snk-cli 0.6.2__tar.gz → 0.7.0__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 (71) hide show
  1. {snk_cli-0.6.2 → snk_cli-0.7.0}/PKG-INFO +1 -1
  2. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/__about__.py +1 -1
  3. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/config/config.py +8 -0
  4. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/snk.yaml +1 -0
  5. {snk_cli-0.6.2 → snk_cli-0.7.0}/.github/workflows/publish.yml +0 -0
  6. {snk_cli-0.6.2 → snk_cli-0.7.0}/.github/workflows/tests.yml +0 -0
  7. {snk_cli-0.6.2 → snk_cli-0.7.0}/.gitignore +0 -0
  8. {snk_cli-0.6.2 → snk_cli-0.7.0}/LICENSE.txt +0 -0
  9. {snk_cli-0.6.2 → snk_cli-0.7.0}/README.md +0 -0
  10. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/index.md +0 -0
  11. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/cli.md +0 -0
  12. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/config.md +0 -0
  13. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/dynamic_typer.md +0 -0
  14. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/options.md +0 -0
  15. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/subcommands.md +0 -0
  16. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/testing.md +0 -0
  17. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/utils.md +0 -0
  18. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/validate.md +0 -0
  19. {snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/workflow.md +0 -0
  20. {snk_cli-0.6.2 → snk_cli-0.7.0}/mkdocs.yml +0 -0
  21. {snk_cli-0.6.2 → snk_cli-0.7.0}/pyproject.toml +0 -0
  22. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/__init__.py +0 -0
  23. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/cli.py +0 -0
  24. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/conda.py +0 -0
  25. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/config/__init__.py +0 -0
  26. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/config/utils.py +0 -0
  27. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/dynamic_typer.py +0 -0
  28. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/options/__init__.py +0 -0
  29. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/options/option.py +0 -0
  30. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/options/utils.py +0 -0
  31. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/__init__.py +0 -0
  32. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/config.py +0 -0
  33. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/env.py +0 -0
  34. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/profile.py +0 -0
  35. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/run.py +0 -0
  36. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/subcommands/script.py +0 -0
  37. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/testing.py +0 -0
  38. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/utils.py +0 -0
  39. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/validate.py +0 -0
  40. {snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/workflow.py +0 -0
  41. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/__init__.py +0 -0
  42. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/conftest.py +0 -0
  43. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/artic_v4.1.bed +0 -0
  44. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/config.yaml +0 -0
  45. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/cov.fasta +0 -0
  46. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/print_config/Snakefile +0 -0
  47. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/print_config/cli.py +0 -0
  48. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/print_config/config.yaml +0 -0
  49. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/print_config/snk.yaml +0 -0
  50. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/cli.py +0 -0
  51. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/config.yaml +0 -0
  52. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/resources/data.txt +0 -0
  53. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/things/__about__.py +0 -0
  54. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/workflow/Snakefile +0 -0
  55. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/workflow/envs/wget.yml +0 -0
  56. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/workflow/profiles/base/config.yaml +0 -0
  57. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/workflow/profiles/slurm/config.yaml +0 -0
  58. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/workflow/scripts/hello.py +0 -0
  59. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_SnkConfig.py +0 -0
  60. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/__init__.py +0 -0
  61. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_dynamic_options.py +0 -0
  62. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_profile.py +0 -0
  63. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_run.py +0 -0
  64. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_snk_config.py +0 -0
  65. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_subcommands.py +0 -0
  66. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_validate.py +0 -0
  67. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_cli/test_workflow_cli.py +0 -0
  68. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_conda_env.py +0 -0
  69. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_dynamic_typer.py +0 -0
  70. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_types.py +0 -0
  71. {snk_cli-0.6.2 → snk_cli-0.7.0}/tests/utils.py +0 -0
{snk_cli-0.6.2 → snk_cli-0.7.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: snk-cli
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- Version: 0.6.2
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+ Version: 0.7.0
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  Project-URL: Documentation, https://github.com/wytamma/snk-cli#readme
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  Project-URL: Issues, https://github.com/wytamma/snk-cli/issues
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  Project-URL: Source, https://github.com/wytamma/snk-cli
{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/__about__.py RENAMED
@@ -1,4 +1,4 @@
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  # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
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  #
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  # SPDX-License-Identifier: MIT
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- __version__ = "0.6.2"
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+ __version__ = "0.7.0"
{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/config/config.py RENAMED
@@ -112,6 +112,14 @@ class SnkConfig:
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  # TODO: remove conda_required in the future
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  snk_config_dict["conda"] = snk_config_dict["conda_required"]
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  del snk_config_dict["conda_required"]
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+ # print warning about any invalid keys
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+ fields = set(cls.__dict__["__dataclass_fields__"])
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+ invalid_config_keys = set(snk_config_dict.keys()) - fields
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+ if invalid_config_keys:
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+ import warnings
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+ warnings.warn(f"invalid keys in `snk.yaml` file: {invalid_config_keys}.")
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+ # filer out any invalid keys
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+ snk_config_dict = {k: v for k, v in snk_config_dict.items() if k in fields}
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  snk_config = cls(**snk_config_dict)
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  snk_config.resources = [
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  snk_config_path.parent / resource for resource in snk_config.resources
{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/workflow/snk.yaml RENAMED
@@ -1,4 +1,5 @@
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  art: null
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+ invalid: false
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  cli:
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  hidden:
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  hidden: true
{snk_cli-0.6.2 → snk_cli-0.7.0}/.gitignore RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/LICENSE.txt RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/README.md RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/docs/index.md RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/cli.md RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/docs/reference/utils.md RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/mkdocs.yml RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/pyproject.toml RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/__init__.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/cli.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/conda.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/testing.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/utils.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/validate.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/src/snk_cli/workflow.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/__init__.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/conftest.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/config.yaml RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/data/cov.fasta RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_SnkConfig.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_conda_env.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/test_types.py RENAMED
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{snk_cli-0.6.2 → snk_cli-0.7.0}/tests/utils.py RENAMED
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