From e700f2f9fa3193b32f2ce2958ffc1158e7deb92f Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 12 Feb 2023 20:40:04 -0800
Subject: [PATCH 1/2] Update Pipenv dependencies

---
 Pipfile.lock | 861 +++++++++++++++++++++++++++++++--------------------
 1 file changed, 522 insertions(+), 339 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index c099eb5..46af44a 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -18,11 +18,10 @@
     "default": {
         "atomicwrites": {
             "hashes": [
-                "sha256:6d1784dea7c0c8d4a5172b6c620f40b6e4cbfdf96d783691f2e1302a7b88e197",
-                "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"
+                "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==1.4.0"
+            "version": "==1.4.1"
         },
         "cycler": {
             "hashes": [
@@ -34,60 +33,85 @@
         },
         "fonttools": {
             "hashes": [
-                "sha256:c0fdcfa8ceebd7c1b2021240bd46ef77aa8e7408cf10434be55df52384865f8e",
-                "sha256:f829c579a8678fa939a1d9e9894d01941db869de44390adb49ce67055a06cc2a"
+                "sha256:2bb244009f9bf3fa100fc3ead6aeb99febe5985fa20afbfbaa2f8946c2fbdaf1",
+                "sha256:820466f43c8be8c3009aef8b87e785014133508f0de64ec469e4efb643ae54fb"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==4.33.3"
+            "version": "==4.38.0"
         },
         "kiwisolver": {
             "hashes": [
-                "sha256:0b7f50a1a25361da3440f07c58cd1d79957c2244209e4f166990e770256b6b0b",
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             ],
             "markers": "python_version >= '3.7'",
-            "version": "==1.4.2"
+            "version": "==1.4.4"
         },
         "lineage": {
             "editable": true,
@@ -95,44 +119,44 @@
         },
         "matplotlib": {
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@@ -173,11 +197,11 @@
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@@ -272,10 +335,10 @@
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@@ -287,89 +350,178 @@
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@@ -478,79 +649,91 @@
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+                "sha256:340bea174e9761308703ae988e982005aedf427de816d1afe98147668cc03036",
+                "sha256:40627dcf047dadb22cd25ea7ecfe9cbf3bbbad0482ee5920b582f3809c97654f",
+                "sha256:40dfd3fefbef579ee058f139733ac336312663c6706d1163b82b3003fb1925c4",
+                "sha256:4cf06cdc1dda95223e9d2d3c58d3b178aa5dacb35ee7e3bbac10e4e1faacb419",
+                "sha256:50c42830a633fa0cf9e7d27664637532791bfc31c731a87b202d2d8ac40c3ea2",
+                "sha256:55f44b440d491028addb3b88f72207d71eeebfb7b5dbf0643f7c023ae1fba619",
+                "sha256:608e7073dfa9e38a85d38474c082d4281f4ce276ac0010224eaba11e929dd53a",
+                "sha256:63ba06c9941e46fa389d389644e2d8225e0e3e5ebcc4ff1ea8506dce646f8c8a",
+                "sha256:65608c35bfb8a76763f37036547f7adfd09270fbdbf96608be2bead319728fcd",
+                "sha256:665a36ae6f8f20a4676b53224e33d456a6f5a72657d9c83c2aa00765072f31f7",
+                "sha256:6d6607f98fcf17e534162f0709aaad3ab7a96032723d8ac8750ffe17ae5a0666",
+                "sha256:7313ce6a199651c4ed9d7e4cfb4aa56fe923b1adf9af3b420ee14e6d9a73df65",
+                "sha256:7668b52e102d0ed87cb082380a7e2e1e78737ddecdde129acadb0eccc5423859",
+                "sha256:7df70907e00c970c60b9ef2938d894a9381f38e6b9db73c5be35e59d92e06625",
+                "sha256:7e007132af78ea9df29495dbf7b5824cb71648d7133cf7848a2a5dd00d36f9ff",
+                "sha256:835fb5e38fd89328e9c81067fd642b3593c33e1e17e2fdbf77f5676abb14a156",
+                "sha256:8bca7e26c1dd751236cfb0c6c72d4ad61d986e9a41bbf76cb445f69488b2a2bd",
+                "sha256:8db032bf0ce9022a8e41a22598eefc802314e81b879ae093f36ce9ddf39ab1ba",
+                "sha256:99625a92da8229df6d44335e6fcc558a5037dd0a760e11d84be2260e6f37002f",
+                "sha256:9cad97ab29dfc3f0249b483412c85c8ef4766d96cdf9dcf5a1e3caa3f3661cf1",
+                "sha256:a4abaec6ca3ad8660690236d11bfe28dfd707778e2442b45addd2f086d6ef094",
+                "sha256:a6e40afa7f45939ca356f348c8e23048e02cb109ced1eb8420961b2f40fb373a",
+                "sha256:a6f2fcca746e8d5910e18782f976489939d54a91f9411c32051b4aab2bd7c513",
+                "sha256:a806db027852538d2ad7555b203300173dd1b77ba116de92da9afbc3a3be3eed",
+                "sha256:abcabc8c2b26036d62d4c746381a6f7cf60aafcc653198ad678306986b09450d",
+                "sha256:b8526c6d437855442cdd3d87eede9c425c4445ea011ca38d937db299382e6fa3",
+                "sha256:bb06feb762bade6bf3c8b844462274db0c76acc95c52abe8dbed28ae3d44a147",
+                "sha256:c0a33bc9f02c2b17c3ea382f91b4db0e6cde90b63b296422a939886a7a80de1c",
+                "sha256:c4a549890a45f57f1ebf99c067a4ad0cb423a05544accaf2b065246827ed9603",
+                "sha256:ca244fa73f50a800cf8c3ebf7fd93149ec37f5cb9596aa8873ae2c1d23498601",
+                "sha256:cf877ab4ed6e302ec1d04952ca358b381a882fbd9d1b07cccbfd61783561f98a",
+                "sha256:d9d971ec1e79906046aa3ca266de79eac42f1dbf3612a05dc9368125952bd1a1",
+                "sha256:da25303d91526aac3672ee6d49a2f3db2d9502a4a60b55519feb1a4c7714e07d",
