From fae5dbfd3dbb7c2904cf7a67f527a2e5892474fc Mon Sep 17 00:00:00 2001
From: Brad Macdonald <bwm03570@gmail.com>
Date: Mon, 12 Feb 2024 14:27:24 -0700
Subject: [PATCH] upgrades pandas and synspseclient versions

---
 Pipfile.lock                             | 2706 ++++++++++------------
 setup.cfg                                |    4 +-
 tests/transform/test_genes_biodomains.py |    4 +-
 3 files changed, 1259 insertions(+), 1455 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 98276be2..44027be0 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -46,11 +46,11 @@
         },
         "appnope": {
             "hashes": [
-                "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24",
-                "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"
+                "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee",
+                "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"
             ],
             "markers": "platform_system == 'Darwin'",
-            "version": "==0.1.3"
+            "version": "==0.1.4"
         },
         "argon2-cffi": {
             "hashes": [
@@ -112,11 +112,11 @@
         },
         "attrs": {
             "hashes": [
-                "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04",
-                "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"
+                "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30",
+                "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==23.1.0"
+            "version": "==23.2.0"
         },
         "babel": {
             "hashes": [
@@ -126,13 +126,21 @@
             "markers": "python_version >= '3.7'",
             "version": "==2.14.0"
         },
+        "backoff": {
+            "hashes": [
+                "sha256:03f829f5bb1923180821643f8753b0502c3b682293992485b0eef2807afa5cba",
+                "sha256:63579f9a0628e06278f7e47b7d7d5b6ce20dc65c5e96a6f3ca99a6adca0396e8"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==2.2.1"
+        },
         "beautifulsoup4": {
             "hashes": [
-                "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da",
-                "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"
+                "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051",
+                "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"
             ],
             "markers": "python_full_version >= '3.6.0'",
-            "version": "==4.12.2"
+            "version": "==4.12.3"
         },
         "bleach": {
             "hashes": [
@@ -144,11 +152,11 @@
         },
         "certifi": {
             "hashes": [
-                "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1",
-                "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"
+                "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f",
+                "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2023.11.17"
+            "version": "==2024.2.2"
         },
         "cffi": {
             "hashes": [
@@ -205,7 +213,7 @@
                 "sha256:fa3a0128b152627161ce47201262d3140edb5a5c3da88d73a1b790a959126956",
                 "sha256:fcc8eb6d5902bb1cf6dc4f187ee3ea80a1eba0a89aba40a5cb20a5087d961357"
             ],
-            "markers": "python_version >= '3.8'",
+            "markers": "platform_python_implementation != 'PyPy'",
             "version": "==1.16.0"
         },
         "charset-normalizer": {
@@ -322,64 +330,77 @@
         },
         "comm": {
             "hashes": [
-                "sha256:2da8d9ebb8dd7bfc247adaff99f24dce705638a8042b85cb995066793e391001",
-                "sha256:a517ea2ca28931c7007a7a99c562a0fa5883cfb48963140cf642c41c948498be"
+                "sha256:0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a",
+                "sha256:87928485c0dfc0e7976fd89fc1e187023cf587e7c353e4a9b417555b44adf021"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==0.2.0"
+            "version": "==0.2.1"
         },
         "cryptography": {
             "hashes": [
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+                "sha256:c9377be063b0b8352ca64ec60d1f94ed402bc48454f098effafa56999438c75a",
+                "sha256:cb105cf46b63848a2623206309fc0f419473286eba34cc605e21a223c8868351",
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+                "sha256:e92fbd578d4bab3cb70478919844bfaf3d04cb0bc841bff9f249ac5730401ced",
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             "markers": "python_version >= '3.7'",
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-            "version": "==1.8.0"
