From e9ecacf935a6ec37f62592f6628231fda9f50c74 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Tue, 22 Jun 2021 22:44:10 -0700
Subject: [PATCH 1/7] Update `__repr__` output

---
 README.rst | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index 85217cd..d6ea2fd 100644
--- a/README.rst
+++ b/README.rst
@@ -74,9 +74,9 @@ Create an ``Individual`` in the context of the ``lineage`` framework to interact
 ``User662`` dataset:
 
 >>> user662 = l.create_individual('User662', ['resources/662.23andme.340.txt.gz', 'resources/662.ftdna-illumina.341.csv.gz'])
-Loading SNPs('resources/662.23andme.340.txt.gz')
-Merging SNPs('resources/662.ftdna-illumina.341.csv.gz')
-SNPs('resources/662.ftdna-illumina.341.csv.gz') has Build 36; remapping to Build 37
+Loading SNPs('662.23andme.340.txt.gz')
+Merging SNPs('662.ftdna-illumina.341.csv.gz')
+SNPs('662.ftdna-illumina.341.csv.gz') has Build 36; remapping to Build 37
 Downloading resources/NCBI36_GRCh37.tar.gz
 27 SNP positions were discrepant; keeping original positions
 151 SNP genotypes were discrepant; marking those as null
@@ -113,7 +113,7 @@ Compare Individuals
 Let's create another ``Individual`` for the ``User663`` dataset:
 
 >>> user663 = l.create_individual('User663', 'resources/663.23andme.305.txt.gz')
-Loading SNPs('resources/663.23andme.305.txt.gz')
+Loading SNPs('663.23andme.305.txt.gz')
 
 Now we can perform some analysis between the ``User662`` and ``User663`` datasets.
 
@@ -201,10 +201,10 @@ For this example, let's create two more ``Individuals`` for the ``User4583`` and
 datasets:
 
 >>> user4583 = l.create_individual('User4583', 'resources/4583.ftdna-illumina.3482.csv.gz')
-Loading SNPs('resources/4583.ftdna-illumina.3482.csv.gz')
+Loading SNPs('4583.ftdna-illumina.3482.csv.gz')
 
 >>> user4584 = l.create_individual('User4584', 'resources/4584.ftdna-illumina.3483.csv.gz')
-Loading SNPs('resources/4584.ftdna-illumina.3483.csv.gz')
+Loading SNPs('4584.ftdna-illumina.3483.csv.gz')
 
 Now let's find the shared genes, specifying a
 `population-specific <https://www.internationalgenome.org/faq/which-populations-are-part-your-study/>`_

From 4691af11f1eb54e8e1ce4de7977bcfd1a691e734 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:01:26 -0800
Subject: [PATCH 2/7] Update Pipenv dependencies

