From c39393667c6f206ac0845d22588b71efd93c737f Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Tue, 19 Mar 2024 22:16:52 -0700
Subject: [PATCH 1/3] Update README

---
 README.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.rst b/README.rst
index f1024a2..d580754 100644
--- a/README.rst
+++ b/README.rst
@@ -246,6 +246,9 @@ Acknowledgements
 Thanks to Whit Athey, Ryan Dale, Binh Bui, Jeff Gill, Gopal Vashishtha,
 `CS50 <https://cs50.harvard.edu>`_, and `openSNP <https://opensnp.org>`_.
 
+``lineage`` incorporates code and concepts generated with the assistance of
+`OpenAI's <https://openai.com>`_ `ChatGPT <https://chat.openai.com>`_ (GPT-3.5). ✨
+
 .. https://github.com/rtfd/readthedocs.org/blob/master/docs/badges.rst
 .. |ci| image:: https://github.com/apriha/lineage/actions/workflows/ci.yml/badge.svg?branch=master
    :target: https://github.com/apriha/lineage/actions/workflows/ci.yml

From 328a01c0ff6e50912fec7d875d31b6cbfc1a9498 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Tue, 19 Mar 2024 22:18:14 -0700
Subject: [PATCH 2/3] Update Pipenv dependencies

---
 Pipfile      |    2 +-
 Pipfile.lock | 1410 ++++++++++++++++++++++++++------------------------
 2 files changed, 726 insertions(+), 686 deletions(-)

diff --git a/Pipfile b/Pipfile
index 40e653a..1d5349b 100644
--- a/Pipfile
+++ b/Pipfile
@@ -14,4 +14,4 @@ black = "*"
 lineage = {editable = true,path = "."}
 
