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‎.cspell.json‎

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// cSpell Settings
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//https://github.com/streetsidesoftware/vscode-spell-checker
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{
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"version": "0.2", // Version of the setting file. Always 0.2
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"language": "en", // language - current active spelling language
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"enabledLanguageIds": [
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"markdown"
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],
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// flagWords - list of words to be always considered incorrect
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// This is useful for offensive words and common spelling errors.
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// For example "hte" should be "the"
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"flagWords": [],
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"allowCompoundWords": true,
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"ignorePaths": [
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"src/archive"
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],
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"words": [
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"Aarse",
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"Abrego",
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"Adib",
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"aggr",
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"Aggr",
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"Aguillon",
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"Aleksandr",
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"Alyx",
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"Andreas",
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"Angelaki",
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"Arlt",
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"Arseny",
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"Asprodini",
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"Athanassios",
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"Atika",
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"Aviv",
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"Baji",
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"Bakshi",
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"Barroso",
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"Bashiri",
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"Behnia",
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"Behr",
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"Behrens",
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"Benda",
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"Berens",
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"Bethge",
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"Bodor",
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"Bonacchi",
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"Branco",
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"Brittain",
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"Brody",
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"Buchanan",
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"Bumbarger",
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"Busse",
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"Cadena",
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"Cadwell",
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"Campagner",
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"Carandini",
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"Cazettes",
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"Celii",
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"Chagas",
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"Chapuis",
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"Chelur",
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"Cheng",
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"Chettih",
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"Chiola",
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"Choi",
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"cholinergic",
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"Christenson",
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"Churchland",
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"Cimorelli",
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"cingulate",
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"Claudi",
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"Cobos",
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"Cohrs",
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"Collman",
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"cond",
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"conda",
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"Connectomics",
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"convolutional",
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"cortico",
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"Corticothalamic",
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"Crombie",
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"Dalkara",
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"dandi",
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"DANDI",
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"Dani",
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"DARPA",
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"DeAngelis",
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"decimalnf",
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"Deisseroth",
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"Denfield",
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"Dichter",
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"Dickman",
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"Ding",
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"djbase",
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"djhub",
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"djlab",
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"djlabhub",
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"djtest",
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"Donato",
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"Drewe",
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"Druckmann",
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"Drugowitsch",
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"Ecker",
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"Economo",
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"Einevoll",
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"elif",
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"Elife",
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"Emmanouil",
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"Eneuro",
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"Engel",
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"entorhinal",
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"EPFL",
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"Ephys",
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"equivariant",
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"Erisken",
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"Fahey",
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"Finkelstein",
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"Fiorini",
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"Fontolan",
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"Franke",
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"Franzen",
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"Froudarakis",
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"Galdamez",
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"Gatys",
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"Geetika",
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"Georgieva",
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"Gerkin",
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"Geue",
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"Ghosh",
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"Goetz",
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"Göttingen",
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"Greenberg",
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"Grewe",
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"Hackathon",
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"Haefner",
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"Halchenko",
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"Harbororatory",
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"Harmin",
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"Hendrik",
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"Henninger",
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"HHMI",
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"Hillman",
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"Hoenselaar",
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"Hulyalkar",
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"Ilana",
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"INCF",
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"Jaerong",
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"Jaffe",
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"Jaramillo",
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"Jeroen",
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"Jessen",
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"Jiang",
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"Josić",
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"jupytext",
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"Jurjut",
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"Jytext",
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"Kabilar",
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"Kahles",
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"Karakostas",
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"Karel",
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"Katzner",
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"Kavli",
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"Khastkhodaei",
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"Kleinfeld",
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"Klindt",
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"Kobak",
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"Kochukov",
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"Kohn",
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"Korympidou",
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"Kotkat",
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"Kushal",
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"Laranjeira",
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"Laturnus",
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"Laurens",
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"Lichtman",
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"Lubenov",
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"Luque",
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"Macke",
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"Macrina",
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"Maho",
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"Mainen",
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"Manivannan",
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"materialx",
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"Maximilians",
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"McClerklin",
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"McGinley",
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"Mesoscale",
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"Mindscope",
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"miniconda",
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"Mizell",
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"mkdocs",
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"Mobarhan",
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"Moser",
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"München",
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"Neuro",
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"neuroanatomical",
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"Neurodata",
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"Neuroinformatics",
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"Neuromatch",
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"neurophotonics",
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"Neurophotonics",
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"Neuropixels",
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"Neurosci",
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"neuroscientists",
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"Obenhaus",
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"Obermüller",
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"objs",
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"openephysgui",
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"Optica",
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"organoids",
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"Oriol",
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"Osmonauts",
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"öttingen",
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"Pachitariu",
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"Palasantza",
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"Papadopoulou",
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"Pede",
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"Pekarek",
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"Pfaffinger",
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"Pharus",
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"Philipp",
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"Pierzchlewicz",
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"Pitani",
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"Pitkow",
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"PLOS",
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"Popeney",
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"Protti",
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"pymdownx",
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"Pytests",
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"Ralf",
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"Reimer",
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"Restivo",
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"Roboto",
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"Rodenkirch",
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"Roncal",
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"Rosón",
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"Rotem",
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"Roukes",
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"RRID",
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"RRIDs",
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"Rxiv",
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"Saavedra",
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"Sabatini",
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"Sachgau",
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"Saggau",
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"Sasaki",
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"Satrajit",
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"Schickard",
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"SDLC",
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"Seung",
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"Shaul",
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"Shcheglovitov",
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"Shen",
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"Shinn",
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"Siapas",
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"silico",
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"Sinz",
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"Sitonic",
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"Slettmoen",
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"Smirnakis",
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"Soupiadis",
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"Spacek",
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"Spampanato",
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"ßner",
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"SSRN",
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"Steffen",
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"Stelios",
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"Storer",
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"striatal",
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"struct",
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"Subramaniyan",
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"Svoboda",
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"Syeda",
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"Szatko",
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"Tarboton",
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"Tiago",
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"Tolga",
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"Tolias",
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"transcriptomic",
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"Tseng",
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"Tsetsenis",
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"Tübingen",
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"Tuthill",
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"twemoji",
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"UCSF",
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"üller",
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"Universität",
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"Urai",
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"Ustyuzhaninov",
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"Vaiceliunaite",
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"Verswijver",
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"Vlasits",
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"Wehr",
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"Weisenhaus",
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"Wellcome",
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"Wießner",
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"Wilhelm",
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"Witten",
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"Yaroslav",
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"Yatsenko",
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"Yilmaz",
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"Zhao",
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"Zhou",
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"Zong",
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"Zuckerman"
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]
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}

