Update PyPI python version and fix a vulnerability (#71)

* update pypi publish to 3.12

* fix vulnerability by upgrading cryptography manually

.devcontainer/docker-compose.yml

@@ -7,7 +7,7 @@ services:
       dockerfile: ./Dockerfile
       args:
         # [Choice] Python version: 3, 3.8, 3.7, 3.6
-        VARIANT: 3.9
+        VARIANT: 3.12
         # [Choice] Install Node.js
         INSTALL_NODE: "true"
         NODE_VERSION: "lts/*"

.github/workflows/pypi_publish.yaml

@@ -12,10 +12,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: '3.12'
 
       - name: Ensure package version and tag name are equal
         run: |

.pyproject_generation/pyproject_custom.toml

@@ -10,6 +10,7 @@ dependencies = [
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
+    "cryptography>=42.0.0"
 ]
 
 [project.urls]

lock/requirements-dev.txt

@@ -304,31 +304,42 @@ coverage==7.3.2 \
     --hash=sha256:fa28e909776dc69efb6ed975a63691bc8172b64ff357e663a1bb06ff3c9b589a \
     --hash=sha256:fe494faa90ce6381770746077243231e0b83ff3f17069d748f645617cefe19d4
     # via pytest-cov
-cryptography==41.0.7 \
-    --hash=sha256:079b85658ea2f59c4f43b70f8119a52414cdb7be34da5d019a77bf96d473b960 \
-    --hash=sha256:09616eeaef406f99046553b8a40fbf8b1e70795a91885ba4c96a70793de5504a \
-    --hash=sha256:13f93ce9bea8016c253b34afc6bd6a75993e5c40672ed5405a9c832f0d4a00bc \
-    --hash=sha256:37a138589b12069efb424220bf78eac59ca68b95696fc622b6ccc1c0a197204a \
-    --hash=sha256:3c78451b78313fa81607fa1b3f1ae0a5ddd8014c38a02d9db0616133987b9cdf \
-    --hash=sha256:43f2552a2378b44869fe8827aa19e69512e3245a219104438692385b0ee119d1 \
-    --hash=sha256:48a0476626da912a44cc078f9893f292f0b3e4c739caf289268168d8f4702a39 \
-    --hash=sha256:49f0805fc0b2ac8d4882dd52f4a3b935b210935d500b6b805f321addc8177406 \
-    --hash=sha256:5429ec739a29df2e29e15d082f1d9ad683701f0ec7709ca479b3ff2708dae65a \
-    --hash=sha256:5a1b41bc97f1ad230a41657d9155113c7521953869ae57ac39ac7f1bb471469a \
-    --hash=sha256:68a2dec79deebc5d26d617bfdf6e8aab065a4f34934b22d3b5010df3ba36612c \
-    --hash=sha256:7a698cb1dac82c35fcf8fe3417a3aaba97de16a01ac914b89a0889d364d2f6be \
-    --hash=sha256:841df4caa01008bad253bce2a6f7b47f86dc9f08df4b433c404def869f590a15 \
-    --hash=sha256:90452ba79b8788fa380dfb587cca692976ef4e757b194b093d845e8d99f612f2 \
-    --hash=sha256:928258ba5d6f8ae644e764d0f996d61a8777559f72dfeb2eea7e2fe0ad6e782d \
-    --hash=sha256:af03b32695b24d85a75d40e1ba39ffe7db7ffcb099fe507b39fd41a565f1b157 \
-    --hash=sha256:b640981bf64a3e978a56167594a0e97db71c89a479da8e175d8bb5be5178c003 \
-    --hash=sha256:c5ca78485a255e03c32b513f8c2bc39fedb7f5c5f8535545bdc223a03b24f248 \
-    --hash=sha256:c7f3201ec47d5207841402594f1d7950879ef890c0c495052fa62f58283fde1a \
-    --hash=sha256:d5ec85080cce7b0513cfd233914eb8b7bbd0633f1d1703aa28d1dd5a72f678ec \
-    --hash=sha256:d6c391c021ab1f7a82da5d8d0b3cee2f4b2c455ec86c8aebbc84837a631ff309 \
-    --hash=sha256:e3114da6d7f95d2dee7d3f4eec16dacff819740bbab931aff8648cb13c5ff5e7 \
-    --hash=sha256:f983596065a18a2183e7f79ab3fd4c475205b839e02cbc0efbbf9666c4b3083d