 [requires]
-python_version = "3.7"
+python_version = "3.12"
diff --git a/Pipfile.lock b/Pipfile.lock
index 46af44a..8712baa 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,11 +1,11 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "4528a55233e15dd3965ebc39ec436e15ad6a06c0115ca57ba35c963a3add12ec"
+            "sha256": "1882bcc4acdb25f4e99eea1d264bc9ceb47031ce3bd77018ddc9ce4e6fb7e0db"
         },
         "pipfile-spec": 6,
         "requires": {
-            "python_version": "3.7"
+            "python_version": "3.12"
         },
         "sources": [
             {
@@ -20,98 +20,223 @@
             "hashes": [
                 "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.4.1"
         },
+        "contourpy": {
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+                "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.14.0"
+            "markers": "python_version >= '3.7'",
+            "version": "==2.17.2"
         },
         "pytest": {
             "hashes": [
-                "sha256:c7c6ca206e93355074ae32f7403e8ea12163b1163c976fee7d4d84027c162be5",
-                "sha256:d45e0952f3727241918b8fd0f376f5ff6b301cc0777c6f9a556935c92d8a7d42"
+                "sha256:2a8386cfc11fa9d2c50ee7b2a57e7d898ef90470a7a34c4b949ff59662bb78b7",
+                "sha256:ac978141a75948948817d360297b7aae0fcb9d6ff6bc9ec6d514b85d5a65c044"
             ],
             "index": "pypi",
-            "version": "==7.2.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==8.1.1"
         },
         "pytest-cov": {
             "hashes": [
-                "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b",
-                "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"
+                "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6",
+                "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"
             ],
             "index": "pypi",
-            "version": "==4.0.0"
-        },
-        "pytz": {
-            "hashes": [
-                "sha256:01a0681c4b9684a28304615eba55d1ab31ae00bf68ec157ec3708a8182dbbcd0",
-                "sha256:78f4f37d8198e0627c5f1143240bb0206b8691d8d7ac6d78fee88b78733f8c4a"
-            ],
-            "version": "==2022.7.1"
+            "markers": "python_version >= '3.7'",
+            "version": "==4.1.0"
         },
         "requests": {
             "hashes": [
-                "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa",
-                "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"
-            ],
-            "markers": "python_version >= '3.7' and python_version < '4'",
-            "version": "==2.28.2"
-        },
-        "setuptools": {
-            "hashes": [
-                "sha256:16ccf598aab3b506593c17378473978908a2734d7336755a8769b480906bec1c",
-                "sha256:b440ee5f7e607bb8c9de15259dba2583dd41a38879a7abc1d43a71c59524da48"
+                "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f",
+                "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==67.2.0"
+            "version": "==2.31.0"
         },
         "snowballstemmer": {
             "hashes": [
@@ -799,51 +891,53 @@
         },
         "sphinx": {
             "hashes": [
-                "sha256:060ca5c9f7ba57a08a1219e547b269fadf125ae25b06b9fa7f66768efb652d6d",
-                "sha256:51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5"
+                "sha256:1e09160a40b956dc623c910118fa636da93bd3ca0b9876a7b3df90f07d691560",
+                "sha256:9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5"
             ],
             "index": "pypi",
-            "version": "==5.3.0"
+            "markers": "python_version >= '3.9'",
+            "version": "==7.2.6"
         },
         "sphinx-rtd-theme": {
             "hashes": [
-                "sha256:a0d8bd1a2ed52e0b338cbe19c4b2eef3c5e7a048769753dac6a9f059c7b641b8",
-                "sha256:f823f7e71890abe0ac6aaa6013361ea2696fc8d3e1fa798f463e82bdb77eeff2"
+                "sha256:bd5d7b80622406762073a04ef8fadc5f9151261563d47027de09910ce03afe6b",
+                "sha256:ec93d0856dc280cf3aee9a4c9807c60e027c7f7b461b77aeffed682e68f0e586"
             ],
             "index": "pypi",
-            "version": "==1.2.0"
+            "markers": "python_version >= '3.6'",
+            "version": "==2.0.0"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
-                "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a",
-                "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"
+                "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619",
+                "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==1.0.2"
+            "markers": "python_version >= '3.9'",
+            "version": "==1.0.8"
         },
         "sphinxcontrib-devhelp": {
             "hashes": [
-                "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e",
-                "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"
+                "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f",
+                "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==1.0.2"
+            "markers": "python_version >= '3.9'",
+            "version": "==1.0.6"
         },
         "sphinxcontrib-htmlhelp": {
             "hashes": [
-                "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07",
-                "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"
+                "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015",
+                "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.0.0"
+            "markers": "python_version >= '3.9'",
+            "version": "==2.0.5"
         },
         "sphinxcontrib-jquery": {
             "hashes": [
-                "sha256:8fb65f6dba84bf7bcd1aea1f02ab3955ac34611d838bcc95d4983b805b234daa",
-                "sha256:ed47fa425c338ffebe3c37e1cdb56e30eb806116b85f01055b158c7057fdb995"
+                "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a",
+                "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"
             ],
-            "markers": "python_version >= '3.1'",
-            "version": "==2.0.0"
+            "markers": "python_version >= '2.7'",
+            "version": "==4.1"
         },
         "sphinxcontrib-jsmath": {
             "hashes": [
@@ -855,81 +949,27 @@
         },
         "sphinxcontrib-qthelp": {
             "hashes": [
-                "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72",
-                "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"
+                "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6",
+                "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==1.0.3"
+            "markers": "python_version >= '3.9'",
+            "version": "==1.0.7"
         },
         "sphinxcontrib-serializinghtml": {
             "hashes": [
-                "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd",
-                "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"
+                "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7",
+                "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"
             ],
-            "markers": "python_version >= '3.5'",
-            "version": "==1.1.5"
-        },
-        "tomli": {
-            "hashes": [
-                "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc",
-                "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"
-            ],
-            "markers": "python_version < '3.11'",
-            "version": "==2.0.1"
-        },
-        "typed-ast": {
-            "hashes": [
-                "sha256:0261195c2062caf107831e92a76764c81227dae162c4f75192c0d489faf751a2",
-                "sha256:0fdbcf2fef0ca421a3f5912555804296f0b0960f0418c440f5d6d3abb549f3e1",
-                "sha256:183afdf0ec5b1b211724dfef3d2cad2d767cbefac291f24d69b00546c1837fb6",
-                "sha256:211260621ab1cd7324e0798d6be953d00b74e0428382991adfddb352252f1d62",
-                "sha256:267e3f78697a6c00c689c03db4876dd1efdfea2f251a5ad6555e82a26847b4ac",
-                "sha256:2efae9db7a8c05ad5547d522e7dbe62c83d838d3906a3716d1478b6c1d61388d",
-                "sha256:370788a63915e82fd6f212865a596a0fefcbb7d408bbbb13dea723d971ed8bdc",
-                "sha256:39e21ceb7388e4bb37f4c679d72707ed46c2fbf2a5609b8b8ebc4b067d977df2",
-                "sha256:3e123d878ba170397916557d31c8f589951e353cc95fb7f24f6bb69adc1a8a97",
-                "sha256:4879da6c9b73443f97e731b617184a596ac1235fe91f98d279a7af36c796da35",
-                "sha256:4e964b4ff86550a7a7d56345c7864b18f403f5bd7380edf44a3c1fb4ee7ac6c6",
-                "sha256:639c5f0b21776605dd6c9dbe592d5228f021404dafd377e2b7ac046b0349b1a1",
-                "sha256:669dd0c4167f6f2cd9f57041e03c3c2ebf9063d0757dc89f79ba1daa2bfca9d4",
-                "sha256:6778e1b2f81dfc7bc58e4b259363b83d2e509a65198e85d5700dfae4c6c8ff1c",
-                "sha256:683407d92dc953c8a7347119596f0b0e6c55eb98ebebd9b23437501b28dcbb8e",
-                "sha256:79b1e0869db7c830ba6a981d58711c88b6677506e648496b1f64ac7d15633aec",
-                "sha256:7d5d014b7daa8b0bf2eaef684295acae12b036d79f54178b92a2b6a56f92278f",
-                "sha256:98f80dee3c03455e92796b58b98ff6ca0b2a6f652120c263efdba4d6c5e58f72",
-                "sha256:a94d55d142c9265f4ea46fab70977a1944ecae359ae867397757d836ea5a3f47",
-                "sha256:a9916d2bb8865f973824fb47436fa45e1ebf2efd920f2b9f99342cb7fab93f72",
-                "sha256:c542eeda69212fa10a7ada75e668876fdec5f856cd3d06829e6aa64ad17c8dfe",
-                "sha256:cf4afcfac006ece570e32d6fa90ab74a17245b83dfd6655a6f68568098345ff6",
-                "sha256:ebd9d7f80ccf7a82ac5f88c521115cc55d84e35bf8b446fcd7836eb6b98929a3",
-                "sha256:ed855bbe3eb3715fca349c80174cfcfd699c2f9de574d40527b8429acae23a66"
-            ],
-            "markers": "python_version < '3.8' and implementation_name == 'cpython'",
-            "version": "==1.5.4"
-        },
-        "typing-extensions": {
-            "hashes": [
-                "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa",
-                "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"
-            ],
-            "markers": "python_version < '3.8'",
-            "version": "==4.4.0"
+            "markers": "python_version >= '3.9'",
+            "version": "==1.1.10"
         },
         "urllib3": {
             "hashes": [
-                "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72",
-                "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"
+                "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d",
+                "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"
             ],
-            "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": [
-                "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6",
-                "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.13.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==2.2.1"
         }
     }
 }

