update numpy version and taxa data

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "OGU"
-version = "1.999"
+version = "2.0.0"
 description = "Organelle Genome Utilities"
 keywords = ['plastid', 'mitochondria', 'organelle genome', 'analysis',
     'Bioinformatics']
@@ -12,14 +12,14 @@ maintainers = [
 ]
 dependencies = [
     "biopython==1.82",
-    "certifi>=2024.6.2",
     "colorama>=0.4.6",
     "coloredlogs>=10.0",
     "matplotlib>=3.0.0",
-    "numpy<2.0",
     "primer3-py==2.0.2",
     "pandas>=2.1.4",
     "pycirclize>=1.7.1",
+    "certifi>=2024.12.14",
+    "numpy>=2.0",
 ]
 requires-python = ">=3.9"
 readme = "README.md"

setup.py

@@ -28,10 +28,10 @@
     long_description_content_type='text/markdown',
     name=name,
     packages=setuptools.find_packages(),
-    python_requires='>=3.8',
+    python_requires='>=3.9',
     entry_points={'console_scripts': ['OGU = OGU:main', 'ogu = OGU:main']},
     url='https://github.com/wpwupingwp/BarcodeFinder',
-    version='1.996',
+    version='2.0.0',
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',
@@ -43,4 +43,4 @@
         'Programming Language :: Python :: 3.10',
         'Topic :: Scientific/Engineering :: Bio-Informatics'
     ],
-)
+)

src/OGU/data/kingdoms.csv

@@ -1 +1 @@
-Helvetiavirae,Bamfordvirae,Pararnavirae,Heunggongvirae,Trapavirae,Viridiplantae,Orthornavirae,Shotokuvirae,Metazoa,Loebvirae,Zilligvirae,Sangervirae,Fungi
+Bacillati,Bamfordvirae,Fusobacteriati,Viridiplantae,Thermoproteati,Shotokuvirae,Zilligvirae,Sangervirae,Trapavirae,Metazoa,Nanobdellati,Pararnavirae,Loebvirae,Pseudomonadati,Heunggongvirae,Thermotogati,Fungi,Orthornavirae,Helvetiavirae,Methanobacteriati,Promethearchaeati