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+                "sha256:e38beb7992b5afd9d5244e96ad5fa9135e94993b0c551ceebf3fe1a5d9beb234",
+                "sha256:edcc9f58ec0fd121a25bc950d4578df47428d72e1a0d66c07403b04eb93bcf98",
+                "sha256:efd3fdd3f67a7e576dd869c184c5dd71d9aaa36ded271939da352880c012e703",
+                "sha256:f696d6be15be87aef621917585f9bb94b1dc9e8aced570db1b8a6fc14e8f9b42",
+                "sha256:fd97ed11a4c7f6d042d320ce03d83b20c3fb40da892f994bc041bbc415d7a099"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==1.8.1"
         },
         "decorator": {
             "hashes": [
@@ -431,10 +452,10 @@
         },
         "fastjsonschema": {
             "hashes": [
-                "sha256:b9fd1a2dd6971dbc7fee280a95bd199ae0dd9ce22beb91cc75e9c1c528a5170e",
-                "sha256:e25df6647e1bc4a26070b700897b07b542ec898dd4f1f6ea013e7f6a88417225"
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-            "version": "==2.19.0"
+            "version": "==2.19.1"
         },
         "fqdn": {
             "hashes": [
@@ -443,6 +464,14 @@
             ],
             "version": "==1.5.1"
         },
+        "googleapis-common-protos": {
+            "hashes": [
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+                "sha256:83f0ece9f94e5672cced82f592d2a5edf527a96ed1794f0bab36d5735c996277"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.62.0"
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         "great-expectations": {
             "hashes": [
                 "sha256:343f89109ea4edd8c367c938d65181509f8add957f07997da4d8d6e7cb9fb756",
@@ -485,19 +514,19 @@
         },
         "importlib-metadata": {
             "hashes": [
-                "sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7",
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+                "sha256:1231cf92d825c9e03cfc4da076a16de6422c863558229ea0b22b675657463443",
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             "markers": "python_version >= '3.8'",
-            "version": "==7.0.0"
+            "version": "==6.11.0"
         },
         "ipykernel": {
             "hashes": [
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-                "sha256:dab88b47f112f9f7df62236511023c9bdeef67abc73af7c652e4ce4441601686"
+                "sha256:3bade28004e3ff624ed57974948116670604ac5f676d12339693f3142176d3f0",
+                "sha256:50384f5c577a260a1d53f1f59a828c7266d321c9b7d00d345693783f66616055"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==6.27.1"
+            "version": "==6.29.2"
         },
         "ipython": {
             "hashes": [
@@ -509,11 +538,11 @@
         },
         "ipywidgets": {
             "hashes": [
-                "sha256:2b88d728656aea3bbfd05d32c747cfd0078f9d7e159cf982433b58ad717eed7f",
-                "sha256:40211efb556adec6fa450ccc2a77d59ca44a060f4f9f136833df59c9f538e6e8"
+                "sha256:bbe43850d79fb5e906b14801d6c01402857996864d1e5b6fa62dd2ee35559f60",
+                "sha256:d0b9b41e49bae926a866e613a39b0f0097745d2b9f1f3dd406641b4a57ec42c9"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==8.1.1"
+            "version": "==8.1.2"
         },
         "isoduration": {
             "hashes": [
@@ -532,11 +561,11 @@
         },
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             "markers": "python_version >= '3.7'",
-            "version": "==2.1.3"
+            "version": "==2.1.5"
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         "marshmallow": {
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@@ -772,11 +793,11 @@
         },
         "nbconvert": {
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@@ -788,19 +809,19 @@
         },
         "nest-asyncio": {
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-            "version": "==1.5.8"
+            "version": "==1.6.0"
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@@ -812,53 +833,101 @@
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@@ -870,33 +939,42 @@
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@@ -916,11 +994,11 @@
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@@ -938,27 +1016,44 @@
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@@ -1539,34 +1609,34 @@
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@@ -1617,11 +1687,11 @@
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@@ -1674,19 +1744,19 @@
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@@ -1698,10 +1768,11 @@
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@@ -1711,6 +1782,14 @@
