snplib 1.0.7__tar.gz → 1.0.8__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 (186) hide show
  1. snplib-1.0.8/.github/workflows/linux.yml +34 -0
  2. snplib-1.0.8/.github/workflows/macos.yml +34 -0
  3. snplib-1.0.8/.github/workflows/windows.yml +34 -0
  4. snplib-1.0.8/.gitignore +25 -0
  5. snplib-1.0.8/.readthedocs.yaml +37 -0
  6. {snplib-1.0.7 → snplib-1.0.8}/LICENSE +674 -674
  7. {snplib-1.0.7/src/snplib.egg-info → snplib-1.0.8}/PKG-INFO +80 -97
  8. {snplib-1.0.7 → snplib-1.0.8}/README.md +59 -75
  9. snplib-1.0.8/__init__.py +0 -0
  10. snplib-1.0.8/docs/Makefile +20 -0
  11. snplib-1.0.8/docs/_build/doctrees/environment.pickle +0 -0
  12. snplib-1.0.8/docs/_build/doctrees/examples.doctree +0 -0
  13. snplib-1.0.8/docs/_build/doctrees/index.doctree +0 -0
  14. snplib-1.0.8/docs/_build/doctrees/install.doctree +0 -0
  15. snplib-1.0.8/docs/_build/doctrees/intro.doctree +0 -0
  16. snplib-1.0.8/docs/_build/doctrees/modules.doctree +0 -0
  17. snplib-1.0.8/docs/_build/doctrees/snplib.doctree +0 -0
  18. snplib-1.0.8/docs/_build/doctrees/snplib.finalreport.doctree +0 -0
  19. snplib-1.0.8/docs/_build/doctrees/snplib.format.doctree +0 -0
  20. snplib-1.0.8/docs/_build/doctrees/snplib.parentage.doctree +0 -0
  21. snplib-1.0.8/docs/_build/doctrees/snplib.statistics.doctree +0 -0
  22. snplib-1.0.8/docs/_build/doctrees/usage.doctree +0 -0
  23. snplib-1.0.8/docs/_build/html/.buildinfo +4 -0
  24. snplib-1.0.8/docs/_build/html/_modules/index.html +113 -0
  25. snplib-1.0.8/docs/_build/html/_modules/snplib/finalreport/_finalreport.html +368 -0
  26. snplib-1.0.8/docs/_build/html/_modules/snplib/format/_plink.html +422 -0
  27. snplib-1.0.8/docs/_build/html/_modules/snplib/format/_snp.html +233 -0
  28. snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_discov.html +213 -0
  29. snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_isagmark.html +126 -0
  30. snplib-1.0.8/docs/_build/html/_modules/snplib/parentage/_verif.html +202 -0
  31. snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_callrate.html +167 -0
  32. snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_freq.html +178 -0
  33. snplib-1.0.8/docs/_build/html/_modules/snplib/statistics/_snphwe.html +243 -0
  34. snplib-1.0.8/docs/_build/html/_sources/examples.rst.txt +647 -0
  35. snplib-1.0.8/docs/_build/html/_sources/index.rst.txt +23 -0
  36. snplib-1.0.8/docs/_build/html/_sources/install.rst.txt +26 -0
  37. snplib-1.0.8/docs/_build/html/_sources/intro.rst.txt +15 -0
  38. snplib-1.0.8/docs/_build/html/_sources/modules.rst.txt +7 -0
  39. snplib-1.0.8/docs/_build/html/_sources/snplib.finalreport.rst.txt +9 -0
  40. snplib-1.0.8/docs/_build/html/_sources/snplib.format.rst.txt +10 -0
  41. snplib-1.0.8/docs/_build/html/_sources/snplib.parentage.rst.txt +12 -0
  42. snplib-1.0.8/docs/_build/html/_sources/snplib.rst.txt +12 -0
  43. snplib-1.0.8/docs/_build/html/_sources/snplib.statistics.rst.txt +13 -0
  44. snplib-1.0.8/docs/_build/html/_sources/usage.rst.txt +26 -0
  45. snplib-1.0.8/docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js +123 -0
  46. snplib-1.0.8/docs/_build/html/_static/basic.css +925 -0
  47. snplib-1.0.8/docs/_build/html/_static/css/badge_only.css +1 -0
  48. snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  49. snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  50. snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  51. snplib-1.0.8/docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  52. snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.eot +0 -0
  53. snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.svg +2671 -0
  54. snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  55. snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff +0 -0
  56. snplib-1.0.8/docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  57. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold-italic.woff +0 -0
  58. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  59. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold.woff +0 -0
  60. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-bold.woff2 +0 -0
  61. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal-italic.woff +0 -0
  62. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  63. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal.woff +0 -0
  64. snplib-1.0.8/docs/_build/html/_static/css/fonts/lato-normal.woff2 +0 -0
  65. snplib-1.0.8/docs/_build/html/_static/css/theme.css +4 -0
  66. snplib-1.0.8/docs/_build/html/_static/doctools.js +156 -0
  67. snplib-1.0.8/docs/_build/html/_static/documentation_options.js +13 -0
  68. snplib-1.0.8/docs/_build/html/_static/file.png +0 -0
  69. snplib-1.0.8/docs/_build/html/_static/jquery.js +2 -0
  70. snplib-1.0.8/docs/_build/html/_static/js/badge_only.js +1 -0
  71. snplib-1.0.8/docs/_build/html/_static/js/html5shiv-printshiv.min.js +4 -0
  72. snplib-1.0.8/docs/_build/html/_static/js/html5shiv.min.js +4 -0
  73. snplib-1.0.8/docs/_build/html/_static/js/theme.js +1 -0
  74. snplib-1.0.8/docs/_build/html/_static/language_data.js +199 -0
  75. snplib-1.0.8/docs/_build/html/_static/logo.png +0 -0
  76. snplib-1.0.8/docs/_build/html/_static/minus.png +0 -0
  77. snplib-1.0.8/docs/_build/html/_static/plus.png +0 -0
  78. snplib-1.0.8/docs/_build/html/_static/pygments.css +75 -0
  79. snplib-1.0.8/docs/_build/html/_static/searchtools.js +574 -0
