From 863e6aaceda648ce79635e2b374a997f8cf4c814 Mon Sep 17 00:00:00 2001
From: Remi Planel <rplanel@pasteur.fr>
Date: Fri, 31 Jan 2020 16:08:17 +0100
Subject: [PATCH] Update to panda 1.0.0

---
 poetry.lock    | 324 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   2 +-
 2 files changed, 160 insertions(+), 166 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index efeb490..de7e5aa 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -20,6 +20,7 @@ pyyaml = "*"
 [[package]]
 category = "dev"
 description = "Atomic file writes."
+marker = "sys_platform == \"win32\""
 name = "atomicwrites"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
@@ -45,7 +46,7 @@ description = "Freely available tools for computational molecular biology."
 name = "biopython"
 optional = false
 python-versions = "*"
-version = "1.75"
+version = "1.76"
 
 [package.dependencies]
 numpy = "*"
@@ -95,8 +96,8 @@ description = "Cross-platform colored terminal text."
 marker = "sys_platform == \"win32\""
 name = "colorama"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.4.1"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "0.4.3"
 
 [[package]]
 category = "dev"
@@ -126,7 +127,7 @@ description = "File identification library for Python"
 name = "identify"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-version = "1.4.9"
+version = "1.4.11"
 
 [package.extras]
 license = ["editdistance"]
@@ -137,8 +138,8 @@ description = "Read metadata from Python packages"
 marker = "python_version < \"3.8\""
 name = "importlib-metadata"
 optional = false
-python-versions = ">=2.7,!=3.0,!=3.1,!=3.2,!=3.3"
-version = "0.23"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+version = "1.5.0"
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -160,8 +161,8 @@ category = "dev"
 description = "More routines for operating on iterables, beyond itertools"
 name = "more-itertools"
 optional = false
-python-versions = ">=3.4"
-version = "7.2.0"
+python-versions = ">=3.5"
+version = "8.2.0"
 
 [[package]]
 category = "dev"
@@ -169,7 +170,7 @@ description = "Node.js virtual environment builder"
 name = "nodeenv"
 optional = false
 python-versions = "*"
-version = "1.3.3"
+version = "1.3.4"
 
 [[package]]
 category = "main"
@@ -177,7 +178,7 @@ description = "NumPy is the fundamental package for array computing with Python.
 name = "numpy"
 optional = false
 python-versions = ">=3.5"
-version = "1.17.4"
+version = "1.18.1"
 
 [[package]]
 category = "dev"
@@ -185,7 +186,7 @@ description = "Core utilities for Python packages"
 name = "packaging"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "19.2"
+version = "20.1"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
@@ -196,8 +197,8 @@ category = "main"
 description = "Powerful data structures for data analysis, time series, and statistics"
 name = "pandas"
 optional = false
-python-versions = ">=3.5.3"
-version = "0.25.3"
+python-versions = ">=3.6.1"
+version = "1.0.0"
 
 [package.dependencies]
 numpy = ">=1.13.3"
@@ -221,7 +222,7 @@ description = "plugin and hook calling mechanisms for python"
 name = "pluggy"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.0"
+version = "0.13.1"
 
 [package.dependencies]
 [package.dependencies.importlib-metadata]
@@ -236,8 +237,8 @@ category = "dev"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 name = "pre-commit"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "1.20.0"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+version = "1.21.0"
 
 [package.dependencies]
 "aspy.yaml" = "*"
@@ -259,7 +260,7 @@ description = "library with cross-python path, ini-parsing, io, code, log facili
 name = "py"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.8.0"
+version = "1.8.1"
 
 [[package]]
 category = "dev"
@@ -283,7 +284,7 @@ description = "Python parsing module"
 name = "pyparsing"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "2.4.5"
+version = "2.4.6"
 
 [[package]]
 category = "dev"
@@ -291,7 +292,7 @@ description = "pytest: simple powerful testing with Python"
 name = "pytest"
 optional = false
 python-versions = ">=3.5"
-version = "5.2.2"
+version = "5.3.5"
 
 [package.dependencies]
 atomicwrites = ">=1.0"
@@ -308,6 +309,7 @@ python = "<3.8"
 version = ">=0.12"
 
 [package.extras]
+checkqa-mypy = ["mypy (v0.761)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
@@ -343,7 +345,7 @@ description = "Alternative regular expression module, to replace re."
 name = "regex"
 optional = false
 python-versions = "*"
-version = "2019.12.20"
+version = "2020.1.8"
 
