Bump biopython from 1.83 to 1.84 in /pipeline/seq_retrieval

Bumps [biopython](https://github.com/biopython/biopython) from 1.83 to 1.84. - [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst) - [Commits](https://github.com/biopython/biopython/commits) --- updated-dependencies: - dependency-name: biopython dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
alliance-genome · Jul 9, 2024 · fa795d9 · fa795d9
1 parent 9c85e5e
commit fa795d9
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Showing 3 changed files with 53 additions and 57 deletions.
diff --git a/pipeline/seq_retrieval/pyproject.toml b/pipeline/seq_retrieval/pyproject.toml
@@ -9,7 +9,7 @@ authors = [
 
 requires-python = "==3.12.*"
 dependencies = [
-    "biopython==1.83",
+    "biopython==1.84",
     "click==8.1.*",
     "pysam==0.22.*",
     "requests==2.32.*",

diff --git a/pipeline/seq_retrieval/requirements.txt b/pipeline/seq_retrieval/requirements.txt
@@ -4,34 +4,32 @@
 #
 #    pip-compile --generate-hashes --output-file=requirements.txt
 #
-biopython==1.83 \
-    --hash=sha256:0496f2a6e6e060d8ff0f34784ad15ed342b10cfe282020efe168286f0c14c479 \
-    --hash=sha256:0b35aa095de0fa8339b70664797d0e83322a1a9d512e2fd52d4e872df5189f56 \
-    --hash=sha256:0d5ce14755a6b49dea4743cf6929570afe5becb66ad222194984c7bf04218f86 \
-    --hash=sha256:118425a210cb3d184c7a78154c5646089366faf124cd46c6056ca7f9302b94ad \
-    --hash=sha256:29708772651d930e808cd24c519fd4f39b2e719668944c0aa1eaf0b1deef9f48 \
-    --hash=sha256:2c3584122a5daca25b3914a32c52785b051c11518cd5e111e9e89ee04a6234fe \
-    --hash=sha256:2df408be9816dd98c28fe181ea93fb6e0d375bf1763ad9ed503ac30bb2df5b1a \
-    --hash=sha256:30fa323694ee640978888d0c8c4f61f951d119ccec52b1dd5fe0668cfffb6648 \
-    --hash=sha256:3686ff61df3f24ecf6f23826e4fe5172c5e5f745099bc8fbb176f5304582f88f \
-    --hash=sha256:4cc011346bc8af264e3d3ea98c665b6ebe20e503f1dd50ee7e0bc913941b4c6e \
-    --hash=sha256:56f03f43c183acb88c082bc31e5f047fcc6d0aceb5270fbd29c31ab769795b86 \
-    --hash=sha256:641c1a860705d6740eb16c6147b2b730b05a8f5974db804c14d5faa8a1446085 \
-    --hash=sha256:741abad84165e4caf0c80e485054135f51c21177e50ac6fcc502a45a6e8f7311 \
-    --hash=sha256:78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7 \
-    --hash=sha256:81d1e2515b380e1876720ba79dbf50f8ef3a38cc38ba5953ef61ec20d0934ee2 \
-    --hash=sha256:8552cc467429b555c604b84fc174c33923bf7e4c735774eda505f1d5a9c2feab \
-    --hash=sha256:94b68e550619e1b6e3784ed8cecb62f201d70d8b87d3a90365291f065ab42bd9 \
-    --hash=sha256:a01dfdad7210f2fd5c4f36606278f91dbfdda6dac02347206d13cc618e79fe32 \
-    --hash=sha256:a0c1c70789c7e2a26563db5ba533fb9fea0cc1f2c7bc7ad240146cb223ba44a3 \
-    --hash=sha256:aae1b156a76907c2abfe9d141776b0aead65695ea914eaecdf12bd1e8991f869 \
-    --hash=sha256:c756c0b81702c705141c87c2805203df01c6d4cf290e8cefd48cbc61a3c85b82 \
-    --hash=sha256:ca94e8ea8907de841a515af55acb1922a9de99b3144c738a193f2a75e4726078 \
-    --hash=sha256:e2cc737906d8de47eedbc4476f711b960c16a65daa8cdd021875398c81999a09 \
-    --hash=sha256:e37884fe39e4560bf5934a4ec4ba7f7fe0e7c091053d03d05b20a70557167717 \
-    --hash=sha256:e914f7161b3831d7c58db33cc5c7ca64b42c9877c5a776a8313e7a5fd494f8de \
-    --hash=sha256:ec82350c24cdcf34a8d4a5f189d0ff7dc025658098a60e6f0e681d24b6a1414e \
-    --hash=sha256:fd9bc6fef3f6a10043635a75e1a77c9dce877375140e81059c67c73d4ce65c4c
+biopython==1.84 \
+    --hash=sha256:0c425a39871f652598f502671aa5f6b5125475a91333a368a47f9c611ca96db1 \
