From a67d1612775e0fe01fd11e8787394feb02f27c26 Mon Sep 17 00:00:00 2001
From: Daniel King <dnlkng13@gmail.com>
Date: Mon, 16 May 2022 09:18:23 -0700
Subject: [PATCH 01/24] build: add PSR as dev dependency

---
 poetry.lock    | 430 ++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |   1 +
 2 files changed, 430 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index fbe190f..f42a550 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -114,6 +114,22 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "bleach"
+version = "5.0.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+six = ">=1.9.0"
+webencodings = "*"
+
+[package.extras]
+css = ["tinycss2 (>=1.1.0)"]
+dev = ["pip-tools (==6.5.1)", "pytest (==7.1.1)", "flake8 (==4.0.1)", "tox (==3.24.5)", "sphinx (==4.3.2)", "twine (==4.0.0)", "wheel (==0.37.1)", "hashin (==0.17.0)", "black (==22.3.0)", "mypy (==0.942)"]
+
 [[package]]
 name = "certifi"
 version = "2021.10.8"
@@ -155,6 +171,17 @@ python-versions = ">=3.7"
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
+[[package]]
+name = "click-log"
+version = "0.4.0"
+description = "Logging integration for Click"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+click = "*"
+
 [[package]]
 name = "codecov"
 version = "2.1.12"
@@ -189,6 +216,25 @@ tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
 [package.extras]
 toml = ["tomli"]
 
+[[package]]
+name = "cryptography"
+version = "37.0.2"
+description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cffi = ">=1.12"
+
+[package.extras]
+docs = ["sphinx (>=1.6.5,!=1.8.0,!=3.1.0,!=3.1.1)", "sphinx-rtd-theme"]
+docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"]
+pep8test = ["black", "flake8", "flake8-import-order", "pep8-naming"]
+sdist = ["setuptools_rust (>=0.11.4)"]
+ssh = ["bcrypt (>=3.1.5)"]
+test = ["pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"]
+
 [[package]]
 name = "debugpy"
 version = "1.6.0"
@@ -213,6 +259,17 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[[package]]
+name = "dotty-dict"
+version = "1.3.0"
+description = "Dictionary wrapper for quick access to deeply nested keys."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+setuptools_scm = "*"
+
 [[package]]
 name = "entrypoints"
 version = "0.4"
@@ -240,6 +297,28 @@ python-versions = "*"
 [package.extras]
 devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
 
+[[package]]
+name = "gitdb"
+version = "4.0.9"
+description = "Git Object Database"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+smmap = ">=3.0.1,<6"
+
+[[package]]
+name = "gitpython"
+version = "3.1.27"
+description = "GitPython is a python library used to interact with Git repositories"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+gitdb = ">=4.0.1,<5"
+
 [[package]]
 name = "greenlet"
 version = "1.1.2"
@@ -291,6 +370,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "invoke"
+version = "1.7.1"
+description = "Pythonic task execution"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "ipykernel"
 version = "6.13.0"
@@ -364,6 +451,18 @@ parso = ">=0.8.0,<0.9.0"
 qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
 testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
 
