Team Ai
Datasetpublic

OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.

sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
github.com__manuquadros__d3text.json2487 linesDownload Raw Back to 25
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/manuquadros/d3text",4 "url": "https://github.com/manuquadros/d3text/releases/tag/v0.1.0",5 "host": "github.com",6 "commit": "dcfa6e57a82ec697bf7f6eacc43a59cfb6b797a4",7 "license": "GPL-3.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "3972dc9744f6499f0f9b2dbf76696f2ae7ad8af9b23dde66d6af86c9dfb36986",14   "language": "License",15   "lines": 674,16   "truncated": false,17   "block": 1,18   "row": 223519  },20  {21   "path": "README.md",22   "sha256": "4fcc05c9fca4a1d65c6a434c956a9b89cee895d778ebe742eb14249d636e4dfe",23   "language": "Text",24   "lines": 28,25   "truncated": false,26   "block": 4,27   "row": 234128  },29  {30   "path": "brenda_references/docs/source/conf.py",31   "sha256": "ed8650ce819d8d8b6d6e75807b1fde14f54ad1690c2d84260f06d4c80f538b6e",32   "language": "Python",33   "lines": 33,34   "truncated": false,35   "block": 3,36   "row": 1922637  },38  {39   "path": "brenda_references/scripts/__init__.py",40   "sha256": "d02a783d8ec44ffde216331e7c15a62207a204f6e6c94127b6adb15e9e28a308",41   "language": "Python",42   "lines": 9,43   "truncated": false,44   "block": 3,45   "row": 1808246  },47  {48   "path": "brenda_references/scripts/clean_data.py",49   "sha256": "41ad9cb2adb688ac66f2272a73a59f3ef39dbc6523c403719f9e5cd57e42f121",50   "language": "Python",51   "lines": 87,52   "truncated": false,53   "block": 3,54   "row": 2108655  },56  {57   "path": "brenda_references/scripts/create_test_docdb.py",58   "sha256": "d1d5113ac3a012344fe68ef808adc66f380f50ad2bbdc636cfddb25cbea060f0",59   "language": "Python",60   "lines": 31,61   "truncated": false,62   "block": 3,63   "row": 1903364  },65  {66   "path": "brenda_references/scripts/fix_missing_strains.py",67   "sha256": "1cd05ec2c8cbef2d02b2b0a05f8e7eb8df335bd2a870870d5c4f2e8b94cb7a0b",68   "language": "Python",69   "lines": 150,70   "truncated": false,71   "block": 3,72   "row": 2328273  },74  {75   "path": "brenda_references/scripts/fix_pubmed_ids.py",76   "sha256": "45b3cc7e6b3b3571eba17ddd388a5160f35fc66579f84d3552fc7db9e6a76cfc",77   "language": "Python",78   "lines": 27,79   "truncated": false,80   "block": 3,81   "row": 1878882  },83  {84   "path": "brenda_references/scripts/fix_taxonomy.py",85   "sha256": "160d065a452fc1e61181d0abb41e669ef55791d5844c5455ece43ed436f01864",86   "language": "Python",87   "lines": 225,88   "truncated": false,89   "block": 3,90   "row": 2485791  },92  {93   "path": "brenda_references/scripts/generate_entity_names_dataset.py",94   "sha256": "233019b5bb5f260d4153c600b4fc633e7b2a56c369212723f06b338bd092cd50",95   "language": "Python",96   "lines": 64,97   "truncated": false,98   "block": 3,99   "row": 20374100  },101  {102   "path": "brenda_references/scripts/generate_json_schemas.py",103   "sha256": "2132138810f77c9ea4831c66197105bad5a60776a751c8a1b5f182c47b220455",104   "language": "Python",105   "lines": 34,106   "truncated": false,107   "block": 3,108   "row": 18778109  },110  {111   "path": "brenda_references/scripts/pull_data.py",112   "sha256": "ae9999784e7474342a47686538c46af0afaa817847fd6d5765094f340c640ea9",113   "language": "Python",114   "lines": 129,115   "truncated": false,116   "block": 3,117   "row": 22006118  },119  {120   "path": "brenda_references/scripts/release.py",121   "sha256": "e3d2a9198611e2bf1d4225f5a018e435df2f5a4719e4bb6589c869663fd1029f",122   "language": "Python",123   "lines": 220,124   "truncated": false,125   "block": 3,126   "row": 24056127  },128  {129   "path": "brenda_references/scripts/retrieve_text.py",130   "sha256": "e7722b163d5c078a549902642eed7119e42044193bd22cea283606dbafaeb497",131   "language": "Python",132   "lines": 117,133   "truncated": false,134   "block": 3,135   "row": 22137136  },137  {138   "path": "brenda_references/scripts/statistics.py",139   "sha256": "e0014f2916247663c90a70a5decbf8dcd4286b3a8ef396da6188d412c72593fd",140   "language": "Python",141   "lines": 294,142   "truncated": false,143   "block": 3,144   "row": 25190145  },146  {147   "path": "brenda_references/scripts/update_pmc_open.py",148   "sha256": "c1ea11843c33baaf9d6b0185d20f08086e919c0099b503065f54cc3f93317073",149   "language": "Python",150   "lines": 31,151   "truncated": false,152   "block": 3,153   "row": 18874154  },155  {156   "path": "brenda_references/src/brenda_references/__init__.py",157   "sha256": "948f2dfb7a0e0aa71c6c810d54bc83a4c1bdbaa5ad8d4246d38dacf22559f7b1",158   "language": "Python",159   "lines": 33,160   "truncated": false,161   "block": 3,162   "row": 18514163  },164  {165   "path": "brenda_references/src/brenda_references/brenda_references.py",166   "sha256": "d19c112c939ed808258e15b1ace6502d844327f0a848a9b8a992002239f7a85f",167   "language": "Python",168   "lines": 873,169   "truncated": false,170   "block": 3,171   "row": 27622172  },173  {174   "path": "brenda_references/src/brenda_references/collection_numbers.py",175   "sha256": "5bb991874caf8859d9615b26099376dd3a262df534e9f51c2473e67fcf204fef",176   "language": "Python",177   "lines": 198,178   "truncated": false,179   "block": 3,180   "row": 22939181  },182  {183   "path": "brenda_references/src/brenda_references/config.py",184   "sha256": "d63e0cf7614e21753a586732668e8df8df1c65b8e12ad4876fc980dc335ffabd",185   "language": "Python",186   "lines": 20,187   "truncated": false,188   "block": 3,189   "row": 18704190  },191  {192   "path": "brenda_references/src/brenda_references/data_paths.py",193   "sha256": "65972551e90812dbc89d410ae9aebbd7fc97b0ada0eeda259e73f75b76ef4f4a",194   "language": "Python",195   "lines": 119,196   "truncated": false,197   "block": 3,198   "row": 22355199  },200  {201   "path": "brenda_references/src/brenda_references/db.py",202   "sha256": "2713f1d08641dbd3f592748e4d3833bdece38a9b48df202435d6f8f1cdb5328d",203   "language": "Python",204   "lines": 305,205   "truncated": false,206   "block": 3,207   "row": 25191208  },209  {210   "path": "brenda_references/src/brenda_references/docdb.py",211   "sha256": "afb693b51676dbe3f09305d70a9d0b7d85873e50f79379860d1982ab7f18a07d",212   "language": "Python",213   "lines": 251,214   "truncated": false,215   "block": 3,216   "row": 25082217  },218  {219   "path": "brenda_references/src/brenda_references/sampling.py",220   "sha256": "622cf20aa363c67b1b2a7971f394525b92ff5fe664994dbc07be7f750d9d3f24",221   "language": "Python",222   "lines": 331,223   "truncated": false,224   "block": 3,225   "row": 25950226  },227  {228   "path": "brenda_references/src/brenda_references/utils/__init__.py",229   "sha256": "d32af8712e47989d334b7bcfa321d3f90445178ab4f29481fc385edc5bcd38f1",230   "language": "Python",231   "lines": 15,232   "truncated": false,233   "block": 3,234   "row": 17808235  },236  {237   "path": "brenda_references/src/brenda_references/utils/utils.py",238   "sha256": "946b1e1c817a0e04952a216e785fdf6bcbed329076e8d6e5c380f3ecc7707168",239   "language": "Python",240   "lines": 66,241   "truncated": false,242   "block": 3,243   "row": 19985244  },245  {246   "path": "brenda_references/tests/test_apis.py",247   "sha256": "ef1aafda7c337c1567a442dad1a0a7a142228062042b2d312b776ed36403b54c",248   "language": "Python",249   "lines": 133,250   "truncated": false,251   "block": 3,252   "row": 22112253  },254  {255   "path": "brenda_references/tests/test_clean_data.py",256   "sha256": "629051223fe83cfe74fdc760da20534d8e3ffcdfe51cb58c852498b54e0783c9",257   "language": "Python",258   "lines": 32,259   "truncated": false,260   "block": 3,261   "row": 19231262  },263  {264   "path": "brenda_references/tests/test_collection_numbers.py",265   "sha256": "edcd129ff6966605bdff7baa493630c1704951f567208f81a19c0b453f85136b",266   "language": "Python",267   "lines": 17,268   "truncated": false,269   "block": 3,270   "row": 18620271  },272  {273   "path": "brenda_references/tests/test_data_paths.py",274   "sha256": "4165f94818a27df3596d0d6af39352f4c58a77214695cf184673695f0c738774",275   "language": "Python",276   "lines": 116,277   "truncated": false,278   "block": 3,279   "row": 22385280  },281  {282   "path": "brenda_references/tests/test_dataset_splits.py",283   "sha256": "21da14ed640674cbcd155a48c5261e3a3dea2816b0cec3bdafeb40e747b239db",284   "language": "Python",285   "lines": 219,286   "truncated": false,287   "block": 3,288   "row": 24369289  },290  {291   "path": "brenda_references/tests/test_docdb.py",292   "sha256": "3c5d611e9ab1af58646f76dea2169e224f361d8988a4695a8f5f9a6381f6008e",293   "language": "Python",294   "lines": 109,295   "truncated": false,296   "block": 3,297   "row": 21772298  },299  {300   "path": "brenda_references/tests/test_fix_missing_strains.py",301   "sha256": "ae6d73ec104170ca52de622329beb72087cf74b4acc50d767f0f244369a781ec",302   "language": "Python",303   "lines": 95,304   "truncated": false,305   "block": 3,306   "row": 21884307  },308  {309   "path": "brenda_references/tests/test_fix_taxonomy_relations.py",310   "sha256": "3153a8362c19a9977ee4ae10e60915362afd4c40538bbb4a2d4047ad8c5ea568",311   "language": "Python",312   "lines": 301,313   "truncated": false,314   "block": 3,315   "row": 25491316  },317  {318   "path": "brenda_references/tests/test_preprocessing.py",319   "sha256": "b0e02a1d706fb4f6c9aa6661ea2068ed3d9734bebcff9c37f6342d85e0df960e",320   "language": "Python",321   "lines": 319,322   "truncated": false,323   "block": 3,324   "row": 26022325  },326  {327   "path": "brenda_references/tests/test_retrieve_text.py",328   "sha256": "de27515fb83f5ac0251b39edcee162d887ec133f4201bf0f79b0e979cf921afe",329   "language": "Python",330   "lines": 87,331   "truncated": false,332   "block": 3,333   "row": 21234334  },335  {336   "path": "brenda_references/tests/test_scripts.py",337   "sha256": "f738db9c0b67f5b8aeee22c297bd849c3e64fd000a05d70ac5dedad971f5faad",338   "language": "Python",339   "lines": 24,340   "truncated": false,341   "block": 3,342   "row": 18886343  },344  {345   "path": "brenda_references/tests/test_statistics.py",346   "sha256": "98afabedd16cb480de36500a1c6e660bedc3cda7071e594410a9b24cb7df785e",347   "language": "Python",348   "lines": 26,349   "truncated": false,350   "block": 3,351   "row": 18850352  },353  {354   "path": "brenda_references/tests/test_straininfo.py",355   "sha256": "7bec4a1b73cb98692f8662c59d0f790f10f2ee2dd24875ac5825318d10f8b36c",356   "language": "Python",357   "lines": 29,358   "truncated": false,359   "block": 3,360   "row": 18604361  },362  {363   "path": "brenda_references/tests/test_sync_doc_db.py",364   "sha256": "76ca7ff5d07a6f40c974fb88010467e8eb720a9a4f890955b8ddebbca9043339",365   "language": "Python",366   "lines": 358,367   "truncated": false,368   "block": 3,369   "row": 25727370  },371  {372   "path": "brenda_references/tests/test_taxonomy.py",373   "sha256": "5ea48f5857e3af9d2bc1b819d1668f2ec5f71a5afab172f03ca3bc9ef82e18fe",374   "language": "Python",375   "lines": 203,376   "truncated": false,377   "block": 3,378   "row": 23992379  },380  {381   "path": "brenda_references/tests/test_update_pmc_open.py",382   "sha256": "2c2f937bdc242526a791579853bfae933d90deb422ff5cc4aeedf2ff829b35d5",383   "language": "Python",384   "lines": 48,385   "truncated": false,386   "block": 3,387   "row": 19712388  },389  {390   "path": "docs/hooks/metric_glossary.py",391   "sha256": "a4370843a018ca203a3e6c3a4db744a7659f8f8e68bb6b7f7ff510c34a80f293",392   "language": "Python",393   "lines": 31,394   "truncated": false,395   "block": 3,396   "row": 18968397  },398  {399   "path": "docs/javascripts/mathjax.js",400   "sha256": "aef103fdac4ed5914233e07a728b0a4237e4c320fa6b5d91be7cfb31963ed6d6",401   "language": "JavaScript",402   "lines": 19,403   "truncated": false,404   "block": 3,405   "row": 6750406  },407  {408   "path": "enzymes.py",409   "sha256": "0d21527cac25be9626ed6c0fa8dc345cb0200b25f52730aadfc264b15102c9b0",410   "language": "Python",411   "lines": 11,412   "truncated": false,413   "block": 3,414   "row": 17702415  },416  {417   "path": "fulltext_retriever.py",418   "sha256": "9f087294e6c1c43678c4f0e66a9b097e0a644186ee8837427ce8bd2357669acc",419   "language": "Python",420   "lines": 73,421   "truncated": false,422   "block": 3,423   "row": 20140424  },425  {426   "path": "get_pmcs.py",427   "sha256": "febb7637733623a640206489d7c89bc38a74faa08881dbcc79cae8294a5f5bd8",428   "language": "Python",429   "lines": 137,430   "truncated": false,431   "block": 3,432   "row": 22299433  },434  {435   "path": "get_reference_list.py",436   "sha256": "3edc6b0e5c09797480e321bd9b2d1fb2aeb7f71aa79a5732564b1893f54770ac",437   "language": "Python",438   "lines": 44,439   "truncated": false,440   "block": 3,441   "row": 19305442  },443  {444   "path": "par_report.py",445   "sha256": "b981bdefef1f654d21b497c2761fd3032834c279514b6299b3cc629a4a3e4919",446   "language": "Python",447   "lines": 56,448   "truncated": false,449   "block": 3,450   "row": 19433451  },452  {453   "path": "scripts/__init__.py",454   "sha256": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",455   "language": "Python",456   "lines": 1,457   "truncated": false,458   "block": 1,459   "row": 4956460  },461  {462   "path": "scripts/benchmarks/bench_codecs.py",463   "sha256": "cbe0058ae9cd2c737d628105a34a9418c7104aa4d4855129c51e45e871c262ec",464   "language": "Python",465   "lines": 268,466   "truncated": false,467   "block": 3,468   "row": 24885469  },470  {471   "path": "scripts/benchmarks/bench_embedding_residency.py",472   "sha256": "e8c8734a35909934f381332801cad6c1e4c240822798c6b7757acb79ee2c6d2a",473   "language": "Python",474   "lines": 451,475   "truncated": false,476   "block": 3,477   "row": 26776478  },479  {480   "path": "scripts/benchmarks/bench_embeddings_backend.py",481   "sha256": "7c99943688a71b66b9e2d2e2d53a8c1728ad9812dd522b0201a2954992993cb0",482   "language": "Python",483   "lines": 216,484   "truncated": false,485   "block": 3,486   "row": 24232487  },488  {489   "path": "scripts/benchmarks/bench_store.py",490   "sha256": "34cd6f18b824ae4a917ef069fc0e03d506ab0fe09c4836aa5980df2c97609786",491   "language": "Python",492   "lines": 155,493   "truncated": false,494   "block": 3,495   "row": 23318496  },497  {498   "path": "scripts/benchmarks/parse_run.py",499   "sha256": "415c151f86a660a28a452325ac8e251aa53dc90d8421f5f814ae211427df22ff",500   "language": "Python",501   "lines": 162,502   "truncated": false,503   "block": 3,504   "row": 23542505  },506  {507   "path": "scripts/benchmarks/perf_baseline.sh",508   "sha256": "03a3443d5e68fb8df7ee065835fad84cd0ef53e2dec80fde406b951036c18ae1",509   "language": "Shell",510   "lines": 93,511   "truncated": false,512   "block": 4,513   "row": 2113514  },515  {516   "path": "scripts/benchmarks/profile_gb10.sh",517   "sha256": "02a2e48630cc6a6f4d18ef316f06642243c29f3169a663ee445db2ec830ae899",518   "language": "Shell",519   "lines": 212,520   "truncated": false,521   "block": 4,522   "row": 2201523  },524  {525   "path": "scripts/build_bacteria_wordlist.py",526   "sha256": "db2b8cb203da624597716c21042cecf9240a3578c289383f9c5117ed1ae100e3",527   "language": "Python",528   "lines": 63,529   "truncated": false,530   "block": 3,531   "row": 20527532  },533  {534   "path": "scripts/build_enzyme_ec_bridge.py",535   "sha256": "fdc0f1eba9b35de3300ed583556bd09a17a6134ece6977d55f2c14d688e39600",536   "language": "Python",537   "lines": 88,538   "truncated": false,539   "block": 3,540   "row": 21252541  },542  {543   "path": "scripts/build_organism_taxid_bridge.py",544   "sha256": "849c2ab67d1f1df5042adec52d02c40b3b91bb0109ba32429e3cdd5ace752c6f",545   "language": "Python",546   "lines": 384,547   "truncated": false,548   "block": 3,549   "row": 26221550  },551  {552   "path": "scripts/build_strain_number_bridge.py",553   "sha256": "9b5d5b108f2cb2ad6fe3d2a3a27146788913a9866abe7698525c54edbe3e25d5",554   "language": "Python",555   "lines": 127,556   "truncated": false,557   "block": 3,558   "row": 22934559  },560  {561   "path": "scripts/check_deadcode.py",562   "sha256": "0e285ad71c36a1b47700319ea747047758666ea2e03548520fd33d33150ce134",563   "language": "Python",564   "lines": 72,565   "truncated": false,566   "block": 3,567   "row": 20430568  },569  {570   "path": "scripts/check_imports.py",571   "sha256": "15e457666a666c098825abf79cefbd4465679e14856f47c21b09ecb6c1212d95",572   "language": "Python",573   "lines": 119,574   "truncated": false,575   "block": 3,576   "row": 22151577  },578  {579   "path": "scripts/collect_microbiology_sample.py",580   "sha256": "315096a6854ef1b360419d7ef52ddb129e9018ec780fe9893bca4ed972d430c4",581   "language": "Python",582   "lines": 440,583   "truncated": false,584   "block": 3,585   "row": 26448586  },587  {588   "path": "scripts/compile_benchmark/compare_arms.py",589   "sha256": "688b3eee2d053cd273f3eeebc1a0adca13f7c269f8a5f15f686337e8c77a5fea",590   "language": "Python",591   "lines": 