tzok/rnapolis-py issues and pull requests

#244 - feat: resolve occupancy related clashes

Pull Request - State: closed - Opened by tzok about 1 month ago

#243 - feat: support alternate locations

Pull Request - State: closed - Opened by tzok about 1 month ago

#242 - build: bump hypothesis from 6.112.1 to 6.112.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 month ago
Labels: dependencies, python

#241 - build: bump pandas from 2.2.2 to 2.2.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#240 - build: bump pytest from 8.3.2 to 8.3.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#239 - build: bump hypothesis from 6.112.0 to 6.112.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies, python

#238 - build: bump numpy from 2.0.1 to 2.1.1

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies, python

#237 - build: bump hypothesis from 6.111.2 to 6.112.0

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies, python

#236 - fix: resolve conflicts in BPSEQ generation

Pull Request - State: closed - Opened by tzok 2 months ago

#235 - build: bump scipy from 1.14.0 to 1.14.1

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, python

#234 - build: bump hypothesis from 6.111.1 to 6.111.2

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#233 - build: bump numpy from 2.0.1 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, python

#232 - build: bump hypothesis from 6.111.0 to 6.111.1

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#231 - fix: incorrect strand sequence

Pull Request - State: closed - Opened by tzok 3 months ago

#230 - fix: dot-bracket encoding with gaps

Pull Request - State: closed - Opened by tzok 3 months ago

#229 - feat: fill BPSEQ with gaps

Pull Request - State: closed - Opened by tzok 3 months ago

#228 - feat: improve mmCIF parsing with unnamed residues

Pull Request - State: closed - Opened by tzok 3 months ago

#227 - feat: support chain filtering

Pull Request - State: closed - Opened by tzok 3 months ago

#226 - build: bump orjson from 3.10.6 to 3.10.7

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#225 - build: bump hypothesis from 6.108.8 to 6.111.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, python

#224 - build: bump hypothesis from 6.108.5 to 6.108.8

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#223 - build: bump black from 24.4.2 to 24.8.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies, python

#222 - build: bump pytest from 8.3.1 to 8.3.2

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#221 - build: bump hypothesis from 6.108.2 to 6.108.5

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#220 - build: bump hypothesis from 6.105.1 to 6.108.2

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#219 - build: bump pytest from 8.2.2 to 8.3.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#218 - build: bump numpy from 2.0.0 to 2.0.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#217 - build: bump hypothesis from 6.105.1 to 6.108.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies, python

#216 - build: bump mmcif from 0.88.0 to 0.89.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#215 - build: bump pulp from 2.8.0 to 2.9.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#214 - build: bump hypothesis from 6.104.2 to 6.105.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#213 - build: bump orjson from 3.10.5 to 3.10.6

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies, python

#212 - feat: support CSV output

Pull Request - State: closed - Opened by tzok 4 months ago

#211 - build: bump hypothesis from 6.103.1 to 6.104.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#210 - build: bump scipy from 1.13.1 to 1.14.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#209 - build: bump hypothesis from 6.103.1 to 6.103.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, python

#208 - build: bump orjson from 3.10.3 to 3.10.5

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#207 - build: bump numpy from 1.26.4 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 2 comments
Labels: dependencies, python

#206 - fix: adjusted the start index for the "Residue name" entries (PDB)

Pull Request - State: closed - Opened by tzok 5 months ago

#205 - "math domain error" during annotator run

Issue - State: closed - Opened by DiegoBarMor 5 months ago - 3 comments

#204 - fix: adjusted the start index for the "Residue name" entries (PDB)

Pull Request - State: closed - Opened by DiegoBarMor 5 months ago - 3 comments

#203 - build: bump pytest from 8.2.1 to 8.2.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#202 - build: bump hypothesis from 6.103.0 to 6.103.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#201 - fix: TypeError in 8BTK caused by invalid label columns in the mmCIF

Pull Request - State: closed - Opened by tzok 5 months ago

#200 - Python exception during annotator run

Issue - State: closed - Opened by morrgant 5 months ago - 2 comments

#199 - build: bump hypothesis from 6.102.6 to 6.103.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#198 - build: bump requests from 2.32.2 to 2.32.3