+[[package]]
+name = "jeepney"
+version = "0.8.0"
+description = "Low-level, pure Python DBus protocol wrapper."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest", "pytest-trio", "pytest-asyncio (>=0.17)", "testpath", "trio", "async-timeout"]
+trio = ["trio", "async-generator"]
+
 [[package]]
 name = "jinja2"
 version = "3.1.2"
@@ -454,6 +553,24 @@ traitlets = "*"
 [package.extras]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
+[[package]]
+name = "keyring"
+version = "23.5.0"
+description = "Store and access your passwords safely."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+importlib-metadata = ">=3.6"
+jeepney = {version = ">=0.4.2", markers = "sys_platform == \"linux\""}
+pywin32-ctypes = {version = "<0.1.0 || >0.1.0,<0.1.1 || >0.1.1", markers = "sys_platform == \"win32\""}
+SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [[package]]
 name = "lazy-object-proxy"
 version = "1.7.1"
@@ -690,6 +807,17 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pkginfo"
+version = "1.8.2"
+description = "Query metadatdata from sdists / bdists / installed packages."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+testing = ["coverage", "nose"]
+
 [[package]]
 name = "pluggy"
 version = "1.0.0"
@@ -844,6 +972,48 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "python-gitlab"
+version = "3.4.0"
+description = "Interact with GitLab API"
+category = "dev"
+optional = false
+python-versions = ">=3.7.0"
+
+[package.dependencies]
+requests = ">=2.25.0"
+requests-toolbelt = ">=0.9.1"
+
+[package.extras]
+autocompletion = ["argcomplete (>=1.10.0,<3)"]
+yaml = ["PyYaml (>=5.2)"]
+
+[[package]]
+name = "python-semantic-release"
+version = "7.28.1"
+description = "Automatic Semantic Versioning for Python projects"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+click = ">=7,<9"
+click-log = ">=0.3,<1"
+dotty-dict = ">=1.3.0,<2"
+gitpython = ">=3.0.8,<4"
+invoke = ">=1.4.1,<2"
+python-gitlab = ">=2,<4"
+requests = ">=2.25,<3"
+semver = ">=2.10,<3"
+tomlkit = ">=0.10.0,<0.11.0"
+twine = ">=3,<4"
+
+[package.extras]
+dev = ["tox", "isort", "black"]
+docs = ["Sphinx (==1.3.6)"]
+mypy = ["mypy", "types-requests"]
+test = ["coverage (>=5,<6)", "pytest (>=5,<6)", "pytest-xdist (>=1,<2)", "pytest-mock (>=2,<3)", "responses (==0.13.3)", "mock (==1.3.0)"]
+
 [[package]]
 name = "pytz"
 version = "2022.1"
@@ -860,6 +1030,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pywin32-ctypes"
+version = "0.2.0"
+description = ""
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -880,6 +1058,22 @@ python-versions = ">=3.6"
 cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 py = {version = "*", markers = "implementation_name == \"pypy\""}
 
+[[package]]
+name = "readme-renderer"
+version = "35.0"
+description = "readme_renderer is a library for rendering \"readme\" descriptions for Warehouse"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+bleach = ">=2.1.0"
+docutils = ">=0.13.1"
+Pygments = ">=2.5.1"
+
+[package.extras]
+md = ["cmarkgfm (>=0.8.0)"]
+
 [[package]]
 name = "requests"
 version = "2.27.1"
@@ -898,6 +1092,28 @@ urllib3 = ">=1.21.1,<1.27"
 socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
 use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
+[[package]]
+name = "requests-toolbelt"
+version = "0.9.1"
+description = "A utility belt for advanced users of python-requests"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+requests = ">=2.0.1,<3.0.0"
+
+[[package]]
+name = "rfc3986"
+version = "2.0.0"
+description = "Validating URI References per RFC 3986"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+idna2008 = ["idna"]
+
 [[package]]
 name = "scipy"
 version = "1.8.0"
@@ -909,6 +1125,42 @@ python-versions = ">=3.8,<3.11"
 [package.dependencies]
 numpy = ">=1.17.3,<1.25.0"
 
+[[package]]
+name = "secretstorage"
+version = "3.3.2"
+description = "Python bindings to FreeDesktop.org Secret Service API"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cryptography = ">=2.0"
+jeepney = ">=0.6"
+
+[[package]]
+name = "semver"
+version = "2.13.0"
+description = "Python helper for Semantic Versioning (http://semver.org/)"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "setuptools-scm"
+version = "6.4.2"
+description = "the blessed package to manage your versions by scm tags"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+packaging = ">=20.0"
+tomli = ">=1.0.0"
+
+[package.extras]
+test = ["pytest (>=6.2)", "virtualenv (>20)"]
+toml = ["setuptools (>=42)"]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -917,6 +1169,14 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "smmap"
+version = "5.0.0"
+description = "A pure Python implementation of a sliding window memory map manager"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "snowballstemmer"
 version = "2.2.0"
@@ -1145,6 +1405,14 @@ category = "dev"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "tomlkit"
+version = "0.10.2"
+description = "Style preserving TOML library"
+category = "dev"
+optional = false
+python-versions = ">=3.6,<4.0"
+
 [[package]]
 name = "toolz"
 version = "0.11.2"
@@ -1161,6 +1429,23 @@ category = "main"
 optional = false
 python-versions = ">= 3.5"
 
+[[package]]
+name = "tqdm"
+version = "4.64.0"
+description = "Fast, Extensible Progress Meter"
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
+telegram = ["requests"]
+
 [[package]]
 name = "traitlets"
 version = "5.2.0"
@@ -1172,6 +1457,26 @@ python-versions = ">=3.7"
 [package.extras]
 test = ["pytest", "pre-commit"]
 
