Merge pull request #215 from hms-dbmi/development

Development
hms-dbmi · Mar 25, 2024 · 11962d1 · 11962d1
2 parents e78089b + 39aac79
commit 11962d1
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diff --git a/.github/workflows/requirements-update.yml b/.github/workflows/requirements-update.yml
@@ -32,7 +32,7 @@ jobs:
     - name: Setup python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.10'
+        python-version: '3.12'
 
     - name: Install dev Python packages
       run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,15 @@
 minimum_pre_commit_version: "2.13.0"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks.git
-    rev: v4.2.0
+    rev: v4.5.0
     hooks:
     - id: trailing-whitespace
     - id: mixed-line-ending
     - id: check-byte-order-marker
     - id: check-merge-conflict
     - id: detect-aws-credentials
   - repo: https://github.com/jazzband/pip-tools
-    rev: 6.6.0
+    rev: 7.4.1
     hooks:
       - id: pip-compile
         name: pip-compile dev-requirements.in

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM hmsdbmitc/dbmisvc:debian11-slim-python3.10-0.5.1 AS builder
+FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.1 AS builder
 
 # Install requirements
 RUN apt-get update \
@@ -22,7 +22,7 @@ RUN pip install -U wheel \
     && pip wheel -r /requirements.txt \
         --wheel-dir=/root/wheels
 
-FROM hmsdbmitc/dbmisvc:debian11-slim-python3.10-0.5.1
+FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.1
 