src/OGU/data/phyla.csv

@@ -1 +1 @@
-candidate division CPR1,Deferribacterota,Rhodophyta,Candidatus Campbellbacteria,Candidatus Fermentibacteria,Candidatus Komeiliibacteriota,Candidatus Cloacimonadota,Candidatus Woesebacteria,Candidatus Abawacaibacteriota,Candidatus Fischeribacteriota,Candidatus Shapirobacteria,Verrucomicrobiota,Negarnaviricota,Hofneiviricota,Aquificota,Atribacterota,Preplasmiviricota,Candidatus Hydrothermarchaeota,Candidatus Magasanikiibacteriota,Candidatus Altarchaeota,Discosea,Kiritimatiellota,Candidatus Melainabacteria,Chlorobiota,Nanoarchaeota,Candidatus Tagaibacteriota,Caldisericota,Nucleocytoviricota,Bacillariophyta,Planctomycetota,Candidatus Huberarchaea,Candidatus Aminicenantota,Candidatus Wukongarchaeota,Candidatus Fraseribacteriota,Phixviricota,Cnidaria,Chytridiomycota,Lentisphaerota,Kinorhyncha,Calditrichota,Fornicata,Candidatus Berkelbacteria,Nematoda,Candidatus Woykeibacteriota,Candidatus Aenigmatarchaeota,Mollusca,Candidatus Geothermarchaeota,Candidatus Lithacetigenota,Cercozoa,Thermoproteota,Blastocladiomycota,Candidatus Falkowbacteria,Preaxostyla,Echinodermata,Coprothermobacterota,Candidatus Eiseniibacteriota,Candidatus Adlerbacteria,Candidatus Anderseniibacteriota,Candidatus Calescamantes,Candidatus Hadarchaeota,Candidatus Electryoneota,Thermosulfidibacterota,Candidatus Vogeliibacteriota,Candidatus Glassiibacteriota,Candidatus Thermoplasmatota,candidate division JL-ETNP-Z39,Evosea,Candidatus Wildermuthiibacteriota,Candidatus Dormiibacterota,Thermotogota,Candidatus Kariarchaeota,Gnathostomulida,Candidatus Spechtiibacteriota,Halobacteriota,Nibbleridia,Porifera,Candidatus Buchananiibacteriota,Euryarchaeota,Nebulidia,Candidatus Handelsmaniibacteriota,candidate division WWE3,Olpidiomycota,Synergistota,Candidatus Rifleibacteriota,Candidatus Harrisoniibacteriota,Streptophyta,Myxococcota,Mucoromycota,Candidatus Hodarchaeota,Candidatus Marsarchaeota,Candidatus Tectimicrobiota,Candidatus Hydrogenedentota,Candidatus Terryibacteriota,Candidatus Geoarchaeota,Acidobacteriota,Chaetognatha,Candidatus Roizmanbacteria,Candidatus Blackallbacteria,Candidatus Doudnaibacteriota,Prasinodermophyta,Basidiomycota,Nitrospinota,Nematomorpha,Picozoa,Candidatus Effluviviacota,Nitrospirota,Candidatus Firestoneibacteriota,candidate division ZB2,Candidatus Lloydiibacteriota,Candidatus Pyropristinus,Rhodothermota,Cycliophora,Microsporidia,Bacillota,Dictyoglomota,Candidatus Amesbacteria,candidate phylum NAG2,Sanchytriomycota,Candidatus Edwardsiibacteriota,Oomycota,Candidatus Wolfebacteria,Placozoa,Platyhelminthes,Thermodesulfobiota,Perkinsozoa,Elusimicrobiota,Artverviricota,Dicyemida,Chlamydiota,Candidatus Giovannonibacteria,Kitrinoviricota,Arthropoda,Bdellovibrionota,Candidatus Goldiibacteriota,Candidatus Azambacteria,Candidatus Neomarinimicrobiota,Cressdnaviricota,Candidatus Parcubacteria,candidate division CPR3,Candidatus Lernaellota,Cossaviricota,Candidatus Zambryskiibacteriota,Candidatus Peregrinibacteria,Candidatus Moraniibacteriota,Candidatus Curtissbacteria,Endomyxa,Heterolobosea,Candidatus Kaiserbacteria,Uroviricota,Candidatus Auribacterota,Candidatus Latescibacterota,Candidatus Muiribacteriota,Candidatus Beckwithbacteria,Candidatus Bathyarchaeota,Gemmatimonadota,Candidatus Yanofskyibacteriota,Candidatus Wirthbacteria,Fibrobacterota,Acanthocephala,Candidatus Ryaniibacteriota,Candidatus