+[[package]]
+name = "twine"
+version = "3.8.0"
+description = "Collection of utilities for publishing packages on PyPI"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = ">=0.4.3"
+importlib-metadata = ">=3.6"
+keyring = ">=15.1"
+pkginfo = ">=1.8.1"
+readme-renderer = ">=21.0"
+requests = ">=2.20"
+requests-toolbelt = ">=0.8.0,<0.9.0 || >0.9.0"
+rfc3986 = ">=1.4.0"
+tqdm = ">=4.14"
+urllib3 = ">=1.26.0"
+
 [[package]]
 name = "typing-extensions"
 version = "4.2.0"
@@ -1209,6 +1514,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "webencodings"
+version = "0.5.1"
+description = "Character encoding aliases for legacy web content"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "wrapt"
 version = "1.14.1"
@@ -1232,7 +1545,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.9, <3.11"
-content-hash = "fb53c9563ce775739c038488982af5ee693be6378004488fb0d5876550bd06a9"
+content-hash = "8613b3abc288fa9a243ab25e3ebd1c6d6ba25ad9c8f3bc5a9cdc27c396ae743c"
 
 [metadata.files]
 alabaster = [
@@ -1275,6 +1588,10 @@ backcall = [
     {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
 ]
+bleach = [
+    {file = "bleach-5.0.0-py3-none-any.whl", hash = "sha256:08a1fe86d253b5c88c92cc3d810fd8048a16d15762e1e5b74d502256e5926aa1"},
+    {file = "bleach-5.0.0.tar.gz", hash = "sha256:c6d6cc054bdc9c83b48b8083e236e5f00f238428666d2ce2e083eaa5fd568565"},
+]
 certifi = [
     {file = "certifi-2021.10.8-py2.py3-none-any.whl", hash = "sha256:d62a0163eb4c2344ac042ab2bdf75399a71a2d8c7d47eac2e2ee91b9d6339569"},
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
@@ -1339,6 +1656,10 @@ click = [
     {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
     {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
 ]
+click-log = [
+    {file = "click-log-0.4.0.tar.gz", hash = "sha256:3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975"},
+    {file = "click_log-0.4.0-py2.py3-none-any.whl", hash = "sha256:a43e394b528d52112af599f2fc9e4b7cf3c15f94e53581f74fa6867e68c91756"},
+]
 codecov = [
     {file = "codecov-2.1.12-py2.py3-none-any.whl", hash = "sha256:585dc217dc3d8185198ceb402f85d5cb5dbfa0c5f350a5abcdf9e347776a5b47"},
     {file = "codecov-2.1.12-py3.8.egg", hash = "sha256:782a8e5352f22593cbc5427a35320b99490eb24d9dcfa2155fd99d2b75cfb635"},
@@ -1391,6 +1712,30 @@ coverage = [
     {file = "coverage-6.3.2-pp36.pp37.pp38-none-any.whl", hash = "sha256:18d520c6860515a771708937d2f78f63cc47ab3b80cb78e86573b0a760161faf"},
     {file = "coverage-6.3.2.tar.gz", hash = "sha256:03e2a7826086b91ef345ff18742ee9fc47a6839ccd517061ef8fa1976e652ce9"},
 ]
+cryptography = [
+    {file = "cryptography-37.0.2-cp36-abi3-macosx_10_10_universal2.whl", hash = "sha256:ef15c2df7656763b4ff20a9bc4381d8352e6640cfeb95c2972c38ef508e75181"},
+    {file = "cryptography-37.0.2-cp36-abi3-macosx_10_10_x86_64.whl", hash = "sha256:3c81599befb4d4f3d7648ed3217e00d21a9341a9a688ecdd615ff72ffbed7336"},
+    {file = "cryptography-37.0.2-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:2bd1096476aaac820426239ab534b636c77d71af66c547b9ddcd76eb9c79e004"},
+    {file = "cryptography-37.0.2-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:31fe38d14d2e5f787e0aecef831457da6cec68e0bb09a35835b0b44ae8b988fe"},
+    {file = "cryptography-37.0.2-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:093cb351031656d3ee2f4fa1be579a8c69c754cf874206be1d4cf3b542042804"},
+    {file = "cryptography-37.0.2-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:59b281eab51e1b6b6afa525af2bd93c16d49358404f814fe2c2410058623928c"},
+    {file = "cryptography-37.0.2-cp36-abi3-manylinux_2_24_x86_64.whl", hash = "sha256:0cc20f655157d4cfc7bada909dc5cc228211b075ba8407c46467f63597c78178"},
+    {file = "cryptography-37.0.2-cp36-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:f8ec91983e638a9bcd75b39f1396e5c0dc2330cbd9ce4accefe68717e6779e0a"},