  80. snplib-1.0.8/docs/_build/html/_static/sphinx_highlight.js +154 -0
  81. snplib-1.0.8/docs/_build/html/examples.html +725 -0
  82. snplib-1.0.8/docs/_build/html/genindex.html +352 -0
  83. snplib-1.0.8/docs/_build/html/index.html +143 -0
  84. snplib-1.0.8/docs/_build/html/install.html +141 -0
  85. snplib-1.0.8/docs/_build/html/intro.html +126 -0
  86. snplib-1.0.8/docs/_build/html/modules.html +127 -0
  87. snplib-1.0.8/docs/_build/html/objects.inv +0 -0
  88. snplib-1.0.8/docs/_build/html/py-modindex.html +144 -0
  89. snplib-1.0.8/docs/_build/html/search.html +124 -0
  90. snplib-1.0.8/docs/_build/html/searchindex.js +1 -0
  91. snplib-1.0.8/docs/_build/html/snplib.finalreport.html +265 -0
  92. snplib-1.0.8/docs/_build/html/snplib.format.html +407 -0
  93. snplib-1.0.8/docs/_build/html/snplib.html +155 -0
  94. snplib-1.0.8/docs/_build/html/snplib.parentage.html +230 -0
  95. snplib-1.0.8/docs/_build/html/snplib.statistics.html +245 -0
  96. snplib-1.0.8/docs/_build/html/usage.html +135 -0
  97. snplib-1.0.8/docs/conf.py +56 -0
  98. snplib-1.0.8/docs/examples.rst +647 -0
  99. snplib-1.0.8/docs/index.rst +23 -0
  100. snplib-1.0.8/docs/install.rst +26 -0
  101. snplib-1.0.8/docs/intro.rst +15 -0
  102. snplib-1.0.8/docs/logo.png +0 -0
  103. snplib-1.0.8/docs/make.bat +35 -0
  104. snplib-1.0.8/docs/modules.rst +7 -0
  105. snplib-1.0.8/docs/snplib.finalreport.rst +9 -0
  106. snplib-1.0.8/docs/snplib.format.rst +10 -0
  107. snplib-1.0.8/docs/snplib.parentage.rst +12 -0
  108. snplib-1.0.8/docs/snplib.rst +12 -0
  109. snplib-1.0.8/docs/snplib.statistics.rst +13 -0
  110. snplib-1.0.8/docs/usage.rst +26 -0
  111. snplib-1.0.8/iconlib.png +0 -0
  112. {snplib-1.0.7 → snplib-1.0.8}/pyproject.toml +44 -32
  113. snplib-1.0.8/requirements.txt +14 -0
  114. {snplib-1.0.7 → snplib-1.0.8}/setup.cfg +4 -4
  115. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/__init__.py +8 -8
  116. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/finalreport/__init__.py +7 -7
  117. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/finalreport/_finalreport.py +251 -251
  118. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/__init__.py +19 -19
  119. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/__settings.py +7 -7
  120. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/_plink.py +305 -305
  121. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/format/_snp.py +113 -113
  122. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/__init__.py +15 -15
  123. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_discov.py +102 -102
  124. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_isagmark.py +15 -15
  125. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/parentage/_verif.py +91 -91
  126. snplib-1.0.8/src/snplib/parentage/isag_disc.pl +0 -0
  127. snplib-1.0.8/src/snplib/parentage/isag_verif.pl +0 -0
  128. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/__init__.py +16 -16
  129. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_callrate.py +59 -59
  130. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_freq.py +67 -67
  131. {snplib-1.0.7 → snplib-1.0.8}/src/snplib/statistics/_snphwe.py +132 -132
  132. {snplib-1.0.7 → snplib-1.0.8/src/snplib.egg-info}/PKG-INFO +80 -97
  133. snplib-1.0.8/src/snplib.egg-info/SOURCES.txt +183 -0
  134. {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/requires.txt +0 -1
  135. snplib-1.0.8/tests/__init__.py +0 -0
  136. {snplib-1.0.7/src/snplib/finalreport/tests → snplib-1.0.8/tests/finalreport}/__init__.py +7 -7
  137. snplib-1.0.8/tests/finalreport/files/fr/file1.txt +28 -0
  138. snplib-1.0.8/tests/finalreport/files/fr/file1.xlsx +0 -0
  139. snplib-1.0.8/tests/finalreport/files/fr/file2.txt +21 -0
  140. snplib-1.0.8/tests/finalreport/files/fr/file2.xlsx +0 -0
  141. snplib-1.0.8/tests/finalreport/files/fr/file3.txt +10 -0
  142. snplib-1.0.8/tests/finalreport/files/fr/file3.xlsx +0 -0
  143. snplib-1.0.8/tests/finalreport/files/fr/file4.txt +16 -0
  144. snplib-1.0.8/tests/finalreport/files/fr/file5.txt +0 -0
  145. snplib-1.0.8/tests/finalreport/files/fr/file5.xlsx +0 -0
  146. snplib-1.0.8/tests/finalreport/files/fr/file6.txt +28 -0
  147. snplib-1.0.8/tests/finalreport/files/fr/file6.xlsx +0 -0
  148. snplib-1.0.8/tests/finalreport/files/fr/file7.txt +28 -0
  149. snplib-1.0.8/tests/finalreport/files/fr/file7.xlsx +0 -0
  150. {snplib-1.0.7/src/snplib/finalreport/tests → snplib-1.0.8/tests/finalreport}/test_finalreport.py +215 -215
  151. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/__init__.py +7 -7
  152. snplib-1.0.8/tests/format/files/fplink/fam/file.pl +0 -0
  153. snplib-1.0.8/tests/format/files/fplink/fam/file2.pl +0 -0
  154. snplib-1.0.8/tests/format/files/fplink/fam/file3.pl +0 -0
  155. snplib-1.0.8/tests/format/files/fplink/fam/file4.pl +0 -0
  156. snplib-1.0.8/tests/format/files/fplink/lgen/file.pl +0 -0
  157. snplib-1.0.8/tests/format/files/fplink/map/file_bovinesnp50.csv +31 -0
  158. snplib-1.0.8/tests/format/files/fplink/ped/file.pl +0 -0
  159. snplib-1.0.8/tests/format/files/fplink/ped/file2.pl +0 -0
  160. snplib-1.0.8/tests/format/files/fplink/ped/file3.pl +0 -0
  161. snplib-1.0.8/tests/format/files/fplink/ped/file4.pl +0 -0
  162. snplib-1.0.8/tests/format/files/fsnp/file1.txt +35 -0
  163. snplib-1.0.8/tests/format/files/fsnp/file2.txt +35 -0
