chatspatial 1.1.0__py3-none-any.whl

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Files changed (67) hide show
  1. chatspatial/__init__.py +11 -0
  2. chatspatial/__main__.py +141 -0
  3. chatspatial/cli/__init__.py +7 -0
  4. chatspatial/config.py +53 -0
  5. chatspatial/models/__init__.py +85 -0
  6. chatspatial/models/analysis.py +513 -0
  7. chatspatial/models/data.py +2462 -0
  8. chatspatial/server.py +1763 -0
  9. chatspatial/spatial_mcp_adapter.py +720 -0
  10. chatspatial/tools/__init__.py +3 -0
  11. chatspatial/tools/annotation.py +1903 -0
  12. chatspatial/tools/cell_communication.py +1603 -0
  13. chatspatial/tools/cnv_analysis.py +605 -0
  14. chatspatial/tools/condition_comparison.py +595 -0
  15. chatspatial/tools/deconvolution/__init__.py +402 -0
  16. chatspatial/tools/deconvolution/base.py +318 -0
  17. chatspatial/tools/deconvolution/card.py +244 -0
  18. chatspatial/tools/deconvolution/cell2location.py +326 -0
  19. chatspatial/tools/deconvolution/destvi.py +144 -0
  20. chatspatial/tools/deconvolution/flashdeconv.py +101 -0
  21. chatspatial/tools/deconvolution/rctd.py +317 -0
  22. chatspatial/tools/deconvolution/spotlight.py +216 -0
  23. chatspatial/tools/deconvolution/stereoscope.py +109 -0
  24. chatspatial/tools/deconvolution/tangram.py +135 -0
  25. chatspatial/tools/differential.py +625 -0
  26. chatspatial/tools/embeddings.py +298 -0
  27. chatspatial/tools/enrichment.py +1863 -0
  28. chatspatial/tools/integration.py +807 -0
  29. chatspatial/tools/preprocessing.py +723 -0
  30. chatspatial/tools/spatial_domains.py +808 -0
  31. chatspatial/tools/spatial_genes.py +836 -0
  32. chatspatial/tools/spatial_registration.py +441 -0
  33. chatspatial/tools/spatial_statistics.py +1476 -0
  34. chatspatial/tools/trajectory.py +495 -0
  35. chatspatial/tools/velocity.py +405 -0
  36. chatspatial/tools/visualization/__init__.py +155 -0
  37. chatspatial/tools/visualization/basic.py +393 -0
  38. chatspatial/tools/visualization/cell_comm.py +699 -0
  39. chatspatial/tools/visualization/cnv.py +320 -0
  40. chatspatial/tools/visualization/core.py +684 -0
  41. chatspatial/tools/visualization/deconvolution.py +852 -0
  42. chatspatial/tools/visualization/enrichment.py +660 -0
  43. chatspatial/tools/visualization/integration.py +205 -0
  44. chatspatial/tools/visualization/main.py +164 -0
  45. chatspatial/tools/visualization/multi_gene.py +739 -0
  46. chatspatial/tools/visualization/persistence.py +335 -0
  47. chatspatial/tools/visualization/spatial_stats.py +469 -0
  48. chatspatial/tools/visualization/trajectory.py +639 -0
  49. chatspatial/tools/visualization/velocity.py +411 -0
  50. chatspatial/utils/__init__.py +115 -0
  51. chatspatial/utils/adata_utils.py +1372 -0
  52. chatspatial/utils/compute.py +327 -0
  53. chatspatial/utils/data_loader.py +499 -0
  54. chatspatial/utils/dependency_manager.py +462 -0
  55. chatspatial/utils/device_utils.py +165 -0
  56. chatspatial/utils/exceptions.py +185 -0
  57. chatspatial/utils/image_utils.py +267 -0
  58. chatspatial/utils/mcp_utils.py +137 -0
  59. chatspatial/utils/path_utils.py +243 -0
  60. chatspatial/utils/persistence.py +78 -0
  61. chatspatial/utils/scipy_compat.py +143 -0
  62. chatspatial-1.1.0.dist-info/METADATA +242 -0
  63. chatspatial-1.1.0.dist-info/RECORD +67 -0
  64. chatspatial-1.1.0.dist-info/WHEEL +5 -0
  65. chatspatial-1.1.0.dist-info/entry_points.txt +2 -0
  66. chatspatial-1.1.0.dist-info/licenses/LICENSE +21 -0
  67. chatspatial-1.1.0.dist-info/top_level.txt +1 -0
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+ chatspatial/config.py,sha256=zOnpaw07T1ddxmezsr8k8EWJySrXYgZsEb9ycaIkKko,1298
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+ chatspatial/server.py,sha256=PWvEq3WsFrh2ui7HbIYGIAG_NJCpg1fTAVvAas7sD-Y,72234
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+ chatspatial/spatial_mcp_adapter.py,sha256=wNcZWmmxm-y8THnLAC7f8wK_KE92zH2ETo0K4Pjk4Kc,26150
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+ chatspatial/cli/__init__.py,sha256=hHuuXHW4tekJ9uJP2WHsZAkfHTXQKTeJpGXV3U8XLLY,139
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+ chatspatial/models/__init__.py,sha256=vHd3JL8KuPbVwwlp9Y3Ku1r3oMMOQlUkhcpiogaDfrs,2140
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+ chatspatial/models/analysis.py,sha256=UvJlz3v3KRPq8epZbsl0C24TBLTSH2bb8nOyJ1giO3Q,17692
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+ chatspatial/models/data.py,sha256=zgu62PkCx-09Q3HInF9GTyXtll1KUZZF4H55RDPpjaA,104729
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+ chatspatial/tools/__init__.py,sha256=_mHxphWoCjSwviNPhIVxb7jXdkEkjw2JCrYxdDwK8hE,57
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+ chatspatial/tools/annotation.py,sha256=iSU4_TzWI-up47wCxF_z_I3eC1dE1T_yBlSIp8TCDVw,72821
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+ chatspatial/tools/cell_communication.py,sha256=QvoUSQDaIA-O37RbIu7HYLhRFTWwxXLW0PND48ceZgY,64716
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+ chatspatial/tools/cnv_analysis.py,sha256=PJj9HgxcOpDmUxbmfMUJ58UyMrxm1PFXmS25FjzmhYc,24197
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+ chatspatial/tools/condition_comparison.py,sha256=6xGHTFgETNemofgg1xjo7P_Bpy3reWptSw8ck8Q0ba4,19795
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+ chatspatial/tools/differential.py,sha256=6aFkCROtnIXHFcEm5qeFGN7Z3ofRjzf9_Y6Z16uMml4,22467
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+ chatspatial/tools/embeddings.py,sha256=WdIogmq9usYbGd8RLvZ9bAaG4HxS2OD9sU0NV_Bhk0Y,9469
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+ chatspatial/tools/enrichment.py,sha256=cKlkDgamNljVx-xSLMSf5uJqY5hAaRGS30e3h8d93Fk,66313
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+ chatspatial/tools/integration.py,sha256=6yrCluko5GGDrkaZN9lupdvPsKSo6cQQFBf5pG1Nwqs,31075
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+ chatspatial/tools/preprocessing.py,sha256=y81xL3Rcwa0JxJTS-GUdIdZlOaS2S49dUlEfESzYoZ0,33556
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+ chatspatial/tools/spatial_domains.py,sha256=E3ww48U3SCBF3Y6TaCh7ocln3QIoH3antT6Gs7sIORo,32363
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+ chatspatial/tools/spatial_genes.py,sha256=iCWfy7Wl74hbxkdv77JHs-WN8fJJXb8qVBl2KK5V9M8,34571
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+ chatspatial/tools/spatial_registration.py,sha256=aaPQN1oieYslSfmY2QE9ResJ_Sa_aPDOdJJVVFvyXyo,14020
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+ chatspatial/tools/spatial_statistics.py,sha256=mM5Q_KROrrVIxY_ENAVCoJHgzJbfRXP0bSgJiVZRn2M,57368
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+ chatspatial/tools/trajectory.py,sha256=ufp_IuTQV_eBj-_3Puim7AcU1IWz32yAvruugeDKhfk,17323
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+ chatspatial/tools/velocity.py,sha256=2taOQsQmlWx3f96ClzRjTs2DEdPquDrLsF40m3JuIoE,13796
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+ chatspatial/tools/deconvolution/__init__.py,sha256=5zIGmSApZnk9cmk7DAA2ZmS3SAK6k9e6ndX_oIQtMeQ,13786
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+ chatspatial/tools/deconvolution/base.py,sha256=TD9ERTd0Svld_U68ffN0aUlZaHCp-tWeHKZmVNGp9s4,10275
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+ chatspatial/tools/deconvolution/card.py,sha256=EPsp6gtUjAJKjK98AoGnAZBkiEAb-aBc8n4gFybD8EM,8460
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+ chatspatial/tools/deconvolution/cell2location.py,sha256=1b1nDf2ivDhP9vIBcGXovXDPaLHJg4IDXJT_tWqS3ok,10929
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+ chatspatial/tools/deconvolution/destvi.py,sha256=IRI-11Zwt5ogLEGmQoKhLScEN930saPYi4sjyKDEuME,4389
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+ chatspatial/tools/deconvolution/flashdeconv.py,sha256=rDp4ae5Fsvlh3YuDuabwRSlCUxae9mglAgZkslf28JU,3188
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+ chatspatial/tools/deconvolution/rctd.py,sha256=Zf8cD-jE96RLzOF0thCsMeJwdMWqcbIV31u4QXa-tFQ,12990
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+ chatspatial/tools/deconvolution/spotlight.py,sha256=uXKRiNmDih1TsLsrO8xoN_KloSxLSpVXtgg6JLqAQn8,7548
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+ chatspatial/tools/deconvolution/stereoscope.py,sha256=Z8zM1q5Qh-fFAAlQ4Wqph9d1rQVeqR1lf1Km353ICXw,3380
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+ chatspatial/tools/deconvolution/tangram.py,sha256=dSuQoezQunQ2aFXSqIGMp_VlC7xNRNumcDmayb3Qrds,4535
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+ chatspatial/tools/visualization/__init__.py,sha256=iFTKGsGlG1sMbBI2297hC2NpGi8eiUsCSkRnwQHj5aQ,4615
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+ chatspatial/tools/visualization/basic.py,sha256=WGrKzmZ66UD_Gss8qQzs0hh7vExzG2A26FWdiiG9MHg,11934
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+ chatspatial/tools/visualization/cell_comm.py,sha256=GUDd_AbuHYeijClaGNkslkw1bGRVepwH04XrwxItgMc,22825
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+ chatspatial/tools/visualization/cnv.py,sha256=hF1r6p69_D2JoxkgNXqtONqHEqRd85FO2RolfPCYM4k,10596
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+ chatspatial/tools/visualization/core.py,sha256=s66YQfVcHumi4q3vdNRHc93H3qTkCUn1uElBJJ6PUKg,21774
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+ chatspatial/tools/visualization/deconvolution.py,sha256=nyDTSWGNqP_vHkZc0n6xkurflxx6JevUMAV6qAj_CJg,28387
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+ chatspatial/tools/visualization/enrichment.py,sha256=rstJrv4Ej1kwuNvN7lU9r8c5q6WNU8bP61szZe3dJeM,21698
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+ chatspatial/tools/visualization/integration.py,sha256=NwirVYdbYCXitDnDW6TFKNtkBzpXXNdhISn8OWVoddE,7021
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+ chatspatial/tools/visualization/main.py,sha256=xYaZ6hT4JtogHCp7HxSqLvPIZHmFxhQmjgJfobapwoE,6044
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+ chatspatial/tools/visualization/multi_gene.py,sha256=fr_fKaqyjXFeadnnFDa0AHKLr_dt76LRyDrYBb4nOeg,24821
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+ chatspatial/tools/visualization/persistence.py,sha256=eRi2TQmOITzvfDNOdXQbOX_nhMnoNXhFAgtkW_HnZiQ,12002
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+ chatspatial/tools/visualization/spatial_stats.py,sha256=NRnudVJL1UZbWcX7JY7NJK-6jXzr8a5tdiM8oStv7Pw,14915
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+ chatspatial/tools/visualization/trajectory.py,sha256=rY5ovNgpnJ_ewQPeESjnqbfH5AnIyEMCSf-z10aAuU0,19661
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+ chatspatial/tools/visualization/velocity.py,sha256=Own1bDIQpGFw8quUtquRlihtGx19H6lMzWdQvjy-fjE,13057
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+ chatspatial/utils/__init__.py,sha256=QsF9woCOW3h6rfZBNG5q1zJ6uhhDGrXH_u3fIXDgBkI,2611
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+ chatspatial/utils/adata_utils.py,sha256=93qv89UBID2Kv_0eV83brFoXMBL1ZXzTzzf6V7bJ35E,46925
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+ chatspatial/utils/compute.py,sha256=5PHNZluw4EWfPuaBPoMFWX57V3fZnySBcQPclf6xQVw,8671
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+ chatspatial/utils/data_loader.py,sha256=fhJA3fYpVMJhd3ka9lsi4unTos86cy7jlymqrF_OgT8,20789
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+ chatspatial/utils/dependency_manager.py,sha256=5OwXXbJUwS3qjJibKK6FEWgUfHusUiIRAicZZA_eXpM,15059
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+ chatspatial/utils/device_utils.py,sha256=g2Ih4ByHIz8B7GgDwCxWyu09m-QhGmj-QsQ1Z8QCCV0,4965
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+ chatspatial/utils/exceptions.py,sha256=lih4UT0XOJJ_o5PfcDi8Tc1UTL-5mmyBGCXLj1GuRB8,6208
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+ chatspatial/utils/image_utils.py,sha256=-oTM0FS-SI9N5h7NlKwAo4vfvzY7JWy8KtSRwY75MQI,8044
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+ chatspatial/utils/mcp_utils.py,sha256=RkBZ5XCZlcRoAsHFstfjli4pfKmepK4kOf8c_zwkAiM,4362
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+ chatspatial/utils/path_utils.py,sha256=usbfTXU_eK-7XwtxcWPwQDBTvnHn5GrcF-gyTbwy8Xk,7115
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+ chatspatial/utils/persistence.py,sha256=Yd4IL9AfMKY6-skCYYUy0FCKgOdLGLkb1vEOU_ATZRw,2237
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+ chatspatial/utils/scipy_compat.py,sha256=63qAaNXBfEKPLTxlHA2y9BVJIbghD_2o68rg5WSE0UU,5123
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+ chatspatial-1.1.0.dist-info/licenses/LICENSE,sha256=ycAwbRDiysfzCDHgU9AjsNmmSGKN1Z6-obB0K_h0bhQ,1080
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+ chatspatial-1.1.0.dist-info/METADATA,sha256=K47wePgT6sUjpgCYimVWVICYPEcRFYvm1J_JEUOZYW0,7286
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+ chatspatial-1.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ chatspatial-1.1.0.dist-info/entry_points.txt,sha256=z57PdLCSwlA7-QrnpJuGrjtCHIcPXkRFbhR-O0RHPWQ,58
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+ chatspatial-1.1.0.dist-info/top_level.txt,sha256=EiZwbRsD5mw_V5500GWU-r37JSH2JwdUAIu_N-LgH_M,12
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+ chatspatial-1.1.0.dist-info/RECORD,,
@@ -0,0 +1,5 @@
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+ Wheel-Version: 1.0
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+ Generator: setuptools (80.9.0)
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+ Root-Is-Purelib: true
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+ Tag: py3-none-any
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+
@@ -0,0 +1,2 @@
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+ [console_scripts]
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+ chatspatial = chatspatial.__main__:main
@@ -0,0 +1,21 @@
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+ MIT License
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+
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+ Copyright (c) 2024 ChatSpatial Contributors
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
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+ chatspatial