+    {file = "cryptography-37.0.2-cp36-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:46f4c544f6557a2fefa7ac8ac7d1b17bf9b647bd20b16decc8fbcab7117fbc15"},
+    {file = "cryptography-37.0.2-cp36-abi3-win32.whl", hash = "sha256:731c8abd27693323b348518ed0e0705713a36d79fdbd969ad968fbef0979a7e0"},
+    {file = "cryptography-37.0.2-cp36-abi3-win_amd64.whl", hash = "sha256:471e0d70201c069f74c837983189949aa0d24bb2d751b57e26e3761f2f782b8d"},
+    {file = "cryptography-37.0.2-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a68254dd88021f24a68b613d8c51d5c5e74d735878b9e32cc0adf19d1f10aaf9"},
+    {file = "cryptography-37.0.2-pp37-pypy37_pp73-manylinux_2_24_x86_64.whl", hash = "sha256:a7d5137e556cc0ea418dca6186deabe9129cee318618eb1ffecbd35bee55ddc1"},
+    {file = "cryptography-37.0.2-pp38-pypy38_pp73-macosx_10_10_x86_64.whl", hash = "sha256:aeaba7b5e756ea52c8861c133c596afe93dd716cbcacae23b80bc238202dc023"},
+    {file = "cryptography-37.0.2-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:95e590dd70642eb2079d280420a888190aa040ad20f19ec8c6e097e38aa29e06"},
+    {file = "cryptography-37.0.2-pp38-pypy38_pp73-manylinux_2_24_x86_64.whl", hash = "sha256:1b9362d34363f2c71b7853f6251219298124aa4cc2075ae2932e64c91a3e2717"},
+    {file = "cryptography-37.0.2-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:e53258e69874a306fcecb88b7534d61820db8a98655662a3dd2ec7f1afd9132f"},
+    {file = "cryptography-37.0.2-pp39-pypy39_pp73-macosx_10_10_x86_64.whl", hash = "sha256:1f3bfbd611db5cb58ca82f3deb35e83af34bb8cf06043fa61500157d50a70982"},
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@@ -1419,6 +1764,9 @@ docutils = [
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@@ -1714,6 +2082,10 @@ pickleshare = [
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@@ -1819,6 +2191,14 @@ python-dateutil = [
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@@ -1839,6 +2219,10 @@ pywin32 = [
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@@ -1923,10 +2307,22 @@ pyzmq = [
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@@ -1952,10 +2348,26 @@ scipy = [
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 snowballstemmer = [
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@@ -2050,6 +2462,10 @@ tomli = [
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@@ -2097,10 +2513,18 @@ tornado = [
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@@ -2117,6 +2541,10 @@ wcwidth = [
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 ]
+webencodings = [
+    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
+    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
+]
 wrapt = [
     {file = "wrapt-1.14.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3"},
     {file = "wrapt-1.14.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:903500616422a40a98a5a3c4ff4ed9d0066f3b4c951fa286018ecdf0750194ef"},
diff --git a/pyproject.toml b/pyproject.toml
index 203792f..970b554 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,6 +21,7 @@ codecov = "^2.1.12"
 myst-nb = {version = "^0.15.0", python = "^3.9"}
 sphinx-autoapi = "^1.8.4"
 sphinx-rtd-theme = "^1.0.0"
+python-semantic-release = "^7.28.1"
 [tool.semantic_release]
 version_variable = "pyproject.toml:version" # version location
 branch = "main"                             # branch to make releases of

From 8905d5980ba4d24451e92cc31f017d06f926a04b Mon Sep 17 00:00:00 2001
From: Daniel King <dnlkng13@gmail.com>
Date: Mon, 16 May 2022 12:10:45 -0700
Subject: [PATCH 02/24] build: add codecov with upload token

---
 .github/workflows/ci-cd.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index 05a8294..dcccd2c 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -26,11 +26,11 @@ jobs:
     - name: Test with pytest
       run: poetry run pytest tests/ --cov=emgdecompy --cov-report=xml
 
