gsMap 1.67__tar.gz → 1.71__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 (77) hide show
  1. {gsmap-1.67 → gsmap-1.71}/.github/workflows/publish-to-pypi.yml +120 -119
  2. {gsmap-1.67 → gsmap-1.71}/.gitignore +257 -257
  3. {gsmap-1.67 → gsmap-1.71}/LICENSE +21 -21
  4. {gsmap-1.67 → gsmap-1.71}/PKG-INFO +28 -22
  5. gsmap-1.71/README.md +46 -0
  6. {gsmap-1.67 → gsmap-1.71}/docs/Makefile +20 -20
  7. {gsmap-1.67 → gsmap-1.71}/docs/make.bat +35 -35
  8. {gsmap-1.67 → gsmap-1.71}/docs/requirements.txt +2 -2
  9. {gsmap-1.67 → gsmap-1.71}/docs/source/_static/schematic.svg +13633 -13633
  10. {gsmap-1.67 → gsmap-1.71}/docs/source/api/cauchy_combination.rst +8 -8
  11. {gsmap-1.67 → gsmap-1.71}/docs/source/api/find_latent_representations.rst +8 -8
  12. {gsmap-1.67 → gsmap-1.71}/docs/source/api/format_sumstats.rst +8 -8
  13. {gsmap-1.67 → gsmap-1.71}/docs/source/api/generate_ldscore.rst +8 -8
  14. {gsmap-1.67 → gsmap-1.71}/docs/source/api/latent_to_gene.rst +8 -8
  15. {gsmap-1.67 → gsmap-1.71}/docs/source/api/quick_mode.rst +7 -7
  16. {gsmap-1.67 → gsmap-1.71}/docs/source/api/report.rst +8 -8
  17. {gsmap-1.67 → gsmap-1.71}/docs/source/api/spatial_ldsc.rst +8 -8
  18. {gsmap-1.67 → gsmap-1.71}/docs/source/api.rst +81 -81
  19. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/cortex/Cortex_151507_Height.json +0 -0
  20. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/cortex/Cortex_151507_IQ.json +0 -0
  21. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/cortex/Cortex_151507_MCHC.json +0 -0
  22. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/cortex/Cortex_151507_SCZ.json +0 -0
  23. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/mouse_embryo/E16.5_E1S1_Height.json +0 -0
  24. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/mouse_embryo/E16.5_E1S1_IQ.json +0 -0
  25. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/mouse_embryo/E16.5_E1S1_MCHC.json +0 -0
  26. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/mouse_embryo/E16.5_E1S1_SCZ.json +0 -0
  27. {gsmap-1.67 → gsmap-1.71}/docs/source/charts/test.json +16 -16
  28. {gsmap-1.67 → gsmap-1.71}/docs/source/conf.py +55 -55
  29. {gsmap-1.67 → gsmap-1.71}/docs/source/data.rst +63 -63
  30. {gsmap-1.67 → gsmap-1.71}/docs/source/data_format.md +63 -63
  31. {gsmap-1.67 → gsmap-1.71}/docs/source/index.rst +68 -68
  32. {gsmap-1.67 → gsmap-1.71}/docs/source/install.rst +26 -26
  33. {gsmap-1.67 → gsmap-1.71}/docs/source/mouse.rst +5 -5
  34. {gsmap-1.67 → gsmap-1.71}/docs/source/mouse_example.md +264 -264
  35. {gsmap-1.67 → gsmap-1.71}/docs/source/quick_mode.md +140 -140
  36. {gsmap-1.67 → gsmap-1.71}/docs/source/release.rst +7 -7
  37. {gsmap-1.67 → gsmap-1.71}/docs/source/tutorials.rst +29 -29
  38. {gsmap-1.67 → gsmap-1.71}/pyproject.toml +83 -85
  39. {gsmap-1.67 → gsmap-1.71}/schematic.png +0 -0
  40. {gsmap-1.67/src/gsMap/GNN_VAE → gsmap-1.71/src/gsMap/GNN}/__init__.py +0 -0
  41. {gsmap-1.67/src/gsMap/GNN_VAE → gsmap-1.71/src/gsMap/GNN}/adjacency_matrix.py +75 -75
  42. {gsmap-1.67/src/gsMap/GNN_VAE → gsmap-1.71/src/gsMap/GNN}/model.py +89 -89
  43. {gsmap-1.67/src/gsMap/GNN_VAE → gsmap-1.71/src/gsMap/GNN}/train.py +88 -86
  44. {gsmap-1.67 → gsmap-1.71}/src/gsMap/__init__.py +5 -5
  45. {gsmap-1.67 → gsmap-1.71}/src/gsMap/__main__.py +2 -2
  46. {gsmap-1.67 → gsmap-1.71}/src/gsMap/cauchy_combination_test.py +141 -141
  47. {gsmap-1.67 → gsmap-1.71}/src/gsMap/config.py +805 -803
  48. {gsmap-1.67 → gsmap-1.71}/src/gsMap/diagnosis.py +273 -273
  49. {gsmap-1.67 → gsmap-1.71}/src/gsMap/find_latent_representation.py +133 -145
  50. {gsmap-1.67 → gsmap-1.71}/src/gsMap/format_sumstats.py +407 -407
  51. {gsmap-1.67 → gsmap-1.71}/src/gsMap/generate_ldscore.py +618 -618
  52. {gsmap-1.67 → gsmap-1.71}/src/gsMap/latent_to_gene.py +234 -234
  53. {gsmap-1.67 → gsmap-1.71}/src/gsMap/main.py +31 -31
  54. {gsmap-1.67 → gsmap-1.71}/src/gsMap/report.py +160 -160
  55. {gsmap-1.67 → gsmap-1.71}/src/gsMap/run_all_mode.py +194 -194
  56. {gsmap-1.67 → gsmap-1.71}/src/gsMap/setup.py +0 -0
  57. {gsmap-1.67 → gsmap-1.71}/src/gsMap/spatial_ldsc_multiple_sumstats.py +380 -380
  58. {gsmap-1.67 → gsmap-1.71}/src/gsMap/templates/report_template.html +198 -198
  59. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/__init__.py +0 -0
  60. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/generate_r2_matrix.py +735 -735
  61. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/jackknife.py +514 -514
  62. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/make_annotations.py +518 -518
  63. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/manhattan_plot.py +639 -639
  64. {gsmap-1.67 → gsmap-1.71}/src/gsMap/utils/regression_read.py +294 -294