---
 Pipfile.lock | 852 +++++++++++++++++++++++++++++----------------------
 1 file changed, 486 insertions(+), 366 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index b722a25..beb412c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -26,48 +26,69 @@
         },
         "cycler": {
             "hashes": [
-                "sha256:1d8a5ae1ff6c5cf9b93e8811e581232ad8920aeec647c37316ceac982b08cb2d",
-                "sha256:cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8"
+                "sha256:3a27e95f763a428a739d2add979fa7494c912a32c17c4c38c4d5f082cad165a3",
+                "sha256:9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f"
             ],
-            "version": "==0.10.0"
+            "markers": "python_version >= '3.6'",
+            "version": "==0.11.0"
+        },
+        "fonttools": {
+            "hashes": [
+                "sha256:545c05d0f7903a863c2020e07b8f0a57517f2c40d940bded77076397872d14ca",
+                "sha256:edf251d5d2cc0580d5f72de4621c338d8c66c5f61abb50cf486640f73c8194d5"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==4.28.5"
         },
         "kiwisolver": {
             "hashes": [
-                "sha256:0cd53f403202159b44528498de18f9285b04482bab2a6fc3f5dd8dbb9352e30d",
-                "sha256:1e1bc12fb773a7b2ffdeb8380609f4f8064777877b2225dec3da711b421fda31",
-                "sha256:225e2e18f271e0ed8157d7f4518ffbf99b9450fca398d561eb5c4a87d0986dd9",
-                "sha256:232c9e11fd7ac3a470d65cd67e4359eee155ec57e822e5220322d7b2ac84fbf0",
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-                "sha256:33449715e0101e4d34f64990352bce4095c8bf13bed1b390773fc0a7295967b3",
-                "sha256:401a2e9afa8588589775fe34fc22d918ae839aaaf0c0e96441c0fdbce6d8ebe6",
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-                "sha256:5989db3b3b34b76c09253deeaf7fbc2707616f130e166996606c284395da3f18",
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-                "sha256:5c3e6455341008a054cccee8c5d24481bcfe1acdbc9add30aa95798e95c65621",
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-                "sha256:72c99e39d005b793fb7d3d4e660aed6b6281b502e8c1eaf8ee8346023c8e03bc",
-                "sha256:78751b33595f7f9511952e7e60ce858c6d64db2e062afb325985ddbd34b5c131",
-                "sha256:834ee27348c4aefc20b479335fd422a2c69db55f7d9ab61721ac8cd83eb78882",
-                "sha256:8be8d84b7d4f2ba4ffff3665bcd0211318aa632395a1a41553250484a871d454",
-                "sha256:950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248",
-                "sha256:a357fd4f15ee49b4a98b44ec23a34a95f1e00292a139d6015c11f55774ef10de",
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-                "sha256:c08e95114951dc2090c4a630c2385bef681cacf12636fb0241accdc6b303fd81",
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+                "sha256:0007840186bacfaa0aba4466d5890334ea5938e0bb7e28078a0eb0e63b5b59d5",
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+                "sha256:a498bcd005e8a3fedd0022bb30ee0ad92728154a8798b703f394484452550507",
+                "sha256:a7a4cf5bbdc861987a7745aed7a536c6405256853c94abc9f3287c3fa401b174",
+                "sha256:b5074fb09429f2b7bc82b6fb4be8645dcbac14e592128beeff5461dcde0af09f",
+                "sha256:b6a5431940f28b6de123de42f0eb47b84a073ee3c3345dc109ad550a3307dd28",
+                "sha256:ba677bcaff9429fd1bf01648ad0901cea56c0d068df383d5f5856d88221fe75b",
+                "sha256:bcadb05c3d4794eb9eee1dddf1c24215c92fb7b55a80beae7a60530a91060560",
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+                "sha256:ec2eba188c1906b05b9b49ae55aae4efd8150c61ba450e6721f64620c50b59eb",
+                "sha256:ee040a7de8d295dbd261ef2d6d3192f13e2b08ec4a954de34a6fb8ff6422e24c",
+                "sha256:eedd3b59190885d1ebdf6c5e0ca56828beb1949b4dfe6e5d0256a461429ac386",
+                "sha256:f441422bb313ab25de7b3dbfd388e790eceb76ce01a18199ec4944b369017009",
+                "sha256:f8eb7b6716f5b50e9c06207a14172cf2de201e41912ebe732846c02c830455b9",
+                "sha256:fc4453705b81d03568d5b808ad8f09c77c47534f6ac2e72e733f9ca4714aa75c"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==1.3.1"
+            "markers": "python_version >= '3.7'",
+            "version": "==1.3.2"
         },
         "lineage": {
             "editable": true,
@@ -75,143 +96,180 @@
         },
         "matplotlib": {
             "hashes": [
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+                "sha256:fe8d40c434a8e2c68d64c6d6a04e77f21791a93ff6afe0dce169597c110d3079"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==3.4.2"
+            "version": "==3.5.1"
         },
         "numpy": {
             "hashes": [
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-            "version": "==2.8.1"
+            "version": "==2.8.2"
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         "pytz": {
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-            "version": "==2021.1"
+            "version": "==2021.3"
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@@ -223,11 +281,11 @@
         },
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-            "markers": "python_full_version >= '3.6.1'",
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+            "markers": "python_full_version >= '3.7.1'",
+            "version": "==2.4.1"
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     "develop": {
@@ -247,11 +305,11 @@
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-            "version": "==21.2.0"
+            "version": "==21.4.0"
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@@ -271,116 +329,114 @@
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@@ -391,43 +447,78 @@
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+                "sha256:bf594cc7cc9d528338d66674c10a5b25e3cde7dd75c3e96784df8f371d77a298",
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+                "sha256:c73d2166e4b210b73d1429c4f1ca97cea9cc090e5302df2a7a0a96ce55373f1c",
+                "sha256:c9099bf89078675c372339011ccfc9ec310310bf6c292b413c013eb90ffdcafc",
+                "sha256:cf0db26a1f76aa6b3aa314a74b8facd586b7a5457d05b64f8082a62c9c49582a",
+                "sha256:d19a34f8a3429bd536996ad53597b805c10352a8561d8382e05830df389d2b43",
+                "sha256:da80047524eac2acf7c04c18ac7a7da05a9136241f642dd2ed94269ef0d0a45a",
+                "sha256:de2923886b5d3214be951bc2ce3f6b8ac0d6dfd4a0d0e2a4d2e5523d8046fdfb",
+                "sha256:defa0652696ff0ba48c8aff5a1fac1eef1ca6ac9c660b047fc8e7623c4eb5093",
+                "sha256:e54a1eb9fd38f2779e973d2f8958fd575b532fe26013405d1afb9ee2374e7ab8",
+                "sha256:e5c31d70a478b0ca22a9d2d76d520ae996214019d39ed7dd93af872c7f301e52",
+                "sha256:ebaeb93f90c0903233b11ce913a7cb8f6ee069158406e056f884854c737d2442",
+                "sha256:ecfe51abf7f045e0b9cdde71ca9e153d11238679ef7b5da6c82093874adf3338",
+                "sha256:f99112aed4fb7cee00c7f77e8b964a9b10f69488cdff626ffd797d02e2e4484f",
+                "sha256:fd914db437ec25bfa410f8aa0aa2f3ba87cdfc04d9919d608d02330947afaeab"
+            ],
+            "version": "==2022.1.18"
         },
         "requests": {
             "hashes": [
-                "sha256:27973dd4a904a4f13b263a19c866c13b92a39ed1c964655f025f3f8d3d75b804",
-                "sha256:c210084e36a42ae6b9219e00e48287def368a26d03a048ddad7bfee44f75871e"
+                "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61",
+                "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==2.25.1"
+            "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"
         },
         "snowballstemmer": {
             "hashes": [
-                "sha256:b51b447bea85f9968c13b650126a888aabd4cb4463fca868ec596826325dedc2",
-                "sha256:e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914"