-# Can't use Codecov because repo is private
-#     - name: Use Codecov to track coverage
-#       uses: codecov/codecov-action@v2
-#       with:
-#         files: ./coverage.xml   # coverage report
+    - name: Use Codecov to track coverage
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml   # coverage report
 
     - name: Build documentation
       run: poetry run make html --directory docs/

From e744a7c704cfdfba43fd37003d47f0bae9de231c Mon Sep 17 00:00:00 2001
From: Rada Rudyak <radawilinofsky@gmail.com>
Date: Mon, 16 May 2022 23:50:06 -0700
Subject: [PATCH 03/24] fix: small change to create_emg_data() function to not
 allow 1 dimensional arrays to be created

---
 tests/test_emgdecompy.py | 87 +++++++++++++++++++++++++---------------
 1 file changed, 55 insertions(+), 32 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index fefb9a8..49f764c 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -1,8 +1,9 @@
 from emgdecompy import emgdecompy as emg
-import random 
+import random
 import numpy as np
 from scipy import linalg
 
+
 def test_extend_input_by_R():
     """
     Run unit tests on extend_input_by_R function from EMGdecomPy.
@@ -15,13 +16,18 @@ def test_extend_input_by_R():
     assert emg.extend_input_by_R(x, R_one)[0][-1] == 0
     assert emg.extend_input_by_R(x, R_one).shape == (len(x), R_one + 1)
     assert emg.extend_input_by_R(x, R_one)[-1][0] == x[-1]
-    assert emg.extend_input_by_R(x, R_one)[0][0] == emg.extend_input_by_R(x, R_one)[1][1]
+    assert (
+        emg.extend_input_by_R(x, R_one)[0][0] == emg.extend_input_by_R(x, R_one)[1][1]
+    )
 
     assert emg.extend_input_by_R(x, R_two)[0][0] == x[0]
     assert emg.extend_input_by_R(x, R_two)[0][-1] == 0
     assert emg.extend_input_by_R(x, R_two).shape == (len(x), R_two + 1)
     assert emg.extend_input_by_R(x, R_two)[-1][0] == x[-1]
-    assert emg.extend_input_by_R(x, R_two)[0][0] == emg.extend_input_by_R(x, R_two)[1][1]
+    assert (
+        emg.extend_input_by_R(x, R_two)[0][0] == emg.extend_input_by_R(x, R_two)[1][1]
+    )
+
 
 def test_extend_all_channels():
     """
@@ -31,28 +37,43 @@ def test_extend_all_channels():
     R_two = 10
     x_mat = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
 
-    assert emg.extend_all_channels(x_mat, R_one).shape == (len(x_mat), len(x_mat[0]), R_one + 1)
-    assert emg.extend_all_channels(x_mat, R_one)[0][0][0] == emg.extend_input_all_channels(x_mat, R_one)[0][1][1]
+    assert emg.extend_all_channels(x_mat, R_one).shape == (
+        len(x_mat),
+        len(x_mat[0]),
+        R_one + 1,
+    )
+    assert (
+        emg.extend_all_channels(x_mat, R_one)[0][0][0]
+        == emg.extend_input_all_channels(x_mat, R_one)[0][1][1]
+    )
     assert emg.extend_all_channels(x_mat, R_one)[0][0][-1] == 0
     assert sum(emg.extend_all_channels(x_mat, R_one)[-1][-1]) == sum(x_mat[-1])
 
-    assert emg.extend_all_channels(x_mat, R_two).shape == (len(x_mat), len(x_mat[0]), R_two + 1)
-    assert emg.extend_all_channels(x_mat, R_two)[0][0][0] == emg.extend_input_all_channels(x_mat, R_two)[0][1][1]
+    assert emg.extend_all_channels(x_mat, R_two).shape == (
+        len(x_mat),
+        len(x_mat[0]),
+        R_two + 1,
+    )
+    assert (
+        emg.extend_all_channels(x_mat, R_two)[0][0][0]
+        == emg.extend_input_all_channels(x_mat, R_two)[0][1][1]
+    )
     assert emg.extend_all_channels(x_mat, R_two)[0][0][-1] == 0
     assert sum(emg.extend_all_channels(x_mat, R_two)[-1][-1]) == sum(x_mat[-1])
 
+
 def create_emg_data(m=13, n=5, q=10):
     """
     Creates array (m, n) of arrays (1, q) with one empty subarray.
-    
+
     Parameters
     ---------
     m : int
         Number of rows to set as outer array size. The default size is 13.
     n : int
-        Number of entries for outer array to have in each row. The default size is 5. 
+        Number of entries for outer array to have in each row. The default size is 5.
     q : int
-        Number of entries for inner array to have in each row. The default size is 10; the default shape is (1, 10). 
+        Number of entries for inner array to have in each row. The default size is 10; the default shape is (1, 10).
 
