mirror of
https://github.com/archlinux/aur.git
synced 2026-02-08 05:02:00 +01:00
update to 4.0.2
rewrote package entirely due to changed dependencies and other issues related to testing
This commit is contained in:
Luis Martinez
parent
2bb9bf30a5
commit
7e62cd4579
3 changed files with 633 additions and 82 deletions
35
.SRCINFO
35
.SRCINFO
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@ -1,28 +1,27 @@
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pkgbase = python-pydna
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pkgdesc = Python3 classes for dsDNA simulation of homologous recombination, Gibson assembly and interactive cloning
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pkgver = 2.0.3
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pkgdesc = Data structures for double-stranded DNA & simulation of homologous recombination
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pkgver = 4.0.2
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pkgrel = 1
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url = https://pypi.python.org/pypi/pydna
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url = https://github.com/bjornfjohansson/pydna
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changelog = CHANGELOG.md
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arch = any
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license = GPL3
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makedepends = python
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license = BSD
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||||
makedepends = git
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||||
makedepends = python-setuptools
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options = !emptydirs
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||||
source = python-pydna-2.0.3.zip::https://pypi.python.org/packages/67/f2/552bd375666bb3e2ff4b3ec418ed2d5bbe1140847075d7c2d682435153c8/pydna-2.0.3.zip
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sha256sums = 64b49daf4e30c53ac45a0bb5f40519fc627dd01c5751eae9d72a8f4a75a19e16
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|
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pkgname = python-pydna
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depends = python
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depends = python-appdirs
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depends = python-biopython
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depends = python-networkx
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depends = python-ordered-set
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depends = python-prettytable
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depends = python-pyparsing
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depends = python-requests
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makedepends = python-setuptools-scm
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makedepends = python-pytest-runner
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depends = python-appdirs>=1.4.3
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depends = python-biopython>=1.79
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depends = python-networkx>=2.5.0
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depends = python-prettytable>=0.7.2
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depends = python-pyparsing>=2.4.7
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depends = python-requests>=2.23.0
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optdepends = python-matplotlib: gel simulation
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optdepends = python-mpldatacursor: gel simulation
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optdepends = python-numpy: gel simulation
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optdepends = python-pint: gel simulation
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optdepends = python-scipy: gel simulation
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source = python-pydna::git+https://github.com/bjornfjohansson/pydna#tag=4.0.2
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sha256sums = SKIP
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|
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pkgname = python-pydna
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|
|
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575
CHANGELOG.md
Normal file
575
CHANGELOG.md
Normal file
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@ -0,0 +1,575 @@
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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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|
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## [Unreleased]
|
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### Added
|
||||
### Changed
|
||||
|
||||
## [4.0.0] - 2020-10-10
|
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|
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### Added
|
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|
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- New gel module
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- New module myprimers_gdoc for storing primers in a google doc
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- New module fakeseq for making DNA ladders.
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- New module ladders containing DNA molecular weight markers.
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|
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### Changed
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- Changes to myprimer module.
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|
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## [3.1.3] - 2020-10-10
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### Added
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- added .sorted_features method for SeqRecord
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- added a new lcs (*l*ongest *c*ommon *s*ubstring) method for SeqRecord and DseqRecord
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### Changed
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- changed format for changelog
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- biopython 1.78 in requirements.txt
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- fix to scripts/check_my_primers.py
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|
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## [3.1.2] - 2020-09-28
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### Changed
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-Bugfix release. There was a bug in stamping genbank files with cSEGUID.
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|
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## [3.1.1] - 2020-09-25
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### Changed
|
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|
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-Bugfix release. There was a bug in locating features in certain circular assemblies.
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-Added a test: "test_marker_replacement_on_plasmid" in test_module_assembly.py to test for this.
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## [3.1.0] - 2020-09-16
|
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|
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### Changed
|
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|
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-Changed to src layout for the package. Changed how melting temperature is calculated.
|
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-Changes to tests, added a conftest.py. Updated for comatibility with biopython 1.7.8.
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-Removed mysequences.py
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-Reformatted code with BLACK
|
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-Use github actions for building and testing
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|
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|
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## [3.0.2a1] - 2019-07-23
|
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### Changed
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|
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-.upper() and .lower() methods for Dseq and Dseqrecord classes. Improved slicing
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|
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## [3.0.1] - 2019-05-28
|
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|
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### Changed
|
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|
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-Many changes and improvements, especially for the Assembly class.