+                "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1",
+                "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"
             ],
-            "version": "==2.1.0"
+            "version": "==2.2.0"
         },
         "sphinx": {
             "hashes": [
-                "sha256:b5c2ae4120bf00c799ba9b3699bc895816d272d120080fbc967292f29b52b48c",
-                "sha256:d1cb10bee9c4231f1700ec2e24a91be3f3a3aba066ea4ca9f3bbe47e59d5a1d4"
+                "sha256:5da895959511473857b6d0200f56865ed62c31e8f82dd338063b84ec022701fe",
+                "sha256:6caad9786055cb1fa22b4a365c1775816b876f91966481765d7d50e9f0dd35cc"
             ],
             "index": "pypi",
-            "version": "==4.0.2"
+            "version": "==4.4.0"
         },
         "sphinx-rtd-theme": {
             "hashes": [
-                "sha256:32bd3b5d13dc8186d7a42fc816a23d32e83a4827d7d9882948e7b837c232da5a",
-                "sha256:4a05bdbe8b1446d77a01e20a23ebc6777c74f43237035e76be89699308987d6f"
+                "sha256:4d35a56f4508cfee4c4fb604373ede6feae2a306731d533f409ef5c3496fdbd8",
+                "sha256:eec6d497e4c2195fa0e8b2016b337532b8a699a68bcb22a512870e16925c6a5c"
             ],
             "index": "pypi",
-            "version": "==0.5.2"
+            "version": "==1.0.0"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
@@ -640,65 +764,61 @@
             "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.10.2"
         },
+        "tomli": {
+            "hashes": [
+                "sha256:b5bde28da1fed24b9bd1d4d2b8cba62300bfb4ec9a6187a957e8ddb9434c5224",
+                "sha256:c292c34f58502a1eb2bbb9f5bbc9a5ebc37bee10ffb8c2d6bbdfa8eb13cc14e1"
+            ],
+            "version": "==2.0.0"
+        },
         "typed-ast": {
             "hashes": [
-                "sha256:01ae5f73431d21eead5015997ab41afa53aa1fbe252f9da060be5dad2c730ace",
-                "sha256:067a74454df670dcaa4e59349a2e5c81e567d8d65458d480a5b3dfecec08c5ff",
-                "sha256:0fb71b8c643187d7492c1f8352f2c15b4c4af3f6338f21681d3681b3dc31a266",
-                "sha256:1b3ead4a96c9101bef08f9f7d1217c096f31667617b58de957f690c92378b528",
-                "sha256:2068531575a125b87a41802130fa7e29f26c09a2833fea68d9a40cf33902eba6",
-                "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808",
-                "sha256:2c726c276d09fc5c414693a2de063f521052d9ea7c240ce553316f70656c84d4",
-                "sha256:398e44cd480f4d2b7ee8d98385ca104e35c81525dd98c519acff1b79bdaac363",
-                "sha256:52b1eb8c83f178ab787f3a4283f68258525f8d70f778a2f6dd54d3b5e5fb4341",
-                "sha256:5feca99c17af94057417d744607b82dd0a664fd5e4ca98061480fd8b14b18d04",
-                "sha256:7538e495704e2ccda9b234b82423a4038f324f3a10c43bc088a1636180f11a41",
-                "sha256:760ad187b1041a154f0e4d0f6aae3e40fdb51d6de16e5c99aedadd9246450e9e",
-                "sha256:777a26c84bea6cd934422ac2e3b78863a37017618b6e5c08f92ef69853e765d3",
-                "sha256:95431a26309a21874005845c21118c83991c63ea800dd44843e42a916aec5899",
-                "sha256:9ad2c92ec681e02baf81fdfa056fe0d818645efa9af1f1cd5fd6f1bd2bdfd805",
-                "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c",
-                "sha256:aee0c1256be6c07bd3e1263ff920c325b59849dc95392a05f258bb9b259cf39c",
-                "sha256:af3d4a73793725138d6b334d9d247ce7e5f084d96284ed23f22ee626a7b88e39",
-                "sha256:b36b4f3920103a25e1d5d024d155c504080959582b928e91cb608a65c3a49e1a",
-                "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3",
-                "sha256:bff6ad71c81b3bba8fa35f0f1921fb24ff4476235a6e94a26ada2e54370e6da7",
-                "sha256:c190f0899e9f9f8b6b7863debfb739abcb21a5c054f911ca3596d12b8a4c4c7f",
-                "sha256:c907f561b1e83e93fad565bac5ba9c22d96a54e7ea0267c708bffe863cbe4075",
-                "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0",
-                "sha256:dd4a21253f42b8d2b48410cb31fe501d32f8b9fbeb1f55063ad102fe9c425e40",
-                "sha256:dde816ca9dac1d9c01dd504ea5967821606f02e510438120091b84e852367428",
-                "sha256:f2362f3cb0f3172c42938946dbc5b7843c2a28aec307c49100c8b38764eb6927",
-                "sha256:f328adcfebed9f11301eaedfa48e15bdece9b519fb27e6a8c01aa52a17ec31b3",
-                "sha256:f8afcf15cc511ada719a88e013cec87c11aff7b91f019295eb4530f96fe5ef2f",
-                "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"
-            ],
-            "version": "==1.4.3"
+                "sha256:24058827d8f5d633f97223f5148a7d22628099a3d2efe06654ce872f46f07cdb",
+                "sha256:256115a5bc7ea9e665c6314ed6671ee2c08ca380f9d5f130bd4d2c1f5848d695",
+                "sha256:38cf5c642fa808300bae1281460d4f9b7617cf864d4e383054a5ef336e344d32",
+                "sha256:484137cab8ecf47e137260daa20bafbba5f4e3ec7fda1c1e69ab299b75fa81c5",
+                "sha256:4f30a2bcd8e68adbb791ce1567fdb897357506f7ea6716f6bbdd3053ac4d9471",
+                "sha256:591bc04e507595887160ed7aa8d6785867fb86c5793911be79ccede61ae96f4d",
+                "sha256:5b6ab14c56bc9c7e3c30228a0a0b54b915b1579613f6e463ba6f4eb1382e7fd4",
+                "sha256:5d8314c92414ce7481eee7ad42b353943679cf6f30237b5ecbf7d835519e1212",
+                "sha256:71dcda943a471d826ea930dd449ac7e76db7be778fcd722deb63642bab32ea3f",
+                "sha256:7c42707ab981b6cf4b73490c16e9d17fcd5227039720ca14abe415d39a173a30",
+                "sha256:9caaf2b440efb39ecbc45e2fabde809cbe56272719131a6318fd9bf08b58e2cb",
+                "sha256:a2b8d7007f6280e36fa42652df47087ac7b0a7d7f09f9468f07792ba646aac2d",
+                "sha256:a6d495c1ef572519a7bac9534dbf6d94c40e5b6a608ef41136133377bba4aa08",
+                "sha256:a80d84f535642420dd17e16ae25bb46c7f4c16ee231105e7f3eb43976a89670a",
+                "sha256:b53ae5de5500529c76225d18eeb060efbcec90ad5e030713fe8dab0fb4531631",
+                "sha256:b6d17f37f6edd879141e64a5db17b67488cfeffeedad8c5cec0392305e9bc775",
+                "sha256:c9bcad65d66d594bffab8575f39420fe0ee96f66e23c4d927ebb4e24354ec1af",
+                "sha256:ca9e8300d8ba0b66d140820cf463438c8e7b4cdc6fd710c059bfcfb1531d03fb",
+                "sha256:de4ecae89c7d8b56169473e08f6bfd2df7f95015591f43126e4ea7865928677e"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.5.1"
         },
         "typing-extensions": {
             "hashes": [
-                "sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497",
-                "sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342",
-                "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"
+                "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e",
+                "sha256:7f001e5ac290a0c0401508864c7ec868be4e701886d5b573a9528ed3973d9d3b"
             ],
             "markers": "python_version < '3.8'",
-            "version": "==3.10.0.0"
+            "version": "==4.0.1"
         },
         "urllib3": {
             "hashes": [
-                "sha256:753a0374df26658f99d826cfe40394a686d05985786d946fbe4165b5148f5a7c",
-                "sha256:a7acd0977125325f516bda9735fa7142b909a8d01e8b2e4c8108d0984e6e0098"
+                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
+                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
             ],
             "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": "==1.26.5"
+            "version": "==1.26.8"
         },
         "zipp": {
             "hashes": [
-                "sha256:3607921face881ba3e026887d8150cca609d517579abe052ac81fc5aeffdbd76",
-                "sha256:51cb66cc54621609dd593d1787f286ee42a5c0adbb4b29abea5a63edc3e03098"
+                "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d",
+                "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==3.4.1"
+            "markers": "python_version >= '3.7'",
+            "version": "==3.7.0"
         }
     }
 }