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#197 - build: bump scipy from 1.13.0 to 1.13.1

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#196 - build: bump requests from 2.32.0 to 2.32.2

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#195 - build: bump hypothesis from 6.102.4 to 6.102.6

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#194 - build: bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#193 - build: bump hypothesis from 6.100.7 to 6.102.4

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#192 - build: bump pytest from 8.2.0 to 8.2.1

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#191 - build: bump hypothesis from 6.100.4 to 6.100.7

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#190 - feat: optimize all dot bracket generation

Pull Request - State: closed - Opened by tzok 6 months ago

#189 - fix: handle non pseudoknotted structures

Pull Request - State: closed - Opened by tzok 6 months ago

#188 - feat: generate all valid dot brackets

Pull Request - State: closed - Opened by tzok 6 months ago

#187 - feat: support IUPAC codes

Pull Request - State: closed - Opened by tzok 6 months ago

#186 - feat: add multi strand dot bracket

Pull Request - State: closed - Opened by tzok 6 months ago

#185 - build: bump mmcif from 0.87.0 to 0.88.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#184 - build: bump hypothesis from 6.100.2 to 6.100.4

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#183 - build: bump orjson from 3.10.1 to 3.10.3

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#182 - build: bump black from 24.3.0 to 24.4.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#181 - build: bump hypothesis from 6.100.1 to 6.100.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#180 - build: bump pytest from 8.1.1 to 8.2.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#179 - build: bump orjson from 3.10.0 to 3.10.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#178 - build: bump hypothesis from 6.100.0 to 6.100.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#177 - build: bump black from 24.3.0 to 24.4.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: dependencies, python

#176 - build: bump scipy from 1.12.0 to 1.13.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#175 - build: bump mmcif from 0.86.0 to 0.87.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies, python

#174 - build: bump orjson from 3.9.15 to 3.10.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#173 - build: bump hypothesis from 6.99.13 to 6.100.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#172 - build: bump dependabot/fetch-metadata from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies, github_actions

#171 - build: bump hypothesis from 6.99.6 to 6.99.13

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#170 - build: bump graphviz from 0.20.1 to 0.20.3

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#169 - fix: select first available model

Pull Request - State: closed - Opened by tzok 8 months ago

#168 - fix: handle multi-model files

Pull Request - State: closed - Opened by tzok 8 months ago

#167 - build: bump graphviz from 0.20.1 to 0.20.2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies, python

#166 - build: bump black from 24.2.0 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#165 - build: bump hypothesis from 6.99.2 to 6.99.6

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#164 - fix: handling of reverse strand

Pull Request - State: closed - Opened by tzok 8 months ago

#163 - fix: match whole sequences in rfam_folder

Pull Request - State: closed - Opened by tzok 8 months ago

#162 - fix: parsing of cmsearch output

Pull Request - State: closed - Opened by tzok 8 months ago

#161 - feat: use rfam defaults for infernal

Pull Request - State: closed - Opened by tzok 8 months ago

#160 - build: bump hypothesis from 6.98.15 to 6.99.2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#159 - build: bump pytest from 8.1.0 to 8.1.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#158 - fix: add threading.Lock to solve synchronization problems

Pull Request - State: closed - Opened by tzok 8 months ago

#157 - build: bump mmcif from 0.85.1 to 0.86.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#156 - build: bump hypothesis from 6.98.12 to 6.98.15

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#155 - build: bump pytest from 8.0.2 to 8.1.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies, python

#154 - build: bump pytest from 8.0.1 to 8.0.2

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#153 - build: bump hypothesis from 6.98.8 to 6.98.12

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#152 - build: bump orjson from 3.9.13 to 3.9.15

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#151 - build: bump pytest from 8.0.0 to 8.0.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#150 - build: bump black from 24.1.1 to 24.2.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#149 - build: bump orjson from 3.9.13 to 3.9.14

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies, python

#148 - build: bump hypothesis from 6.98.3 to 6.98.8

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#147 - build: bump numpy from 1.26.3 to 1.26.4

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#146 - build: bump hypothesis from 6.97.1 to 6.98.3

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, python

#145 - build: bump hypothesis from 6.97.1 to 6.98.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies, python

GitHub / tzok/rnapolis-py issues and pull requests