From 099915e230177872715f076cf85ef0e40dc90e54 Mon Sep 17 00:00:00 2001
From: Patrick Kunzmann <padix.key@gmail.com>
Date: Mon, 23 Dec 2024 14:00:18 +0100
Subject: [PATCH 1/2] Use trusted publishing

---
 .github/workflows/test_and_deploy.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index d57390fbb..d3b80f4a2 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -326,6 +326,7 @@ jobs:
     name: Upload package to GitHub Releases & PyPI
     permissions:
       contents: write
+      id-token: write
     needs:
     - lint
     - test-and-build
@@ -333,6 +334,9 @@ jobs:
     - test-interfaces
     - test-muscle5
     runs-on: ubuntu-latest
+    environment:
+      name: publish
+      url: https://pypi.org/p/biotite
     steps:
     - uses: actions/download-artifact@v4
       with:
@@ -347,10 +351,8 @@ jobs:
       with:
         files: dist//*
     - name: Upload to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.9.0
+      uses: pypa/gh-action-pypi-publish@release/v1
       if: github.event_name == 'release' && github.event.action == 'published'
-      with:
-        password: ${{ secrets.PYPI_TOKEN }}
 
 
   upload-ccd:

From 197a8fc218545e18be13bb361df59abb8ebe41de Mon Sep 17 00:00:00 2001
From: Patrick Kunzmann <padix.key@gmail.com>
Date: Mon, 23 Dec 2024 14:27:12 +0100
Subject: [PATCH 2/2] Use preamble also for example gallery

---
 doc/conf.py               |  4 ++--
 doc/key.py                | 11 -----------
 doc/preamble.py           | 29 +++++++++++++++++++++++++++++
 doc/tutorial/preamble.rst | 24 ++++--------------------
 4 files changed, 35 insertions(+), 33 deletions(-)
 delete mode 100644 doc/key.py
 create mode 100644 doc/preamble.py

diff --git a/doc/conf.py b/doc/conf.py
index d9d511858..eee7fc572 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -30,7 +30,7 @@
 sys.path.insert(0, DOC_PATH)
 import apidoc
 import bibliography
-import key
+import preamble
 import scraper
 import switcher
 import viewcode
@@ -206,7 +206,7 @@
     "backreferences_dir": "examples/backreferences",
     "doc_module": ("biotite",),
     # Set the NCBI API key
-    "reset_modules": (key.set_ncbi_api_key_from_env,),
+    "reset_modules": (preamble.setup_script),
     "remove_config_comments": True,
 }
 
diff --git a/doc/key.py b/doc/key.py
deleted file mode 100644
index b7a2b4334..000000000
--- a/doc/key.py
+++ /dev/null
@@ -1,11 +0,0 @@
-import os
-
-
-def set_ncbi_api_key_from_env(*args, **kwargs):
-    # Import inside function as Biotite may not be known
-    # at the time of function definition
-    import biotite.database.entrez as entrez
-
-    ncbi_api_key = os.environ.get("NCBI_API_KEY")
-    if ncbi_api_key is not None and ncbi_api_key != "":
-        entrez.set_api_key(ncbi_api_key)
diff --git a/doc/preamble.py b/doc/preamble.py
new file mode 100644
index 000000000..93ee07e33
--- /dev/null
+++ b/doc/preamble.py
@@ -0,0 +1,29 @@
+import os
+import numpy as np
+
+
+def setup_script():
+    """
+    Prepare API keys, formatting, etc. for running a tutorial or example script.
+    """
+    # Import inside function as Biotite may not be known
+    # at the time of function definition
+    import biotite.application.blast as blast
+    import biotite.database.entrez as entrez
+
+    # Improve readability of large arrays
+    np.set_printoptions(precision=2)
+
+    # Use API key to increase request limit
+    ncbi_api_key = os.environ.get("NCBI_API_KEY")
+    if ncbi_api_key is not None and ncbi_api_key != "":
+        entrez.set_api_key(ncbi_api_key)
+
+    # Mock the BlastWebApp class
+    # to allow subsequent BLAST calls when building the tutorial
+    class MockedBlastApp(blast.BlastWebApp):
+        def __init__(self, *args, **kwargs):
+            kwargs["obey_rules"] = False
+            super().__init__(*args, **kwargs)
+
+    blast.BlastWebApp = MockedBlastApp
diff --git a/doc/tutorial/preamble.rst b/doc/tutorial/preamble.rst
index 14079a70f..710ca0c69 100644
--- a/doc/tutorial/preamble.rst
+++ b/doc/tutorial/preamble.rst
@@ -1,23 +1,7 @@
-.. jupyter-execute::
+.. jupyter-execute:: /preamble.py
     :hide-code:
 
-    import os
-    import numpy as np
-    import biotite.database.entrez as entrez
-    import biotite.application.blast as blast
-
-    # Improve readability of large arrays
-    np.set_printoptions(precision=2)
-
-    # Use API key to increase request limit
-    ncbi_api_key = os.environ.get("NCBI_API_KEY")
-    if ncbi_api_key is not None and ncbi_api_key != "":
-        entrez.set_api_key(ncbi_api_key)
+.. jupyter-execute::
+    :hide-code:
 
-    # Mock the BlastWebApp class
-    # to allow subsequent BLAST calls when building the tutorial
-    class MockedBlastApp(blast.BlastWebApp):
-        def __init__(self, *args, **kwargs):
-            kwargs["obey_rules"] = False
-            super().__init__(*args, **kwargs)
-    blast.BlastWebApp = MockedBlastApp
\ No newline at end of file
+    setup_script()
\ No newline at end of file