+    --hash=sha256:25f4ef193a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e \
+    --hash=sha256:2cb8e839ab472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20 \
+    --hash=sha256:2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4 \
+    --hash=sha256:2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4 \
+    --hash=sha256:3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b \
+    --hash=sha256:4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad \
+    --hash=sha256:507ac3956f3107e77fee362ecb048dafb5f97cbcf110012d091418430c3227c7 \
+    --hash=sha256:52b6098f47d6b90fc8a5e8579b81ee50047e9108f0976e69c891ae0c4817e42d \
+    --hash=sha256:60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4 \
+    --hash=sha256:61765b71f84814a1eeb55ab222f43330aa7ad3e55ab91e8b444706149c67a281 \
+    --hash=sha256:7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089 \
+    --hash=sha256:7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f \
+    --hash=sha256:894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a13e7585ff4 \
+    --hash=sha256:89ef3967f5a88b5bb6344bef75ae83386de53fed3966d5c8c334ad885f8db08a \
+    --hash=sha256:9e3f7476fd81f31e048965d7be2826f018686e870d96870f440b609002953954 \
+    --hash=sha256:9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da7 \
+    --hash=sha256:b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4 \
+    --hash=sha256:b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b479118 \
+    --hash=sha256:ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4f96d0059 \
+    --hash=sha256:c792508988fc3ccf18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c \
+    --hash=sha256:ca8d6a88b9a9718074b3f5b450f9ea5adf7112a7dbaed55d82d5b623f5859a01 \
+    --hash=sha256:ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c \
+    --hash=sha256:ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae \
+    --hash=sha256:f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c
     # via seq-retrieval (pyproject.toml)
 certifi==2024.7.4 \
     --hash=sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b \

diff --git a/pipeline/seq_retrieval/tests/requirements.txt b/pipeline/seq_retrieval/tests/requirements.txt
@@ -4,34 +4,32 @@
 #
 #    pip-compile --extra=test --generate-hashes --output-file=tests/requirements.txt
 #
-biopython==1.83 \
-    --hash=sha256:0496f2a6e6e060d8ff0f34784ad15ed342b10cfe282020efe168286f0c14c479 \
-    --hash=sha256:0b35aa095de0fa8339b70664797d0e83322a1a9d512e2fd52d4e872df5189f56 \
-    --hash=sha256:0d5ce14755a6b49dea4743cf6929570afe5becb66ad222194984c7bf04218f86 \
-    --hash=sha256:118425a210cb3d184c7a78154c5646089366faf124cd46c6056ca7f9302b94ad \
-    --hash=sha256:29708772651d930e808cd24c519fd4f39b2e719668944c0aa1eaf0b1deef9f48 \
-    --hash=sha256:2c3584122a5daca25b3914a32c52785b051c11518cd5e111e9e89ee04a6234fe \
-    --hash=sha256:2df408be9816dd98c28fe181ea93fb6e0d375bf1763ad9ed503ac30bb2df5b1a \
-    --hash=sha256:30fa323694ee640978888d0c8c4f61f951d119ccec52b1dd5fe0668cfffb6648 \
-    --hash=sha256:3686ff61df3f24ecf6f23826e4fe5172c5e5f745099bc8fbb176f5304582f88f \
-    --hash=sha256:4cc011346bc8af264e3d3ea98c665b6ebe20e503f1dd50ee7e0bc913941b4c6e \
-    --hash=sha256:56f03f43c183acb88c082bc31e5f047fcc6d0aceb5270fbd29c31ab769795b86 \
-    --hash=sha256:641c1a860705d6740eb16c6147b2b730b05a8f5974db804c14d5faa8a1446085 \
-    --hash=sha256:741abad84165e4caf0c80e485054135f51c21177e50ac6fcc502a45a6e8f7311 \
