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Carlos Aznarán Laos 2023-05-21 14:54:49 -05:00
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.SRCINFO
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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

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CHANGELOG.md
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# 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]: https://github.com/BjornFJohansson/pydna/compare/3.1.0a0..3.1.0
[3.1.0]: https://github.com/BjornFJohansson/pydna/compare/3.1.0..3.0.2a5
[3.0.2a5]: https://github.com/BjornFJohansson/pydna/compare/3.0.2a5..3.0.2a4
[3.0.2a4]: https://github.com/BjornFJohansson/pydna/compare/3.0.2a4..3.0.2a3
[3.0.2a3]: https://github.com/BjornFJohansson/pydna/compare/3.0.2a3..3.0.2a2
[3.0.2a2]: https://github.com/BjornFJohansson/pydna/compare/3.0.2a2..3.0.2a1
[3.0.2a1]: https://github.com/BjornFJohansson/pydna/compare/3.0.2a1..3.0.2
[3.0.2]: https://github.com/BjornFJohansson/pydna/compare/3.0.2..3.0.1
[3.0.1]: https://github.com/BjornFJohansson/pydna/compare/3.0.1..3.0.0a9
[3.0.0a9]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a9..3.0.0a8
[3.0.0a8]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a8..3.0.0a7
[3.0.0a7]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a7..3.0.0a6
[3.0.0a6]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a6..3.0.0a5
[3.0.0a5]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a5..3.0.0a46
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[3.0.0a44]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a44..3.0.0a43
[3.0.0a43]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a43..3.0.0a42
[3.0.0a42]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a42..3.0.0a41
[3.0.0a41]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a41..3.0.0a40
[3.0.0a40]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a40..3.0.0a4
[3.0.0a4]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a4..3.0.0a39
[3.0.0a39]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a39..3.0.0a38
[3.0.0a38]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a38..3.0.0a37
[3.0.0a37]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a37..3.0.0a36
[3.0.0a36]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a36..3.0.0a35
[3.0.0a35]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a35..3.0.0a32
[3.0.0a32]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a32..3.0.0a31
[3.0.0a31]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a31..3.0.0a30
[3.0.0a30]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a30..3.0.0a3
[3.0.0a3]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a3..3.0.0a29
[3.0.0a29]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a29..3.0.0a28
[3.0.0a28]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a28..3.0.0a27
[3.0.0a27]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a27..3.0.0a26
[3.0.0a26]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a26..3.0.0a25
[3.0.0a25]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a25..3.0.0a24
[3.0.0a24]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a24..3.0.0a23
[3.0.0a23]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a23..3.0.0a22
[3.0.0a22]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a22..3.0.0a21
[3.0.0a21]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a21..3.0.0a20
[3.0.0a20]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a20..3.0.0a2
[3.0.0a2]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a2..3.0.0a19
[3.0.0a19]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a19..3.0.0a18
[3.0.0a18]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a18..3.0.0a17
[3.0.0a17]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a17..3.0.0a16
[3.0.0a16]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a16..3.0.0a15
[3.0.0a15]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a15..3.0.0a14
[3.0.0a14]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a14..3.0.0a13
[3.0.0a13]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a13..3.0.0a12
[3.0.0a12]: 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

74
PKGBUILD
View file

@ -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/"
}