liberu-genealogy / php-dna Goto Github PK
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License: MIT License
php-dna's Issues
Sweep: update readme.md to describe how to call matchkits from cli or handler
Sweep: convert python
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/ensembl.py
Update src/Snps/Ensembl.php
Sweep: snps
Details
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/snps.py
Update src/Snps/Snps.php
Do this so that matchkits still works or will now work
Checklist
- Create
src/Snps/PythonDependencyAdapter.php✓ 56fda3c Edit - Running GitHub Actions for
src/Snps/PythonDependencyAdapter.php✓ Edit - Modify
src/Snps/Utils.php✓ 31315be Edit - Running GitHub Actions for
src/Snps/Utils.php✓ Edit - Modify
src/Snps/SNPs.php✓ c33d651 Edit - Running GitHub Actions for
src/Snps/SNPs.php✓ Edit - Modify
src/Snps/IO/Reader.php✓ f9e1ff2 Edit - Running GitHub Actions for
src/Snps/IO/Reader.php✓ Edit - Modify
src/Snps/IO/Writer.php✓ a50a107 Edit - Running GitHub Actions for
src/Snps/IO/Writer.php✓ Edit
Sweep: update snps
Details
Details
Convert the following file from python 3 into php 8.3:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/snps.py
Update src/Snps/Snps.php in this project and refactor for php 8.3
Sweep:
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/snps.py
Update src/Snps/Snps.php
Checklist
- Modify
src/Snps/SNPs.php✓ 95dbafd Edit - Running GitHub Actions for
src/Snps/SNPs.php✓ Edit - Create
src/Snps/Utils/MathOperations.php✓ 09cab11 Edit - Running GitHub Actions for
src/Snps/Utils/MathOperations.php✓ Edit - Create
src/Snps/Utils/DataFrame.php✓ c5ffadd Edit - Running GitHub Actions for
src/Snps/Utils/DataFrame.php✓ Edit - Modify
src/Snps/IO/Reader.php✓ 018aa34 Edit - Running GitHub Actions for
src/Snps/IO/Reader.php✓ Edit - Modify
src/Snps/IO/Writer.php✓ 850d6a2 Edit - Running GitHub Actions for
src/Snps/IO/Writer.php✓ Edit
Sweep: improve modularization of the project and efficiency
Checklist
- Create
src/Snps/ReferenceSequenceManager.php✓ 822b8b7 Edit - Running GitHub Actions for
src/Snps/ReferenceSequenceManager.php✓ Edit - Create
src/Snps/AssemblyMappingManager.php✓ 129c643 Edit - Running GitHub Actions for
src/Snps/AssemblyMappingManager.php✓ Edit - Create
src/Snps/DatasetDownloader.php✓ 6f94880 Edit - Running GitHub Actions for
src/Snps/DatasetDownloader.php✓ Edit - Modify
src/Snps/SNPsResources.php! No changes made Edit - Running GitHub Actions for
src/Snps/SNPsResources.php✗ Edit
Sweep:
Details
Finish converting from python 3 into php 8.3 the following file https://github.com/apriha/snps/blob/master/src%2Fsnps%2Fio%2Freader.py and update src/Snps/IO/Reader.php also convert all the python called external files into php 8.3 and place in src/Snps/IO
Checklist
- Modify
src/Snps/IO/Reader.php✓ 26719e9 Edit - Running GitHub Actions for
src/Snps/IO/Reader.php✓ Edit - Modify
src/Snps/IO/ExtraTabsFilter.php✓ 2f008e9 Edit - Running GitHub Actions for
src/Snps/IO/ExtraTabsFilter.php✓ Edit - Modify
src/Snps/SNPsResources.php! No changes made Edit - Running GitHub Actions for
src/Snps/SNPsResources.php✗ Edit - Modify
src/Snps/IO/CsvReader.php✓ e5ebcc9 Edit - Running GitHub Actions for
src/Snps/IO/CsvReader.php✓ Edit
Sweep: add triangulation to matchkits to compare multiple kits
Sweep: update snps
Details
Convert the following file from python 3 into php 8.3:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/snps.py
Update src/Snps/Snps.php in this project and refactor for php 8.3
Checklist
- Modify
src/Snps/SNPs.php! No changes made Edit - Running GitHub Actions for
src/Snps/SNPs.php✗ Edit - Modify
src/Snps/Utils.php✓ b5cdfd8 Edit - Running GitHub Actions for
src/Snps/Utils.php✓ Edit - Create
src/Snps/IO/DataParser.php✓ 08c6015 Edit - Running GitHub Actions for
src/Snps/IO/DataParser.php✓ Edit
Sweep: update to vite 5.2
Sweep: finish visualisation
Details
Finish converting the python 3 file at https://github.com/apriha/lineage/blob/master/src%2Flineage%2Fvisualization.py to the php 8.3 file at src/Visualization.php
Sweep: finish visulation
Details
Finish converting the python 3 file at https://github.com/apriha/lineage/blob/master/src%2Flineage%2Fvisualization.py to the php 8.3 file at src/Visualisation.php