From a3564a732b5358a2743e451bd0cf9cff9bf77bb5 Mon Sep 17 00:00:00 2001
From: Andrew Riha <apriha@gmail.com>
Date: Tue, 19 Mar 2024 22:25:48 -0700
Subject: [PATCH 3/3] Support modern Python versions

---
 .github/workflows/ci.yml | 50 ++++++++++++++++++----------------------
 README.rst               |  2 +-
 setup.py                 |  5 ++--
 3 files changed, 26 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c095bb6..3af5bc4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,8 +19,10 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
     - name: Install Black
       run: |
         pip install black
@@ -31,8 +33,10 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
     - name: Install Sphinx
       run: |
         pip install -r docs/requirements.txt
@@ -46,33 +50,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         include:
-          - os: ubuntu-latest
-            python-version: '3.7'
-            job_id: 0
-          - os: ubuntu-latest
-            python-version: '3.8'
-            job_id: 1
-          - os: ubuntu-latest
-            python-version: '3.9'
-            job_id: 2
-          - os: ubuntu-latest
-            python-version: '3.10'
-            job_id: 3
           - os: macos-latest
-            python-version: '3.10'
-            job_id: 4
+            python-version: '3.12'
           - os: windows-latest
-            python-version: '3.10'
-            job_id: 5
+            python-version: '3.12'
+
+    env:
+      JOB_ID: ${{ strategy.job-index }}
+      NUM_JOBS: ${{ strategy.job-total }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         persist-credentials: false
     - name: Setup Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Determine if downloads are enabled for this job
@@ -80,9 +76,6 @@ jobs:
       # PRs and the master branch; note that the master branch is tested weekly via `cron`,
       # so this ensures all Python versions will be periodically integration tested with the
       # resource servers
-      env:
-        NUM_JOBS: 6
-        JOB_ID: ${{ matrix.job_id }}
       if: ${{ github.event_name == 'pull_request' || github.ref == 'refs/heads/master' }}
       shell: bash
       run: |
@@ -110,6 +103,7 @@ jobs:
       working-directory: C:\a\lineage\lineage
       run: |
         pytest --cov=lineage tests
-    - name: Upload coverage to Codecov (Ubuntu & macOS)
-      if: ${{ matrix.os != 'windows-latest' }}
-      uses: codecov/codecov-action@v3
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4.1.0
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.rst b/README.rst
index d580754..b1ced0a 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>`_ 3.7.1+ and the following Python packages:
+``lineage`` requires `Python <https://www.python.org>`_ 3.8+ and the following Python packages:
 
 - `numpy <https://numpy.org>`_
 - `pandas <https://pandas.pydata.org>`_
diff --git a/setup.py b/setup.py
index 04436fd..8e2d2fa 100644
--- a/setup.py
+++ b/setup.py
@@ -97,10 +97,11 @@
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",
@@ -115,6 +116,6 @@
     keywords="dna genes genetics genealogy snps chromosomes genotype "
     "bioinformatics ancestry",
     install_requires=["numpy", "pandas", "matplotlib", "atomicwrites", "snps"],
-    python_requires=">=3.7.1",
+    python_requires=">=3.8",
     platforms=["any"],
 )