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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]: 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