Undinarchaeota,Candidatus Sigynarchaeota,Thermomicrobiota,Candidatus Walliibacteriota,Balneolota,Microcaldota,Duplornaviricota,Candidatus Brenneribacteriota,Brachiopoda,Candidatus Vebleniibacteriota,Candidatus Borrarchaeota,Candidatus Schekmaniibacteriota,Candidatus Freyarchaeota,Candidatus Zixiibacteriota,Candidatus Odinarchaeota,Vulcanimicrobiota,Thermodesulfobacteriota,Candidatus Gottesmanbacteria,Candidatus Hermodarchaeota,Chrysiogenota,Dividoviricota,Candidatus Tayloriibacteriota,Candidatus Sungiibacteriota,Mycoplasmatota,Candidatus Thorarchaeota,Candidatus Chisholmiibacteriota,Nemertea,Fusobacteriota,Candidatus Nealsoniibacteriota,candidate division CPR2,Hemimastigophora,Candidatus Staskawicziibacteriota,Chordata,Ciliophora,Candidatus Fervidibacterota,Candidatus Korarchaeota,Spirochaetota,Candidatus Methylomirabilota,Candidatus Parvarchaeota,Nitrososphaerota,Candidatus Yonathiibacteriota,Candidatus Delongiibacteriota,Onychophora,Candidatus Omnitrophota,Candidatus Binatota,Candidatus Tharpellota,Priapulida,Candidatus Hydrothermota,Candidatus Baldrarchaeota,Candidatus Paceibacterota,candidate division CSSED10-310,Candidatus Sumerlaeota,Candidatus Desantisbacteria,Candidatus Helarchaeota,Candidatus Kerfeldiibacteriota,Cryptomycota,Chlorophyta,Pisuviricota,Candidatus Gribaldobacteria,Bacteroidota,Candidatus Niyogiibacteriota,candidate division WOR-3,Candidatus Daviesbacteria,candidate division KD3-62,Ascomycota,Parabasalia,Candidatus Bipolaricaulota,Candidatus Portnoyibacteriota,candidate division LCP-89,Candidatus Mcinerneyibacteriota,Candidatus Rokuibacteriota,Candidatus Coatesiibacteriota,Rotifera,Candidatus Jacksoniibacteriota,Gastrotricha,Candidatus Diapherotrites,Hemichordata,Candidatus Nanohalarchaeota,Candidatus Uhrbacteria,Peploviricota,Candidatus Micrarchaeota,candidate division GAL15,Saleviricota,Cyanobacteriota,Candidatus Lokiarchaeota,Candidatus Methanomethylicota,Candidatus Krumholzibacteriota,Phoronida,Candidatus Heimdallarchaeota,Zoopagomycota,Candidatus Woesearchaeota,Orthonectida,Bryozoa,Candidatus Blackburniibacteriota,Candidatus Microgenomates,Candidatus Deferrimicrobiota,Haptophyta,Loricifera,Candidatus Kuenenbacteria,Candidatus Absconditabacteria,Lenarviricota,Candidatus Raymondiibacteriota,Candidatus Cryosericota,Chloroflexota,Candidatus Caldatribacteriota,Candidatus Collierbacteria,Candidatus Liptoniibacteriota,Annelida,Candidatus Jorgensenbacteria,Apicomplexa,Candidatus Cerribacteria,Candidatus Kryptoniota,Actinomycetota,candidate division FCPU426,Candidatus Njordarchaeota,Candidatus Levyibacteriota,Candidatus Gerdarchaeota,Abditibacteriota,Candidatus Moduliflexota,Candidatus Culexarchaeota,Candidatus Colwelliibacteriota,Foraminifera,Candidatus Nezhaarchaeota,Candidatus Poribacteria,Candidatus Nomurabacteria,Candidatus Gefionarchaeota,Deinococcota,Entoprocta,Armatimonadota,Pseudomonadota,Candidatus Hinthialibacterota,Euglenozoa,Candidatus Sifarchaeota,Candidatus Margulisiibacteriota,Candidatus Ratteibacteria,Candidatus Friggarchaeota,Tubulinea,Ctenophora,Campylobacterota,Candidatus Elulimicrobiota,Candidatus Salinosulfoleibacteria,Candidatus Lindowiibacteriota,Taleaviricota,Candidatus Gracilibacteria,Candidatus Aerophobetes,Xenacoelomorpha,Candidatus Saccharibacteria,Candidatus Idunnarchaeota,Tardigrada,Ignavibacteriota,Candidatus Brockarchaeota