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@@ -2040,21 +2030,13 @@
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@@ -2064,40 +2046,48 @@
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@@ -2548,11 +2476,11 @@
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@@ -2564,11 +2492,11 @@
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@@ -2580,11 +2508,11 @@
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@@ -2596,11 +2524,11 @@
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@@ -2619,11 +2547,11 @@
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@@ -2650,19 +2578,19 @@
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@@ -2674,11 +2602,11 @@
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@@ -2690,35 +2618,35 @@
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@@ -2738,19 +2666,11 @@
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@@ -2761,77 +2681,77 @@
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@@ -2947,11 +2787,11 @@
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@@ -2963,11 +2803,11 @@
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@@ -2979,11 +2819,11 @@
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         "packaging": {
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@@ -3053,33 +2941,42 @@
         },
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@@ -3144,27 +3041,44 @@
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@@ -3425,6 +3313,7 @@
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@@ -3830,11 +3719,11 @@
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@@ -3862,11 +3751,11 @@
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@@ -3887,19 +3776,19 @@
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@@ -3911,10 +3800,11 @@
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@@ -3924,6 +3814,14 @@
             "markers": "python_version >= '3.8'",
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@@ -3957,10 +3855,10 @@
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@@ -3986,11 +3884,11 @@
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@@ -4068,102 +3966,6 @@
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-                "sha256:bac8d525a8dbc2a1507ec731d2867025d11ceadcb4dd421423a5d42c56818541",
-                "sha256:bef596fdaa8f26e3d66af846bbe77057237cb6e8efff8cd7cc8dff9a62278bbf",
-                "sha256:c0ec0ed476f77db9fb29bca17f0a8fcc7bc97ad4c6c1d8959c507decb22e8572",
-                "sha256:c38c9ddb6103ceae4e4498f9c08fac9b590c5c71b0370f98714768e22ac6fa66",
-                "sha256:c7224cab95645c7ab53791022ae77a4509472613e839dab722a72abe5a684575",
-                "sha256:c74018551e31269d56fab81a728f683667e7c28c04e807ba08f8c9e3bba32f14",
-                "sha256:ca06675212f94e7a610e85ca36948bb8fc023e458dd6c63ef71abfd482481aa5",
-                "sha256:d1d2532b340b692880261c15aee4dc94dd22ca5d61b9db9a8a361953d36410b1",
-                "sha256:d25039a474c4c72a5ad4b52495056f843a7ff07b632c1b92ea9043a3d9950f6e",
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-                "sha256:ee04010f26d5102399bd17f8df8bc38dc7ccd7701dc77f4a68c5b8d733406958",
-                "sha256:f3bc6af6e2b8f92eced34ef6a96ffb248e863af20ef4fde9448cc8c9b858b749",
-                "sha256:f7d6b36dd2e029b6bcb8a13cf19664c7b8e19ab3a58e0fefbb5b8461447ed5ec"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==1.9.4"
-        },
         "zipp": {
             "hashes": [
                 "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31",
diff --git a/setup.cfg b/setup.cfg
index c741eda0..3ffe4f41 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -33,10 +33,10 @@ package_dir =
     = src
 packages = find:
 install_requires =
-    pandas==1.2.4
+    pandas~=2.0.0
     numpy~=1.21
     setuptools~=67.0.0
-    synapseclient~=3.1.1
+    synapseclient~=4.0.0
     PyYAML~=6.0
     pyarrow~=14.0.1
     typer~=0.7.0
diff --git a/tests/transform/test_genes_biodomains.py b/tests/transform/test_genes_biodomains.py
index dfce32a2..799853c8 100644
--- a/tests/transform/test_genes_biodomains.py
+++ b/tests/transform/test_genes_biodomains.py
@@ -83,7 +83,9 @@ def test_transform_genes_biodomains_should_pass(
 
     @pytest.mark.parametrize("input_file", fail_test_data, ids=fail_test_ids)
     def test_transform_genes_biodomains_should_fail(self, input_file):
-        with pytest.raises(KeyError):
+        with pytest.raises(
+            ValueError, match="cannot insert ensembl_gene_id, already exists"
+        ):
             input_df = pd.read_csv(
                 os.path.join(self.data_files_path, "input", input_file)
             )