From c724f8ab583bf2e33038a596e54f78bc31076ff0 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:12:33 -0800
Subject: [PATCH 3/7] Change minimum supported Python version

---
 .github/workflows/ci.yml | 15 ++++++---------
 README.rst               |  2 +-
 setup.py                 |  3 +--
 3 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f7eb3a6..9df0b25 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -47,24 +47,21 @@ jobs:
     strategy:
       matrix:
         include:
-          - os: ubuntu-latest
-            python-version: 3.6
-            job_id: 0
           - os: ubuntu-latest
             python-version: 3.7
-            job_id: 1
+            job_id: 0
           - os: ubuntu-latest
             python-version: 3.8
-            job_id: 2
+            job_id: 1
           - os: ubuntu-latest
             python-version: 3.9
-            job_id: 3
+            job_id: 2
           - os: macos-latest
             python-version: 3.9
-            job_id: 4
+            job_id: 3
           - os: windows-latest
             python-version: 3.9
-            job_id: 5
+            job_id: 4
 
     steps:
     - uses: actions/checkout@v2
@@ -80,7 +77,7 @@ jobs:
       # so this ensures all Python versions will be periodically integration tested with the
       # resource servers
       env:
-        NUM_JOBS: 6
+        NUM_JOBS: 5
         JOB_ID: ${{ matrix.job_id }}
       if: ${{ github.event_name == 'pull_request' || github.ref == 'refs/heads/master' }}
       shell: bash
diff --git a/README.rst b/README.rst
index d6ea2fd..de12d9b 100644
--- a/README.rst
+++ b/README.rst
@@ -31,7 +31,7 @@ Also see the `installation documentation <https://lineage.readthedocs.io/en/stab
 
 Dependencies
 ------------
-``lineage`` requires `Python <https://www.python.org>`_ 3.6.1+ and the following Python packages:
+``lineage`` requires `Python <https://www.python.org>`_ 3.7.1+ and the following Python packages:
 
 - `numpy <https://numpy.org>`_
 - `pandas <https://pandas.pydata.org>`_
diff --git a/setup.py b/setup.py
index c003ec4..f5641d4 100644
--- a/setup.py
+++ b/setup.py
@@ -97,7 +97,6 @@
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
@@ -115,6 +114,6 @@
     keywords="dna genes genetics genealogy snps chromosomes genotype "
     "bioinformatics ancestry",
     install_requires=["numpy", "pandas", "matplotlib", "atomicwrites", "snps"],
-    python_requires=">=3.6.1",
+    python_requires=">=3.7.1",
     platforms=["any"],
 )

From 663d1ee28dc44fd40b7e0c25e3ab6f431c6cf432 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:20:10 -0800
Subject: [PATCH 4/7] Support current version of `black`

---
 .github/workflows/ci.yml |   2 +-
 Pipfile                  |   2 +-
 Pipfile.lock             | 117 ++++++++-------------------------------
 3 files changed, 25 insertions(+), 96 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9df0b25..dda2832 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,7 +23,7 @@ jobs:
     - uses: actions/setup-python@v2
     - name: Install Black
       run: |
-        pip install black==19.10b0
+        pip install black
     - name: Lint with Black
       run: |
         black --check --diff .
diff --git a/Pipfile b/Pipfile
index 0e19146..f623350 100644
--- a/Pipfile
+++ b/Pipfile
@@ -8,7 +8,7 @@ pytest = "*"
 pytest-cov = "*"
 sphinx = "*"
 sphinx-rtd-theme = "*"
-black = "==19.10b0"
+black = "==21.12b0"
 