-    # via jwcrypto
+cryptography==42.0.7 \
+    --hash=sha256:02c0eee2d7133bdbbc5e24441258d5d2244beb31da5ed19fbb80315f4bbbff55 \
+    --hash=sha256:0d563795db98b4cd57742a78a288cdbdc9daedac29f2239793071fe114f13785 \
+    --hash=sha256:16268d46086bb8ad5bf0a2b5544d8a9ed87a0e33f5e77dd3c3301e63d941a83b \
+    --hash=sha256:1a58839984d9cb34c855197043eaae2c187d930ca6d644612843b4fe8513c886 \
+    --hash=sha256:2954fccea107026512b15afb4aa664a5640cd0af630e2ee3962f2602693f0c82 \
+    --hash=sha256:2e47577f9b18723fa294b0ea9a17d5e53a227867a0a4904a1a076d1646d45ca1 \
+    --hash=sha256:31adb7d06fe4383226c3e963471f6837742889b3c4caa55aac20ad951bc8ffda \
+    --hash=sha256:3577d029bc3f4827dd5bf8bf7710cac13527b470bbf1820a3f394adb38ed7d5f \
+    --hash=sha256:36017400817987670037fbb0324d71489b6ead6231c9604f8fc1f7d008087c68 \
+    --hash=sha256:362e7197754c231797ec45ee081f3088a27a47c6c01eff2ac83f60f85a50fe60 \
+    --hash=sha256:3de9a45d3b2b7d8088c3fbf1ed4395dfeff79d07842217b38df14ef09ce1d8d7 \
+    --hash=sha256:4f698edacf9c9e0371112792558d2f705b5645076cc0aaae02f816a0171770fd \
+    --hash=sha256:5482e789294854c28237bba77c4c83be698be740e31a3ae5e879ee5444166582 \
+    --hash=sha256:5e44507bf8d14b36b8389b226665d597bc0f18ea035d75b4e53c7b1ea84583cc \
+    --hash=sha256:779245e13b9a6638df14641d029add5dc17edbef6ec915688f3acb9e720a5858 \
+    --hash=sha256:789caea816c6704f63f6241a519bfa347f72fbd67ba28d04636b7c6b7da94b0b \
+    --hash=sha256:7f8b25fa616d8b846aef64b15c606bb0828dbc35faf90566eb139aa9cff67af2 \
+    --hash=sha256:8cb8ce7c3347fcf9446f201dc30e2d5a3c898d009126010cbd1f443f28b52678 \
+    --hash=sha256:93a3209f6bb2b33e725ed08ee0991b92976dfdcf4e8b38646540674fc7508e13 \
+    --hash=sha256:a3a5ac8b56fe37f3125e5b72b61dcde43283e5370827f5233893d461b7360cd4 \
+    --hash=sha256:a47787a5e3649008a1102d3df55424e86606c9bae6fb77ac59afe06d234605f8 \
+    --hash=sha256:a79165431551042cc9d1d90e6145d5d0d3ab0f2d66326c201d9b0e7f5bf43604 \
+    --hash=sha256:a987f840718078212fdf4504d0fd4c6effe34a7e4740378e59d47696e8dfb477 \
+    --hash=sha256:a9bc127cdc4ecf87a5ea22a2556cab6c7eda2923f84e4f3cc588e8470ce4e42e \
+    --hash=sha256:bd13b5e9b543532453de08bcdc3cc7cebec6f9883e886fd20a92f26940fd3e7a \
+    --hash=sha256:c65f96dad14f8528a447414125e1fc8feb2ad5a272b8f68477abbcc1ea7d94b9 \
+    --hash=sha256:d8e3098721b84392ee45af2dd554c947c32cc52f862b6a3ae982dbb90f577f14 \
+    --hash=sha256:e6b79d0adb01aae87e8a44c2b64bc3f3fe59515280e00fb6d57a7267a2583cda \
+    --hash=sha256:e6b8f1881dac458c34778d0a424ae5769de30544fc678eac51c1c8bb2183e9da \
+    --hash=sha256:e9b2a6309f14c0497f348d08a065d52f3020656f675819fc405fb63bbcd26562 \
+    --hash=sha256:ecbfbc00bf55888edda9868a4cf927205de8499e7fabe6c050322298382953f2 \
+    --hash=sha256:efd0bf5205240182e0f13bcaea41be4fdf5c22c5129fc7ced4a0282ac86998c9
+    # via
+    #   metldata (pyproject.toml)
+    #   jwcrypto
 curies==0.7.4 \
     --hash=sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39 \
     --hash=sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718