+Sanchytriomycota,Candidatus Sigynarchaeota,Candidatus Daviesbacteria,Candidatus Blackallbacteria,Microsporidia,Candidatus Nanohalarchaeota,Bacillariophyta,candidate division CPR2,candidate division LCP-89,Candidatus Baldrarchaeota,Gnathostomulida,Candidatus Wukongarchaeota,Fornicata,Candidatus Kerfeldiibacteriota,Candidatus Iainarchaeota,Chlorophyta,Kiritimatiellota,Candidatus Beckwithbacteria,Candidatus Hinthialibacterota,Atribacterota,Gemmatimonadota,Zoopagomycota,Nemertea,Candidatus Pyropristinus,Candidatus Gottesmanbacteria,Candidatus Blackburniibacteriota,Candidatus Staskawicziibacteriota,Candidatus Uhrbacteria,Candidatus Huberarchaeota,Candidatus Undinarchaeota,Acanthocephala,Kinorhyncha,Candidatus Nealsoniibacteriota,candidate division KD3-62,Candidatus Collierbacteria,Balneolota,Candidatus Peregrinibacteria,Armatimonadota,Candidatus Levyibacteriota,Chloroflexota,Nebulidia,Dicyemida,Candidatus Lernaellota,Candidatus Zixiibacteriota,Pisuviricota,Candidatus Colwelliibacteriota,candidate division WWE3,Taleaviricota,Dividoviricota,Candidatus Eiseniibacteriota,Mycoplasmatota,Candidatus Falkowbacteria,Candidatus Edwardsiibacteriota,Kitrinoviricota,Candidatus Geoarchaeota,Candidatus Fervidibacterota,Candidatus Ryaniibacteriota,Preplasmiviricota,Candidatus Kryptoniota,Chlamydiota,Candidatus Aerophobetes,Duplornaviricota,Candidatus Gefionarchaeota,Deferribacterota,Mucoromycota,Cressdnaviricota,Nematoda,Candidatus Fischeribacteriota,Candidatus Tagaibacteriota,Candidatus Campbellbacteria,candidate division JL-ETNP-Z39,Artverviricota,Promethearchaeota,Candidatus Yanofskyibacteriota,Acidobacteriota,Thermodesulfobiota,Candidatus Komeiliibacteriota,Candidatus Raymondiibacteriota,Candidatus Sifarchaeota,Basidiomycota,Candidatus Margulisiibacteriota,Candidatus Fermentibacterota,Entoprocta,Candidatus Thorarchaeota,Xenacoelomorpha,Fibrobacterota,Lentisphaerota,Candidatus Lithacetigenota,Candidatus Omnitrophota,Spirochaetota,Oomycota,Candidatus Moduliflexota,Elusimicrobiota,Abditibacteriota,Candidatus Helarchaeota,Candidatus Goldiibacteriota,Candidatus Chisholmiibacteriota,Brachiopoda,Candidatus Kuenenbacteria,Candidatus Parcubacteria,Chrysiogenota,Candidatus Kapaibacteriota,Nitrososphaerota,Candidatus Woykeibacteriota,Candidatus Friggarchaeota,Candidatus Terryibacteriota,Candidatus Salinosulfoleibacteria,Candidatus Effluviviacota,Candidatus Borrarchaeota,Candidatus Wildermuthiibacteriota,Dictyoglomota,Candidatus Woesearchaeota,Candidatus Shapirobacteria,Candidatus Absconditibacteriota,Uroviricota,Thermomicrobiota,Candidatus Caldatribacteriota,Tubulinea,Cnidaria,Candidatus Altarchaeota,Candidatus Parvarchaeota,Candidatus Melainabacteria,Bacillota,Chordata,Candidatus Lloydiibacteriota,Endomyxa,Discosea,Candidatus Gerdarchaeota,Candidatus Elulimicrobiota,Bdellovibrionota,Candidatus Brockarchaeota,Caldisericota,Foraminifera,Candidatus Hydrothermarchaeota,Candidatus Tayloriibacteriota,Candidatus Dormiibacterota,Actinomycetota,Candidatus Adlerbacteria,Porifera,Saleviricota,Thermosulfidibacterota,Candidatus Vogeliibacteriota,Annelida,Candidatus Handelsmaniibacteriota,Candidatus Krumholzibacteriota,Candidatus Hadarchaeota,Candidatus Saccharibacteria,Candidatus Hermodarchaeota,Candidatus Deferrimicrobiota,Prasinodermophyta,Negarnaviricota,Candidatus Walliibacteriota,Candidatus Sysuimicrobiota,Candidatus Firestoneibacteriota,Candidatus Hydrothermota,Candidatus