From 7cfd902c61efde1d4f4704fae23bac21768fb562 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 5 Jun 2023 12:58:56 -0700
Subject: [PATCH] Add HIVIntact to our python dependencies

---
 Pipfile      |   1 +
 Pipfile.lock | 188 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 setup.py     |   1 +
 3 files changed, 187 insertions(+), 3 deletions(-)

diff --git a/Pipfile b/Pipfile
index a039031..a9d403d 100644
--- a/Pipfile
+++ b/Pipfile
@@ -10,6 +10,7 @@ python-levenshtein = "==0.12.0"
 pandas = "==2.0.2"
 requests = "==2.31.0"
 pyyaml = "*"
+intactness-pipeline = {ref = "cfe-1.2", git = "https://github.com/cfe-lab/HIVIntact"}
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 5bc34d3..aed6c1c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "73432848a2ff11546bd4d06f2cabd2c46876a987e2d0a9e8c0d379cdfd9eb4f5"
+            "sha256": "100f2cea5bdbda87105a66b042daed34e24cc3e092e8382794b6f03c5553b02d"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,6 +16,43 @@
         ]
     },
     "default": {
+        "appdirs": {
+            "hashes": [
+                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
+                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
+            ],
+            "version": "==1.4.4"
+        },
+        "biopython": {
+            "hashes": [
+                "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
+                "sha256:2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0",
+                "sha256:2f9cfaf16d55ab80d514e7aebe5710dabe4e4ff47ede851031202e33b3249da3",
+                "sha256:35506e39822c52d11cf09a3951e82375ca1bb9303960b4286acf02c9a6f6c4cc",
+                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
+                "sha256:655df416936662c0c8a06a549cb25e1560e1fea5067d850f34fb714b8a3fae6c",
+                "sha256:65b93b513ce9dd7b2ce058720eadf42cd03f312db3409356efeb93123d1320aa",
+                "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b",
+                "sha256:762c6c43a8486b5fcd07f136a3217b87d24755618b9ea9da1f17124ff44c2ad6",
+                "sha256:793c42a376cd63f62f8a088ce39b7dc6b5c55e4e9031d887c434de1595bfa4b8",
+                "sha256:7a168709694e10b338718c18d967edd5b56c237dc88642c22275796007a70000",
+                "sha256:7c5c07123ff5f44c9e6b5369df854a38afd3c0c50ef58498a0ae8f7eb799f3e8",
+                "sha256:811796f8d222aa3869a50e31e54ce62b69106b47cd8bb06934867c0d843297b5",
+                "sha256:8bb0c690c7368f255ed45236bf0f5464b476b8c083c8f634533921af78278261",
+                "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275",
+                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
+                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
+                "sha256:a51d9c1d1b4b634447535da74a644fae59bc234fbbf9001e2dc6b6fbabb98019",
+                "sha256:b09efcb4733c8770f25eab5fe555a96a08f5ab9e1bc36939e08ebf2ffbf3e0f1",
+                "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81",
+                "sha256:ccd729249fd5f586dd4c2a3507c2ea2456825d7e615e97c07c409c850eaf4594",
+                "sha256:e41b55edcfd448630e77bf4de66a7235324a8a149621499891da6bd1d5085b9a",
+                "sha256:ee51bb1cd7decffd24da6b76d5e01b7e2fd818ab85cf0c180226cbb5793a3abd",
+                "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.81"
+        },
         "certifi": {
             "hashes": [
                 "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7",
@@ -105,6 +142,14 @@
             "markers": "python_full_version >= '3.7.0'",
             "version": "==3.2.0"
         },
+        "click": {
+            "hashes": [
+                "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd",
+                "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==8.1.6"
+        },
         "gotoh": {
             "git": "https://github.com/cfe-lab/MiCall.git",
             "ref": "f1687e7b7c7f1f3a6f3cb63107f1cf9b2b210f26",
@@ -118,6 +163,118 @@
             "markers": "python_version >= '3.5'",
             "version": "==3.4"
         },
+        "intactness-pipeline": {
+            "git": "https://github.com/cfe-lab/HIVIntact",
+            "ref": "14f571d873131d2521a6bddcefbf795914ac78c7"
+        },
+        "jarowinkler": {
+            "hashes": [
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+                "sha256:18e3af57ac066a617bd688d62b9d0da11da32dca977d9fe5c1726040be26ad2e",
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+                "sha256:21869871774ea4a34222538c33704234ee8e1b4c1a82fe95471215994575e631",
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+                "sha256:28654c3cfd1f917900a44650cee3a6827210c1f1783ef5aca3399ee31ee2cd17",
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+                "sha256:fa55d91bcf097b464df6efa92762434aa3026a9774ab2509895a1948bf64b121",
+                "sha256:fbcb4aafadf3ac758de12deb3c90c4e4b6497a104d00ecc8cb6585757af3ab90",
+                "sha256:fd4b9111a2092eaaaabd7dd33aa8703d734075a2f75ec87976eab0a2b60273ac"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.2.3"
+        },
         "numpy": {
             "hashes": [
                 "sha256:012097b5b0d00a11070e8f2e261128c44157a8689f7dedcf35576e525893f4fe",
@@ -185,7 +342,7 @@
                 "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86",
                 "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==2.8.2"
         },
         "python-levenshtein": {
@@ -256,6 +413,31 @@
             "index": "pypi",
             "version": "==2.31.0"
         },
+        "scipy": {
+            "hashes": [
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+                "sha256:ba94eeef3c9caa4cea7b402a35bb02a5714ee1ee77eb98aca1eed4543beb0f4c",
+                "sha256:be8c962a821957fdde8c4044efdab7a140c13294997a407eaee777acf63cbf0c",
+                "sha256:cce154372f0ebe88556ed06d7b196e9c2e0c13080ecb58d0f35062dc7cc28b47",
+                "sha256:d51565560565a0307ed06fa0ec4c6f21ff094947d4844d6068ed04400c72d0c3",
+                "sha256:e866514bc2d660608447b6ba95c8900d591f2865c07cca0aa4f7ff3c4ca70f30",
+                "sha256:fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289",
+                "sha256:ffb28e3fa31b9c376d0fb1f74c1f13911c8c154a760312fbee87a21eb21efe31"
+            ],
+            "markers": "python_version < '3.13' and python_version >= '3.9'",
+            "version": "==1.11.1"
+        },
         "setuptools": {
             "hashes": [
                 "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f",
@@ -269,7 +451,7 @@
                 "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
                 "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==1.16.0"
         },
         "tzdata": {
diff --git a/setup.py b/setup.py
index 069adcc..8fc0cd8 100644
--- a/setup.py
+++ b/setup.py
@@ -10,6 +10,7 @@
         'python-Levenshtein==0.12.0',
         'pandas==2.0.2',
         'requests==2.31.0',
+        'intactness-pipeline @ git+https://github.com/cfe-lab/HIVIntact.git@cfe-1.2',
         'pyyaml'
     ],
     package_data={