phykit 2.1.89__tar.gz → 2.1.90__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (149) hide show
  1. {phykit-2.1.89 → phykit-2.1.90}/PKG-INFO +1 -1
  2. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/transfer_annotations.py +8 -0
  3. phykit-2.1.90/phykit/version.py +1 -0
  4. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/PKG-INFO +1 -1
  5. phykit-2.1.89/phykit/version.py +0 -1
  6. {phykit-2.1.89 → phykit-2.1.90}/LICENSE.md +0 -0
  7. {phykit-2.1.89 → phykit-2.1.90}/README.md +0 -0
  8. {phykit-2.1.89 → phykit-2.1.90}/phykit/__init__.py +0 -0
  9. {phykit-2.1.89 → phykit-2.1.90}/phykit/__main__.py +0 -0
  10. {phykit-2.1.89 → phykit-2.1.90}/phykit/cli_registry.py +0 -0
  11. {phykit-2.1.89 → phykit-2.1.90}/phykit/errors.py +0 -0
  12. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/__init__.py +0 -0
  13. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/boolean_argument_parsing.py +0 -0
  14. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/caching.py +0 -0
  15. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/circular_layout.py +0 -0
  16. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/color_annotations.py +0 -0
  17. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/discrete_models.py +0 -0
  18. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/files.py +0 -0
  19. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/geological_timescale.py +0 -0
  20. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/json_output.py +0 -0
  21. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/parallel.py +0 -0
  22. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/parsimony_utils.py +0 -0
  23. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/pgls_utils.py +0 -0
  24. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/plot_config.py +0 -0
  25. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/quartet_utils.py +0 -0
  26. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/stats_summary.py +0 -0
  27. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/streaming.py +0 -0
  28. {phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/trait_parsing.py +0 -0
  29. {phykit-2.1.89 → phykit-2.1.90}/phykit/phykit.py +0 -0
  30. {phykit-2.1.89 → phykit-2.1.90}/phykit/service_factories.py +0 -0
  31. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/__init__.py +0 -0
  32. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/__init__.py +0 -0
  33. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_entropy.py +0 -0
  34. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_length.py +0 -0
  35. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_length_no_gaps.py +0 -0
  36. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_outlier_taxa.py +0 -0
  37. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_recoding.py +0 -0
  38. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/alignment_subsample.py +0 -0
  39. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/base.py +0 -0
  40. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/column_score.py +0 -0
  41. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/composition_per_taxon.py +0 -0
  42. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/compositional_bias_per_site.py +0 -0
  43. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/create_concatenation_matrix.py +0 -0
  44. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/dfoil.py +0 -0
  45. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/dna_threader.py +0 -0
  46. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/dstatistic.py +0 -0
  47. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/evolutionary_rate_per_site.py +0 -0
  48. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/faidx.py +0 -0
  49. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/gc_content.py +0 -0
  50. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/identity_matrix.py +0 -0
  51. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/mask_alignment.py +0 -0
  52. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/occupancy_filter.py +0 -0
  53. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/occupancy_per_taxon.py +0 -0
  54. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/pairwise_identity.py +0 -0
  55. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/parsimony_informative_sites.py +0 -0
  56. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/phylo_gwas.py +0 -0
  57. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/plot_alignment_qc.py +0 -0
  58. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/rcv.py +0 -0
  59. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/rcvt.py +0 -0
  60. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/rename_fasta_entries.py +0 -0
  61. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/sum_of_pairs_score.py +0 -0
  62. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/taxon_groups.py +0 -0
  63. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/alignment/variable_sites.py +0 -0
  64. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/base.py +0 -0
  65. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/__init__.py +0 -0
  66. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/ancestral_reconstruction.py +0 -0
  67. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/base.py +0 -0
  68. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/bipartition_support_stats.py +0 -0
  69. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/branch_length_multiplier.py +0 -0
  70. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/character_map.py +0 -0
  71. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/chronogram.py +0 -0
  72. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/collapse_branches.py +0 -0
  73. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/concordance_asr.py +0 -0
  74. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/consensus_network.py +0 -0
  75. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/consensus_tree.py +0 -0
  76. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/cont_map.py +0 -0
  77. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/cophylo.py +0 -0
  78. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/covarying_evolutionary_rates.py +0 -0
  79. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/density_map.py +0 -0
  80. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/discordance_asymmetry.py +0 -0
  81. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/dtt.py +0 -0
  82. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/dvmc.py +0 -0
  83. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/evo_tempo_map.py +0 -0
  84. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/evolutionary_rate.py +0 -0
  85. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/fit_continuous.py +0 -0
  86. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/fit_discrete.py +0 -0
  87. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/hidden_paralogy_check.py +0 -0
  88. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/hybridization.py +0 -0
  89. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/independent_contrasts.py +0 -0
  90. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/internal_branch_stats.py +0 -0
  91. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/internode_labeler.py +0 -0
  92. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/kf_distance.py +0 -0
  93. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/last_common_ancestor_subtree.py +0 -0
  94. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/lb_score.py +0 -0
  95. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/ltt.py +0 -0
  96. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/monophyly_check.py +0 -0
  97. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/nearest_neighbor_interchange.py +0 -0
  98. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/neighbor_net.py +0 -0
  99. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/network_signal.py +0 -0
  100. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/ou_shift_detection.py +0 -0
