pyjess 0.7.0a4__tar.gz → 0.7.0a5__tar.gz

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  1. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/CHANGELOG.md +8 -1
  2. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/PKG-INFO +1 -1
  3. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/TessAtom.c.patch +12 -2
  4. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/pyproject.toml +1 -1
  5. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.github/workflows/package.yml +0 -0
  6. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.github/workflows/requirements.txt +0 -0
  7. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.github/workflows/test.yml +0 -0
  8. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.gitignore +0 -0
  9. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.gitmodules +0 -0
  10. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/.readthedocs.yaml +0 -0
  11. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/CMakeLists.txt +0 -0
  12. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/CONTRIBUTING.md +0 -0
  13. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/COPYING +0 -0
  14. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/README.md +0 -0
  15. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/.gitignore +0 -0
  16. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/Makefile +0 -0
  17. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/_static/css/main.css +0 -0
  18. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/_static/js/custom-icon.js +0 -0
  19. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/_static/json/switcher.json +0 -0
  20. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/api/index.rst +0 -0
  21. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/api/jess.rst +0 -0
  22. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/api/molecule.rst +0 -0
  23. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/api/template.rst +0 -0
  24. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/conf.py +0 -0
  25. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/changes.md +0 -0
  26. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/contributing.md +0 -0
  27. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/copyright.rst +0 -0
  28. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/index.rst +0 -0
  29. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/install.rst +0 -0
  30. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/guide/optimizations.rst +0 -0
  31. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/index.rst +0 -0
  32. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/make.bat +0 -0
  33. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/docs/requirements.txt +0 -0
  34. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/__init__.pxd +0 -0
  35. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/annulus.pxd +0 -0
  36. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/atom.pxd +0 -0
  37. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/candidate_set.pxd +0 -0
  38. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/jess.pxd +0 -0
  39. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/join.pxd +0 -0
  40. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/kdtree.pxd +0 -0
  41. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/molecule.pxd +0 -0
  42. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/region.pxd +0 -0
  43. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/res_index.pxd +0 -0
  44. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/scanner.pxd +0 -0
  45. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/super.pxd +0 -0
  46. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/template.pxd +0 -0
  47. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/tess_atom.pxd +0 -0
  48. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/include/jess/tess_template.pxd +0 -0
  49. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Annulus.c.patch +0 -0
  50. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Annulus.h.patch +0 -0
  51. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Atom.c.patch +0 -0
  52. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Atom.h.patch +0 -0
  53. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Box.c.patch +0 -0
  54. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Box.h.patch +0 -0
  55. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/CMakeLists.txt.patch +0 -0
  56. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/CandidateSet.c.patch +0 -0
  57. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/CandidateSet.h.patch +0 -0
  58. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Jess.c.patch +0 -0
  59. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Jess.h.patch +0 -0
  60. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Join.c.patch +0 -0
  61. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Join.h.patch +0 -0
  62. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/KdTree.c.patch +0 -0
  63. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/KdTree.h.patch +0 -0
  64. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Main.c.patch +0 -0
  65. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Molecule.c.patch +0 -0
  66. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Molecule.h.patch +0 -0
  67. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/ResIndex.c.patch +0 -0
  68. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/ResIndex.h.patch +0 -0
  69. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Scanner.c.patch +0 -0
  70. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Scanner.h.patch +0 -0
  71. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Super.c.patch +0 -0
  72. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/Template.h.patch +0 -0
  73. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/TessAtom.h.patch +0 -0
  74. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/TessTemplate.c.patch +0 -0
  75. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/TessTemplate.h.patch +0 -0
  76. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/qselect.h.patch +0 -0
  77. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/pkg/aur/PKGBUILD.in +0 -0
  78. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/CMakeLists.txt +0 -0
  79. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/jess/CMakeLists.txt +0 -0
  80. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/.gitignore +0 -0
  81. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/CMakeLists.txt +0 -0
  82. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/__init__.py +0 -0
  83. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/_jess.pyi +0 -0
  84. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/_jess.pyx +0 -0
  85. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/py.typed +0 -0
  86. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/__init__.py +0 -0
  87. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/1.3.3.tpl +0 -0
  88. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/1AMY+1.3.3.txt +0 -0
  89. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/1AMY.cif +0 -0
  90. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/1AMY.pdb +0 -0
  91. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/1sur.qry +0 -0
  92. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/4.1.2.tpl +0 -0
  93. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/5ayx.EF.pdb +0 -0
  94. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/__init__.py +0 -0
  95. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/pdb1lnb.pdb +0 -0
  96. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/template_01.qry +0 -0
  97. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/data/template_02.qry +0 -0
  98. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_atom.py +0 -0
  99. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_hit.py +0 -0
  100. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_jess.py +0 -0