337,592   "truncated": false,593   "block": 3,594   "row": 25588595  },596  {597   "path": "scripts/compile_benchmark/run.sh",598   "sha256": "ac45bbff41a3e30fe08906ccb26430499d101b9b4b8f40e22fe3b41300bbb4cc",599   "language": "Shell",600   "lines": 71,601   "truncated": false,602   "block": 4,603   "row": 2088604  },605  {606   "path": "scripts/compile_benchmark/run_arms.py",607   "sha256": "a2abe551dbcecaa6e6a36463fef7a737d38ae9dc8ceaba0336e477e6c2c69201",608   "language": "Python",609   "lines": 365,610   "truncated": false,611   "block": 3,612   "row": 25918613  },614  {615   "path": "scripts/compile_benchmark/train_json.py",616   "sha256": "6f45c019df1a1b2ef6818f6f3d4c16672886dd2d5bfd7e79bd0d6a20631df645",617   "language": "Python",618   "lines": 182,619   "truncated": false,620   "block": 3,621   "row": 23982622  },623  {624   "path": "scripts/dec02_probe/localization_probe.py",625   "sha256": "d0a9f908d62a367064c3752c78e082161c6e154a611dde8b8616337dff1574ba",626   "language": "Python",627   "lines": 829,628   "truncated": false,629   "block": 3,630   "row": 27541631  },632  {633   "path": "scripts/dec04_full/compare.py",634   "sha256": "f7a81806ed34d6b4f8a1b97236b0ced9b2e2533a7da903df976ed20f2897307b",635   "language": "Python",636   "lines": 136,637   "truncated": false,638   "block": 3,639   "row": 23100640  },641  {642   "path": "scripts/dec04_full/label_audit.py",643   "sha256": "a76fef88c2948f05513c489b75dd508f247af27c4569b6f1fa4cc2e6da13a4ae",644   "language": "Python",645   "lines": 223,646   "truncated": false,647   "block": 3,648   "row": 24437649  },650  {651   "path": "scripts/dec04_full/negative_ablation_compare.py",652   "sha256": "401fb51be59bc94c6a2fbd934d9a625374e522959d34fde91c4f144a5cbd3492",653   "language": "Python",654   "lines": 117,655   "truncated": false,656   "block": 3,657   "row": 22156658  },659  {660   "path": "scripts/dec04_full/vm/preflight.py",661   "sha256": "a98dcf91b387d3f04975bfdf9e47d23d3d0505865fd9fe1829a1531804095197",662   "language": "Python",663   "lines": 185,664   "truncated": false,665   "block": 3,666   "row": 24161667  },668  {669   "path": "scripts/dec04_full/vm/run.sh",670   "sha256": "1cd70e46a4b355dd3d77d976bfc81e9771f1ebec6ca1b0375cd3e5038e5e5af1",671   "language": "Shell",672   "lines": 350,673   "truncated": false,674   "block": 4,675   "row": 2260676  },677  {678   "path": "scripts/dec04_full/vm/run_downweight_ablation.sh",679   "sha256": "991500926eefeb90a4705cee8a2da3002df51f03f8b074bd2aaea2c36c720af9",680   "language": "Shell",681   "lines": 198,682   "truncated": false,683   "block": 4,684   "row": 2218685  },686  {687   "path": "scripts/dec04_full/vm/run_negative_ablation.sh",688   "sha256": "669e2df0d4b7f42f897e6e0fca0cb3306fb12e2a3e80667fc15989230226a6b9",689   "language": "Shell",690   "lines": 211,691   "truncated": false,692   "block": 4,693   "row": 2240694  },695  {696   "path": "scripts/feat10_recall/compare_arms.py",697   "sha256": "2b1366f4a55056fb455f91fb5a9e64bdd5169346f8819adfb6da34c1fcbe1c51",698   "language": "Python",699   "lines": 140,700   "truncated": false,701   "block": 3,702   "row": 22923703  },704  {705   "path": "scripts/feat10_recall/evaluate_json.py",706   "sha256": "67cab99da42cdec199d218936e835e0c6a68e76fa90d9f9150542dcde67585bc",707   "language": "Python",708   "lines": 46,709   "truncated": false,710   "block": 3,711   "row": 19619712  },713  {714   "path": "scripts/feat10_recall/vm/run.sh",715   "sha256": "3d6a287ec20c5efc1d24e998e23198361d92804e5c0afed17df0d256417636f2",716   "language": "Shell",717   "lines": 334,718   "truncated": false,719   "block": 4,720   "row": 2258721  },722  {723   "path": "scripts/generate_embeddings.py",724   "sha256": "0fb272a074559849f5cb5f548bdec3366738b036972d54cdc27e39087c8b964c",725   "language": "Python",726   "lines": 111,727   "truncated": false,728   "block": 3,729   "row": 21657730  },731  {732   "path": "scripts/generate_splits.py",733   "sha256": "06bbc95aee5e86120a3d10d77510fa326ca5a5aaf52756c9a760aa4c1fe12d66",734   "language": "Python",735   "lines": 166,736   "truncated": false,737   "block": 3,738   "row": 23355739  },740  {741   "path": "scripts/release.py",742   "sha256": "5fe34d7cde6a193cf7e7ea5f8e55d79d86881f6e25f1f56821677d2ef1b3f1df",743   "language": "Python",744   "lines": 221,745   "truncated": false,746   "block": 3,747   "row": 24169748  },749  {750   "path": "scripts/score_enzyme_linking.py",751   "sha256": "140eefdc5a581e37d77273c3cc0cdc8e279f7ac8b3b716d2825dc633936366d5",752   "language": "Python",753   "lines": 121,754   "truncated": false,755   "block": 3,756   "row": 22653757  },758  {759   "path": "scripts/score_species_linking.py",760   "sha256": "22f5b50ae11f1256541792759425c6900ab8b1a315d23e5ce8de9a83042da788",761   "language": "Python",762   "lines": 116,763   "truncated": false,764   "block": 3,765   "row": 22160766  },767  {768   "path": "scripts/score_strain_linking.py",769   "sha256": "4a83024a75e863cbe12eab011221d26c85ec78ce3cd3545e653cc84d70283cb7",770   "language": "Python",771   "lines": 165,772   "truncated": false,773   "block": 3,774   "row": 23643775  },776  {777   "path": "scripts/wily.sh",778   "sha256": "729bea126e11763541053d6f9230fc132c2d68c2b300f6651dadae404ce298f8",779   "language": "Shell",780   "lines": 85,781   "truncated": false,782   "block": 4,783   "row": 2116784  },785  {786   "path": "src/d3text/__init__.py",787   "sha256": "623f97e7d40dbbeb7a1c0b4fad0664d119ab1e9ec8e942e7fde91e9090e6bffb",788   "language": "Python",789   "lines": 23,790   "truncated": false,791   "block": 3,792   "row": 18622793  },794  {795   "path": "src/d3text/annotation_hub.py",796   "sha256": "13d91cbd281f667db38a3744e66142029d5b0f3e494dda4b11a6a008f9ca1262",797   "language": "Python",798   "lines": 259,799   "truncated": false,800   "block": 3,801   "row": 24804802  },803  {804   "path": "src/d3text/checkpoint.py",805   "sha256": "1d8b5d33516bbd2e3b9331eff5706be9e03b27f28717ea79446372fa150f2219",806   "language": "Python",807   "lines": 195,808   "truncated": false,809   "block": 3,810   "row": 24678811  },812  {813   "path": "src/d3text/cli/args.py",814   "sha256": "e5ebe90066461ce4ecc555e64ecf60c5a41e65483448be53cd828ad8d077442e",815   "language": "Python",816   "lines": 75,817   "truncated": false,818   "block": 3,819   "row": 21092820  },821  {822   "path": "src/d3text/cli/evaluate.py",823   "sha256": "e9ebdd79ae56bcab01d3f6844d6e5a43f8d599fed21fcab1f4ab7fded722bdc6",824   "language": "Python",825   "lines": 411,826   "truncated": false,827   "block": 3,828   "row": 26553829  },830  {831   "path": "src/d3text/cli/infer.py",832   "sha256": "54f3cbd130638f2bf95fed9c2e50a2e39bda56f61615a6b43b5d971e694fe574",833   "language": "Python",834   "lines": 276,835   "truncated": false,836   "block": 3,837   "row": 25407838  },839  {840   "path": "src/d3text/cli/precompute_embeddings.py",841   "sha256": "1b52f8577fa0d2db14d6e3cd898cf3d3232b32c25fc15d55f18b8e3a8a203ed5",842   "language": "Python",843   "lines": 951,844   "truncated": false,845   "block": 3,846   "row": 27772847  },848  {849   "path": "src/d3text/cli/precompute_encodings.py",850   "sha256": "5587db6bfe3dfede2f7485b1e6142a1a4aa1a4b3c982d9de39d0e02d26c392fd",851   "language": "Python",852   "lines": 354,853   "truncated": false,854   "block": 3,855   "row": 26153856  },857  {858   "path": "src/d3text/cli/precompute_token_labels.py",859   "sha256": "3f9e1b41e8b7be85e67ed864b3a7225f11aafa95f2137d3babef5a7b7d1a6ebc",860   "language": "Python",861   "lines": 537,862   "truncated": false,863   "block": 3,864   "row": 27195865  },866  {867   "path": "src/d3text/cli/train.py",868   "sha256": "fae72596953189da0d80a650359463b203bd01105fe97c99c43d2fe39d6e987c",869   "language": "Python",870   "lines": 306,871   "truncated": false,872   "block": 3,873   "row": 25775874  },875  {876   "path": "src/d3text/cli/tune.py",877   "sha256": "fa4952dc8f13a56f23a6efea6a46eddd7a0d55d4adee7670186f7376e189a7b3",878   "language": "Python",879   "lines": 223,880   "truncated": false,881   "block": 3,882   "row": 24941883  },884  {885   "path": "src/d3text/constraints.py",886   "sha256": "f963c2ad8571698d72d01619d0c64d2d588cc917c0615f815d3222b46b0b93bf",887   "language": "Python",888   "lines": 54,889   "truncated": false,890   "block": 3,891   "row": 20266892  },893  {894   "path": "src/d3text/corpus.py",895   "sha256": "acc89f99f4f7a8e9331d8d6e9bd02d57f475b30dc74b9e0533eae59e829bd89b",896   "language": "Python",897   "lines": 340,898   "truncated": false,899   "block": 3,900   "row": 26041901  },902  {903   "path": "src/d3text/data/__init__.py",904   "sha256": "3fc41765fb49b623fa5014b7badb4176f954db7dfb17b34691f1c4f95216c567",905   "language": "Python",906   "lines": 15,907   "truncated": false,908   "block": 3,909   "row": 17859910  },911  {912   "path": "src/d3text/data/data.py",913   "sha256": "a10c6e948f8b21ec75e05d0585e6c8c2d9c86e79ebb453f5de92ff58249346e9",914   "language": "Python",915   "lines": 616,916   "truncated": false,917   "block": 3,918   "row": 27374919  },920  {921   "path": "src/d3text/datasets/__init__.py",922   "sha256": "3fd2d2ae739a46639c7d4152a4812528ac2bad64809b4cabdf0cfadd1dfeb5f8",923   "language": "Python",924   "lines": 22,925   "truncated": false,926   "block": 3,927   "row": 18639928  },929  {930   "path": "src/d3text/datasets/brenda.py",931   "sha256": "0c2dcbf3e782456feb5e1b7b49977e9d8e30b703100b02e3bf16a8112913ca27",932   "language": "Python",933   "lines": 319,934   "truncated": false,935   "block": 3,936   "row": 26043937  },938  {939   "path": "src/d3text/datasets/culture_numbers.py",940   "sha256": "0b3fae81f845813308687f534af41f9e0c853d396962996165cad4753d283161",941   "language": "Python",942   "lines": 108,943   "truncated": false,944   "block": 3,945   "row": 22050946  },947  {948   "path": "src/d3text/datasets/enzymener.py",949   "sha256": "1dd464354acab96a99842bc9d062d317d56933492d1a02f076e8dd27a4dec6a6",950   "language": "Python",951   "lines": 226,952   "truncated": false,953   "block": 3,954   "row": 24497955  },956  {957   "path": "src/d3text/datasets/expasy.py",958   "sha256": "6fd2a1c9ff6ffe7d9e1c71186421ad0b42328e690add07225ec1c71dc81129d7",959   "language": "Python",960   "lines": 241,961   "truncated": false,962   "block": 3,963   "row": 24642964  },965  {966   "path": "src/d3text/datasets/nlp4pheno.py",967   "sha256": "dbeedb05eb6d759de0db2dd0c3398cb810efb43dadb5e3f8ef3d7b479d898478",968   "language": "Python",969   "lines": 178,970   "truncated": false,971   "block": 3,972   "row": 23784973  },974  {975   "path": "src/d3text/datasets/s800.py",976   "sha256": "42e77aaff1c3e2630f3bec6f2412dd40d97e334d31538d7c6a00b56a5bece63e",977   "language": "Python",978   "lines": 177,979   "truncated": false,980   "block": 3,981   "row": 23505982  },983  {984   "path": "src/d3text/embeddings_store.py",985   "sha256": "fde2b7d3ccfd263be2042ed76111b44aa5b2c692ac98b0e3a387fe555ed9d048",986   "language": "Python",987   "lines": 895,988   "truncated": false,989   "block": 3,990   "row": 27720991  },992  {993   "path": "src/d3text/encodings_store.py",994   "sha256": "1f74804257233fd644f8b8c8ac6a969664774cd8229739f9355d287a6f3f250b",995   "language": "Python",996   "lines": 580,997   "truncated": false,998   "block": 3,999   "row": 273191000  },1001  {1002   "path": "src/d3text/excepthook.py",1003   "sha256": "43e34720fab4a81760ad194fe8715c6d292ab730a2db115237fbc673f76773e1",1004   "language": "Python",1005   "lines": 50,1006   "truncated": false,1007   "block": 3,1008   "row": 197611009  },1010  {1011   "path": "src/d3text/factory.py",1012   "sha256": "8f680842a790e744476736eb95567da7ba562e72c0357601423944632fd101a1",1013   "language": "Python",1014   "lines": 209,1015   "truncated": false,1016   "block": 3,1017   "row": 246831018  },1019  {1020   "path": "src/d3text/identifier_bridge.py",1021   "sha256": "08e533e2e1ee833ceb1f9ccd5c5c88aae8a111f2d08e1ae9d61b901520dd4be6",1022   "language": "Python",1023   "lines": 274,1024   "truncated": false,1025   "block": 3,1026   "row": 253621027  },1028  {1029   "path": "src/d3text/linking.py",1030   "sha256": "6a722d94d092e90a1cfcabc1517f31c1ee37072528f0fc9a02868be279baa000",1031   "language": "Python",1032   "lines": 73,1033   "truncated": false,1034   "block": 3,1035   "row": 207761036  },1037  {1038   "path": "src/d3text/linking_corpora.py",1039   "sha256": "c2e278b37ea2a78010d9eb65ea895ac75bb30bc24e2d44fe1f724d6809e9feb5",1040   "language": "Python",1041   "lines": 810,1042   "truncated": false,1043   "block": 3,1044   "row": 275771045  },1046  {1047   "path": "src/d3text/linking_eval.py",1048   "sha256": "102dc0340eaed302b58b61ec30da64a9f86667caba6039bb41b3a7a81ec3c50b",1049   "language": "Python",1050   "lines": 614,1051   "truncated": false,1052   "block": 3,1053   "row": 273321054  },1055  {1056   "path": "src/d3text/logs.py",1057   "sha256": "d340e7eb5a129926782ad62a5a9aee580eb526e47cb75dfca06295444adf6f17",1058   "language": "Python",1059   "lines": 152,1060   "truncated": false,1061   "block": 3,1062   "row": 232421063  },1064  {1065   "path": "src/d3text/mention_metrics.py",1066   "sha256": "7b7276d16d737286bd0979f935193e7b12ac34081164701e0b2569d1935e0650",1067   "language": "Python",1068   "lines": 796,1069   "truncated": false,1070   "block": 3,1071   "row": 275151072  },1073  {1074   "path": "src/d3text/metric_docs.py",1075   "sha256": "f0c775580f89dcabd3233f0de70798e3e39dc3f88bd8b71cd2d6d7b7b4cad919",1076   "language": "Python",1077   "lines": 523,1078   "truncated": false,1079   "block": 3,1080   "row": 271281081  },1082  {1083   "path": "src/d3text/models/__init__.py",1084   "sha256": "31cf6fed29b4a95382578496727525b4a11d63e583cb6278d04e236e4778b087",1085   "language": "Python",1086   "lines": 45,1087   "truncated": false,1088   "block": 3,1089   "row": 196211090  },1091  {1092   "path": "src/d3text/models/base.py",1093   "sha256": "f981d86d04d0a7ac346c4bf6797c2d5f064d6cda1795a79db5d38363f8746036",1094   "language": "Python",1095   "lines": 2536,1096   "truncated": false,1097   "block": 4,1098   "row": 951099  },1100  {1101   "path": "src/d3text/models/config.py",1102   "sha256": "b775b39d7e3f6b43bbf6c58c0c1015e799e50810d2c51d7898e0efe4eb02f1fd",1103   "language": "Python",1104   "lines": 411,1105   "truncated": false,1106   "block": 3,1107   "row": 266321108  },1109  {1110   "path": "src/d3text/models/entity_linking.py",1111   "sha256": "2b7f1b372b3b3fd4ad65398dd852d14dbb05940dd19df16e57cca7d6ba1928ef",1112   "language": "Python",1113   "lines": 654,1114   "truncated": false,1115   "block": 3,1116   "row": 274731117  },1118  {1119   "path": "src/d3text/models/ete.py",1120   "sha256": "9c46d290f065b0dd56c07bba3fb0636713fcd1ddeb345f5e17054237dc6c31af",1121   "language": "Python",1122   "lines": 1667,1123   "truncated": false,1124   "block": 4,1125   "row": 351126  },1127  {1128   "path": "src/d3text/models/heads.py",1129   "sha256": "52add9ae12174cf84e06a84cd81479cc2d9ca154cd41f819e5f85a401c30e5a0",1130   "language": "Python",1131   "lines": 242,1132   "truncated": false,1133   "block": 3,1134   "row": 250711135  },1136  {1137   "path": "src/d3text/models/model_types.py",1138   "sha256": "239f869c1db274cbd2233ba2c3c49967d5a908c734e681b7035db7e3901fbac0",1139   "language": "Python",1140   "lines": 96,1141   "truncated": false,1142   "block": 3,1143   "row": 216881144  },1145  {1146   "path": "src/d3text/models/ner.py",1147   "sha256": "ae7954e1a5240f28252a7e2523df426d0450b5ea3b8336e5a85c679854dacc53",1148   "language": "Python",1149   "lines": 252,1150   "truncated": false,1151   "block": 3,1152   "row": 246741153  },1154  {1155   "path": "src/d3text/models/token_supervision.py",1156   "sha256": "8910bdb97dddfaea6cfb2b7fc20e73a2ff3c8273e8d61edf8816f1a6b8807c36",1157   "language": "Python",1158   "lines": 989,1159   "truncated": false,1160   "block": 3,1161   "row": 278571162  },1163  {1164   "path": "src/d3text/negative_screen.py",1165   "sha256": "cdc2c8747efadb1f8caec46218b164b5931b9382499686f37c0839871e8bce0a",1166   "language": "Python",1167   "lines": 249,1168   "truncated": false,1169   "block": 3,1170   "row": 252051171  },1172  {1173   "path": "src/d3text/progress.py",1174   "sha256": "69a48e797501d0f984c87cc4292991b3e4eca1702e51379eeb7ce26af9dcc424",1175   "language": "Python",1176   "lines": 92,1177   "truncated": false,1178   "block": 3,1179   "row": 211951180  },1181  {1182   "path": "src/d3text/runtime.py",1183   "sha256": "a9e59d83ad610052d29fcdc0e706bf020e9f32e19ef91008dc3992c7a6353750",1184   "language": "Python",1185   "lines": 382,1186   "truncated": false,1187   "block": 3,1188   "row": 264641189  },1190  {1191   "path": "src/d3text/schema.py",1192   "sha256": "2fc05a92a46f6b0379fc37493b938fa39531b9a169bf42be81a98eab5f523456",1193   "language": "Python",1194   "lines": 328,1195   "truncated": false,1196   "block": 3,1197   "row": 261841198  },1199  {1200   "path": "src/d3text/surface_forms.py",

Showing the first 1,200 of 2487 lines. Download the file for the rest.