 [packages]
 lineage = {editable = true,path = "."}
diff --git a/Pipfile.lock b/Pipfile.lock
index beb412c..261829c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "168f3338878ceaa0179b13cbefdde2458352de0ec53b752b1bcb472ca6d1d38b"
+            "sha256": "c50d8f3f2224e1d099448f1866a26158b5a8a0509e6e2ca9671d3bc15b4d4e92"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -296,13 +296,6 @@
             ],
             "version": "==0.7.12"
         },
-        "appdirs": {
-            "hashes": [
-                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
-                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
-            ],
-            "version": "==1.4.4"
-        },
         "attrs": {
             "hashes": [
                 "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4",
@@ -321,11 +314,11 @@
         },
         "black": {
             "hashes": [
-                "sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b",
-                "sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"
+                "sha256:77b80f693a569e2e527958459634f18df9b0ba2625ba4e0c2d5da5be42e6f2b3",
+                "sha256:a615e69ae185e08fdd73e4715e260e2479c861b5740057fde6e8b4e3b7dd589f"
             ],
             "index": "pypi",
-            "version": "==19.10b0"
+            "version": "==21.12b0"
         },
         "certifi": {
             "hashes": [
@@ -528,6 +521,13 @@
             "markers": "python_version >= '3.6'",
             "version": "==2.0.1"
         },
+        "mypy-extensions": {
+            "hashes": [
+                "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d",
+                "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"
+            ],
+            "version": "==0.4.3"
+        },
         "packaging": {
             "hashes": [
                 "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb",
@@ -543,6 +543,14 @@
             ],
             "version": "==0.9.0"
         },
+        "platformdirs": {
+            "hashes": [
+                "sha256:1d7385c7db91728b83efd0ca99a5afb296cab9d0ed8313a45ed8ba17967ecfca",
+                "sha256:440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==2.4.1"
+        },
         "pluggy": {
             "hashes": [
                 "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159",
@@ -598,85 +606,6 @@
             ],
             "version": "==2021.3"
         },
-        "regex": {
-            "hashes": [
-                "sha256:04611cc0f627fc4a50bc4a9a2e6178a974c6a6a4aa9c1cca921635d2c47b9c87",
-                "sha256:0b5d6f9aed3153487252d00a18e53f19b7f52a1651bc1d0c4b5844bc286dfa52",
-                "sha256:0d2f5c3f7057530afd7b739ed42eb04f1011203bc5e4663e1e1d01bb50f813e3",
-                "sha256:11772be1eb1748e0e197a40ffb82fb8fd0d6914cd147d841d9703e2bef24d288",
-                "sha256:1333b3ce73269f986b1fa4d5d395643810074dc2de5b9d262eb258daf37dc98f",
-                "sha256:16f81025bb3556eccb0681d7946e2b35ff254f9f888cff7d2120e8826330315c",
-                "sha256:1a171eaac36a08964d023eeff740b18a415f79aeb212169080c170ec42dd5184",
-                "sha256:1d6301f5288e9bdca65fab3de6b7de17362c5016d6bf8ee4ba4cbe833b2eda0f",
-                "sha256:1e031899cb2bc92c0cf4d45389eff5b078d1936860a1be3aa8c94fa25fb46ed8",
-                "sha256:1f8c0ae0a0de4e19fddaaff036f508db175f6f03db318c80bbc239a1def62d02",
-                "sha256:2245441445099411b528379dee83e56eadf449db924648e5feb9b747473f42e3",
-                "sha256:22709d701e7037e64dae2a04855021b62efd64a66c3ceed99dfd684bfef09e38",
-                "sha256:24c89346734a4e4d60ecf9b27cac4c1fee3431a413f7aa00be7c4d7bbacc2c4d",
-                "sha256:25716aa70a0d153cd844fe861d4f3315a6ccafce22b39d8aadbf7fcadff2b633",
-                "sha256:2dacb3dae6b8cc579637a7b72f008bff50a94cde5e36e432352f4ca57b9e54c4",
-                "sha256:34316bf693b1d2d29c087ee7e4bb10cdfa39da5f9c50fa15b07489b4ab93a1b5",
-                "sha256:36b2d700a27e168fa96272b42d28c7ac3ff72030c67b32f37c05616ebd22a202",
-                "sha256:37978254d9d00cda01acc1997513f786b6b971e57b778fbe7c20e30ae81a97f3",
-                "sha256:38289f1690a7e27aacd049e420769b996826f3728756859420eeee21cc857118",
-                "sha256:385ccf6d011b97768a640e9d4de25412204fbe8d6b9ae39ff115d4ff03f6fe5d",
-                "sha256:3c7ea86b9ca83e30fa4d4cd0eaf01db3ebcc7b2726a25990966627e39577d729",
-                "sha256:49810f907dfe6de8da5da7d2b238d343e6add62f01a15d03e2195afc180059ed",
-                "sha256:519c0b3a6fbb68afaa0febf0d28f6c4b0a1074aefc484802ecb9709faf181607",
-                "sha256:51f02ca184518702975b56affde6c573ebad4e411599005ce4468b1014b4786c",
-                "sha256:552a39987ac6655dad4bf6f17dd2b55c7b0c6e949d933b8846d2e312ee80005a",
-                "sha256:596f5ae2eeddb79b595583c2e0285312b2783b0ec759930c272dbf02f851ff75",
-                "sha256:6014038f52b4b2ac1fa41a58d439a8a00f015b5c0735a0cd4b09afe344c94899",
-                "sha256:61ebbcd208d78658b09e19c78920f1ad38936a0aa0f9c459c46c197d11c580a0",
-                "sha256:6213713ac743b190ecbf3f316d6e41d099e774812d470422b3a0f137ea635832",
-                "sha256:637e27ea1ebe4a561db75a880ac659ff439dec7f55588212e71700bb1ddd5af9",
-                "sha256:6aa427c55a0abec450bca10b64446331b5ca8f79b648531138f357569705bc4a",
-                "sha256:6ca45359d7a21644793de0e29de497ef7f1ae7268e346c4faf87b421fea364e6",
-                "sha256:6db1b52c6f2c04fafc8da17ea506608e6be7086715dab498570c3e55e4f8fbd1",
-                "sha256:752e7ddfb743344d447367baa85bccd3629c2c3940f70506eb5f01abce98ee68",
-                "sha256:760c54ad1b8a9b81951030a7e8e7c3ec0964c1cb9fee585a03ff53d9e531bb8e",
-                "sha256:768632fd8172ae03852e3245f11c8a425d95f65ff444ce46b3e673ae5b057b74",
-                "sha256:7a0b9f6a1a15d494b35f25ed07abda03209fa76c33564c09c9e81d34f4b919d7",
-                "sha256:7e070d3aef50ac3856f2ef5ec7214798453da878bb5e5a16c16a61edf1817cc3",
-                "sha256:7e12949e5071c20ec49ef00c75121ed2b076972132fc1913ddf5f76cae8d10b4",
-                "sha256:7e26eac9e52e8ce86f915fd33380f1b6896a2b51994e40bb094841e5003429b4",
-                "sha256:85ffd6b1cb0dfb037ede50ff3bef80d9bf7fa60515d192403af6745524524f3b",
-                "sha256:8618d9213a863c468a865e9d2ec50221015f7abf52221bc927152ef26c484b4c",
-                "sha256:8acef4d8a4353f6678fd1035422a937c2170de58a2b29f7da045d5249e934101",
-                "sha256:8d2f355a951f60f0843f2368b39970e4667517e54e86b1508e76f92b44811a8a",
-                "sha256:90b6840b6448203228a9d8464a7a0d99aa8fa9f027ef95fe230579abaf8a6ee1",
-                "sha256:9187500d83fd0cef4669385cbb0961e227a41c0c9bc39219044e35810793edf7",
-                "sha256:93c20777a72cae8620203ac11c4010365706062aa13aaedd1a21bb07adbb9d5d",
-                "sha256:93cce7d422a0093cfb3606beae38a8e47a25232eea0f292c878af580a9dc7605",
-                "sha256:94c623c331a48a5ccc7d25271399aff29729fa202c737ae3b4b28b89d2b0976d",
-                "sha256:97f32dc03a8054a4c4a5ab5d761ed4861e828b2c200febd4e46857069a483916",
-                "sha256:9a2bf98ac92f58777c0fafc772bf0493e67fcf677302e0c0a630ee517a43b949",
-                "sha256:a602bdc8607c99eb5b391592d58c92618dcd1537fdd87df1813f03fed49957a6",
-                "sha256:a9d24b03daf7415f78abc2d25a208f234e2c585e5e6f92f0204d2ab7b9ab48e3",
-                "sha256:abfcb0ef78df0ee9df4ea81f03beea41849340ce33a4c4bd4dbb99e23ec781b6",
-                "sha256:b013f759cd69cb0a62de954d6d2096d648bc210034b79b1881406b07ed0a83f9",
-                "sha256:b02e3e72665cd02afafb933453b0c9f6c59ff6e3708bd28d0d8580450e7e88af",
-                "sha256:b52cc45e71657bc4743a5606d9023459de929b2a198d545868e11898ba1c3f59",
-                "sha256:ba37f11e1d020969e8a779c06b4af866ffb6b854d7229db63c5fdddfceaa917f",
-                "sha256:bb804c7d0bfbd7e3f33924ff49757de9106c44e27979e2492819c16972ec0da2",
-                "sha256:bf594cc7cc9d528338d66674c10a5b25e3cde7dd75c3e96784df8f371d77a298",
-                "sha256:c38baee6bdb7fe1b110b6b3aaa555e6e872d322206b7245aa39572d3fc991ee4",
-                "sha256:c73d2166e4b210b73d1429c4f1ca97cea9cc090e5302df2a7a0a96ce55373f1c",
-                "sha256:c9099bf89078675c372339011ccfc9ec310310bf6c292b413c013eb90ffdcafc",
-                "sha256:cf0db26a1f76aa6b3aa314a74b8facd586b7a5457d05b64f8082a62c9c49582a",
-                "sha256:d19a34f8a3429bd536996ad53597b805c10352a8561d8382e05830df389d2b43",
-                "sha256:da80047524eac2acf7c04c18ac7a7da05a9136241f642dd2ed94269ef0d0a45a",
-                "sha256:de2923886b5d3214be951bc2ce3f6b8ac0d6dfd4a0d0e2a4d2e5523d8046fdfb",
-                "sha256:defa0652696ff0ba48c8aff5a1fac1eef1ca6ac9c660b047fc8e7623c4eb5093",
-                "sha256:e54a1eb9fd38f2779e973d2f8958fd575b532fe26013405d1afb9ee2374e7ab8",
-                "sha256:e5c31d70a478b0ca22a9d2d76d520ae996214019d39ed7dd93af872c7f301e52",
-                "sha256:ebaeb93f90c0903233b11ce913a7cb8f6ee069158406e056f884854c737d2442",
-                "sha256:ecfe51abf7f045e0b9cdde71ca9e153d11238679ef7b5da6c82093874adf3338",
-                "sha256:f99112aed4fb7cee00c7f77e8b964a9b10f69488cdff626ffd797d02e2e4484f",
-                "sha256:fd914db437ec25bfa410f8aa0aa2f3ba87cdfc04d9919d608d02330947afaeab"
-            ],
-            "version": "==2022.1.18"
-        },
         "requests": {
             "hashes": [
                 "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61",
@@ -766,10 +695,10 @@
         },
         "tomli": {
             "hashes": [
-                "sha256:b5bde28da1fed24b9bd1d4d2b8cba62300bfb4ec9a6187a957e8ddb9434c5224",
-                "sha256:c292c34f58502a1eb2bbb9f5bbc9a5ebc37bee10ffb8c2d6bbdfa8eb13cc14e1"
+                "sha256:05b6166bff487dc068d322585c7ea4ef78deed501cc124060e0f238e89a9231f",
+                "sha256:e3069e4be3ead9668e21cb9b074cd948f7b3113fd9c8bba083f48247aab8b11c"
             ],
-            "version": "==2.0.0"
+            "version": "==1.2.3"
         },
         "typed-ast": {
             "hashes": [
@@ -793,7 +722,7 @@
                 "sha256:ca9e8300d8ba0b66d140820cf463438c8e7b4cdc6fd710c059bfcfb1531d03fb",
                 "sha256:de4ecae89c7d8b56169473e08f6bfd2df7f95015591f43126e4ea7865928677e"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_version < '3.8' and implementation_name == 'cpython'",
             "version": "==1.5.1"
         },
         "typing-extensions": {

