ipyrad2 0.1.9__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 (191) hide show
  1. ipyrad2-0.1.9/.github/workflows/publish-pypi.yml +51 -0
  2. ipyrad2-0.1.9/.gitignore +14 -0
  3. ipyrad2-0.1.9/LICENSE.txt +674 -0
  4. ipyrad2-0.1.9/PKG-INFO +749 -0
  5. ipyrad2-0.1.9/README.md +47 -0
  6. ipyrad2-0.1.9/TODO.md +106 -0
  7. ipyrad2-0.1.9/conda.recipe/meta.yaml +57 -0
  8. ipyrad2-0.1.9/docs/_templates/README.md +28 -0
  9. ipyrad2-0.1.9/docs/_templates/command-reference.md +51 -0
  10. ipyrad2-0.1.9/docs/_templates/concept-guide.md +39 -0
  11. ipyrad2-0.1.9/docs/_templates/section-landing.md +32 -0
  12. ipyrad2-0.1.9/docs/analyses/dapc.md +282 -0
  13. ipyrad2-0.1.9/docs/analyses/index.md +35 -0
  14. ipyrad2-0.1.9/docs/analyses/pca.md +327 -0
  15. ipyrad2-0.1.9/docs/analyses/popgen.md +369 -0
  16. ipyrad2-0.1.9/docs/assembly/assemble.md +309 -0
  17. ipyrad2-0.1.9/docs/assembly/demux.md +192 -0
  18. ipyrad2-0.1.9/docs/assembly/denovo.md +385 -0
  19. ipyrad2-0.1.9/docs/assembly/index.md +72 -0
  20. ipyrad2-0.1.9/docs/assembly/map.md +222 -0
  21. ipyrad2-0.1.9/docs/assembly/trim.md +223 -0
  22. ipyrad2-0.1.9/docs/css/notebook-markdown.css +114 -0
  23. ipyrad2-0.1.9/docs/getting-started/ethos.md +28 -0
  24. ipyrad2-0.1.9/docs/getting-started/files-and-data-types.md +187 -0
  25. ipyrad2-0.1.9/docs/getting-started/installation.md +96 -0
  26. ipyrad2-0.1.9/docs/getting-started/what-is-ipyrad.md +43 -0
  27. ipyrad2-0.1.9/docs/index.md +36 -0
  28. ipyrad2-0.1.9/docs/recipes/index.md +28 -0
  29. ipyrad2-0.1.9/docs/recipes/sample-name-parsing.md +136 -0
  30. ipyrad2-0.1.9/docs/writing-outputs/index.md +67 -0
  31. ipyrad2-0.1.9/docs/writing-outputs/lex.md +51 -0
  32. ipyrad2-0.1.9/docs/writing-outputs/snpex.md +178 -0
  33. ipyrad2-0.1.9/docs/writing-outputs/wex.md +290 -0
  34. ipyrad2-0.1.9/environment.yml +21 -0
  35. ipyrad2-0.1.9/ipyrad2/__init__.py +16 -0
  36. ipyrad2-0.1.9/ipyrad2/_version.py +24 -0
  37. ipyrad2-0.1.9/ipyrad2/analysis/__init__.py +61 -0
  38. ipyrad2-0.1.9/ipyrad2/analysis/converters/__init__.py +22 -0
  39. ipyrad2-0.1.9/ipyrad2/analysis/converters/vcf_to_hdf5.py +656 -0
  40. ipyrad2-0.1.9/ipyrad2/analysis/extracters/__init__.py +33 -0
  41. ipyrad2-0.1.9/ipyrad2/analysis/extracters/locus_extracter.py +472 -0
  42. ipyrad2-0.1.9/ipyrad2/analysis/extracters/sequence_common.py +230 -0
  43. ipyrad2-0.1.9/ipyrad2/analysis/extracters/snps_extracter.py +1399 -0
  44. ipyrad2-0.1.9/ipyrad2/analysis/extracters/window_extracter.py +991 -0
  45. ipyrad2-0.1.9/ipyrad2/analysis/methods/__init__.py +47 -0
  46. ipyrad2-0.1.9/ipyrad2/analysis/methods/admixture.py +346 -0
  47. ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/__init__.py +21 -0
  48. ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/models.py +79 -0
  49. ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/runner.py +1822 -0
  50. ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp.py +756 -0
  51. ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp_posteriors.py +105 -0
  52. ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp_summary.py +123 -0
  53. ipyrad2-0.1.9/ipyrad2/analysis/methods/common.py +688 -0
  54. ipyrad2-0.1.9/ipyrad2/analysis/methods/dapc.py +256 -0
  55. ipyrad2-0.1.9/ipyrad2/analysis/methods/pca.py +800 -0
  56. ipyrad2-0.1.9/ipyrad2/analysis/methods/pca_drawing.py +286 -0
  57. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/__init__.py +21 -0
  58. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/common.py +193 -0
  59. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/estimators.py +406 -0
  60. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/models.py +185 -0
  61. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/runner.py +451 -0
  62. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/seq_backend.py +1314 -0
