loqusdb 2.7.22__tar.gz → 2.7.23__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 (95) hide show
  1. {loqusdb-2.7.22 → loqusdb-2.7.23}/PKG-INFO +7 -3
  2. {loqusdb-2.7.22 → loqusdb-2.7.23}/README.md +3 -0
  3. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/__init__.py +1 -1
  4. {loqusdb-2.7.22 → loqusdb-2.7.23}/pyproject.toml +12 -3
  5. {loqusdb-2.7.22 → loqusdb-2.7.23}/LICENSE +0 -0
  6. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/__main__.py +0 -0
  7. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/build_models/__init__.py +0 -0
  8. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/build_models/case.py +0 -0
  9. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/build_models/profile_variant.py +0 -0
  10. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/build_models/variant.py +0 -0
  11. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/__init__.py +0 -0
  12. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/annotate.py +0 -0
  13. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/cli.py +0 -0
  14. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/delete.py +0 -0
  15. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/export.py +0 -0
  16. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/identity.py +0 -0
  17. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/load.py +0 -0
  18. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/load_profile.py +0 -0
  19. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/migrate.py +0 -0
  20. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/restore.py +0 -0
  21. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/update.py +0 -0
  22. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/view.py +0 -0
  23. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/commands/wipe.py +0 -0
  24. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/constants/__init__.py +0 -0
  25. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/exceptions/__init__.py +0 -0
  26. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/exceptions/case.py +0 -0
  27. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/exceptions/profile.py +0 -0
  28. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/exceptions/vcf.py +0 -0
  29. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/log.py +0 -0
  30. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/models/__init__.py +0 -0
  31. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/models/case.py +0 -0
  32. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/models/identity.py +0 -0
  33. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/models/profile_variant.py +0 -0
  34. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/models/variant.py +0 -0
  35. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/__init__.py +0 -0
  36. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/__init__.py +0 -0
  37. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/adapter.py +0 -0
  38. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/case.py +0 -0
  39. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/profile_variant.py +0 -0
  40. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/structural_variant.py +0 -0
  41. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/plugins/mongo/variant.py +0 -0
  42. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/resources/__init__.py +0 -0
  43. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/resources/loqusdb.20181005.gz +0 -0
  44. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/resources/maf_50_sites_GRCh37.vcf.gz +0 -0
  45. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/resources/maf_50_sites_GRCh38.vcf.gz +0 -0
  46. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/__init__.py +0 -0
  47. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/annotate.py +0 -0
  48. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/case.py +0 -0
  49. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/delete.py +0 -0
  50. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/load.py +0 -0
  51. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/migrate.py +0 -0
  52. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/profiling.py +0 -0
  53. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/update.py +0 -0
  54. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/variant.py +0 -0
  55. {loqusdb-2.7.22 → loqusdb-2.7.23}/loqusdb/utils/vcf.py +0 -0
  56. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/build_models/test_build_case.py +0 -0
  57. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/build_models/test_build_variant.py +0 -0
  58. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/build_models/test_is_greater.py +0 -0
  59. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/commands/test_export.py +0 -0
  60. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/commands/test_identity.py +0 -0
  61. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/commands/test_view.py +0 -0
  62. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/conftest.py +0 -0
  63. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/643594.clinical.SV.vcf +0 -0
  64. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/643594.clinical.vcf.gz +0 -0
  65. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/double_variant.vcf +0 -0
  66. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/funny_trio.ped +0 -0
  67. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/profile_snv.vcf +0 -0
  68. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/recessive_trio.ped +0 -0
  69. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/test.SV.vcf +0 -0
  70. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/test.vcf +0 -0
  71. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/test.vcf.gz +0 -0
  72. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/test.vcf.gz.tbi +0 -0
  73. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/fixtures/unsorted.vcf +0 -0
  74. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/functional/test_cli.py +0 -0
  75. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_case_operations.py +0 -0
  76. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_connect.py +0 -0
  77. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_flask_extension.py +0 -0
  78. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_get_sv.py +0 -0
  79. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_load_svs.py +0 -0
  80. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/plugins/mongo/test_variant_operations.py +0 -0
  81. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_case.py +0 -0
  82. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_delete.py +0 -0
  83. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_delete_family.py +0 -0
  84. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_delete_variant.py +0 -0
  85. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_get_family.py +0 -0
  86. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_load_database.py +0 -0
  87. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_load_family.py +0 -0
  88. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_load_variants.py +0 -0
  89. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_migrate.py +0 -0
  90. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/utils/test_profiling.py +0 -0
  91. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/vcf_tools/test_check_par.py +0 -0
  92. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/vcf_tools/test_check_vcf.py +0 -0
  93. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/vcf_tools/test_format_sv_variant.py +0 -0
  94. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/vcf_tools/test_format_variant.py +0 -0
  95. {loqusdb-2.7.22 → loqusdb-2.7.23}/tests/vcf_tools/test_vcf.py +0 -0
@@ -1,10 +1,11 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: loqusdb
3
- Version: 2.7.22
3
+ Version: 2.7.23
4
4
  Summary: A simple observation count database
5
5
  License: MIT
6
- Author: Your Name
7
- Author-email: you@example.com
6
+ Author: Mans Magnuson
7
+ Author-email: monsunas@gmail.com
8
+ Maintainer: Clinical Genomics Bioinformatics Team
8
9
  Requires-Python: >=3.12,<4.0
9
10
  Classifier: License :: OSI Approved :: MIT License
10
11
  Classifier: Programming Language :: Python :: 3
@@ -34,6 +35,8 @@ Right now **Locusdb** uses [mongodb][mongodb] as backend for
34
35
  storing variants, but there should not be a huge difference to use another
35
36
  database manager.
36
37
 