From 0b7771e09888cae0853b8539b0534577913bdddf Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:21:53 -0800
Subject: [PATCH 5/7] Reformat with current verison of `black`

---
 src/lineage/__init__.py      | 14 ++++++-------
 src/lineage/individual.py    |  6 +++---
 src/lineage/resources.py     | 40 ++++++++++++++++++------------------
 src/lineage/visualization.py |  4 ++--
 tests/__init__.py            |  2 +-
 tests/test_lineage.py        | 27 ++++++++++++++++++------
 6 files changed, 54 insertions(+), 39 deletions(-)

diff --git a/src/lineage/__init__.py b/src/lineage/__init__.py
index 5403792..c3af334 100644
--- a/src/lineage/__init__.py
+++ b/src/lineage/__init__.py
@@ -52,7 +52,7 @@
 
 
 class Lineage:
-    """ Object used to interact with the `lineage` framework. """
+    """Object used to interact with the `lineage` framework."""
 
     def __init__(
         self,
@@ -61,7 +61,7 @@ def __init__(
         parallelize=False,
         processes=os.cpu_count(),
     ):
-        """ Initialize a ``Lineage`` object.
+        """Initialize a ``Lineage`` object.
 
         Parameters
         ----------
@@ -80,7 +80,7 @@ def __init__(
         self._parallelizer = Parallelizer(parallelize=parallelize, processes=processes)
 
     def create_individual(self, name, raw_data=(), **kwargs):
-        """ Initialize an individual in the context of the `lineage` framework.
+        """Initialize an individual in the context of the `lineage` framework.
 
         Parameters
         ----------
@@ -104,7 +104,7 @@ def create_individual(self, name, raw_data=(), **kwargs):
         return Individual(name, raw_data, **kwargs)
 
     def download_example_datasets(self):
-        """ Download example datasets from `openSNP <https://opensnp.org>`_.
+        """Download example datasets from `openSNP <https://opensnp.org>`_.
 
         Per openSNP, "the data is donated into the public domain using `CC0 1.0
         <http://creativecommons.org/publicdomain/zero/1.0/>`_."
@@ -130,7 +130,7 @@ def download_example_datasets(self):
     def find_discordant_snps(
         self, individual1, individual2, individual3=None, save_output=False
     ):
-        """ Find discordant SNPs between two or three individuals.
+        """Find discordant SNPs between two or three individuals.
 
         Parameters
         ----------
@@ -282,7 +282,7 @@ def find_shared_dna(
         save_output=True,
         genetic_map="HapMap2",
     ):
-        """ Find the shared DNA between individuals.
+        """Find the shared DNA between individuals.
 
         Computes the genetic distance in centiMorgans (cMs) between SNPs using the specified genetic
         map. Applies thresholds to determine the shared DNA. Plots shared DNA. Optionally determines
@@ -696,7 +696,7 @@ def _is_one_individual_male(self, individuals):
         return False
 
     def _compute_snp_distances(self, task):
-        """ Compute genetic distance in cMs between SNPs.
+        """Compute genetic distance in cMs between SNPs.
 
         Parameters
         ----------
diff --git a/src/lineage/individual.py b/src/lineage/individual.py
index 6287102..102ffcf 100644
--- a/src/lineage/individual.py
+++ b/src/lineage/individual.py
@@ -31,7 +31,7 @@
 
 
 class Individual(SNPs):
-    """ Object used to represent and interact with an individual.
+    """Object used to represent and interact with an individual.
 
