with BLACK --Use github actions for building and testing - - -## [3.0.2a1] - 2019-07-23 - -### Changed - --.upper() and .lower() methods for Dseq and Dseqrecord classes. Improved slicing - -## [3.0.1] - 2019-05-28 - -### Changed - --Many changes and improvements, especially for the Assembly class. - -## [3.0.0] - 2019-05-17 - -### Changed - - --- - -## [2.0.3] - 2017-12-14 - -### Changed - - --- - -## [2.0.3a1] - 2017-12-14 - -### Changed - --pcr function now takes an amplicon. This way an amplicon can easily be rerun after - modification of primers or template - -## [2.0.3a0] - 2017-12-03 - -### Changed - - --- - -## [2.0.2] - 2017-08-26 - -### Changed - - --- - -## [2.0.2] - 2017-08-26 - -### Changed - - --- - -## [2.0.1] - 2017-08-24 - -### Changed - - --- - -## [2.0.0] - 2017-06-23 - -### Changed - --First release of 2.0.0. This version adds changes in the alpha versions - -## [2.0.0a4] - 2017-05-05 - -### Changed - --Fixed bug in _multiply_circular - -## [2.0.0a3] - 2017-04-04 - -### Changed - --added the all module, from pydna.all import *, now imports a set of useful pydna modules - into the main namespace. --Finer control over cache, genbank download is now on by default. - Bug fix in assembly_fragments function that created too long primer tails. - -## [2.0.0a2] - --- - -### Changed - - ---- - - -## [2.0.0a1] - - -### Changed - --removed setting functions for cache in __init_ and the delete_cache function for simplicity --removed these functions --pydna.design.print_primer_pair --pydna.design.cloning_primers --pydna.design.integration_primers --pydna.design.assembly_primers - -## [2.0.0a0] - 2017-03-15 - -### Changed - --alpha release, removed imports in __init__ --This version breaks compatibility. - -## [1.2.0] - 2017-03-10 - -### Changed - --New and simpler primer design api, especially for gibson assembly primers. See docstrings --Dseqrecord.find method that allows finding subsequences "over the edge" of circular sequences. - -## [1.1.5] - 2016-12-16 - -### Changed - --added message for Dseqrecord write - -## [1.1.4] - 2016-12-15 - -### Changed - --split some files into more logical and smaller chunks. --The Primer class is now the same in primer design and amplify modules --less modules are imported in __init__.py --pydna.getcache returns the pydna_cache environment variable --pydna.cached sets pydna_cache to "cached" --pydna.nocache sets pydna_cache to "nocache" --pydna.refresh sets pydna_cache to "refresh" --Many of the Classes have new __repr__ methods compatible with the Jupyter notebook. --One Jupyter notebook is now run as a part of the test suite using pytest/nbval --pydna.parse_primers now return a list of Primer class objects --pydna.read_primer now a Primer class object --pydna.read_url and pydna.parse_url removed, since they are too risky. --it is better to use pydna.download_text in combination with read or parse. - this way, the intermediate text can be inspected and genbankfixer can be applied if - necessary - -## [1.1.1] - 2016-11-20 - -### Changed - --New module genbankfixer for salvaging broken genbank files (pydna.gbtext_clean). --New pydna.readprimer function (shortcut for reading to Biopython.SeqRecord). --Tests merged to pytest. --read_url function --parse_url function --download_text function --New key function for cache of Assemblies. - -## [1.0.2] - 2016-10-08 - -### Changed - --Python 3 only! --pydna.open_cache -> pydna.open_cache_folder; opens the cache folder in the file browser --logging level is not "info" - added the possiblity to specify a text file containing primers and - a path to the ApE plasmid editor (http://biologylabs.utah.edu/jorgensen/wayned/ape/) - These settings can be made in the pydna.ini file that is located in the - "user_config_dir" specified on each platform by the appdirs module. - on linux it is in ~/.config/pydna --Bugfix: invisible gel bands in the gel module. - -## [1.0.1] - 2016-03-10 - -### Changed - --Bugfix: for errors in IPython import if IPython is too old ( < 4.0) --Bugfix: Large genbank records were not downloaded completely. - -## [1.0.0] - - - -### Changed - --Gel simulation added - -## [0.9.3] - 2015-06-03 - -### Changed - --Shelve does not work under MacOS under certain conditions. --This release tries to solve this by not specifying file extensions - for the cache files. Two functions are added, pydna. - -## [0.9.2] - 2015-05-28 - -### Changed - --pydna_data_dir is encoded to a string in __init__.py instead of - unicode. The Popen module does not accept environment variables that - are not strings. - -## [0.9.1] - 2015-05-26 - -### Changed - --fixed critical error in the calculation of seguid and cseguid - checksums - -## [0.9.0] - 2015-05-26 - -### Changed - --seguid and cseguid are now url safe so they can be part of urls and - file names. --Dseqrecord.locus is an alias of Dseqrecord.name --Dseqrecord.accession is an alias of Dseqrecord.id --Dseqrecord.definition is an alias of Dseqrecord.description --changed how circular assembly products are identified to use cseguid. --removed proxy handling when proxy not set in download module. --added CHANGELOG.md, currently empty. --environment variable datadir is now pydna_data_dir. --removed environmental variable pydna_dna_dir. --if Dseqrecord is initiated with a name property that is longer than - 16 characters, it is truncated to 16 chars and a warning is issued. --Default Dseqrecord name property is "na". --Default Dseqrecord id property is "-". --Default Dseqrecord description property is "@". --Dseqrecord __eq__ and __ne__ methods defined. --Dseqrecord.write now overwrites an old sequence with the same --filename if the primary sequence is the same. --Dseqrecord.read now only looks in current working directory. --fixed ipynb_import test code. - -## [0.8.4] - 2015-04-17 - -### Changed - --Bugfix for parsing text files with unicode characters. -## [0.8.3] - - - -### Changed - - - -## [0.8.2] - - - -### Changed - - - -## [0.8.1] - 2015-03-07 - -### Changed - - Bugfix for windows. The data directory was not created. - -## [0.8.0] - 2015-02-06 - -### Changed - --Mapping reads added. - -## [0.7.2] - 2014-11-21 - -### Changed - --First public release with the changes from 0.7.0 and 0.7.1. --Added a Pretty_str class to beautify output of strings in - the IPython shell. - -## [0.7.1] - notpublic - -### Changed - --Short linkers can be incorporated in PCR primers in the - assembly_primers function. - -## [0.7.0] - notpublic - -### Changed - --Caching to speed up Amplify, Assembly, download and the --Desqrecord synced method. The data is stored in four shelf - files in the users application directory. - --amplify.shelf --assembly.shelf --genbank.shelf --synced.shelf - --The location is os specific. --See the documentation of appdirs - https://pypi.python.org/pypi/appdirs/1.4.0 - -## [0.6.6] - - -### Changed - --new function nopcr. - -## [0.6.5] - 2014-07-31 - -### Changed - --bugfix: cutting an amplicon object now preserves features --Changed requirement for NetworkX to 1.8.1 - -## [0.6.4] - 2014-07-09 - -### Changed - --The pcr function and Anneal class can now deal with primers - with ambiguous codons like R = A or G. In the resulting PCR - product, the ambiguous nucleotides are preserved in the tails - i.e. the primer part not annealing. The annealing part will - have the sequence corresponding to the template. - -## [0.6.3] - 2014-07-06 - -### Changed - --Dseqrecord.add_feature can now take a string or some other - sequence as input. The assembly primers function can now produce - primers for a circular assembly. - -## [0.6.2] - 2014-06-13 - -### Changed - --Dseqrecord gained three new methods: - --isorf() method returning True or False. - --List_features() method returns a list of all features as a - formatted ASCII table. - --Extract_feature() extracts a feature in the form os a new - Dseqrecord object. - --Changes to how the primer_design functions work, especially - assembly primers. - -## [0.6.1] - 2014-04-25 - -### Changed - --Fixed a bug in the Dseqrecord synced method and removed the - utils synced function. - -## [0.6.0] - 2014-04-18 - -### Changed - --Bugfixes and improvements in documentation. - -## [0.5.0] - 2013-12-16 - -### Changed - --Changes to how the amplify and assembly