38
+ Find more detailed instructions and examples in the [documentation][docs].
39
+
37
40
  ## Installation ##
38
41
 
39
42
 
@@ -166,6 +169,7 @@ The collections are defined as follows:
166
169
  }
167
170
  ```
168
171
 
172
+ [docs]: https://clinical-genomics.github.io/loqusdb
169
173
  [mongodb]: https://www.mongodb.org
170
174
  [publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
171
175
  [pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square
@@ -10,6 +10,8 @@ Right now **Locusdb** uses [mongodb][mongodb] as backend for
10
10
  storing variants, but there should not be a huge difference to use another
11
11
  database manager.
12
12
 
13
+ Find more detailed instructions and examples in the [documentation][docs].
14
+
13
15
  ## Installation ##
14
16
 
15
17
 
@@ -142,6 +144,7 @@ The collections are defined as follows:
142
144
  }
143
145
  ```
144
146
 
147
+ [docs]: https://clinical-genomics.github.io/loqusdb
145
148
  [mongodb]: https://www.mongodb.org
146
149
  [publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
147
150
  [pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square
@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
4
4
 
5
5
  logger = logging.getLogger(__name__)
6
6
 
7
- __version__ = "2.7.22"
7
+ __version__ = "2.7.23"
8
8
 
9
9
  INDEXES = {
10
10
  "variant": [
@@ -1,10 +1,14 @@
1
- [tool.poetry]
1
+ [project]
2
2
  name = "loqusdb"
3
- version = "2.7.22"
3
+
4
4
  description = "A simple observation count database"
5
- authors = ["Your Name <you@example.com>"]
5
+ authors = [{name="Mans Magnuson", email="monsunas@gmail.com"}, {name="Adam Rosenbaum", email="adam.rosenbaum@regionvasterbotten.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Jesper Eisfeldt", email="jesper.eisfeldt@scilifelab.se"}, {name="Henrik Stranneheim"},]
6
+ maintainers = [ {name="Clinical Genomics Bioinformatics Team"}, {name="Clinical Genomics System Development Team"}, {name="Clinical Genomics Scout Team"}]
6
7
  license = "MIT"
7
8
  readme = "README.md"
9
+ version = "2.7.23"
10
+
11
+ [tool.poetry]
8
12
  include = [
9
13
  "README.md",
10
14
  "loqusdb/**/*",
@@ -31,6 +35,11 @@ pre-commit = "*"
31
35
  pytest = "*"
32
36
  pytest-cov = "*"
33
37
 
38
+ [tool.poetry.group.docs.dependencies]
39
+ mkdocs = "*"
40
+ mkdocs-material = "*"
41
+ markdown-include = "*"
42
+
34
43
  [tool.poetry.scripts]
35
44
  loqusdb = "loqusdb.commands.cli:cli"
36
45
 
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes
File without changes