gsMap 1.71.1__tar.gz → 1.71.2__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 (76) hide show
  1. {gsmap-1.71.1 → gsmap-1.71.2}/.github/workflows/publish-to-pypi.yml +96 -96
  2. {gsmap-1.71.1 → gsmap-1.71.2}/.gitignore +257 -257
  3. {gsmap-1.71.1 → gsmap-1.71.2}/LICENSE +21 -21
  4. {gsmap-1.71.1 → gsmap-1.71.2}/PKG-INFO +3 -3
  5. {gsmap-1.71.1 → gsmap-1.71.2}/README.md +46 -46
  6. {gsmap-1.71.1 → gsmap-1.71.2}/docs/Makefile +20 -20
  7. {gsmap-1.71.1/visualization_web_docs → gsmap-1.71.2/docs}/make.bat +35 -35
  8. {gsmap-1.71.1 → gsmap-1.71.2}/docs/requirements.txt +2 -2
  9. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/_static/schematic.svg +13633 -13633
  10. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/cauchy_combination.rst +8 -8
  11. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/find_latent_representations.rst +8 -8
  12. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/format_sumstats.rst +8 -8
  13. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/generate_ldscore.rst +8 -8
  14. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/latent_to_gene.rst +8 -8
  15. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/quick_mode.rst +7 -7
  16. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/report.rst +8 -8
  17. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api/spatial_ldsc.rst +8 -8
  18. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/api.rst +81 -81
  19. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/cortex/Cortex_151507_Height.json +0 -0
  20. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/cortex/Cortex_151507_IQ.json +0 -0
  21. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/cortex/Cortex_151507_MCHC.json +0 -0
  22. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/cortex/Cortex_151507_SCZ.json +0 -0
  23. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/mouse_embryo/E16.5_E1S1_Height.json +0 -0
  24. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/mouse_embryo/E16.5_E1S1_IQ.json +0 -0
  25. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/mouse_embryo/E16.5_E1S1_MCHC.json +0 -0
  26. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/mouse_embryo/E16.5_E1S1_SCZ.json +0 -0
  27. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/charts/test.json +16 -16
  28. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/conf.py +55 -55
  29. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/data.rst +63 -63
  30. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/data_format.md +63 -63
  31. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/index.rst +68 -68
  32. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/install.rst +26 -26
  33. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/mouse.rst +5 -5
  34. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/mouse_example.md +264 -264
  35. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/quick_mode.md +140 -140
  36. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/release.rst +7 -7
  37. {gsmap-1.71.1 → gsmap-1.71.2}/docs/source/tutorials.rst +29 -29
  38. {gsmap-1.71.1 → gsmap-1.71.2}/pyproject.toml +83 -83
  39. {gsmap-1.71.1 → gsmap-1.71.2}/schematic.png +0 -0
  40. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/GNN/__init__.py +0 -0
  41. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/GNN/adjacency_matrix.py +75 -75
  42. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/GNN/model.py +90 -90
  43. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/GNN/train.py +0 -0
  44. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/__init__.py +5 -5
  45. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/__main__.py +2 -2
  46. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/cauchy_combination_test.py +141 -141
  47. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/config.py +806 -805
  48. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/diagnosis.py +274 -273
  49. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/find_latent_representation.py +139 -133
  50. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/format_sumstats.py +407 -407
  51. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/generate_ldscore.py +618 -618
  52. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/latent_to_gene.py +252 -234
  53. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/main.py +31 -31
  54. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/report.py +160 -160
  55. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/run_all_mode.py +194 -194
  56. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/setup.py +0 -0
  57. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/spatial_ldsc_multiple_sumstats.py +360 -380
  58. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/templates/report_template.html +198 -198
  59. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/__init__.py +0 -0
  60. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/generate_r2_matrix.py +735 -735
  61. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/jackknife.py +514 -514
  62. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/make_annotations.py +518 -518
  63. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/manhattan_plot.py +639 -639
  64. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/utils/regression_read.py +294 -294
  65. {gsmap-1.71.1 → gsmap-1.71.2}/src/gsMap/visualize.py +198 -198
  66. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/Makefile +20 -20
  67. {gsmap-1.71.1/docs → gsmap-1.71.2/visualization_web_docs}/make.bat +35 -35
  68. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/requirements.txt +2 -2
  69. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/raw1_add_txt.svg +37003 -37003
  70. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/raw2_add_txt.svg +29429 -29429
  71. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/raw3_add_txt.svg +36689 -36689
  72. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/raw4_add_txt.svg +17587 -17587
  73. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/raw5_add_txt.svg +20469 -20469
  74. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/_static/schematic.svg +13633 -13633
  75. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/conf.py +57 -57
  76. {gsmap-1.71.1 → gsmap-1.71.2}/visualization_web_docs/source/index.rst +44 -44
{gsmap-1.71.1 → gsmap-1.71.2}/.github/workflows/publish-to-pypi.yml RENAMED
@@ -1,96 +1,96 @@
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- name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
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-
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- on: push
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-
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- jobs:
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- build:
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- name: Build distribution 📦
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- runs-on: ubuntu-latest
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-
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- steps:
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- - uses: actions/checkout@v4
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- - name: Set up Python
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- uses: actions/setup-python@v4
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- with:
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- python-version: "3.x"
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- - name: Install pypa/build
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- run: >-
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- python3 -m
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- pip install
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- flit
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- --user
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- - name: Build a binary wheel and a source tarball
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- run: |
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- flit build
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- ls -lh dist
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- - name: Store the distribution packages
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- if: startsWith(github.ref, 'refs/tags/') # store only on tag pushes
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- uses: actions/upload-artifact@v3
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- with:
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- name: python-package-distributions
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- path: dist/
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-
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- publish-to-pypi:
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- name: >-
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- Publish Python 🐍 distribution 📦 to PyPI
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- if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
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- needs:
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- - build
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- runs-on: ubuntu-latest
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- environment:
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- name: pypi
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- url: https://pypi.org/p/gsMap
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- permissions:
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- id-token: write # IMPORTANT: mandatory for trusted publishing
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-
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- steps:
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- - name: Download all the dists
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- uses: actions/download-artifact@v3
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- with:
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- name: python-package-distributions
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- path: dist/
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- - name: Publish distribution 📦 to PyPI
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- uses: pypa/gh-action-pypi-publish@release/v1