‎.docker/Dockerfile‎

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FROM datajoint/miniconda3:4.10.3-py3.9-alpine
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ARG GITHUB_TOKEN
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WORKDIR /main
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COPY --chown=anaconda:anaconda ./.docker/pip_requirements.txt ${PIP_REQUIREMENTS}
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COPY --chown=anaconda:anaconda ./.docker/apk_requirements.txt ${APK_REQUIREMENTS}
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RUN \
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/entrypoint.sh echo "Dependencies installed" && \
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rm ${PIP_REQUIREMENTS} && \
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rm ${APK_REQUIREMENTS}
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RUN \
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pip install --no-cache git+https://${GITHUB_TOKEN}@github.com/guzman-raphael/mkdocs-material-insiders.git@master || \
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echo "using public mkdocs-material..."
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COPY --chown=anaconda:anaconda ./mkdocs.yaml /main/mkdocs.yaml
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COPY --chown=anaconda:anaconda ./src /main/src

‎.docker/apk_requirements.txt‎

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git

‎.docker/pip_requirements.txt‎

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mkdocs-material
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mkdocs-redirects
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mkdocs-exclude
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mdx_truly_sane_lists
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mkdocs-pymdownx-material-extras
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pymdown-extensions
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mkdocs-section-index

‎.github/workflows/development.yml‎

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branches:
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- main
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jobs:
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deploy:
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deploy-docs:
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runs-on: ubuntu-latest
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env:
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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DJBOT_GH_TOKEN: ${{secrets.djbot_gh_token}}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- name: Compile docs static artifacts
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run: |
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GITHUB_TOKEN=$DJBOT_GH_TOKEN MODE=BUILD HOST_UID=$(id -u) docker-compose up --exit-code-from docs --build
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- name: Commit documentation changes
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run: |
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git clone https://github.com/${GITHUB_REPOSITORY}.git \
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--branch gh-pages --single-branch gh-pages
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rm -R gh-pages/*
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cp -r site/* gh-pages/
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cd gh-pages
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Action"
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git add . --all
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git commit -m "Update documentation" -a || true
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# The above command will fail if no changes were present, so we ignore
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# the return code.
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- name: Push changes
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uses: ad-m/github-push-action@master
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with:
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python-version: 3.x
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- run: pip install mkdocs-material
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- run: mkdocs gh-deploy --force
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branch: gh-pages
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directory: gh-pages
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github_token: ${{secrets.GITHUB_TOKEN}}

‎.gitignore‎

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site
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.env
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.DS_Store
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temp*

‎.gitmodules‎

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