lock/requirements.txt

@@ -269,32 +269,42 @@ colorama==0.4.6 \
     # via
     #   -c lock/requirements-dev.txt
     #   tox
-cryptography==41.0.7 \
-    --hash=sha256:079b85658ea2f59c4f43b70f8119a52414cdb7be34da5d019a77bf96d473b960 \
-    --hash=sha256:09616eeaef406f99046553b8a40fbf8b1e70795a91885ba4c96a70793de5504a \
-    --hash=sha256:13f93ce9bea8016c253b34afc6bd6a75993e5c40672ed5405a9c832f0d4a00bc \
-    --hash=sha256:37a138589b12069efb424220bf78eac59ca68b95696fc622b6ccc1c0a197204a \
-    --hash=sha256:3c78451b78313fa81607fa1b3f1ae0a5ddd8014c38a02d9db0616133987b9cdf \
-    --hash=sha256:43f2552a2378b44869fe8827aa19e69512e3245a219104438692385b0ee119d1 \
-    --hash=sha256:48a0476626da912a44cc078f9893f292f0b3e4c739caf289268168d8f4702a39 \
-    --hash=sha256:49f0805fc0b2ac8d4882dd52f4a3b935b210935d500b6b805f321addc8177406 \
-    --hash=sha256:5429ec739a29df2e29e15d082f1d9ad683701f0ec7709ca479b3ff2708dae65a \
-    --hash=sha256:5a1b41bc97f1ad230a41657d9155113c7521953869ae57ac39ac7f1bb471469a \
-    --hash=sha256:68a2dec79deebc5d26d617bfdf6e8aab065a4f34934b22d3b5010df3ba36612c \
-    --hash=sha256:7a698cb1dac82c35fcf8fe3417a3aaba97de16a01ac914b89a0889d364d2f6be \
-    --hash=sha256:841df4caa01008bad253bce2a6f7b47f86dc9f08df4b433c404def869f590a15 \
-    --hash=sha256:90452ba79b8788fa380dfb587cca692976ef4e757b194b093d845e8d99f612f2 \
-    --hash=sha256:928258ba5d6f8ae644e764d0f996d61a8777559f72dfeb2eea7e2fe0ad6e782d \
-    --hash=sha256:af03b32695b24d85a75d40e1ba39ffe7db7ffcb099fe507b39fd41a565f1b157 \
-    --hash=sha256:b640981bf64a3e978a56167594a0e97db71c89a479da8e175d8bb5be5178c003 \
-    --hash=sha256:c5ca78485a255e03c32b513f8c2bc39fedb7f5c5f8535545bdc223a03b24f248 \
-    --hash=sha256:c7f3201ec47d5207841402594f1d7950879ef890c0c495052fa62f58283fde1a \
-    --hash=sha256:d5ec85080cce7b0513cfd233914eb8b7bbd0633f1d1703aa28d1dd5a72f678ec \
-    --hash=sha256:d6c391c021ab1f7a82da5d8d0b3cee2f4b2c455ec86c8aebbc84837a631ff309 \
-    --hash=sha256:e3114da6d7f95d2dee7d3f4eec16dacff819740bbab931aff8648cb13c5ff5e7 \
-    --hash=sha256:f983596065a18a2183e7f79ab3fd4c475205b839e02cbc0efbbf9666c4b3083d
+cryptography==42.0.7 \
+    --hash=sha256:02c0eee2d7133bdbbc5e24441258d5d2244beb31da5ed19fbb80315f4bbbff55 \
+    --hash=sha256:0d563795db98b4cd57742a78a288cdbdc9daedac29f2239793071fe114f13785 \
+    --hash=sha256:16268d46086bb8ad5bf0a2b5544d8a9ed87a0e33f5e77dd3c3301e63d941a83b \
+    --hash=sha256:1a58839984d9cb34c855197043eaae2c187d930ca6d644612843b4fe8513c886 \
+    --hash=sha256:2954fccea107026512b15afb4aa664a5640cd0af630e2ee3962f2602693f0c82 \