  63. ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/snp_backend.py +296 -0
  64. ipyrad2-0.1.9/ipyrad2/analysis/methods/snmf.py +635 -0
  65. ipyrad2-0.1.9/ipyrad2/analysis/methods/snps_imputer.py +182 -0
  66. ipyrad2-0.1.9/ipyrad2/analysis/methods/treeslider.py +1140 -0
  67. ipyrad2-0.1.9/ipyrad2/analysis/utils.py +163 -0
  68. ipyrad2-0.1.9/ipyrad2/assembler/__init__.py +3 -0
  69. ipyrad2-0.1.9/ipyrad2/assembler/assemble.py +2257 -0
  70. ipyrad2-0.1.9/ipyrad2/assembler/beds.py +826 -0
  71. ipyrad2-0.1.9/ipyrad2/assembler/hdf5_utils.py +163 -0
  72. ipyrad2-0.1.9/ipyrad2/assembler/loci.py +1897 -0
  73. ipyrad2-0.1.9/ipyrad2/assembler/paralogs.py +913 -0
  74. ipyrad2-0.1.9/ipyrad2/assembler/read_filters.py +352 -0
  75. ipyrad2-0.1.9/ipyrad2/assembler/sort_utils.py +12 -0
  76. ipyrad2-0.1.9/ipyrad2/assembler/variants.py +1495 -0
  77. ipyrad2-0.1.9/ipyrad2/assembler/write_seqs.py +384 -0
  78. ipyrad2-0.1.9/ipyrad2/assembler/write_snps.py +700 -0
  79. ipyrad2-0.1.9/ipyrad2/classic/__init__.py +3 -0
  80. ipyrad2-0.1.9/ipyrad2/classic/cli_classic.py +234 -0
  81. ipyrad2-0.1.9/ipyrad2/cli/__init__.py +3 -0
  82. ipyrad2-0.1.9/ipyrad2/cli/cli_admixture.py +139 -0
  83. ipyrad2-0.1.9/ipyrad2/cli/cli_analysis.py +570 -0
  84. ipyrad2-0.1.9/ipyrad2/cli/cli_assemble.py +217 -0
  85. ipyrad2-0.1.9/ipyrad2/cli/cli_baba.py +149 -0
  86. ipyrad2-0.1.9/ipyrad2/cli/cli_bpp.py +167 -0
  87. ipyrad2-0.1.9/ipyrad2/cli/cli_dapc.py +135 -0
  88. ipyrad2-0.1.9/ipyrad2/cli/cli_demux.py +169 -0
  89. ipyrad2-0.1.9/ipyrad2/cli/cli_denovo.py +166 -0
  90. ipyrad2-0.1.9/ipyrad2/cli/cli_lex.py +114 -0
  91. ipyrad2-0.1.9/ipyrad2/cli/cli_main.py +483 -0
  92. ipyrad2-0.1.9/ipyrad2/cli/cli_map.py +100 -0
  93. ipyrad2-0.1.9/ipyrad2/cli/cli_pca.py +163 -0
  94. ipyrad2-0.1.9/ipyrad2/cli/cli_popgen.py +152 -0
  95. ipyrad2-0.1.9/ipyrad2/cli/cli_snmf.py +158 -0
  96. ipyrad2-0.1.9/ipyrad2/cli/cli_snpex.py +147 -0
  97. ipyrad2-0.1.9/ipyrad2/cli/cli_treeslider.py +153 -0
  98. ipyrad2-0.1.9/ipyrad2/cli/cli_trim.py +179 -0
  99. ipyrad2-0.1.9/ipyrad2/cli/cli_vcf_to_hdf5.py +65 -0
  100. ipyrad2-0.1.9/ipyrad2/cli/cli_wex.py +113 -0
  101. ipyrad2-0.1.9/ipyrad2/cli/command_log.py +68 -0
  102. ipyrad2-0.1.9/ipyrad2/cli/common.py +24 -0
  103. ipyrad2-0.1.9/ipyrad2/demuxer/__init__.py +3 -0
  104. ipyrad2-0.1.9/ipyrad2/demuxer/demux.py +1162 -0
  105. ipyrad2-0.1.9/ipyrad2/demuxer/demux_pipeline.py +869 -0
  106. ipyrad2-0.1.9/ipyrad2/demuxer/demux_report.py +471 -0
  107. ipyrad2-0.1.9/ipyrad2/demuxer/match.py +975 -0
  108. ipyrad2-0.1.9/ipyrad2/demuxer/sample_names.py +37 -0
  109. ipyrad2-0.1.9/ipyrad2/denovo/__init__.py +2 -0
  110. ipyrad2-0.1.9/ipyrad2/denovo/align.py +1346 -0
  111. ipyrad2-0.1.9/ipyrad2/denovo/cluster.py +163 -0
  112. ipyrad2-0.1.9/ipyrad2/denovo/common.py +75 -0
  113. ipyrad2-0.1.9/ipyrad2/denovo/denovo.py +1702 -0
  114. ipyrad2-0.1.9/ipyrad2/denovo/graph.py +1334 -0
  115. ipyrad2-0.1.9/ipyrad2/denovo/graph_split.py +269 -0
  116. ipyrad2-0.1.9/ipyrad2/mapper/__init__.py +8 -0
  117. ipyrad2-0.1.9/ipyrad2/mapper/legacy_map_bams.py +453 -0
  118. ipyrad2-0.1.9/ipyrad2/mapper/map_samples_prep.py +304 -0
  119. ipyrad2-0.1.9/ipyrad2/mapper/map_stats.py +604 -0
  120. ipyrad2-0.1.9/ipyrad2/mapper/mapper.py +599 -0
  121. ipyrad2-0.1.9/ipyrad2/trimmer/__init__.py +2 -0
  122. ipyrad2-0.1.9/ipyrad2/trimmer/adapters.fa +14 -0
  123. ipyrad2-0.1.9/ipyrad2/trimmer/trim_fastqs.py +730 -0
  124. ipyrad2-0.1.9/ipyrad2/utils/__init__.py +0 -0
  125. ipyrad2-0.1.9/ipyrad2/utils/exceptions.py +11 -0
  126. ipyrad2-0.1.9/ipyrad2/utils/jit_funcs.py +91 -0
  127. ipyrad2-0.1.9/ipyrad2/utils/kmers.py +1177 -0
  128. ipyrad2-0.1.9/ipyrad2/utils/logger.py +104 -0
  129. ipyrad2-0.1.9/ipyrad2/utils/names.py +699 -0
  130. ipyrad2-0.1.9/ipyrad2/utils/parallel/__init__.py +22 -0
  131. ipyrad2-0.1.9/ipyrad2/utils/parallel/pipeline.py +681 -0