     The ``Individual`` object maintains information about an individual. The object provides
     methods for loading an individual's genetic data (SNPs) and normalizing it for use with the
@@ -42,7 +42,7 @@ class Individual(SNPs):
     """
 
     def __init__(self, name, raw_data=(), **kwargs):
-        """ Initialize an ``Individual`` object.
+        """Initialize an ``Individual`` object.
 
         Parameters
         ----------
@@ -85,7 +85,7 @@ def __repr__(self):
 
     @property
     def name(self):
-        """ Get this ``Individual``'s name.
+        """Get this ``Individual``'s name.
 
         Returns
         -------
diff --git a/src/lineage/resources.py b/src/lineage/resources.py
index 60fb7ef..b4e99fd 100644
--- a/src/lineage/resources.py
+++ b/src/lineage/resources.py
@@ -64,10 +64,10 @@
 
 
 class Resources(SNPsResources):
-    """ Object used to manage resources required by `lineage`. """
+    """Object used to manage resources required by `lineage`."""
 
     def __init__(self, resources_dir="resources"):
-        """ Initialize a ``Resources`` object.
+        """Initialize a ``Resources`` object.
 
         Parameters
         ----------
@@ -83,7 +83,7 @@ def __init__(self, resources_dir="resources"):
         self._kgXref_hg19 = pd.DataFrame()
 
     def get_genetic_map(self, genetic_map):
-        """ Get specified genetic map.
+        """Get specified genetic map.
 
         Parameters
         ----------
@@ -132,7 +132,7 @@ def get_genetic_map(self, genetic_map):
             return self.get_genetic_map_1000G_GRCh37(genetic_map)
 
     def get_genetic_map_HapMapII_GRCh37(self):
-        """ Get International HapMap Consortium HapMap Phase II genetic map for Build 37.
+        """Get International HapMap Consortium HapMap Phase II genetic map for Build 37.
         [#InternationalHapMapConsortium]_ [#Auton2010]_
 
         Returns
@@ -158,7 +158,7 @@ def get_genetic_map_HapMapII_GRCh37(self):
         return self._genetic_map
 
     def get_genetic_map_1000G_GRCh37(self, pop):
-        """ Get population-specific 1000 Genomes Project genetic map. [#Auton2013]_ [#Auton2015]_
+        """Get population-specific 1000 Genomes Project genetic map. [#Auton2013]_ [#Auton2015]_
 
         Notes
         -----
@@ -210,7 +210,7 @@ def get_genetic_map_1000G_GRCh37(self, pop):
         return self._genetic_map
 
     def get_cytoBand_hg19(self):
-        """ Get UCSC cytoBand table for Build 37.
+        """Get UCSC cytoBand table for Build 37.
 
         Returns
         -------
@@ -228,7 +228,7 @@ def get_cytoBand_hg19(self):
         return self._cytoBand_hg19
 
     def get_knownGene_hg19(self):
-        """ Get UCSC knownGene table for Build 37.
+        """Get UCSC knownGene table for Build 37.
 
         Returns
         -------
@@ -241,7 +241,7 @@ def get_knownGene_hg19(self):
         return self._knownGene_hg19
 
     def get_kgXref_hg19(self):
-        """ Get UCSC kgXref table for Build 37.
+        """Get UCSC kgXref table for Build 37.
 
         Returns
         -------
@@ -254,7 +254,7 @@ def get_kgXref_hg19(self):
         return self._kgXref_hg19
 
     def download_example_datasets(self):
-        """ Download example datasets from `openSNP <https://opensnp.org>`_.
+        """Download example datasets from `openSNP <https://opensnp.org>`_.
 
         Per openSNP, "the data is donated into the public domain using `CC0 1.0
         <http://creativecommons.org/publicdomain/zero/1.0/>`_."
@@ -297,7 +297,7 @@ def download_example_datasets(self):
         ]
 
     def get_all_resources(self):
-        """ Get / download all resources (except reference sequences) used throughout `lineage`.
+        """Get / download all resources (except reference sequences) used throughout `lineage`.
 
         Returns
         -------
@@ -315,7 +315,7 @@ def get_all_resources(self):
 
     @staticmethod
     def _load_genetic_map_HapMapII_GRCh37(filename):
-        """ Load HapMapII genetic map.
+        """Load HapMapII genetic map.
 
         Parameters
         ----------
@@ -361,7 +361,7 @@ def _load_genetic_map_HapMapII_GRCh37(filename):
 
     @staticmethod
     def _load_genetic_map_1000G_GRCh37(filename):
-        """ Load 1000 Genomes Project genetic map.
+        """Load 1000 Genomes Project genetic map.
 
         Parameters
         ----------
@@ -402,7 +402,7 @@ def _load_genetic_map_1000G_GRCh37(filename):
 
     @staticmethod
     def _load_cytoBand(filename):
-        """ Load UCSC cytoBand table.
+        """Load UCSC cytoBand table.
 
         Parameters
         ----------
@@ -423,7 +423,7 @@ def _load_cytoBand(filename):
 
     @staticmethod
     def _load_knownGene(filename):
-        """ Load UCSC knownGene table.
+        """Load UCSC knownGene table.
 
         Parameters
         ----------
@@ -459,7 +459,7 @@ def _load_knownGene(filename):
 
     @staticmethod
     def _load_kgXref(filename):
-        """ Load UCSC kgXref table.
+        """Load UCSC kgXref table.
 
         Parameters
         ----------
@@ -492,7 +492,7 @@ def _load_kgXref(filename):
         return df
 
     def _get_path_cytoBand_hg19(self):
-        """ Get local path to cytoBand file for hg19 / GRCh37 from UCSC, downloading if necessary.
+        """Get local path to cytoBand file for hg19 / GRCh37 from UCSC, downloading if necessary.
 
         Returns
         -------
@@ -505,7 +505,7 @@ def _get_path_cytoBand_hg19(self):
         )
 
     def _get_path_genetic_map_HapMapII_GRCh37(self):
-        """ Get local path to HapMap Phase II genetic map for hg19 / GRCh37 (HapMapII),
+        """Get local path to HapMap Phase II genetic map for hg19 / GRCh37 (HapMapII),
         downloading if necessary.
 