     Returns
     -------
@@ -64,78 +85,80 @@ def create_emg_data(m=13, n=5, q=10):
 
     fake_data = np.zeros([m, n], dtype=object)
 
+    # list of five sets of fake data
     for i in range(0, m):
-        fake_data[i, :] = [np.random.randn(1,q)] # same sequence for each row in array
+        fake_data[i, :] = [np.random.randn(1, q)]  # same sequence for each row in array
 
     fake_data[empty_row, empty_col] = np.array([])
-    
+
     return fake_data
 
+
 def test_flatten_signal():
     """
     Run unit tests on flatten_signal function from EMGdecomPy.
     """
-    # create fake data 
+    # create fake data
     fake_data = []
 
-    for i in range(0,4):
-        m = np.random.randint(1, 150)
-        n = np.random.randint(1, 150)
-        q = np.random.randint(1, 150)
+    for i in range(0, 4):
+        m = np.random.randint(2, 150)
+        n = np.random.randint(2, 150)
+        q = np.random.randint(2, 150)
 
         fake_data.append(create_emg_data(m, n, q))
-           
 
     # run tests on fake datasets
     for i in fake_data:
-    
+
         # test that input is correct
         assert type(i) == np.ndarray, "Input is not type numpy.ndarray"
-        assert i.shape != (1,1), "Input array is already one-dimensional."
+        assert i.shape != (1, 1), "Input array is already one-dimensional."
 
         flat = emg.flatten_signal(i)
-        
-        # shape of fake data 
+
+        # shape of fake data
         m, n = i.shape
         q = flat.shape[1]
-        
-        # test that inner arrays are correct length 
+
+        # test that inner arrays are correct length
         assert i[0][0].shape[1] == q, "Dimensions of inner array not the same."
-        
-        # test that empty channel has been removed 
+
+        # test that empty channel has been removed
         assert (m * n) != flat.shape[0], "Empty array not removed"
 
+
 def test_center_matrix():
     """
     Run unit tests on center_matrix function from EMGdecomPy.
     """
     x1 = np.array([[1, 2, 3], [4, 6, 8]])
     x2 = np.array([[[1, 2, 3], [4, 6, 8]], [[10, 13, 16], [17, 21, 25]]])
-    
+
     # assert center_matrix works on a 2D array
     assert (emg.center_matrix(x1)[0] == x1[0] - x1[0].mean()).all()
     assert (emg.center_matrix(x1)[1] == x1[1] - x1[1].mean()).all()
-    
+
     # assert center_matrix works on a 3D array
     assert (emg.center_matrix(x2)[0][0] == x2[0][0] - x2[0][0].mean()).all()
     assert (emg.center_matrix(x2)[0][1] == x2[0][1] - x2[0][1].mean()).all()
     assert (emg.center_matrix(x2)[1][0] == x2[1][0] - x2[1][0].mean()).all()
     assert (emg.center_matrix(x2)[1][1] == x2[1][1] - x2[1][1].mean()).all()
 
+
 def test_whiten():
     """
     Run unit test on whitening function from EMGdecomPy.
     """
-    x = np.array([[1, 2, 3, 4],
-                  [5, 6, 7, 8]])
+    x = np.array([[1, 2, 3, 4], [5, 6, 7, 8]])
     x_cent = emg.center_matrix(x)
     cov_mat = np.cov(x_cent, rowvar=True, bias=True)
     w, v = linalg.eig(cov_mat)
-    #w += w[:len(w) / 2].mean()
+    # w += w[:len(w) / 2].mean()
     D = np.diag(w)
     D = np.sqrt(linalg.inv(D))
     D = D.real.round(4)
     W = np.dot(np.dot(v, D), v.T)
     np.dot(W, x_cent)
 