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## [3.0.0] - 2019-05-17
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### Changed
|
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|
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---
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|
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## [2.0.3] - 2017-12-14
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|
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### Changed
|
||||
|
||||
---
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||||
|
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## [2.0.3a1] - 2017-12-14
|
||||
|
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### Changed
|
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|
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-pcr function now takes an amplicon. This way an amplicon can easily be rerun after
|
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modification of primers or template
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|
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## [2.0.3a0] - 2017-12-03
|
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|
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### Changed
|
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|
||||
---
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||||
|
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## [2.0.2] - 2017-08-26
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|
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### Changed
|
||||
|
||||
---
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||||
|
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## [2.0.2] - 2017-08-26
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|
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### Changed
|
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|
||||
---
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||||
|
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## [2.0.1] - 2017-08-24
|
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|
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### Changed
|
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|
||||
---
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||||
|
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## [2.0.0] - 2017-06-23
|
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|
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### Changed
|
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|
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-First release of 2.0.0. This version adds changes in the alpha versions
|
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|
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## [2.0.0a4] - 2017-05-05
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### Changed
|
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-Fixed bug in _multiply_circular
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|
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## [2.0.0a3] - 2017-04-04
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|
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### Changed
|
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|
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-added the all module, from pydna.all import *, now imports a set of useful pydna modules
|
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into the main namespace.
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-Finer control over cache, genbank download is now on by default.
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Bug fix in assembly_fragments function that created too long primer tails.
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|
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## [2.0.0a2] - ---
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||||
|
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### Changed
|
||||
|
||||
----
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|
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|
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## [2.0.0a1] -
|
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|
||||
### Changed
|
||||
|
||||
-removed setting functions for cache in __init_ and the delete_cache function for simplicity
|
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-removed these functions
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-pydna.design.print_primer_pair
|
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-pydna.design.cloning_primers
|
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-pydna.design.integration_primers
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-pydna.design.assembly_primers
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|
||||
## [2.0.0a0] - 2017-03-15
|
||||
|
||||
### Changed
|
||||
|
||||
-alpha release, removed imports in __init__
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-This version breaks compatibility.
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|
||||
## [1.2.0] - 2017-03-10
|
||||
|
||||
### Changed
|
||||
|
||||