  164. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_fam.py +121 -121
  165. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_lgen.py +106 -106
  166. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_map.py +42 -42
  167. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_plink_ped.py +136 -136
  168. {snplib-1.0.7/src/snplib/format/tests → snplib-1.0.8/tests/format}/test_snp.py +128 -128
  169. {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/__init__.py +7 -7
  170. snplib-1.0.8/tests/parentage/data/parentage_test_disc.csv +623 -0
  171. snplib-1.0.8/tests/parentage/data/parentage_test_verf.csv +245 -0
  172. {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/test_discov.py +164 -164
  173. {snplib-1.0.7/src/snplib/parentage/tests → snplib-1.0.8/tests/parentage}/test_verif.py +160 -160
  174. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/__init__.py +7 -7
  175. snplib-1.0.8/tests/statistics/data/cr/file_cra.pl +0 -0
  176. snplib-1.0.8/tests/statistics/data/cr/file_crm.pl +0 -0
  177. snplib-1.0.8/tests/statistics/data/freq/etalon.txt +8 -0
  178. snplib-1.0.8/tests/statistics/data/freq/file.pl +0 -0
  179. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_callrate.py +171 -171
  180. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_freq_allele.py +87 -87
  181. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_freq_maf.py +17 -17
  182. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_hwe_t.py +41 -41
  183. {snplib-1.0.7/src/snplib/statistics/tests → snplib-1.0.8/tests/statistics}/test_snphwe.py +41 -41
  184. snplib-1.0.7/src/snplib.egg-info/SOURCES.txt +0 -40
  185. {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/dependency_links.txt +0 -0
  186. {snplib-1.0.7 → snplib-1.0.8}/src/snplib.egg-info/top_level.txt +0 -0
@@ -0,0 +1,34 @@
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+ name: Test on Linux
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+
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+ on:
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+ push:
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+ branches: ["dev_v1"]
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+
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+ pull_request:
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+ branches: ["main"]
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+
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+
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+ jobs:
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+ test_lin:
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+
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+ runs-on: ubuntu-latest
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+ strategy:
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+ fail-fast: false
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+
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+ matrix:
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+ python-version: ["3.10", "3.11", "3.12"]
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+
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+ steps:
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+ - uses: actions/checkout@v3
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+ - name: Set up Python ${{ matrix.python-version }}
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+ uses: actions/setup-python@v3
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ pip install -r requirements.txt
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+
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+ - name: Test with pytest
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+ run: pytest
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+ name: Test on MacOs
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+
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+ on:
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+ push:
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+ branches: ["dev_v1"]
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+
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+ pull_request:
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+ branches: ["main"]
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+
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+
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+ jobs:
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+ test_mac:
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+
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+ runs-on: macos-latest
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+ strategy:
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+ fail-fast: false
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+
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+ matrix:
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+ python-version: ['3.10', '3.11', '3.12']
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+
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+ steps:
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+ - uses: actions/checkout@v3
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+ - name: Set up Python ${{ matrix.python-version }}
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+ uses: actions/setup-python@v3