+                "sha256:e55e40ff0cc8cc5c07996915ad367fa47da6b3fc091fdadca7f5403239c5fec3",
+                "sha256:f03a532d7dee1bed20bc4884194a16160a2de9ffc6354b3878ec9682bb623c54",
+                "sha256:f1cd098434e83e656abf198f103a8207a8187c0fc110306691a2e94a78d0abb2",
+                "sha256:f2bfb563d0211ce16b63c7cb9395d2c682a23187f54c3d79bfec33e6705473c6",
+                "sha256:f8ffb705ffcf5ddd0e80b65ddf7bed7ee4f5a441ea7d3419e861a12eaf41af58"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.1"
+            "version": "==2.1.2"
         },
         "mypy-extensions": {
             "hashes": [
-                "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d",
-                "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"
+                "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d",
+                "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"
             ],
-            "version": "==0.4.3"
+            "markers": "python_version >= '3.5'",
+            "version": "==1.0.0"
         },
         "packaging": {
             "hashes": [
-                "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb",
-                "sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522"
+                "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2",
+                "sha256:b6ad297f8907de0fa2fe1ccbd26fdaf387f5f47c7275fedf8cce89f99446cf97"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==21.3"
+            "markers": "python_version >= '3.7'",
+            "version": "==23.0"
         },
         "pathspec": {
             "hashes": [
-                "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a",
-                "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"
+                "sha256:3a66eb970cbac598f9e5ccb5b2cf58930cd8e3ed86d393d541eaf2d8b1705229",
+                "sha256:64d338d4e0914e91c1792321e6907b5a593f1ab1851de7fc269557a21b30ebbc"
             ],
-            "version": "==0.9.0"
+            "markers": "python_version >= '3.7'",
+            "version": "==0.11.0"
         },
         "platformdirs": {
             "hashes": [
-                "sha256:027d8e83a2d7de06bbac4e5ef7e023c02b863d7ea5d079477e722bb41ab25788",
-                "sha256:58c8abb07dcb441e6ee4b11d8df0ac856038f944ab98b7be6b27b2a3c7feef19"
+                "sha256:8a1228abb1ef82d788f74139988b137e78692984ec7b08eaa6c65f1723af28f9",
+                "sha256:b1d5eb14f221506f50d6604a561f4c5786d9e80355219694a1b244bcd96f4567"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.5.2"
+            "version": "==3.0.0"
         },
         "pluggy": {
             "hashes": [
@@ -560,60 +743,52 @@
             "markers": "python_version >= '3.6'",
             "version": "==1.0.0"
         },
-        "py": {
-            "hashes": [
-                "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719",
-                "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"
-            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==1.11.0"
-        },
         "pygments": {
             "hashes": [
-                "sha256:5eb116118f9612ff1ee89ac96437bb6b49e8f04d8a13b514ba26f620208e26eb",
-                "sha256:dc9c10fb40944260f6ed4c688ece0cd2048414940f1cea51b8b226318411c519"
+                "sha256:b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297",
+                "sha256:fa7bd7bd2771287c0de303af8bfdfc731f51bd2c6a47ab69d117138893b82717"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2.12.0"
-        },
-        "pyparsing": {
-            "hashes": [
-                "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb",
-                "sha256:5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc"
-            ],
-            "markers": "python_full_version >= '3.6.8'",
-            "version": "==3.0.9"
+            "version": "==2.14.0"
         },
         "pytest": {
             "hashes": [
-                "sha256:13d0e3ccfc2b6e26be000cb6568c832ba67ba32e719443bfe725814d3c42433c",
-                "sha256:a06a0425453864a270bc45e71f783330a7428defb4230fb5e6a731fde06ecd45"
+                "sha256:c7c6ca206e93355074ae32f7403e8ea12163b1163c976fee7d4d84027c162be5",
+                "sha256:d45e0952f3727241918b8fd0f376f5ff6b301cc0777c6f9a556935c92d8a7d42"
             ],
             "index": "pypi",
-            "version": "==7.1.2"
+            "version": "==7.2.1"
         },
         "pytest-cov": {
             "hashes": [
-                "sha256:578d5d15ac4a25e5f961c938b85a05b09fdaae9deef3bb6de9a6e766622ca7a6",
-                "sha256:e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470"
+                "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b",
+                "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"
             ],
             "index": "pypi",
-            "version": "==3.0.0"
+            "version": "==4.0.0"
         },
         "pytz": {
             "hashes": [
-                "sha256:1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7",
-                "sha256:e68985985296d9a66a881eb3193b0906246245294a881e7c8afe623866ac6a5c"