-    assert np.allclose(np.dot(W, x_cent), emg.whiten(x))
\ No newline at end of file
+    assert np.allclose(np.dot(W, x_cent), emg.whiten(x))

From a7c0da45dd6f07dc81c05a7409505e6723cbbac1 Mon Sep 17 00:00:00 2001
From: Rada Rudyak <radawilinofsky@gmail.com>
Date: Tue, 17 May 2022 00:18:25 -0700
Subject: [PATCH 04/24] fix: tweak test_flatten_signal to test for empty arrays
 pre-flatten

---
 tests/test_emgdecompy.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index 49f764c..5aa5be4 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -122,7 +122,11 @@ def test_flatten_signal():
         q = flat.shape[1]
 
         # test that inner arrays are correct length
-        assert i[0][0].shape[1] == q, "Dimensions of inner array not the same."
+        # test that inner arrays are correct length
+        if 0 not in i[0][0].shape:
+            assert i[0][0].shape[1] == q, "Dimensions of inner array not the same."
+        else:
+            assert i[0][1].shape[1] == q, "Dimensions of inner array not the same."
 
         # test that empty channel has been removed
         assert (m * n) != flat.shape[0], "Empty array not removed"

From 97d67c9ef6c663e4aab3c31167dd6775a1a313c1 Mon Sep 17 00:00:00 2001
From: Rada Rudyak <radawilinofsky@gmail.com>
Date: Tue, 17 May 2022 00:19:24 -0700
Subject: [PATCH 05/24] fix: tweak create_emg_data to use np.empty so that
 shape is consistent with real data

---
 tests/test_emgdecompy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index 5aa5be4..f435ff9 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -89,7 +89,7 @@ def create_emg_data(m=13, n=5, q=10):
     for i in range(0, m):
         fake_data[i, :] = [np.random.randn(1, q)]  # same sequence for each row in array
 
-    fake_data[empty_row, empty_col] = np.array([])
+    fake_data[empty_row, empty_col] = np.empty([0,0])
 
     return fake_data
 

From 539b38630789fcac6e257530db95b23f49d45e46 Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Tue, 17 May 2022 16:20:41 -0700
Subject: [PATCH 06/24] test: update extend_input_by_R tests

---
 tests/test_emgdecompy.py | 41 ++++++++++++++++++++++++----------------
 1 file changed, 25 insertions(+), 16 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index fefb9a8..c5ee923 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -5,23 +5,32 @@
 
 def test_extend_input_by_R():
     """
-    Run unit tests on extend_input_by_R function from EMGdecomPy.
+    Run unit tests on extend_input_by_R function from emg-decomPy
     """
-    R_one = 5
-    R_two = 10
-    x = np.array([1, 2, 3, 4, 5, 6, 7])
-
-    assert emg.extend_input_by_R(x, R_one)[0][0] == x[0]
-    assert emg.extend_input_by_R(x, R_one)[0][-1] == 0
-    assert emg.extend_input_by_R(x, R_one).shape == (len(x), R_one + 1)
-    assert emg.extend_input_by_R(x, R_one)[-1][0] == x[-1]
-    assert emg.extend_input_by_R(x, R_one)[0][0] == emg.extend_input_by_R(x, R_one)[1][1]
-
-    assert emg.extend_input_by_R(x, R_two)[0][0] == x[0]
-    assert emg.extend_input_by_R(x, R_two)[0][-1] == 0
-    assert emg.extend_input_by_R(x, R_two).shape == (len(x), R_two + 1)
-    assert emg.extend_input_by_R(x, R_two)[-1][0] == x[-1]
-    assert emg.extend_input_by_R(x, R_two)[0][0] == emg.extend_input_by_R(x, R_two)[1][1]
+
+    for i in range(0, 15): 
+        R = np.random.randint(1, 100) # to extend 
+        
+        assert R % 1 == 0, "Value of R is not an integer."  
+        assert R > 0 , "Value of R must be greater than zero."
+
+        # length of input array 
+        if R == 1:
+            q = 1 
+
+        else: 
+            q = np.random.randint(1, R)
+
+        middle = round(q/2)    
+        x = np.random.rand(q) # create input array
+
+        testing = emg.extend_input_by_R(x, R)
+
+        assert testing[1][0] == 0, "Array not extended properly." # check first value 
+        assert testing[middle][middle] == x[0] # check middle value 
+        assert testing[q-1][q-1] == x[0], "Array not extended properly." # check end value 
+        assert testing.shape == (R+1, x.shape[0]), "Shape of extended array incorrect"
+
 
 def test_extend_all_channels():
     """