-    --hash=sha256:78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7 \
-    --hash=sha256:81d1e2515b380e1876720ba79dbf50f8ef3a38cc38ba5953ef61ec20d0934ee2 \
-    --hash=sha256:8552cc467429b555c604b84fc174c33923bf7e4c735774eda505f1d5a9c2feab \
-    --hash=sha256:94b68e550619e1b6e3784ed8cecb62f201d70d8b87d3a90365291f065ab42bd9 \
-    --hash=sha256:a01dfdad7210f2fd5c4f36606278f91dbfdda6dac02347206d13cc618e79fe32 \
-    --hash=sha256:a0c1c70789c7e2a26563db5ba533fb9fea0cc1f2c7bc7ad240146cb223ba44a3 \
-    --hash=sha256:aae1b156a76907c2abfe9d141776b0aead65695ea914eaecdf12bd1e8991f869 \
-    --hash=sha256:c756c0b81702c705141c87c2805203df01c6d4cf290e8cefd48cbc61a3c85b82 \
-    --hash=sha256:ca94e8ea8907de841a515af55acb1922a9de99b3144c738a193f2a75e4726078 \
-    --hash=sha256:e2cc737906d8de47eedbc4476f711b960c16a65daa8cdd021875398c81999a09 \
-    --hash=sha256:e37884fe39e4560bf5934a4ec4ba7f7fe0e7c091053d03d05b20a70557167717 \
-    --hash=sha256:e914f7161b3831d7c58db33cc5c7ca64b42c9877c5a776a8313e7a5fd494f8de \
-    --hash=sha256:ec82350c24cdcf34a8d4a5f189d0ff7dc025658098a60e6f0e681d24b6a1414e \
-    --hash=sha256:fd9bc6fef3f6a10043635a75e1a77c9dce877375140e81059c67c73d4ce65c4c
+biopython==1.84 \
+    --hash=sha256:0c425a39871f652598f502671aa5f6b5125475a91333a368a47f9c611ca96db1 \
+    --hash=sha256:25f4ef193a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e \
+    --hash=sha256:2cb8e839ab472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20 \
+    --hash=sha256:2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4 \
+    --hash=sha256:2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4 \
+    --hash=sha256:3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b \
+    --hash=sha256:4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad \
+    --hash=sha256:507ac3956f3107e77fee362ecb048dafb5f97cbcf110012d091418430c3227c7 \
+    --hash=sha256:52b6098f47d6b90fc8a5e8579b81ee50047e9108f0976e69c891ae0c4817e42d \
+    --hash=sha256:60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4 \
+    --hash=sha256:61765b71f84814a1eeb55ab222f43330aa7ad3e55ab91e8b444706149c67a281 \
+    --hash=sha256:7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089 \
+    --hash=sha256:7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f \
+    --hash=sha256:894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a13e7585ff4 \
+    --hash=sha256:89ef3967f5a88b5bb6344bef75ae83386de53fed3966d5c8c334ad885f8db08a \
+    --hash=sha256:9e3f7476fd81f31e048965d7be2826f018686e870d96870f440b609002953954 \
+    --hash=sha256:9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da7 \
+    --hash=sha256:b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4 \
+    --hash=sha256:b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b479118 \
+    --hash=sha256:ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4f96d0059 \
+    --hash=sha256:c792508988fc3ccf18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c \
+    --hash=sha256:ca8d6a88b9a9718074b3f5b450f9ea5adf7112a7dbaed55d82d5b623f5859a01 \
+    --hash=sha256:ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c \
+    --hash=sha256:ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae \
+    --hash=sha256:f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c
     # via seq-retrieval (pyproject.toml)
 certifi==2024.7.4 \
     --hash=sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b \