  65. {gsmap-1.67 → gsmap-1.71}/src/gsMap/visualize.py +198 -198
  66. gsmap-1.71/visualization_web_docs/Makefile +20 -0
  67. gsmap-1.71/visualization_web_docs/make.bat +35 -0
  68. gsmap-1.71/visualization_web_docs/requirements.txt +2 -0
  69. gsmap-1.71/visualization_web_docs/source/_static/raw1_add_txt.svg +37003 -0
  70. gsmap-1.71/visualization_web_docs/source/_static/raw2_add_txt.svg +29429 -0
  71. gsmap-1.71/visualization_web_docs/source/_static/raw3_add_txt.svg +36689 -0
  72. gsmap-1.71/visualization_web_docs/source/_static/raw4_add_txt.svg +17587 -0
  73. gsmap-1.71/visualization_web_docs/source/_static/raw5_add_txt.svg +20469 -0
  74. gsmap-1.71/visualization_web_docs/source/_static/schematic.svg +13633 -0
  75. gsmap-1.71/visualization_web_docs/source/conf.py +57 -0
  76. gsmap-1.71/visualization_web_docs/source/index.rst +44 -0
  77. gsmap-1.67/README.md +0 -39
@@ -1,120 +1,121 @@
1
- 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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- 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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-
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- publish-to-testpypi:
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- name: Publish Python 🐍 distribution 📦 to TestPyPI
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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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-
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- environment:
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- name: testpypi
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- url: https://test.pypi.org/p/gsMap
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-
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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 TestPyPI
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- uses: pypa/gh-action-pypi-publish@release/v1
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- with:
1
+ name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
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+
3
+ on: push
4
+
5
+ jobs:
6
+ build:
7
+ name: Build distribution 📦
8
+ runs-on: ubuntu-latest
9
+
10
+ steps:
11
+ - uses: actions/checkout@v4
12
+ - name: Set up Python
13
+ uses: actions/setup-python@v4
14
+ with:
15
+ python-version: "3.x"
16
+ - name: Install pypa/build
17
+ run: >-
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+ python3 -m
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+ pip install
20
+ flit
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+ --user
22
+ - name: Build a binary wheel and a source tarball
23
+ run: |
24
+ flit build
25
+ ls -lh dist
26
+ - name: Store the distribution packages
27
+ 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: >-
35
+ Publish Python 🐍 distribution 📦 to PyPI
36
+ if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
37
+ needs:
38
+ - build
39
+ runs-on: ubuntu-latest
40
+ environment:
41
+ 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
54
+
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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
65
+ id-token: write # IMPORTANT: mandatory for sigstore
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+
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+ steps:
68
+ - 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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+
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+ publish-to-testpypi:
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+ name: Publish Python 🐍 distribution 📦 to TestPyPI
100
+ if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
101
+ needs:
102
+ - build
103
+ runs-on: ubuntu-latest
104
+
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+ environment:
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+ name: testpypi
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+ url: https://test.pypi.org/p/gsMap
108
+
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+ permissions:
110
+ id-token: write # IMPORTANT: mandatory for trusted publishing
111
+
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+ steps:
113
+ - name: Download all the dists
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+ uses: actions/download-artifact@v3
115
+ with:
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+ name: python-package-distributions
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+ path: dist/
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+ - name: Publish distribution 📦 to TestPyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+ with:
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  repository-url: https://test.pypi.org/legacy/