 # Copy PhantomJS binary
 COPY --from=builder /tmp/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin/phantomjs

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -1,111 +1,129 @@
 #
-# This file is autogenerated by pip-compile with python 3.10
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.12
+# by the following command:
 #
 #    pip-compile --allow-unsafe --generate-hashes --output-file=dev-requirements.txt dev-requirements.in
 #
-cfgv==3.3.1 \
-    --hash=sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426 \
-    --hash=sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736
+build==1.1.1 \
+    --hash=sha256:8ed0851ee76e6e38adce47e4bee3b51c771d86c64cf578d0c2245567ee200e73 \
+    --hash=sha256:8eea65bb45b1aac2e734ba2cc8dad3a6d97d97901a395bd0ed3e7b46953d2a31
+    # via pip-tools
+cfgv==3.4.0 \
+    --hash=sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9 \
+    --hash=sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560
     # via pre-commit
-click==8.1.3 \
-    --hash=sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e \
-    --hash=sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48
+click==8.1.7 \
+    --hash=sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28 \
+    --hash=sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de
     # via pip-tools
-distlib==0.3.4 \
-    --hash=sha256:6564fe0a8f51e734df6333d08b8b94d4ea8ee6b99b5ed50613f731fd4089f34b \
-    --hash=sha256:e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579
+distlib==0.3.8 \
+    --hash=sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784 \
+    --hash=sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64
     # via virtualenv
-filelock==3.6.0 \
-    --hash=sha256:9cd540a9352e432c7246a48fe4e8712b10acb1df2ad1f30e8c070b82ae1fed85 \
-    --hash=sha256:f8314284bfffbdcfa0ff3d7992b023d4c628ced6feb957351d4c48d059f56bc0
+filelock==3.13.1 \
+    --hash=sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e \
+    --hash=sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c
     # via virtualenv
-identify==2.5.0 \
-    --hash=sha256:3acfe15a96e4272b4ec5662ee3e231ceba976ef63fd9980ed2ce9cc415df393f \
-    --hash=sha256:c83af514ea50bf2be2c4a3f2fb349442b59dc87284558ae9ff54191bff3541d2
+identify==2.5.35 \
+    --hash=sha256:10a7ca245cfcd756a554a7288159f72ff105ad233c7c4b9c6f0f4d108f5f6791 \
+    --hash=sha256:c4de0081837b211594f8e877a6b4fad7ca32bbfc1a9307fdd61c28bfe923f13e
     # via pre-commit
-nodeenv==1.6.0 \
-    --hash=sha256:3ef13ff90291ba2a4a7a4ff9a979b63ffdd00a464dbe04acf0ea6471517a4c2b \
-    --hash=sha256:621e6b7076565ddcacd2db0294c0381e01fd28945ab36bcf00f41c5daf63bef7
+nodeenv==1.8.0 \
+    --hash=sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2 \
+    --hash=sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec
     # via pre-commit
-pep517==0.12.0 \
-    --hash=sha256:931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0 \
-    --hash=sha256:dd884c326898e2c6e11f9e0b64940606a93eb10ea022a2e067959f3a110cf161
-    # via pip-tools
-pip-tools==6.6.0 \
-    --hash=sha256:66318bc2e884b61fafa1cb2cf01b35fdd779ab9ce82cc1bce277adb8cf3ab845 \
-    --hash=sha256:98aa24004440a1c0489d71a567a4e8afdf23c7782bff483d1219881e7302de83
+packaging==24.0 \
+    --hash=sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5 \
+    --hash=sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9
+    # via build
+pip-tools==7.4.1 \
+    --hash=sha256:4c690e5fbae2f21e87843e89c26191f0d9454f362d8acdbd695716493ec8b3a9 \
+    --hash=sha256:864826f5073864450e24dbeeb85ce3920cdfb09848a3d69ebf537b521f14bcc9
     # via -r dev-requirements.in
-platformdirs==2.5.2 \
-    --hash=sha256:027d8e83a2d7de06bbac4e5ef7e023c02b863d7ea5d079477e722bb41ab25788 \
-    --hash=sha256:58c8abb07dcb441e6ee4b11d8df0ac856038f944ab98b7be6b27b2a3c7feef19
+platformdirs==4.2.0 \
+    --hash=sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068 \
+    --hash=sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768
     # via virtualenv
-pre-commit==2.19.0 \
-    --hash=sha256:10c62741aa5704faea2ad69cb550ca78082efe5697d6f04e5710c3c229afdd10 \
-    --hash=sha256:4233a1e38621c87d9dda9808c6606d7e7ba0e087cd56d3fe03202a01d2919615
+pre-commit==3.6.2 \
+    --hash=sha256:ba637c2d7a670c10daedc059f5c49b5bd0aadbccfcd7ec15592cf9665117532c \
+    --hash=sha256:c3ef34f463045c88658c5b99f38c1e297abdcc0ff13f98d3370055fbbfabc67e
     # via -r dev-requirements.in
-pyyaml==6.0 \
-    --hash=sha256:0283c35a6a9fbf047493e3a0ce8d79ef5030852c51e9d911a27badfde0605293 \
-    --hash=sha256:055d937d65826939cb044fc8c9b08889e8c743fdc6a32b33e2390f66013e449b \
-    --hash=sha256:07751360502caac1c067a8132d150cf3d61339af5691fe9e87803040dbc5db57 \
-    --hash=sha256:0b4624f379dab24d3725ffde76559cff63d9ec94e1736b556dacdfebe5ab6d4b \
-    --hash=sha256:0ce82d761c532fe4ec3f87fc45688bdd3a4c1dc5e0b4a19814b9009a29baefd4 \
-    --hash=sha256:1e4747bc279b4f613a09eb64bba2ba602d8a6664c6ce6396a4d0cd413a50ce07 \
-    --hash=sha256:213c60cd50106436cc818accf5baa1aba61c0189ff610f64f4a3e8c6726218ba \
-    --hash=sha256:231710d57adfd809ef5d34183b8ed1eeae3f76459c18fb4a0b373ad56bedcdd9 \
-    --hash=sha256:277a0ef2981ca40581a47093e9e2d13b3f1fbbeffae064c1d21bfceba2030287 \
-    --hash=sha256:2cd5df3de48857ed0544b34e2d40e9fac445930039f3cfe4bcc592a1f836d513 \
-    --hash=sha256:40527857252b61eacd1d9af500c3337ba8deb8fc298940291486c465c8b46ec0 \
-    --hash=sha256:473f9edb243cb1935ab5a084eb238d842fb8f404ed2193a915d1784b5a6b5fc0 \
-    --hash=sha256:48c346915c114f5fdb3ead70312bd042a953a8ce5c7106d5bfb1a5254e47da92 \
-    --hash=sha256:50602afada6d6cbfad699b0c7bb50d5ccffa7e46a3d738092afddc1f9758427f \
-    --hash=sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2 \
-    --hash=sha256:77f396e6ef4c73fdc33a9157446466f1cff553d979bd00ecb64385760c6babdc \
-    --hash=sha256:819b3830a1543db06c4d4b865e70ded25be52a2e0631ccd2f6a47a2822f2fd7c \
-    --hash=sha256:897b80890765f037df3403d22bab41627ca8811ae55e9a722fd0392850ec4d86 \
-    --hash=sha256:98c4d36e99714e55cfbaaee6dd5badbc9a1ec339ebfc3b1f52e293aee6bb71a4 \
-    --hash=sha256:9df7ed3b3d2e0ecfe09e14741b857df43adb5a3ddadc919a2d94fbdf78fea53c \
-    --hash=sha256:9fa600030013c4de8165339db93d182b9431076eb98eb40ee068700c9c813e34 \
-    --hash=sha256:a80a78046a72361de73f8f395f1f1e49f956c6be882eed58505a15f3e430962b \
-    --hash=sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c \
-    --hash=sha256:b5b9eccad747aabaaffbc6064800670f0c297e52c12754eb1d976c57e4f74dcb \
-    --hash=sha256:c5687b8d43cf58545ade1fe3e055f70eac7a5a1a0bf42824308d868289a95737 \
-    --hash=sha256:cba8c411ef271aa037d7357a2bc8f9ee8b58b9965831d9e51baf703280dc73d3 \