  101. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/ouwie.py +0 -0
  102. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/parsimony_score.py +0 -0
  103. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/patristic_distances.py +0 -0
  104. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phenogram.py +0 -0
  105. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylo_anova.py +0 -0
  106. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylo_heatmap.py +0 -0
  107. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylo_impute.py +0 -0
  108. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylo_logistic.py +0 -0
  109. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylo_path.py +0 -0
  110. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylogenetic_glm.py +0 -0
  111. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylogenetic_ordination.py +0 -0
  112. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylogenetic_regression.py +0 -0
  113. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylogenetic_signal.py +0 -0
  114. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/phylomorphospace.py +0 -0
  115. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/polytomy_test.py +0 -0
  116. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/print_tree.py +0 -0
  117. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/prune_tree.py +0 -0
  118. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/quartet_network.py +0 -0
  119. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/quartet_pie.py +0 -0
  120. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/rate_heterogeneity.py +0 -0
  121. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/relative_rate_test.py +0 -0
  122. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/rename_tree_tips.py +0 -0
  123. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/rf_distance.py +0 -0
  124. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/root_tree.py +0 -0
  125. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/saturation.py +0 -0
  126. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/simmap_summary.py +0 -0
  127. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/spectral_discordance.py +0 -0
  128. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/spr.py +0 -0
  129. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/spurious_sequence.py +0 -0
  130. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/stochastic_character_map.py +0 -0
  131. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/terminal_branch_stats.py +0 -0
  132. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/threshold_model.py +0 -0
  133. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/tip_labels.py +0 -0
  134. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/tip_to_tip_distance.py +0 -0
  135. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/tip_to_tip_node_distance.py +0 -0
  136. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/total_tree_length.py +0 -0
  137. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/trait_correlation.py +0 -0
  138. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/trait_rate_map.py +0 -0
  139. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/tree_space.py +0 -0
  140. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/treeness.py +0 -0
  141. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/treeness_over_rcv.py +0 -0
  142. {phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/vcv_utils.py +0 -0
  143. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/SOURCES.txt +0 -0
  144. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/dependency_links.txt +0 -0
  145. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/entry_points.txt +0 -0
  146. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/requires.txt +0 -0
  147. {phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/top_level.txt +0 -0
  148. {phykit-2.1.89 → phykit-2.1.90}/setup.cfg +0 -0
  149. {phykit-2.1.89 → phykit-2.1.90}/setup.py +0 -0
{phykit-2.1.89 → phykit-2.1.90}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: phykit
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- Version: 2.1.89
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+ Version: 2.1.90
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  Home-page: https://github.com/jlsteenwyk/phykit
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  Author: Jacob L. Steenwyk
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  Author-email: jlsteenwyk@gmail.com
{phykit-2.1.89 → phykit-2.1.90}/phykit/services/tree/transfer_annotations.py RENAMED
@@ -114,6 +114,12 @@ class TransferAnnotations(Tree):
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  annotation = clade.comment or clade.name or ""
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  if not annotation:
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  continue
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+ # wASTRAL --support 3 wraps annotations as '[key=val;...]'
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+ # which BioPython parses as a quoted node name including the
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+ # brackets. Strip them so BioPython's comment writer can
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+ # re-add proper brackets on output.
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+ if annotation.startswith("[") and annotation.endswith("]"):
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+ annotation = annotation[1:-1]
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  bp = self._get_bipartition(clade, all_taxa)
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  if bp:
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  annotations[bp] = annotation
@@ -149,6 +155,8 @@ class TransferAnnotations(Tree):
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  content = f.read()
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  # Remove the & prefix that BioPython adds
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  content = content.replace("[&", "[")
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+ # BioPython may also backslash-escape brackets inside comments
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+ content = content.replace("\\[", "[").replace("\\]", "]")
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  with open(output_path, "w") as f:
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  f.write(content)
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phykit-2.1.90/phykit/version.py ADDED
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+ __version__ = "2.1.90"
{phykit-2.1.89 → phykit-2.1.90}/phykit.egg-info/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: phykit
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- Version: 2.1.89
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+ Version: 2.1.90
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  Home-page: https://github.com/jlsteenwyk/phykit
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  Author: Jacob L. Steenwyk
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  Author-email: jlsteenwyk@gmail.com
phykit-2.1.89/phykit/version.py DELETED
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- __version__ = "2.1.89"
{phykit-2.1.89 → phykit-2.1.90}/LICENSE.md RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/README.md RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/__init__.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/__main__.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/cli_registry.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/errors.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/helpers/files.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/phykit.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/phykit/services/base.py RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/setup.cfg RENAMED
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{phykit-2.1.89 → phykit-2.1.90}/setup.py RENAMED
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