  132. ipyrad2-0.1.9/ipyrad2/utils/parallel/pool.py +544 -0
  133. ipyrad2-0.1.9/ipyrad2/utils/params.py +222 -0
  134. ipyrad2-0.1.9/ipyrad2/utils/pops.py +228 -0
  135. ipyrad2-0.1.9/ipyrad2/utils/profiling.py +83 -0
  136. ipyrad2-0.1.9/ipyrad2/utils/progress.py +58 -0
  137. ipyrad2-0.1.9/ipyrad2/utils/seqs.py +46 -0
  138. ipyrad2-0.1.9/ipyrad2.egg-info/PKG-INFO +749 -0
  139. ipyrad2-0.1.9/ipyrad2.egg-info/SOURCES.txt +189 -0
  140. ipyrad2-0.1.9/ipyrad2.egg-info/dependency_links.txt +1 -0
  141. ipyrad2-0.1.9/ipyrad2.egg-info/entry_points.txt +3 -0
  142. ipyrad2-0.1.9/ipyrad2.egg-info/requires.txt +14 -0
  143. ipyrad2-0.1.9/ipyrad2.egg-info/scm_file_list.json +184 -0
  144. ipyrad2-0.1.9/ipyrad2.egg-info/scm_version.json +8 -0
  145. ipyrad2-0.1.9/ipyrad2.egg-info/top_level.txt +1 -0
  146. ipyrad2-0.1.9/pyproject.toml +63 -0
  147. ipyrad2-0.1.9/scripts/benchmark_denovo_split.py +204 -0
  148. ipyrad2-0.1.9/scripts/migrate_legacy_map_bams.py +73 -0
  149. ipyrad2-0.1.9/setup.cfg +4 -0
  150. ipyrad2-0.1.9/tests/test_analysis_admixture.py +319 -0
  151. ipyrad2-0.1.9/tests/test_analysis_baba.py +525 -0
  152. ipyrad2-0.1.9/tests/test_analysis_bpp.py +288 -0
  153. ipyrad2-0.1.9/tests/test_analysis_cluster_tools.py +315 -0
  154. ipyrad2-0.1.9/tests/test_analysis_extractors.py +1001 -0
  155. ipyrad2-0.1.9/tests/test_analysis_pca.py +966 -0
  156. ipyrad2-0.1.9/tests/test_analysis_popgen.py +888 -0
  157. ipyrad2-0.1.9/tests/test_analysis_snmf.py +136 -0
  158. ipyrad2-0.1.9/tests/test_analysis_snp_imputer.py +213 -0
  159. ipyrad2-0.1.9/tests/test_analysis_snp_tools.py +956 -0
  160. ipyrad2-0.1.9/tests/test_analysis_treeslider.py +724 -0
  161. ipyrad2-0.1.9/tests/test_assemble_callable_regions.py +410 -0
  162. ipyrad2-0.1.9/tests/test_assemble_paralogs.py +329 -0
  163. ipyrad2-0.1.9/tests/test_assemble_read_filters.py +6210 -0
  164. ipyrad2-0.1.9/tests/test_cli_analysis_help.py +852 -0
  165. ipyrad2-0.1.9/tests/test_cli_assemble_help.py +221 -0
  166. ipyrad2-0.1.9/tests/test_cli_command_log.py +117 -0
  167. ipyrad2-0.1.9/tests/test_cli_demux_help.py +213 -0
  168. ipyrad2-0.1.9/tests/test_cli_denovo_help.py +117 -0
  169. ipyrad2-0.1.9/tests/test_cli_lazy_imports.py +148 -0
  170. ipyrad2-0.1.9/tests/test_cli_map_help.py +99 -0
  171. ipyrad2-0.1.9/tests/test_cli_trim_help.py +153 -0
  172. ipyrad2-0.1.9/tests/test_demux_interrupt.py +343 -0
  173. ipyrad2-0.1.9/tests/test_demux_matching.py +2306 -0
  174. ipyrad2-0.1.9/tests/test_denovo.py +3902 -0
  175. ipyrad2-0.1.9/tests/test_kmers.py +506 -0
  176. ipyrad2-0.1.9/tests/test_legacy_map_bams.py +353 -0
  177. ipyrad2-0.1.9/tests/test_map_samples_prep.py +293 -0
  178. ipyrad2-0.1.9/tests/test_map_stats.py +157 -0
  179. ipyrad2-0.1.9/tests/test_mapper.py +582 -0
  180. ipyrad2-0.1.9/tests/test_names.py +369 -0
  181. ipyrad2-0.1.9/tests/test_parallel_ctrl_c.py +239 -0
  182. ipyrad2-0.1.9/tests/test_parallel_pipeline.py +240 -0
  183. ipyrad2-0.1.9/tests/test_parallel_pool.py +402 -0
  184. ipyrad2-0.1.9/tests/test_parallel_streaming.py +128 -0
  185. ipyrad2-0.1.9/tests/test_pops.py +91 -0
  186. ipyrad2-0.1.9/tests/test_profiling.py +112 -0
  187. ipyrad2-0.1.9/tests/test_progress_logging.py +100 -0
  188. ipyrad2-0.1.9/tests/test_trim_fastqs.py +768 -0
  189. ipyrad2-0.1.9/tests/test_trim_fastqs_outputs.py +1029 -0
  190. ipyrad2-0.1.9/tests/test_version.py +23 -0
  191. ipyrad2-0.1.9/zensical.toml +33 -0
@@ -0,0 +1,51 @@
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+ name: Publish PyPI Release
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+
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+ on:
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+ push:
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+ tags:
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+ - "v*"
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+
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+ permissions:
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+ contents: read
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+ id-token: write
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+
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+ jobs:
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+ build-and-publish:
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+ runs-on: ubuntu-latest
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+
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+ steps:
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+ - name: Check out repository
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+ uses: actions/checkout@v4
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+ with:
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+ fetch-depth: 0
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v5
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+ with:
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+ python-version: "3.12"
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+
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+ - name: Classify tag
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+ id: tag_kind
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+ shell: bash
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+ run: |
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+ tag="${GITHUB_REF_NAME}"
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+ if [[ "$tag" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
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+ echo "stable=true" >> "$GITHUB_OUTPUT"
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+ else
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+ echo "stable=false" >> "$GITHUB_OUTPUT"
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+ fi
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+
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+ - name: Install build tooling
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+ run: |
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+ python -m pip install --upgrade pip
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+ python -m pip install build
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+
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+ - name: Build distributions
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+ run: python -m build
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+
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+ - name: Show built artifacts
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+ run: ls -lh dist
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+
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+ - name: Publish stable release to PyPI
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+ if: steps.tag_kind.outputs.stable == 'true'
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+
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+ ## ignore these files
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+ params-*
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+ *.pyc
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+ *~
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+ .DS_Store
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+ *.ipynb_checkpoints
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+ .ipynb_checkpoints
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+ build
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+ dist
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+ *.egg-info
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+ *.sublime-*
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+ __pycache__
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+