-    --hash=sha256:d15a181d1ecd0d4270dc32edb46f7cb7733c7c508857278d3d378d14d606db2d \
-    --hash=sha256:d4db7c7aef085872ef65a8fd7d6d09a14ae91f691dec3e87ee5ee0539d516f53 \
-    --hash=sha256:d4eccecf9adf6fbcc6861a38015c2a64f38b9d94838ac1810a9023a0609e1b78 \
-    --hash=sha256:d67d839ede4ed1b28a4e8909735fc992a923cdb84e618544973d7dfc71540803 \
-    --hash=sha256:daf496c58a8c52083df09b80c860005194014c3698698d1a57cbcfa182142a3a \
-    --hash=sha256:e61ceaab6f49fb8bdfaa0f92c4b57bcfbea54c09277b1b4f7ac376bfb7a7c174 \
-    --hash=sha256:f84fbc98b019fef2ee9a1cb3ce93e3187a6df0b2538a651bfb890254ba9f90b5
+pyproject-hooks==1.0.0 \
+    --hash=sha256:283c11acd6b928d2f6a7c73fa0d01cb2bdc5f07c57a2eeb6e83d5e56b97976f8 \
+    --hash=sha256:f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5
+    # via
+    #   build
+    #   pip-tools
+pyyaml==6.0.1 \
+    --hash=sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5 \
+    --hash=sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc \
+    --hash=sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df \
+    --hash=sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741 \
+    --hash=sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206 \
+    --hash=sha256:18aeb1bf9a78867dc38b259769503436b7c72f7a1f1f4c93ff9a17de54319b27 \
+    --hash=sha256:1d4c7e777c441b20e32f52bd377e0c409713e8bb1386e1099c2415f26e479595 \
+    --hash=sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62 \
+    --hash=sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98 \
+    --hash=sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696 \
+    --hash=sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290 \
+    --hash=sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9 \
+    --hash=sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d \
+    --hash=sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6 \
+    --hash=sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867 \
+    --hash=sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47 \
+    --hash=sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486 \
+    --hash=sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6 \
+    --hash=sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3 \
+    --hash=sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007 \
+    --hash=sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938 \
+    --hash=sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0 \
+    --hash=sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c \
+    --hash=sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735 \
+    --hash=sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d \
+    --hash=sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28 \
+    --hash=sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4 \
+    --hash=sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba \
+    --hash=sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8 \
+    --hash=sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef \
+    --hash=sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5 \
+    --hash=sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd \
+    --hash=sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3 \
+    --hash=sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0 \
+    --hash=sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515 \
+    --hash=sha256:baa90d3f661d43131ca170712d903e6295d1f7a0f595074f151c0aed377c9b9c \
+    --hash=sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c \
+    --hash=sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924 \
+    --hash=sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34 \
+    --hash=sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43 \
+    --hash=sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859 \
+    --hash=sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673 \
+    --hash=sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54 \
+    --hash=sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a \
+    --hash=sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b \
+    --hash=sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab \
+    --hash=sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa \
+    --hash=sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c \
+    --hash=sha256:fca0e3a251908a499833aa292323f32437106001d436eca0e6e7833256674585 \
+    --hash=sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d \
+    --hash=sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f
     # via pre-commit
-six==1.16.0 \
-    --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
-    --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
-    # via virtualenv
-toml==0.10.2 \
-    --hash=sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b \
-    --hash=sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f
+virtualenv==20.25.1 \
+    --hash=sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a \
+    --hash=sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197
     # via pre-commit
-tomli==2.0.1 \
-    --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \
-    --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f
-    # via pep517
-virtualenv==20.14.1 \
-    --hash=sha256:e617f16e25b42eb4f6e74096b9c9e37713cf10bf30168fb4a739f3fa8f898a3a \
-    --hash=sha256:ef589a79795589aada0c1c5b319486797c03b67ac3984c48c669c0e4f50df3a5
-    # via pre-commit
-wheel==0.37.1 \
-    --hash=sha256:4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a \
-    --hash=sha256:e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4
+wheel==0.43.0 \
+    --hash=sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85 \
+    --hash=sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81
     # via pip-tools
 
 # The following packages are considered to be unsafe in a requirements file:
-pip==22.0.4 \
-    --hash=sha256:b3a9de2c6ef801e9247d1527a4b16f92f2cc141cd1489f3fffaf6a9e96729764 \
-    --hash=sha256:c6aca0f2f081363f689f041d90dab2a07a9a07fb840284db2218117a52da800b
-    # via pip-tools
-setuptools==62.1.0 \
-    --hash=sha256:26ead7d1f93efc0f8c804d9fafafbe4a44b179580a7105754b245155f9af05a8 \
-    --hash=sha256:47c7b0c0f8fc10eec4cf1e71c6fdadf8decaa74ffa087e68cd1c20db7ad6a592
+pip==24.0 \
+    --hash=sha256:ba0d021a166865d2265246961bec0152ff124de910c5cc39f1156ce3fa7c69dc \
+    --hash=sha256:ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2
     # via pip-tools
+setuptools==69.2.0 \
+    --hash=sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e \
+    --hash=sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c
+    # via
+    #   nodeenv
+    #   pip-tools