+                "sha256:01a0681c4b9684a28304615eba55d1ab31ae00bf68ec157ec3708a8182dbbcd0",
+                "sha256:78f4f37d8198e0627c5f1143240bb0206b8691d8d7ac6d78fee88b78733f8c4a"
             ],
-            "version": "==2022.1"
+            "version": "==2022.7.1"
         },
         "requests": {
             "hashes": [
-                "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61",
-                "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d"
+                "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa",
+                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==2.27.1"
+            "markers": "python_version >= '3.7' and python_version < '4'",
+            "version": "==2.28.2"
+        },
+        "setuptools": {
+            "hashes": [
+                "sha256:16ccf598aab3b506593c17378473978908a2734d7336755a8769b480906bec1c",
+                "sha256:b440ee5f7e607bb8c9de15259dba2583dd41a38879a7abc1d43a71c59524da48"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==67.2.0"
         },
         "snowballstemmer": {
             "hashes": [
@@ -624,19 +799,19 @@
         },
         "sphinx": {
             "hashes": [
-                "sha256:36aa2a3c2f6d5230be94585bc5d74badd5f9ed8f3388b8eedc1726fe45b1ad30",
-                "sha256:f4da1187785a5bc7312cc271b0e867a93946c319d106363e102936a3d9857306"
+                "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d",
+                "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"
             ],
             "index": "pypi",
-            "version": "==5.0.1"
+            "version": "==5.3.0"
         },
         "sphinx-rtd-theme": {
             "hashes": [
-                "sha256:4d35a56f4508cfee4c4fb604373ede6feae2a306731d533f409ef5c3496fdbd8",
-                "sha256:eec6d497e4c2195fa0e8b2016b337532b8a699a68bcb22a512870e16925c6a5c"
+                "sha256:a0d8bd1a2ed52e0b338cbe19c4b2eef3c5e7a048769753dac6a9f059c7b641b8",
+                "sha256:f823f7e71890abe0ac6aaa6013361ea2696fc8d3e1fa798f463e82bdb77eeff2"
             ],
             "index": "pypi",
-            "version": "==1.0.0"
+            "version": "==1.2.0"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
@@ -662,6 +837,14 @@
             "markers": "python_version >= '3.6'",
             "version": "==2.0.0"
         },
+        "sphinxcontrib-jquery": {
+            "hashes": [
+                "sha256:8fb65f6dba84bf7bcd1aea1f02ab3955ac34611d838bcc95d4983b805b234daa",
+                "sha256:ed47fa425c338ffebe3c37e1cdb56e30eb806116b85f01055b158c7057fdb995"
+            ],
+            "markers": "python_version >= '3.1'",
+            "version": "==2.0.0"
+        },
         "sphinxcontrib-jsmath": {
             "hashes": [
                 "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178",
@@ -726,27 +909,27 @@
         },
         "typing-extensions": {
             "hashes": [
-                "sha256:6657594ee297170d19f67d55c05852a874e7eb634f4f753dbd667855e07c1708",
-                "sha256:f1c24655a0da0d1b67f07e17a5e6b2a105894e6824b92096378bb3668ef02376"
+                "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa",
+                "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"
             ],
             "markers": "python_version < '3.8'",
-            "version": "==4.2.0"
+            "version": "==4.4.0"
         },
         "urllib3": {
             "hashes": [
-                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
-                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
+                "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72",
+                "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.9"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
+            "version": "==1.26.14"
         },
         "zipp": {
             "hashes": [
-                "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad",
-                "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"
+                "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6",
+                "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==3.8.0"
+            "version": "==3.13.0"
         }
     }
 }

From 51e25703c282b4e81d3bf1fc2bcf12ce58015ed0 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 12 Feb 2023 20:44:08 -0800
Subject: [PATCH 2/2] Reformat with current version of `black`

---
 docs/conf.py            | 1 +
 src/lineage/__init__.py | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index c028eea..ab6120f 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -190,6 +190,7 @@
     )
 ]
 
+
 # document __init__ methods
 # https://stackoverflow.com/a/5599712
 def skip(app, what, name, obj, would_skip, options):
diff --git a/src/lineage/__init__.py b/src/lineage/__init__.py
index 40cd50c..8e48bfa 100644
--- a/src/lineage/__init__.py
+++ b/src/lineage/__init__.py
@@ -632,7 +632,6 @@ def _find_shared_dna_return_helper(
         one_chrom_discrepant_snps,
         two_chrom_discrepant_snps,
     ):
-
         return {
             "one_chrom_shared_dna": one_chrom_shared_dna,
             "two_chrom_shared_dna": two_chrom_shared_dna,