Jorgensenbacteria,Candidatus Njordarchaeota,Nibbleridia,Arthropoda,candidate phylum NAG2,Pseudomonadota,Euglenozoa,Cyanobacteriota,Ignavibacteriota,Aquificota,Candidatus Roizmanbacteria,Myxococcota,Chlorobiota,Nucleocytoviricota,Candidatus Paceibacterota,Cercozoa,Perkinsozoa,Candidatus Micrarchaeota,Candidatus Bipolaricaulota,Candidatus Magasanikiibacteriota,Thermoproteota,candidate division WOR-3,Candidatus Giovannonibacteria,Onychophora,Peploviricota,Rhodothermota,Candidatus Kariarchaeota,Verrucomicrobiota,Evosea,Candidatus Moraniibacteriota,Candidatus Tharpellota,Candidatus Bathyarchaeota,Candidatus Aminicenantota,Candidatus Jacksoniibacteriota,Vulcanimicrobiota,Candidatus Glassiibacteriota,Olpidiomycota,Candidatus Harrisoniibacteriota,Candidatus Gribaldobacteria,Microcaldota,Rotifera,Candidatus Delongiibacteriota,Deinococcota,Orthonectida,Cycliophora,Candidatus Amesbacteria,Candidatus Sumerlaeota,Candidatus Electryoneota,candidate division CSSED10-310,Candidatus Sungiibacteriota,Chytridiomycota,Thermodesulfobacteriota,Candidatus Calescamantes,Candidatus Vebleniibacteriota,Candidatus Heimdallarchaeota,Tardigrada,Hofneiviricota,Candidatus Cerribacteria,Haptophyta,Candidatus Niyogiibacteriota,Candidatus Aenigmatarchaeota,Candidatus Yonathiibacteriota,Methanobacteriota,Candidatus Azambacteria,Candidatus Kaiserbacteria,Hemimastigophora,Ascomycota,Ctenophora,Candidatus Geothermarchaeota,Candidatus Culexarchaeota,Preaxostyla,Halobacteriota,Streptophyta,Thermoplasmatota,Candidatus Schekmaniibacteriota,Hemichordata,Candidatus Liptoniibacteriota,candidate division AD1,Echinodermata,candidate division FCPU426,Candidatus Cryosericota,Candidatus Buchananiibacteriota,Calditrichota,Phixviricota,Coprothermobacterota,Candidatus Auribacterota,Cossaviricota,Candidatus Microgenomates,Candidatus Doudnaibacteriota,Candidatus Rifleibacteriota,Fidelibacterota,Candidatus Lindowiibacteriota,Candidatus Wirthbacteria,Candidatus Spechtiibacteriota,Synergistota,Candidatus Nomurabacteria,Nematomorpha,Candidatus Berkelbacteria,Candidatus Tectimicrobiota,candidate division ZB2,Candidatus Hydrogenedentota,Ciliophora,Candidatus Poribacteria,Gastrotricha,Parabasalia,Candidatus Idunnarchaeota,Planctomycetota,Candidatus Coatesiibacteriota,Candidatus Woesebacteria,Apicomplexa,Blastocladiomycota,Placozoa,Cryptomycota,Picozoa,Candidatus Binatota,Candidatus Methanomethylicota,Candidatus Zambryskiibacteriota,Phoronida,Candidatus Hodarchaeota,Candidatus Mcinerneyibacteriota,Bacteroidota,Heterolobosea,Nanobdellota,Bryozoa,Platyhelminthes,Lenarviricota,Candidatus Freyarchaeota,Chaetognatha,Thermotogota,candidate division CPR1,Candidatus Wolfebacteria,Campylobacterota,Nitrospirota,Candidatus Curtissbacteria,Nitrospinota,Loricifera,Candidatus Marsarchaeota,Fusobacteriota,Candidatus Abawacaibacteriota,Candidatus Brenneribacteriota,Candidatus Desantisbacteria,Candidatus Fraseribacteriota,Candidatus Portnoyibacteriota,Candidatus Rokuibacteriota,Priapulida,Candidatus Latescibacterota,Candidatus Nezhaarchaeota,Rhodophyta,Candidatus Cloacimonadota,Candidatus Ratteibacteria,Candidatus Altimarinota,Mollusca,candidate division CPR3,Candidatus Methylomirabilota,Candidatus Muiribacteriota,Candidatus Anderseniibacteriota,Candidatus Odinarchaeota

src/OGU/data/superkingdoms.csv

@@ -1 +1 @@
-Viruses,Bacteria,Eukaryota,Archaea
+Bacteria,Archaea,Viruses,Eukaryota