+    --hash=sha256:2e47577f9b18723fa294b0ea9a17d5e53a227867a0a4904a1a076d1646d45ca1 \
+    --hash=sha256:31adb7d06fe4383226c3e963471f6837742889b3c4caa55aac20ad951bc8ffda \
+    --hash=sha256:3577d029bc3f4827dd5bf8bf7710cac13527b470bbf1820a3f394adb38ed7d5f \
+    --hash=sha256:36017400817987670037fbb0324d71489b6ead6231c9604f8fc1f7d008087c68 \
+    --hash=sha256:362e7197754c231797ec45ee081f3088a27a47c6c01eff2ac83f60f85a50fe60 \
+    --hash=sha256:3de9a45d3b2b7d8088c3fbf1ed4395dfeff79d07842217b38df14ef09ce1d8d7 \
+    --hash=sha256:4f698edacf9c9e0371112792558d2f705b5645076cc0aaae02f816a0171770fd \
+    --hash=sha256:5482e789294854c28237bba77c4c83be698be740e31a3ae5e879ee5444166582 \
+    --hash=sha256:5e44507bf8d14b36b8389b226665d597bc0f18ea035d75b4e53c7b1ea84583cc \
+    --hash=sha256:779245e13b9a6638df14641d029add5dc17edbef6ec915688f3acb9e720a5858 \
+    --hash=sha256:789caea816c6704f63f6241a519bfa347f72fbd67ba28d04636b7c6b7da94b0b \
+    --hash=sha256:7f8b25fa616d8b846aef64b15c606bb0828dbc35faf90566eb139aa9cff67af2 \
+    --hash=sha256:8cb8ce7c3347fcf9446f201dc30e2d5a3c898d009126010cbd1f443f28b52678 \
+    --hash=sha256:93a3209f6bb2b33e725ed08ee0991b92976dfdcf4e8b38646540674fc7508e13 \
+    --hash=sha256:a3a5ac8b56fe37f3125e5b72b61dcde43283e5370827f5233893d461b7360cd4 \
+    --hash=sha256:a47787a5e3649008a1102d3df55424e86606c9bae6fb77ac59afe06d234605f8 \
+    --hash=sha256:a79165431551042cc9d1d90e6145d5d0d3ab0f2d66326c201d9b0e7f5bf43604 \
+    --hash=sha256:a987f840718078212fdf4504d0fd4c6effe34a7e4740378e59d47696e8dfb477 \
+    --hash=sha256:a9bc127cdc4ecf87a5ea22a2556cab6c7eda2923f84e4f3cc588e8470ce4e42e \
+    --hash=sha256:bd13b5e9b543532453de08bcdc3cc7cebec6f9883e886fd20a92f26940fd3e7a \
+    --hash=sha256:c65f96dad14f8528a447414125e1fc8feb2ad5a272b8f68477abbcc1ea7d94b9 \
+    --hash=sha256:d8e3098721b84392ee45af2dd554c947c32cc52f862b6a3ae982dbb90f577f14 \
+    --hash=sha256:e6b79d0adb01aae87e8a44c2b64bc3f3fe59515280e00fb6d57a7267a2583cda \
+    --hash=sha256:e6b8f1881dac458c34778d0a424ae5769de30544fc678eac51c1c8bb2183e9da \
+    --hash=sha256:e9b2a6309f14c0497f348d08a065d52f3020656f675819fc405fb63bbcd26562 \
+    --hash=sha256:ecbfbc00bf55888edda9868a4cf927205de8499e7fabe6c050322298382953f2 \
+    --hash=sha256:efd0bf5205240182e0f13bcaea41be4fdf5c22c5129fc7ced4a0282ac86998c9
     # via
     #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
     #   jwcrypto
 curies==0.7.4 \
     --hash=sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39 \

pyproject.toml

@@ -31,6 +31,7 @@ dependencies = [
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
+    "cryptography>=42.0.0",
 ]
 
 [project.license]