  101. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_molecule.py +0 -0
  102. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_template.py +0 -0
  103. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/test_template_atom.py +0 -0
  104. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/pyjess/tests/utils.py +0 -0
  105. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/scripts/apply_patch.py +0 -0
  106. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/scripts/cmake/CythonExtension.cmake +0 -0
  107. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/scripts/cmake/pystate_patch.h +0 -0
  108. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/src/scripts/generate_patches.py +0 -0
  109. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/.gitignore +0 -0
  110. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/README.md +0 -0
  111. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/examples/template_01.qry +0 -0
  112. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/examples/template_02.qry +0 -0
  113. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/examples/test_pdbs/pdb1lnb.ent +0 -0
  114. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/filter_output.py +0 -0
  115. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Annulus.c +0 -0
  116. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Annulus.h +0 -0
  117. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Atom.c +0 -0
  118. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Atom.h +0 -0
  119. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Jess.c +0 -0
  120. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Jess.h +0 -0
  121. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Join.c +0 -0
  122. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Join.h +0 -0
  123. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/KdTree.c +0 -0
  124. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/KdTree.h +0 -0
  125. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Main.c +0 -0
  126. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Molecule.c +0 -0
  127. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Molecule.h +0 -0
  128. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Region.c +0 -0
  129. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Region.h +0 -0
  130. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Scanner.c +0 -0
  131. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Scanner.h +0 -0
  132. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Super.c +0 -0
  133. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Super.h +0 -0
  134. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/Template.h +0 -0
  135. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/TessAtom.c +0 -0
  136. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/TessAtom.h +0 -0
  137. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/TessTemplate.c +0 -0
  138. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/TessTemplate.h +0 -0
  139. {pyjess-0.7.0a4 → pyjess-0.7.0a5}/vendor/jess/src/jess +0 -0
{pyjess-0.7.0a4 → pyjess-0.7.0a5}/CHANGELOG.md RENAMED
@@ -6,7 +6,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
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  ## [Unreleased]
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- [Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.4...HEAD
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+ [Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.5...HEAD
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+
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+
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+ ## [v0.7.0-alpha.5] - 2025-09-03
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+ [v0.7.0-alpha.5]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.5...v0.7.0-alpha.5
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+
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+ ### Fixed
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+ - Issue with new residue support introduced in `v0.7.0-alpha.4`.
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  ## [v0.7.0-alpha.4] - 2025-09-03
{pyjess-0.7.0a4 → pyjess-0.7.0a5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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  Name: pyjess
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- Version: 0.7.0a4
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+ Version: 0.7.0a5
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  Summary: Cython bindings and Python interface to JESS, a 3D template matching software.
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  Keywords: bioinformatics,structure,template,matching
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  Author-Email: Martin Larralde <martin.larralde@embl.de>
{pyjess-0.7.0a4 → pyjess-0.7.0a5}/patches/TessAtom.c.patch RENAMED
@@ -1,5 +1,5 @@
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  diff --git a/src/TessAtom.c b/src/TessAtom.c
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- index e1cce1a..eecf682 100644
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+ index e1cce1a..3f06daa 100644
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  --- a/src/TessAtom.c
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  +++ b/src/TessAtom.c
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  @@ -7,40 +7,13 @@
@@ -54,7 +54,7 @@ index e1cce1a..eecf682 100644
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  {
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  { 'A',"ALA" },
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  { 'C',"CYS" },
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- @@ -66,10 +39,12 @@ static const char *TessAtom_convertResidue(char p)
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+ @@ -66,18 +39,20 @@ static const char *TessAtom_convertResidue(char p)
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  { 'M',"MET" },
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  { 'N',"ASN" },
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  { 'P',"PRO" },
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  { 'V',"VAL" },
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  { 'W',"TRP" },
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  { 'Y',"TYR" },
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+ { 'X',"XXX" }
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+ };
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+
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+ - for(k=0; k<21 && p!=table[k].one; k++);
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+ - return k<21 ? table[k].three:NULL;
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+ + for(k=0; k<23 && p!=table[k].one; k++);
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+ + return k<23 ? table[k].three:NULL;
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+ }
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+
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+ TessAtom *TessAtom_create(const char *s)
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  @@ -91,7 +66,7 @@ TessAtom *TessAtom_create(const char *s)
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  int rq;
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  const char *q;
{pyjess-0.7.0a4 → pyjess-0.7.0a5}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
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  [project]
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  name = "pyjess"
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- version = "0.7.0-alpha.4"
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+ version = "0.7.0-alpha.5"
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  description = "Cython bindings and Python interface to JESS, a 3D template matching software."
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  readme = "README.md"
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  requires-python = ">=3.7"
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