modules work - the Amplicon and Assembly classes are now subclasses of - Dseqrecord. - -## [0.2.2] - 2013-11-05 - -### Changed - --bugfix: changed the handling of compound features - to fit with the new version of BioPython (1.62) which is - now a requirement. - -## [0.2.1] - 2013-08-18 - -### Changed - - --- - -## [0.1.8] - 2013-06-02 - -### Changed - --bugfix: changed the SeqFeatures added to PCR products in the --amplify module to a dict of list of strings instead of - a dict of strings. - -## [0.1.7] - 2013-05-29 - -### Changed - --Changed the code in amplify.Amplicon to handle features - spanning the origin of circular sequences. - -## [0.1.6] - 2013-04-22 - -### Changed - --Changed the behaviour of the find method of the Dseq object - to find substrings that span the origin. Slicing for circular - Dseq objects now works slightly different. - -## [0.1.5] - 2013-04-18 - -### Changed - --Changed the setup.py script to permit installation - of the source installer without access to a c compiler. - -## [0.1.4] - 2013-04-10 - -### Changed - --Cleaned up some docstrings --Renamed Drecord -> Dseqrecord to be more consistent with --Dseq and Biopython Seq/SeqRecord. - --Changed name of keyword argument for read and parse. --ds=True returns Dseqrecord(s) while ds=False returns SeqRecords. - -## [0.1.3] - 2013-04-09 - -### Changed - --pydna created from Python-dna. - -[unreleased]: https://github.com/BjornFJohansson/pydna/compare/HEAD..3.1.3 -[3.1.3]: https://github.com/BjornFJohansson/pydna/compare/3.1.3..3.1.2 -[3.1.2]: https://github.com/BjornFJohansson/pydna/compare/3.1.2..3.1.1 -[3.1.1]: https://github.com/BjornFJohansson/pydna/compare/3.1.1..3.1.0a1 -[3.1.0a1]: https://github.com/BjornFJohansson/pydna/compare/3.1.0a1..3.1.0a0 -[3.1.0a0]: 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https://github.com/BjornFJohansson/pydna/compare/3.0.0a12..3.0.0a11 -[3.0.0a11]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a11..3.0.0a10 -[3.0.0a10]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a10..3.0.0a1 -[3.0.0a1]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a1..3.0.0a0 -[3.0.0a0]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a0..3.0.0 -[3.0.0]: https://github.com/BjornFJohansson/pydna/compare/3.0.0..2.0.4a5 -[2.0.4a5]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a5..2.0.4a4 -[2.0.4a4]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a4..2.0.4a3 -[2.0.4a3]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a3..2.0.4a2 -[2.0.4a2]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a2..2.0.4a1 -[2.0.4a1]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a1..2.0.4a0 -[2.0.4a0]: https://github.com/BjornFJohansson/pydna/compare/2.0.4a0..2.0.3a0 -[2.0.3a0]: https://github.com/BjornFJohansson/pydna/compare/2.0.3a0..2.0.3 -[2.0.3]: https://github.com/BjornFJohansson/pydna/compare/2.0.3..2.0.2a0 -[2.0.2a0]: https://github.com/BjornFJohansson/pydna/compare/2.0.2a0..2.0.2 -[2.0.2]: https://github.com/BjornFJohansson/pydna/compare/2.0.2..2.0.1 -[2.0.1]: https://github.com/BjornFJohansson/pydna/compare/2.0.1..2.0.0a8 -[2.0.0a8]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a8..2.0.0a7 -[2.0.0a7]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a7..2.0.0a6 -[2.0.0a6]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a6..2.0.0a5 -[2.0.0a5]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a5..2.0.0a4 -[2.0.0a4]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a4..2.0.0a3 -[2.0.0a3]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a3..2.0.0a2 -[2.0.0a2]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a2..2.0.0a0 -[2.0.0a0]: https://github.com/BjornFJohansson/pydna/compare/2.0.0a0..2.0.0 -[2.0.0]: https://github.com/BjornFJohansson/pydna/compare/2.0.0..1.2.0a1 -[1.2.0a1]: https://github.com/BjornFJohansson/pydna/compare/1.2.0a1..1.2.0a0 -[1.2.0a0]: https://github.com/BjornFJohansson/pydna/compare/1.2.0a0..1.2.0 -[1.2.0]: https://github.com/BjornFJohansson/pydna/compare/1.2.0..1.1.6a4 -[1.1.6a4]: https://github.com/BjornFJohansson/pydna/compare/1.1.6a4..1.1.5 -[1.1.5]: https://github.com/BjornFJohansson/pydna/compare/1.1.5..1.1.4 -[1.1.4]: https://github.com/BjornFJohansson/pydna/compare/1.1.4..1.1.1 -[1.1.1]: https://github.com/BjornFJohansson/pydna/compare/1.1.1..1.0.2 -[1.0.2]: https://github.com/BjornFJohansson/pydna/compare/1.0.2..1.0.1 -[1.0.1]: https://github.com/BjornFJohansson/pydna/compare/1.0.1..1.0.0 -[1.0.0]: https://github.com/BjornFJohansson/pydna/compare/1.0.0..0.9.9 -[0.9.9]: https://github.com/BjornFJohansson/pydna/compare/0.9.9..0.9.8 -[0.9.8]: https://github.com/BjornFJohansson/pydna/compare/0.9.8..0.9.7 -[0.9.7]: https://github.com/BjornFJohansson/pydna/compare/0.9.7..0.9.6 -[0.9.6]: https://github.com/BjornFJohansson/pydna/compare/0.9.6..0.9.5 -[0.9.5]: https://github.com/BjornFJohansson/pydna/compare/0.9.5..0.9.4 -[0.9.4]: https://github.com/BjornFJohansson/pydna/compare/0.9.4..0.9.3 -[0.9.3]: https://github.com/BjornFJohansson/pydna/compare/0.9.3..0.9.2 -[0.9.2]: https://github.com/BjornFJohansson/pydna/compare/0.9.2..0.9.1 -[0.9.1]: https://github.com/BjornFJohansson/pydna/compare/0.9.1..0.9.0 -[0.9.0]: https://github.com/BjornFJohansson/pydna/compare/0.9.0..0.8.4 -[0.8.4]: https://github.com/BjornFJohansson/pydna/compare/0.8.4..0.8.3 -[0.8.3]: https://github.com/BjornFJohansson/pydna/compare/0.8.3..0.8.2 -[0.8.2]: https://github.com/BjornFJohansson/pydna/compare/0.8.2..0.8.1 -[0.8.1]: https://github.com/BjornFJohansson/pydna/compare/0.8.1..0.8.0 @@ -1,54 +1,40 @@ -# Maintainer: Luis Martinez <luis dot martinez at disroot dot org> +# Maintainer: Carlos Aznarán <caznaranl@uni.pe> +# Contributor: Luis Martinez <luis dot martinez at disroot dot org> # Contributor: Clint Valentine <valentine.clint@gmail.com> - -pkgname=python-pydna -pkgver=4.0.7 -pkgrel=2 -pkgdesc='Data structures for double-stranded DNA & simulation of homologous recombination' -arch=('any') -url='https://github.com/bjornfjohansson/pydna' -license=('BSD') -depends=( - 'python-appdirs' - 'python-biopython' - 'python-networkx' - 'python-prettytable' - 'python-pyparsing' - 'python-requests') -optdepends=( - 'python-matplotlib: gel simulation' - 'python-mpldatacursor: gel simulation' - 'python-numpy: gel simulation' - 'python-pint: gel simulation' - 'python-scipy: gel simulation') -makedepends=( - 'git' - 'python-build' - 'python-installer' - 'python-wheel' - 'python-sphinx' - 'python-setuptools' - 'python-setuptools-scm' - 'python-pytest-runner') -checkdepends=('python-requests-mock' 'ipython' 'python-codon-adaptation-index') -changelog=CHANGELOG.md -source=("$pkgname::git+$url#tag=$pkgver") -sha256sums=('SKIP') +_base=pydna +pkgname=python-${_base} +pkgver=5.2.0 +pkgrel=1 +pkgdesc="Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules" +arch=(any) +url="https://github.com/bjornfjohansson/${_base}" +license=('custom:BSD-3-clause') +depends=(python-appdirs python-biopython python-networkx python-prettytable python-pyperclip python-pyfiglet) +makedepends=(python-build python-installer python-poetry-dynamic-versioning python-wheel git) +checkdepends=(python-pytest python-requests-mock ipython) # python-cai2 +optdepends=('python-scipy: gel simulation' + 'python-matplotlib: gel simulation' + 'python-pyparsing: download' + 'python-requests: download' + 'python-cai2: express') +source=("git+${url}.git?#tag=v${pkgver}") +sha512sums=('SKIP') build() { - cd "$pkgname" - python -m build --wheel --no-isolation + cd ${_base} + python -m build --wheel --skip-dependency-check --no-isolation } check() { - cd "$pkgname" - PYTHONPATH=./src pytest -x --disable-warnings + cd ${_base} + python -m venv --system-site-packages test-env + test-env/bin/python -m installer dist/*.whl + test-env/bin/python -m pytest } package() { - export PYTHONHASHSEED=0 - cd "$pkgname" - python -m installer --destdir="$pkgdir/" dist/*.whl - install -Dm644 LICENSE.txt "$pkgdir/usr/share/licenses/$pkgname/LICENSE" - install -Dm644 README.md -t "$pkgdir/usr/share/doc/$pkgname/" + cd ${_base} + PYTHONPYCACHEPREFIX="${PWD}/.cache/cpython/" python -m installer --destdir="${pkgdir}" dist/*.whl + install -Dm644 LICENSE.txt "$pkgdir/usr/share/licenses/$pkgname/LICENSE" + install -Dm644 README.md -t "$pkgdir/usr/share/doc/$pkgname/" } |