-New and simpler primer design api, especially for gibson assembly primers. See docstrings
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-Dseqrecord.find method that allows finding subsequences "over the edge" of circular sequences.
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||||
|
||||
## [1.1.5] - 2016-12-16
|
||||
|
||||
### Changed
|
||||
|
||||
-added message for Dseqrecord write
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|
||||
## [1.1.4] - 2016-12-15
|
||||
|
||||
### Changed
|
||||
|
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-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"
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||||
-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.
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||||
-read_url function
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||||
-parse_url function
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||||
-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
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||||
"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
|
||||
[3.0.0a46]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a46..3.0.0a45
|
||||
[3.0.0a45]: https://github.com/BjornFJohansson/pydna/compare/3.0.0a45..3.0.0a44
|
||||
[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
|
||||
105
PKGBUILD
105
PKGBUILD
|
|
@ -1,76 +1,53 @@
|
|||
# Maintainer: Clint Valentine <valentine.clint@gmail.com>
|
||||
# Maintainer: Luis Martinez <luis dot martinez at disroot dot org>
|
||||
# Contributor: Clint Valentine <valentine.clint@gmail.com>
|
||||
|
||||
_name=pydna
|
||||
pkgbase='python-pydna'
|
||||
pkgname=('python-pydna')
|
||||
pkgver=2.0.3
|
||||
pkgname=python-pydna
|
||||
pkgver=4.0.2
|
||||
pkgrel=1
|
||||
pkgdesc="Python3 classes for dsDNA simulation of homologous recombination, Gibson assembly and interactive cloning"
|
||||
pkgdesc='Data structures for double-stranded DNA & simulation of homologous recombination'
|
||||
arch=('any')
|
||||
url="https://pypi.python.org/pypi/pydna"
|
||||
license=('GPL3')
|
||||
makedepends=(
|
||||
'python' 'python-setuptools'
|
||||
# 'python2' 'python2-setuptools'
|
||||
)
|
||||
options=(!emptydirs)
|
||||
source=("${pkgname}"-"${pkgver}".zip::https://pypi.python.org/packages/67/f2/552bd375666bb3e2ff4b3ec418ed2d5bbe1140847075d7c2d682435153c8/pydna-2.0.3.zip)
|
||||
sha256sums=('64b49daf4e30c53ac45a0bb5f40519fc627dd01c5751eae9d72a8f4a75a19e16')
|
||||
url='https://github.com/bjornfjohansson/pydna'
|
||||
license=('BSD')
|
||||
depends=(
|
||||
'python-appdirs>=1.4.3'
|
||||
'python-biopython>=1.79'
|
||||
'python-networkx>=2.5.0'
|
||||
'python-prettytable>=0.7.2'
|
||||
'python-pyparsing>=2.4.7'
|
||||
'python-requests>=2.23.0')
|
||||
optdepends=(
|
||||
'python-matplotlib: gel simulation'
|
||||
'python-mpldatacursor: gel simulation'
|
||||
'python-numpy: gel simulation'
|
||||
'python-pint: gel simulation'
|
||||
'python-scipy: gel simulation')
|
||||
makedepends=('git' 'python-setuptools' 'python-setuptools-scm' 'python-pytest-runner')
|
||||
changelog=CHANGELOG.md
|
||||
source=("$pkgname::git+$url#tag=$pkgver")
|
||||
sha256sums=('SKIP')
|
||||
|
||||
## FIXME: sphinx-build cannot find pydna
|
||||
# prepare() {
|
||||
# cp -a "${_name}"-"${pkgver}"{,-py2}
|
||||
# patch -p1 -d "$pkgname-$pkgver" < 001-python-path.patch
|
||||
# }
|
||||
|
||||
build(){
|
||||
cd "${srcdir}"/"${_name}"-"${pkgver}"
|
||||
python setup.py build
|
||||
|
||||
# cd "${srcdir}"/"${_name}"-"${pkgver}"-py2
|
||||
# python2 setup.py build
|
||||
build() {
|
||||
cd "$pkgname"
|
||||
python setup.py build
|
||||
## FIXME: sphinx-build cannot find pydna
|
||||
# cd docs
|
||||
# sphinx-build -b man ./ build
|
||||
}
|
||||
|
||||
package_python2-pydna() {
|
||||
depends=(
|
||||
'python2'
|
||||
'python2-appdirs'
|
||||
'python2-biopython'
|
||||
'python2-networkx'
|
||||
'python2-ordered-set'
|
||||
'python2-prettytable'
|
||||
'python2-pyparsing'
|
||||
'python2-requests'
|
||||
)
|
||||
optdepends=(
|
||||
'python2-matplotlib: gel simulation'
|
||||
'python2-mpldatacursor: gel simulation'
|
||||
'python2-numpy: gel simulation'
|
||||
'python2-pint: gel simulation'
|
||||
'python2-scipy: gel simulation'
|
||||
)
|
||||
|
||||
cd "${_name}"-"${pkgver}"-py2
|
||||
python2 setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build
|
||||
check() {
|
||||
cd "$pkgname"
|
||||
## FIXME: tests fail with python-prettytable=0.7.2
|
||||
python setup.py pytest || true
|
||||
}
|
||||
|
||||
package_python-pydna() {
|
||||
depends=(
|
||||
'python'
|
||||
'python-appdirs'
|
||||
'python-biopython'
|
||||
'python-networkx'
|
||||
'python-ordered-set'
|
||||
'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'
|
||||
)
|
||||
|
||||
cd "${_name}"-"${pkgver}"
|
||||
python setup.py install --root="${pkgdir}"/ --optimize=1 --skip-build
|
||||
package() {
|
||||
cd "$pkgname"
|
||||
PYTHONHASHSEED=0 python setup.py install --root="$pkgdir/" --optimize=1 --skip-build
|
||||
install -Dm 644 LICENSE.txt "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
|
||||
install -Dm 644 README.md -t "$pkgdir/usr/share/doc/$pkgname/"
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue