synkit 0.0.17__tar.gz → 1.0.1__tar.gz

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Files changed (163) hide show
  1. {synkit-0.0.17 → synkit-1.0.1}/PKG-INFO +3 -3
  2. {synkit-0.0.17 → synkit-1.0.1}/README.md +2 -2
  3. {synkit-0.0.17 → synkit-1.0.1}/pyproject.toml +5 -7
  4. synkit-1.0.1/synkit/Graph/Feature/Descriptors/topology.py +854 -0
  5. synkit-1.0.1/synkit/Graph/Matcher/automorphism.py +151 -0
  6. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/syn_reactor.py +23 -10
  7. synkit-0.0.17/synkit/Data/aldol.json.gz +0 -1
  8. synkit-0.0.17/synkit/Data/paracetamol.json.gz +0 -1
  9. {synkit-0.0.17 → synkit-1.0.1}/.gitignore +0 -0
  10. {synkit-0.0.17 → synkit-1.0.1}/LICENSE +0 -0
  11. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Cluster/__init__.py +0 -0
  12. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Cluster/butina.py +0 -0
  13. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Fingerprint/__init__.py +0 -0
  14. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Fingerprint/fp_calculator.py +0 -0
  15. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Fingerprint/smiles_featurizer.py +0 -0
  16. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Fingerprint/transformation_fp.py +0 -0
  17. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Molecule/__init__.py +0 -0
  18. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Molecule/standardize.py +0 -0
  19. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/__init__.py +0 -0
  20. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/aam_validator.py +0 -0
  21. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/balance_check.py +0 -0
  22. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/canon_rsmi.py +0 -0
  23. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/cleaning.py +0 -0
  24. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/deionize.py +0 -0
  25. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/fix_aam.py +0 -0
  26. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/neutralize.py +0 -0
  27. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/radical_wildcard.py +0 -0
  28. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/standardize.py +0 -0
  29. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/Reaction/tautomerize.py +0 -0
  30. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/__init__.py +0 -0
  31. {synkit-0.0.17 → synkit-1.0.1}/synkit/Chem/utils.py +0 -0
  32. {synkit-0.0.17 → synkit-1.0.1}/synkit/Data/__init__.py +0 -0
  33. {synkit-0.0.17 → synkit-1.0.1}/synkit/Data/gen_partial_aam.py +0 -0
  34. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Canon/__init__.py +0 -0
  35. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Canon/canon_algs.py +0 -0
  36. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Canon/canon_graph.py +0 -0
  37. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Canon/nauty.py +0 -0
  38. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Context/__init__.py +0 -0
  39. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Context/hier_context.py +0 -0
  40. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Context/radius_expand.py +0 -0
  41. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/Fingerprint/__init__.py +0 -0
  42. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/Fingerprint/wl_rxn_fps.py +0 -0
  43. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/__init__.py +0 -0
  44. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/graph_descriptors.py +0 -0
  45. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/graph_fps.py +0 -0
  46. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/graph_signature.py +0 -0
  47. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/hash_fps.py +0 -0
  48. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/morgan_fps.py +0 -0
  49. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/path_fps.py +0 -0
  50. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Feature/wl_hash.py +0 -0
  51. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Hyrogen/__init__.py +0 -0
  52. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Hyrogen/_misc.py +0 -0
  53. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Hyrogen/hcomplete.py +0 -0
  54. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Hyrogen/hextend.py +0 -0
  55. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/__init__.py +0 -0
  56. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_builder.py +0 -0
  57. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_construction.py +0 -0
  58. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_decompose.py +0 -0
  59. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_destruction.py +0 -0
  60. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_expand.py +0 -0
  61. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/its_relabel.py +0 -0
  62. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/normalize_aam.py +0 -0
  63. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/ITS/partial_its.py +0 -0
  64. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/__init__.py +0 -0
  65. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/group_comp.py +0 -0
  66. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/groupoid.py +0 -0
  67. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/mcs_matcher.py +0 -0
  68. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/mtg.py +0 -0
  69. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/mtg_explore.py +0 -0
  70. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/MTG/utils.py +0 -0
  71. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/__init__.py +0 -0
  72. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/batch_cluster.py +0 -0
  73. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/graph_cluster.py +0 -0
  74. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/graph_matcher.py +0 -0
  75. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/graph_morphism.py +0 -0
  76. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/mcs_matcher.py +0 -0
  77. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/multi_turbo_iso.py +0 -0
  78. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/partial_matcher.py +0 -0
  79. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/sing.py +0 -0
  80. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/subgraph_matcher.py +0 -0
  81. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Matcher/turbo_iso.py +0 -0
  82. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Wildcard/__init__.py +0 -0
  83. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Wildcard/fuse_graph.py +0 -0
  84. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Wildcard/radwc.py +0 -0
  85. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/Wildcard/wildcard.py +0 -0
  86. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/__init__.py +0 -0
  87. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/canon_graph.py +0 -0
  88. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/syn_graph.py +0 -0
  89. {synkit-0.0.17 → synkit-1.0.1}/synkit/Graph/utils.py +0 -0
  90. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/__init__.py +0 -0
  91. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/chem_converter.py +0 -0
  92. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/__init__.py +0 -0
  93. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/gml_to_graph.py +0 -0
  94. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/graph_to_gml.py +0 -0
  95. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/graph_to_smarts.py +0 -0
  96. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/smarts_expander.py +0 -0
  97. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/smarts_generalizer.py +0 -0
  98. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/combinatorial/smarts_to_graph.py +0 -0
  99. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/data_io.py +0 -0
  100. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/data_process.py +0 -0
  101. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/debug.py +0 -0
  102. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/dg_to_gml.py +0 -0
  103. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/gml_to_nx.py +0 -0
  104. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/graph_to_mol.py +0 -0
  105. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/mol_to_graph.py +0 -0
  106. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/nx_to_gml.py +0 -0
  107. {synkit-0.0.17 → synkit-1.0.1}/synkit/IO/smiles_to_id.py +0 -0
  108. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Apply/__init__.py +0 -0
  109. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Apply/reactor_rule.py +0 -0
  110. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Apply/retro_reactor.py +0 -0
  111. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Apply/rule_matcher.py +0 -0
  112. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Apply/rule_rbl.py +0 -0
  113. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/__init__.py +0 -0
  114. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/compose_rule.py +0 -0
  115. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/rule_compose.py +0 -0
  116. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/rule_mapping.py +0 -0
  117. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/seq_comp.py +0 -0
  118. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Compose/valence_constrain.py +0 -0
  119. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/__init__.py +0 -0
  120. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/implict_rule.py +0 -0
  121. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/longest_path.py +0 -0
  122. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/molecule_rule.py +0 -0
  123. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/prune_templates.py +0 -0
  124. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/rule_utils.py +0 -0
  125. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/Modify/strip_rule.py +0 -0
  126. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/__init__.py +0 -0
  127. {synkit-0.0.17 → synkit-1.0.1}/synkit/Rule/syn_rule.py +0 -0
  128. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/CRN/__init__.py +0 -0
  129. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/CRN/crn.py +0 -0
  130. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/CRN/dcrn.py +0 -0
  131. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/CRN/mod_crn.py +0 -0
  132. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/MSR/__init__.py +0 -0
  133. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/MSR/multi_steps.py +0 -0
  134. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/MSR/path_finder.py +0 -0
  135. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Metrics/__init__.py +0 -0
  136. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Metrics/_base.py +0 -0
  137. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Metrics/_plot.py +0 -0
  138. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Metrics/_ranking.py +0 -0
  139. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/__init__.py +0 -0
  140. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/batch_reactor.py +0 -0
  141. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/benchmark.py +0 -0
  142. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/imba_engine.py +0 -0
  143. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/mod_aam.py +0 -0
  144. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/mod_reactor.py +0 -0
  145. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/partial_engine.py +0 -0
  146. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/post_syn.py +0 -0
  147. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/rbl_engine.py +0 -0
  148. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/rule_filter.py +0 -0
  149. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/single_predictor.py +0 -0
  150. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/Reactor/strategy.py +0 -0
  151. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/__init__.py +0 -0
  152. {synkit-0.0.17 → synkit-1.0.1}/synkit/Synthesis/reactor_utils.py +0 -0
  153. {synkit-0.0.17 → synkit-1.0.1}/synkit/Utils/__init__.py +0 -0
  154. {synkit-0.0.17 → synkit-1.0.1}/synkit/Utils/utils.py +0 -0
  155. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/__init__.py +0 -0
  156. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/chemical_space.py +0 -0
  157. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/embedding.py +0 -0
  158. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/graph_visualizer.py +0 -0
  159. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/pdf_writer.py +0 -0
  160. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/rule_vis.py +0 -0
  161. {synkit-0.0.17 → synkit-1.0.1}/synkit/Vis/rxn_vis.py +0 -0
  162. {synkit-0.0.17 → synkit-1.0.1}/synkit/__init__.py +0 -0
  163. {synkit-0.0.17 → synkit-1.0.1}/synkit/examples.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: synkit
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- Version: 0.0.17
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+ Version: 1.0.1
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  Summary: Utility for reaction modeling using graph grammar
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  Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
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  Project-URL: source, https://github.com/TieuLongPhan/SynKit
@@ -44,7 +44,7 @@ Description-Content-Type: text/markdown
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  **Toolkit for Synthesis Planning**
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- SynKit is a collection of tools designed to support the planning and execution of chemical synthesis.
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+ SynKit is a collection of tools designed to support the planning and execution of chemical synthesis. Check out the [documentation](https://tieulongphan.github.io/SynKit/) for a comprehensive description of its features.
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  ![SynKit](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit.png)
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@@ -96,7 +96,7 @@ For more details on each utility within the repository, please refer to the docu
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  ```bash
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  docker pull tieulongphan/synkit:latest
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  # or a specific version:
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- docker pull tieulongphan/synkit:0.1.0
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+ docker pull tieulongphan/synkit:1.0.0
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  ```
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  Run a container (sanity check):
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  ```
@@ -13,7 +13,7 @@
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  **Toolkit for Synthesis Planning**
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- SynKit is a collection of tools designed to support the planning and execution of chemical synthesis.
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+ SynKit is a collection of tools designed to support the planning and execution of chemical synthesis. Check out the [documentation](https://tieulongphan.github.io/SynKit/) for a comprehensive description of its features.
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  ![SynKit](https://raw.githubusercontent.com/TieuLongPhan/SynKit/main/Data/Figure/synkit.png)
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@@ -65,7 +65,7 @@ For more details on each utility within the repository, please refer to the docu
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  ```bash
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  docker pull tieulongphan/synkit:latest
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  # or a specific version:
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- docker pull tieulongphan/synkit:0.1.0
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+ docker pull tieulongphan/synkit:1.0.0
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  ```
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  Run a container (sanity check):
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  ```
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
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  [project]
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  name = "synkit"
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- version = "0.0.17"
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+ version = "1.0.1"
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  description = "Utility for reaction modeling using graph grammar"
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  readme = "README.md"
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  long-description = { file = "CHANGELOG.md" }
@@ -45,12 +45,10 @@ issues = "https://github.com/TieuLongPhan/SynKit/issues"
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  documentation = "https://tieulongphan.github.io/SynKit/"
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  [tool.hatch.build]
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- # ship your code as normal
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  packages = ["synkit"]
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- # Force-include the entire Data directory (recursively)
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- [tool.hatch.build.targets.wheel.force-include]
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- "synkit/Data" = "synkit/Data"
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+ [tool.hatch.build.targets.wheel]
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+ include = ["synkit/Data/**"]
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- [tool.hatch.build.targets.sdist.force-include]
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- "synkit/Data" = "synkit/Data"
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+ [tool.hatch.build.targets.sdist]
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+ include = ["synkit/Data/**"]