Sweep: Refactor
Details
Refactor src/Snps/Snps.php to be more modular and efficient
Checklist
- Create
src/Snps/IO/SnpFileReader.php✓ 8bd4255 Edit - Running GitHub Actions for
src/Snps/IO/SnpFileReader.php✓ Edit - Create
src/Snps/Analysis/BuildDetector.php✓ 2f1e204 Edit - Running GitHub Actions for
src/Snps/Analysis/BuildDetector.php✓ Edit - Create
src/Snps/Analysis/ClusterOverlapCalculator.php✓ 61b745c Edit - Running GitHub Actions for
src/Snps/Analysis/ClusterOverlapCalculator.php✓ Edit - Modify
src/Snps/SNPs.php✓ 9ed4e94 Edit - Running GitHub Actions for
src/Snps/SNPs.php✓ Edit
Sweep: write
Details
Details
Finish converting from python 3 into php 8.3 the following file https://github.com/apriha/snps/blob/master/src%2Fsnps%2Fio%2Fwriter.py and update src/Snps/IO/Writer.php also convert all the python called external files into php 8.3 and place in src/Snps/IO
Sweep: snps
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/snps.py
Update src/Snps/Snps.php
Do this so that matchkits still works or will now work
Sweep: Refactor codebase to use php 8.3 and improve code overall
Checklist
- Modify
src/Snps/IO/Reader.php✓ 937ceab Edit - Running GitHub Actions for
src/Snps/IO/Reader.php✓ Edit - Modify
src/Snps/IO/Writer.php✓ 1227a1d Edit - Running GitHub Actions for
src/Snps/IO/Writer.php✓ Edit - Modify
src/Snps/Utils.php✓ 9f16ca7 Edit - Running GitHub Actions for
src/Snps/Utils.php✓ Edit - Modify
tests/Snps/ResourcesTest.php✓ 55aa9cb Edit - Running GitHub Actions for
tests/Snps/ResourcesTest.php✓ Edit - Modify
src/Snps/IO/ExtraTabsFilter.php✓ a73943b Edit - Running GitHub Actions for
src/Snps/IO/ExtraTabsFilter.php✓ Edit - Modify
src/Snps/EnsemblRestClient.php✓ 3e3050f Edit - Running GitHub Actions for
src/Snps/EnsemblRestClient.php✓ Edit - Modify
src/Snps/SNPs.php✓ 5993646 Edit - Running GitHub Actions for
src/Snps/SNPs.php✓ Edit - Modify
src/Snps/ReferenceSequence.php✓ cec5ca9 Edit - Running GitHub Actions for
src/Snps/ReferenceSequence.php✓ Edit
Sweep: writer
Details
Finish converting from python 3 into php 8.3 the following file https://github.com/apriha/snps/blob/master/src%2Fsnps%2Fio%2Fwriter.py and update src/Snps/IO/Wruter.php also convert all the python called external files into php 8.3 and place in src/Snps/IO
Sweep: handling
Details
Create entry point to match two kits using the current code
Sweep: improve gd
Details
Improve and add php GD image library support to src/Visualization.php so that beautiful chromosome outputs are generated using png and svg. Also generate a csv with information of the matching data
Checklist
- Modify
src/Visualization.php✓ 9a2699f Edit - Running GitHub Actions for
src/Visualization.php✓ Edit - Modify
src/MatchKits.php✓ bd2795d Edit - Running GitHub Actions for
src/MatchKits.php✓ Edit - Create
src/Helpers/CSVGenerator.php✓ 037a6f5 Edit - Running GitHub Actions for
src/Helpers/CSVGenerator.php✓ Edit - Modify
src/Visualization.php✓ 0665716 Edit - Running GitHub Actions for
src/Visualization.php✓ Edit
Sweep: improve chromosome visualisation quality in src/Visualization.php
Sweep:
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/utils.py
Update src/Snps/Utils.php
Sweep:
Details
Convert the following files from python 3 into php 8.3 and refactor:
https://raw.githubusercontent.com/apriha/snps/master/src/snps/resources.py
Update src/Snps/Resources.php
Sweep: finish resources
Details
Finish converting the python 3 file at https://github.com/apriha/lineage/blob/master/src%2Flineage%2Fresources.py to the php 8.3 file at src/Resources.php
Sweep: Refactor for php 8.3
Checklist
- Modify
composer.json✓ d576635 Edit - Running GitHub Actions for
composer.json✓ Edit - Modify
src/Snps/SNPs.php✓ 01570df Edit - Running GitHub Actions for
src/Snps/SNPs.php✓ Edit - Modify
src/Snps/EnsemblRestClient.php! No changes made Edit - Running GitHub Actions for
src/Snps/EnsemblRestClient.php✗ Edit - Modify
src/Snps/IO/Reader.php✓ ad09040 Edit - Running GitHub Actions for
src/Snps/IO/Reader.php✓ Edit - Modify
src/Snps/Utils.php✓ 02b08d6 Edit - Running GitHub Actions for
src/Snps/Utils.php✓ Edit
Sweep: update readme.md
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