         Returns
@@ -520,7 +520,7 @@ def _get_path_genetic_map_HapMapII_GRCh37(self):
         )
 
     def _get_path_genetic_map_1000G_GRCh37(self, pop):
-        """ Get local path to population-specific 1000 Genomes Project genetic map,
+        """Get local path to population-specific 1000 Genomes Project genetic map,
         downloading if necessary.
 
         Returns
@@ -535,7 +535,7 @@ def _get_path_genetic_map_1000G_GRCh37(self, pop):
         )
 
     def _get_path_knownGene_hg19(self):
-        """ Get local path to knownGene file for hg19 / GRCh37 from UCSC, downloading if necessary.
+        """Get local path to knownGene file for hg19 / GRCh37 from UCSC, downloading if necessary.
 
         Returns
         -------
@@ -548,7 +548,7 @@ def _get_path_knownGene_hg19(self):
         )
 
     def _get_path_kgXref_hg19(self):
-        """ Get local path to kgXref file for hg19 / GRCh37 from UCSC, downloading if necessary.
+        """Get local path to kgXref file for hg19 / GRCh37 from UCSC, downloading if necessary.
 
         Returns
         -------
diff --git a/src/lineage/visualization.py b/src/lineage/visualization.py
index a62d118..898df94 100644
--- a/src/lineage/visualization.py
+++ b/src/lineage/visualization.py
@@ -77,7 +77,7 @@
 
 
 def plot_chromosomes(one_chrom_match, two_chrom_match, cytobands, path, title, build):
-    """ Plots chromosomes with designated markers.
+    """Plots chromosomes with designated markers.
 
     Parameters
     ----------
@@ -218,7 +218,7 @@ def _chromosome_collections(df, y_positions, height, **kwargs):
 
 
 def _patch_chromosomal_features(cytobands, one_chrom_match, two_chrom_match):
-    """ Highlight positions for each chromosome segment / feature.
+    """Highlight positions for each chromosome segment / feature.
 
     Parameters
     ----------
diff --git a/tests/__init__.py b/tests/__init__.py
index 2ed64b9..feab9f6 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -136,7 +136,7 @@ def generic_snps(self):
 
     @property
     def downloads_enabled(self):
-        """ Property indicating if downloads are enabled.
+        """Property indicating if downloads are enabled.
 
         Only download from external resources when an environment variable named
         "DOWNLOADS_ENABLED" is set to "true".
diff --git a/tests/test_lineage.py b/tests/test_lineage.py
index 6b6324c..be36e76 100644
--- a/tests/test_lineage.py
+++ b/tests/test_lineage.py
@@ -55,7 +55,13 @@ def _generate_test_genetic_map(
         **kwargs,
     ):
         return {
-            chrom: pd.DataFrame({"pos": pos, "rate": rate, "map": map_cMs,}),
+            chrom: pd.DataFrame(
+                {
+                    "pos": pos,
+                    "rate": rate,
+                    "map": map_cMs,
+                }
+            ),
         }
 
     def _generate_test_cytoBand_hg19(self):
@@ -159,7 +165,8 @@ def run_find_shared_dna_test(self, f, HapMap2=True, **kwargs):
             kg, kgXref = self._generate_test_gene_dfs(**kwargs)
 
             with patch(
-                genetic_map_patch, Mock(return_value=genetic_map),
+                genetic_map_patch,
+                Mock(return_value=genetic_map),
             ):
                 with patch(
                     "lineage.resources.Resources.get_cytoBand_hg19",
@@ -579,10 +586,14 @@ def _test_find_shared_dna_X_chrom_two_individuals_male(self):
             assert len(d["one_chrom_discrepant_snps"]) == 0
             assert len(d["two_chrom_discrepant_snps"]) == 0
             np.testing.assert_allclose(
-                d["one_chrom_shared_dna"].loc[1]["cMs"], 202.022891, rtol=1e-5,
+                d["one_chrom_shared_dna"].loc[1]["cMs"],
+                202.022891,
+                rtol=1e-5,
             )
             np.testing.assert_allclose(
-                d["two_chrom_shared_dna"].loc[1]["cMs"], 20.837792, rtol=1e-3,
+                d["two_chrom_shared_dna"].loc[1]["cMs"],
+                20.837792,
+                rtol=1e-3,
             )
             self._make_file_exist_assertions("ind1_ind2", output_dir=tmpdir)
 
@@ -617,10 +628,14 @@ def _test_find_shared_dna_X_chrom_two_individuals_female(self):
             assert len(d["one_chrom_discrepant_snps"]) == 0
             assert len(d["two_chrom_discrepant_snps"]) == 0
             np.testing.assert_allclose(
-                d["one_chrom_shared_dna"].loc[1]["cMs"], 202.022891, rtol=1e-5,
+                d["one_chrom_shared_dna"].loc[1]["cMs"],
+                202.022891,
+                rtol=1e-5,
             )
             np.testing.assert_allclose(
-                d["two_chrom_shared_dna"].loc[1]["cMs"], 202.022891, rtol=1e-5,
+                d["two_chrom_shared_dna"].loc[1]["cMs"],
+                202.022891,
+                rtol=1e-5,
             )
             self._make_file_exist_assertions("ind1_ind2", output_dir=tmpdir)
 

From eb6d67f249bd720f03aae13a3fc3f7dfb53fdc24 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:26:31 -0800
Subject: [PATCH 6/7] Configure Read the Docs builds

https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
---
 .readthedocs.yaml     | 20 ++++++++++++++++++++
 docs/requirements.txt |  2 ++
 2 files changed, 22 insertions(+)
 create mode 100644 .readthedocs.yaml
 create mode 100644 docs/requirements.txt

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..c082f85
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,20 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/conf.py
+
+formats: all
+
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 0000000..d9286ce
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1,2 @@
+sphinx==4.4.0
+sphinx-rtd-theme==1.0.0

From c1c040127f8f47bb831f7cb655a6fefff2a938ea Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Sun, 23 Jan 2022 20:46:59 -0800
Subject: [PATCH 7/7] Fix DeprecationWarning

---
 src/lineage/resources.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/lineage/resources.py b/src/lineage/resources.py
index b4e99fd..8882d18 100644
--- a/src/lineage/resources.py
+++ b/src/lineage/resources.py
@@ -385,7 +385,7 @@ def _load_genetic_map_1000G_GRCh37(filename):
                 df = pd.read_csv(
                     tar.extractfile(member),
                     compression="gzip",
-                    sep="\s+",
+                    sep=r"\s+",
                     usecols=["Position(bp)", "Rate(cM/Mb)", "Map(cM)"],
                 )
                 df = df.rename(