updated pypi publish script

.github/workflows/python-publish.yml

@@ -1,6 +1,3 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Upload Python Package
 
 on:
@@ -9,9 +6,10 @@ on:
 
 jobs:
   deploy:
-
+    name: upload release to PyPI
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -23,9 +21,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

docs_jupyter/python-usage.ipynb

@@ -138,7 +138,13 @@
     }
    ],
    "source": [
-    "geof = Geofetcher(processed=True, data_source=\"all\", const_limit_project = 20, const_limit_discard = 500, attr_limit_truncate = 10000 )"
+    "geof = Geofetcher(\n",
+    "    processed=True,\n",
+    "    data_source=\"all\",\n",
+    "    const_limit_project=20,\n",
+    "    const_limit_discard=500,\n",
+    "    attr_limit_truncate=10000,\n",
+    ")"
    ]
   },
   {
@@ -418,7 +424,7 @@
     }
    ],
    "source": [
-    "len(projects['GSE95654_samples'].samples)"
+    "len(projects[\"GSE95654_samples\"].samples)"
    ]
   },
   {
@@ -684,7 +690,7 @@
     }
    ],
    "source": [
-    "projects['GSE95654_samples'].sample_table.iloc[:15 , :5]"
+    "projects[\"GSE95654_samples\"].sample_table.iloc[:15, :5]"
    ]
   }
  ],