 [[package]]
 category = "main"
@@ -361,8 +363,8 @@ category = "main"
 description = "Python 2 and 3 compatibility utilities"
 name = "six"
 optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*"
-version = "1.13.0"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+version = "1.14.0"
 
 [[package]]
 category = "dev"
@@ -378,7 +380,7 @@ description = "a fork of Python 2 and 3 ast modules with type comment support"
 name = "typed-ast"
 optional = false
 python-versions = "*"
-version = "1.4.0"
+version = "1.4.1"
 
 [[package]]
 category = "dev"
@@ -398,7 +400,7 @@ description = "Measures number of Terminal column cells of wide-character codes"
 name = "wcwidth"
 optional = false
 python-versions = "*"
-version = "0.1.7"
+version = "0.1.8"
 
 [[package]]
 category = "dev"
@@ -406,18 +408,15 @@ description = "Backport of pathlib-compatible object wrapper for zip files"
 marker = "python_version < \"3.8\""
 name = "zipp"
 optional = false
-python-versions = ">=2.7"
-version = "0.6.0"
-
-[package.dependencies]
-more-itertools = "*"
+python-versions = ">=3.6"
+version = "2.1.0"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["pathlib2", "contextlib2", "unittest2"]
+testing = ["jaraco.itertools"]
 
 [metadata]
-content-hash = "fd6a383dbb81068f75ead2da55eccaea5f426d79758f22ebaf6eef7ac197234a"
+content-hash = "0215f7f3ee571b2a0728522af2e5306a325632e4c9b4c4a3dafda203f9522d1b"
 python-versions = "^3.7"
 
 [metadata.files]
@@ -438,32 +437,31 @@ attrs = [
     {file = "attrs-19.3.0.tar.gz", hash = "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"},
 ]
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+    {file = "biopython-1.76-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:b1a29524cbea4eb7d6ef9c2626c8fdc3d21a1a0790b7a5a6725bfc57e129be39"},
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+    {file = "biopython-1.76-cp38-cp38-win_amd64.whl", hash = "sha256:20550cad24f66d4c47be556464e892c3e7cadeadb83e28cd3118297dd4bc361b"},
+    {file = "biopython-1.76.tar.gz", hash = "sha256:3873cb98dad5e28d5e3f2215a012565345a398d3d2c4eebf7cd701757b828c72"},
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 black = [
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@@ -478,8 +476,8 @@ click = [
     {file = "Click-7.0.tar.gz", hash = "sha256:5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7"},
 ]
 colorama = [
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+    {file = "colorama-0.4.3.tar.gz", hash = "sha256:e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1"},
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 entrypoints = [
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@@ -490,87 +488,82 @@ flake8 = [
     {file = "flake8-3.7.9.tar.gz", hash = "sha256:45681a117ecc81e870cbf1262835ae4af5e7a8b08e40b944a8a6e6b895914cfb"},
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+    {file = "identify-1.4.11.tar.gz", hash = "sha256:d824ebe21f38325c771c41b08a95a761db1982f1fc0eee37c6c97df3f1636b96"},
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 wcwidth = [
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-    {file = "wcwidth-0.1.7.tar.gz", hash = "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e"},
+    {file = "wcwidth-0.1.8-py2.py3-none-any.whl", hash = "sha256:8fd29383f539be45b20bd4df0dc29c20ba48654a41e661925e612311e9f3c603"},
+    {file = "wcwidth-0.1.8.tar.gz", hash = "sha256:f28b3e8a6483e5d49e7f8949ac1a78314e740333ae305b4ba5defd3e74fb37a8"},
 ]
 zipp = [
-    {file = "zipp-0.6.0-py2.py3-none-any.whl", hash = "sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335"},
-    {file = "zipp-0.6.0.tar.gz", hash = "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e"},
+    {file = "zipp-2.1.0-py3-none-any.whl", hash = "sha256:ccc94ed0909b58ffe34430ea5451f07bc0c76467d7081619a454bf5c98b89e28"},
+    {file = "zipp-2.1.0.tar.gz", hash = "sha256:feae2f18633c32fc71f2de629bfb3bd3c9325cd4419642b1f1da42ee488d9b98"},
 ]
diff --git a/pyproject.toml b/pyproject.toml
index ad950ce..875168c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ numpy = "^1.17"
 click = "^7.0"
 biopython = "^1.75"
 rope = "^0.16.0"
-pandas = "^0.25.3"
+pandas = "^1.0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
-- 
GitLab