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-
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- github-release:
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- name: >-
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- Sign the Python 🐍 distribution 📦 with Sigstore
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- and upload them to GitHub Release
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- needs:
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- - publish-to-pypi
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- runs-on: ubuntu-latest
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-
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- permissions:
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- contents: write # IMPORTANT: mandatory for making GitHub Releases
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- id-token: write # IMPORTANT: mandatory for sigstore
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-
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- steps:
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- - name: Download all the dists
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- uses: actions/download-artifact@v3
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- with:
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- name: python-package-distributions
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- path: dist/
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- - name: Sign the dists with Sigstore
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- uses: sigstore/gh-action-sigstore-python@v1.2.3
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- with:
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- inputs: >-
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- ./dist/*.tar.gz
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- ./dist/*.whl
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- - name: Create GitHub Release
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- env:
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- GITHUB_TOKEN: ${{ github.token }}
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- run: >-
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- gh release create
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- '${{ github.ref_name }}'
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- --repo '${{ github.repository }}'
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- --notes ""
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- - name: Upload artifact signatures to GitHub Release
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- env:
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- GITHUB_TOKEN: ${{ github.token }}
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- # Upload to GitHub Release using the `gh` CLI.
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- # `dist/` contains the built packages, and the
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- # sigstore-produced signatures and certificates.
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- run: >-
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- gh release upload
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- '${{ github.ref_name }}' dist/**
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- --repo '${{ github.repository }}'
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+ name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
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+
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+ on: push
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+
5
+ jobs:
6
+ build:
7
+ name: Build distribution 📦
8
+ runs-on: ubuntu-latest
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+
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+ steps:
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+ - uses: actions/checkout@v4
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+ - name: Set up Python
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+ uses: actions/setup-python@v4
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+ with:
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+ python-version: "3.x"
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+ - name: Install pypa/build
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+ run: >-
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+ python3 -m
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+ pip install
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+ flit
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+ --user
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+ - name: Build a binary wheel and a source tarball
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+ run: |
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+ flit build
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+ ls -lh dist
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+ - name: Store the distribution packages
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+ if: startsWith(github.ref, 'refs/tags/') # store only on tag pushes
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+ uses: actions/upload-artifact@v3
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+ with:
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+ name: python-package-distributions
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+ path: dist/
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+
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+ publish-to-pypi:
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+ name: >-
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+ Publish Python 🐍 distribution 📦 to PyPI
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+ if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
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+ needs:
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+ - build
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+ runs-on: ubuntu-latest
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+ environment:
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+ name: pypi
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+ url: https://pypi.org/p/gsMap
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+ permissions:
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+ id-token: write # IMPORTANT: mandatory for trusted publishing
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+
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+ steps:
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+ - name: Download all the dists
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+ uses: actions/download-artifact@v3
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+ with:
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+ name: python-package-distributions
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+ path: dist/
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+ - name: Publish distribution 📦 to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+
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+ github-release:
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+ name: >-
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+ Sign the Python 🐍 distribution 📦 with Sigstore
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+ and upload them to GitHub Release
59
+ needs:
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+ - publish-to-pypi
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+ runs-on: ubuntu-latest
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+
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+ permissions:
64
+ contents: write # IMPORTANT: mandatory for making GitHub Releases
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+ id-token: write # IMPORTANT: mandatory for sigstore
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+
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+ steps:
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+ - name: Download all the dists
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+ uses: actions/download-artifact@v3
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+ with:
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+ name: python-package-distributions
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+ path: dist/
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+ - name: Sign the dists with Sigstore
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+ uses: sigstore/gh-action-sigstore-python@v1.2.3
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+ with:
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+ inputs: >-
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+ ./dist/*.tar.gz
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+ ./dist/*.whl
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+ - name: Create GitHub Release
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+ env:
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+ GITHUB_TOKEN: ${{ github.token }}
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+ run: >-
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+ gh release create
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+ '${{ github.ref_name }}'
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+ --repo '${{ github.repository }}'
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+ --notes ""
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+ - name: Upload artifact signatures to GitHub Release
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+ env:
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+ GITHUB_TOKEN: ${{ github.token }}
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+ # Upload to GitHub Release using the `gh` CLI.
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+ # `dist/` contains the built packages, and the
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+ # sigstore-produced signatures and certificates.
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+ run: >-
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+ gh release upload
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+ '${{ github.ref_name }}' dist/**
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+ --repo '${{ github.repository }}'