update to 4.0.2

rewrote package entirely due to changed dependencies and other issues
related to testing

3 files changed, 634 insertions, 83 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 9111cff16058..301036603e47 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,28 +1,27 @@
 pkgbase = python-pydna
-	pkgdesc = Python3 classes for dsDNA simulation of homologous recombination, Gibson assembly and interactive cloning
-	pkgver = 2.0.3
+	pkgdesc = Data structures for double-stranded DNA & simulation of homologous recombination
+	pkgver = 4.0.2
 	pkgrel = 1
-	url = https://pypi.python.org/pypi/pydna
+	url = https://github.com/bjornfjohansson/pydna
+	changelog = CHANGELOG.md
 	arch = any
-	license = GPL3
-	makedepends = python
+	license = BSD
+	makedepends = git
 	makedepends = python-setuptools
-	options = !emptydirs
-	source = python-pydna-2.0.3.zip::https://pypi.python.org/packages/67/f2/552bd375666bb3e2ff4b3ec418ed2d5bbe1140847075d7c2d682435153c8/pydna-2.0.3.zip
-	sha256sums = 64b49daf4e30c53ac45a0bb5f40519fc627dd01c5751eae9d72a8f4a75a19e16
-
-pkgname = python-pydna
-	depends = python
-	depends = python-appdirs
-	depends = python-biopython
-	depends = python-networkx
-	depends = python-ordered-set
-	depends = python-prettytable
-	depends = python-pyparsing
-	depends = python-requests
+	makedepends = python-setuptools-scm
+	makedepends = python-pytest-runner
+	depends = python-appdirs>=1.4.3
+	depends = python-biopython>=1.79
+	depends = python-networkx>=2.5.0
+	depends = python-prettytable>=0.7.2
+	depends = python-pyparsing>=2.4.7
+	depends = python-requests>=2.23.0
 	optdepends = python-matplotlib: gel simulation
 	optdepends = python-mpldatacursor: gel simulation
 	optdepends = python-numpy: gel simulation
 	optdepends = python-pint: gel simulation
 	optdepends = python-scipy: gel simulation
+	source = python-pydna::git+https://github.com/bjornfjohansson/pydna#tag=4.0.2
+	sha256sums = SKIP
 
+pkgname = python-pydna
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 000000000000..96b3a997801d
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,575 @@
+# 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
+[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
diff --git a/PKGBUILD b/PKGBUILD
index 98f2262a6438..631bff6b1264 100644
--- a/PKGBUILD
+++ b/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/"
 }