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ pip install -r requirements.txt
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+
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+ - name: Test with pytest
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+ run: pytest
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+ name: Test on Windows
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+
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+ on:
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+ push:
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+ branches: ["dev_v1"]
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+
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+ pull_request:
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+ branches: ["main"]
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+
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+
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+ jobs:
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+ test_wind:
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+
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+ runs-on: windows-latest
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+ strategy:
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+ fail-fast: false
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+
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+ matrix:
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+ python-version: ['3.10', '3.11', '3.12']
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+
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+ steps:
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+ - uses: actions/checkout@v3
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+ - name: Set up Python ${{ matrix.python-version }}
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+ uses: actions/setup-python@v3
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ pip install -r requirements.txt
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+
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+ - name: Test with pytest
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+ run: pytest
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+ /.venv
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+
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+ *.bz2
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+ *.jpg
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+ *.log
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+ *.html
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+ *.rar
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+ *.zip
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+ *.txt
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+ *.csv
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+ *.npz
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+ *.xlsx
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+ *.7z
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+ *.ipynb
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+ *.docx
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+
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+ !requirements.txt
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+ !/tests/*/**
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+ !/docs/*/**
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+
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+ *.idea*
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+ *__pycache__*
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+ *.pytest_cache*
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+ *.ipynb_checkpoints*
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+
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+ # Read the Docs configuration file for Sphinx projects
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+ # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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+
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+ # Required
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+ version: 2
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+
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+ # Set the OS, Python version and other tools you might need
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+ build:
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+ os: ubuntu-22.04
10
+ tools:
11
+ python: "3.11"
12
+ # You can also specify other tool versions:
13
+ # nodejs: "20"
14
+ # rust: "1.70"
15
+ # golang: "1.20"
16
+
17
+ # Build documentation in the "docs/" directory with Sphinx
18
+ sphinx:
19
+ builder: html
20
+ configuration: docs/conf.py
21
+ fail_on_warning: true
22
+ # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
23
+ # builder: "dirhtml"
24
+ # Fail on all warnings to avoid broken references
25
+ # fail_on_warning: true
26
+
27
+ # Optionally build your docs in additional formats such as PDF and ePub
28
+ # formats:
29
+ # - pdf
30
+ # - epub
31
+
32
+ # Optional but recommended, declare the Python requirements required
33
+ # to build your documentation
34
+ # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
35
+ python:
36
+ install:
37
+ - requirements: requirements.txt