From 79490f462fa946c123b747b38187e2cc919c0fc7 Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Tue, 17 May 2022 16:27:59 -0700
Subject: [PATCH 07/24] docs: fix doc string for test_extend_by_R()

---
 tests/test_emgdecompy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index c5ee923..568feec 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -5,7 +5,7 @@
 
 def test_extend_input_by_R():
     """
-    Run unit tests on extend_input_by_R function from emg-decomPy
+    Run unit tests on extend_input_by_R function from EMGdecomPy.
     """
 
     for i in range(0, 15): 

From bcc735cbed770547beacf584a1579ab481e3ba00 Mon Sep 17 00:00:00 2001
From: Rada Rudyak <radawilinofsky@gmail.com>
Date: Tue, 17 May 2022 16:28:58 -0700
Subject: [PATCH 08/24] docs: add clarification comment to test_flatten()
 according to Jasmine's feedback

---
 tests/test_emgdecompy.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index f435ff9..2684b9d 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -89,7 +89,7 @@ def create_emg_data(m=13, n=5, q=10):
     for i in range(0, m):
         fake_data[i, :] = [np.random.randn(1, q)]  # same sequence for each row in array
 
-    fake_data[empty_row, empty_col] = np.empty([0,0])
+    fake_data[empty_row, empty_col] = np.empty([0, 0])
 
     return fake_data
 
@@ -122,7 +122,9 @@ def test_flatten_signal():
         q = flat.shape[1]
 
         # test that inner arrays are correct length
-        # test that inner arrays are correct length
+
+        # if the first element is null array that was removed in flat,
+        # check the second element's shape for consistency
         if 0 not in i[0][0].shape:
             assert i[0][0].shape[1] == q, "Dimensions of inner array not the same."
         else:

From 6c3ac94e8f56b96ae9f216f177027bb116a80906 Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 13:38:08 -0700
Subject: [PATCH 09/24] test: update unit tests for extend_input_all_channels()

---
 tests/test_emgdecompy.py | 48 +++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 11 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index 568feec..b3e6050 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -36,20 +36,46 @@ def test_extend_all_channels():
     """
     Run unit tests on extend_input_all_channels function from EMGdecomPy.
     """
-    R_one = 5
-    R_two = 10
-    x_mat = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    for i in range(0, 15):
+    
+        # initalize dimensions of test data 
+        x = np.random.randint(2, 100)
+        y = np.random.randint(2, 100)
+        z = np.random.randint(2, 1000) 
+
+        # create test data + flatten
+        fake = emg.create_emg_data(x, y, z)
+        flat = emg.flatten_signal(fake)
+
+        # input array must be two dimensional 
+        assert sum(flat.shape) > flat.shape[0], "Input array is not of shape M x K"
+
+        m, k = flat.shape
+
+        # ensure that correct shape can be outputted
+        assert m > 0, "Input array cannot be empty."
+        assert k > 1, "Input array must contain more than one channel." 
+
+        # Negro, et al used R = 16
+        R = np.random.randint(1, 30)
+
+        # test input parameters of extend_all_channels()
+        assert R > 0, "Value of R must be greater than 0."
+        assert R % 1 == 0, "Value of R must be an integer."
 
-    assert emg.extend_all_channels(x_mat, R_one).shape == (len(x_mat), len(x_mat[0]), R_one + 1)
-    assert emg.extend_all_channels(x_mat, R_one)[0][0][0] == emg.extend_input_all_channels(x_mat, R_one)[0][1][1]
-    assert emg.extend_all_channels(x_mat, R_one)[0][0][-1] == 0
-    assert sum(emg.extend_all_channels(x_mat, R_one)[-1][-1]) == sum(x_mat[-1])
+        # extend channels
+        ext = emg.extend_all_channels(flat, R)
 
-    assert emg.extend_all_channels(x_mat, R_two).shape == (len(x_mat), len(x_mat[0]), R_two + 1)
-    assert emg.extend_all_channels(x_mat, R_two)[0][0][0] == emg.extend_input_all_channels(x_mat, R_two)[0][1][1]
-    assert emg.extend_all_channels(x_mat, R_two)[0][0][-1] == 0
-    assert sum(emg.extend_all_channels(x_mat, R_two)[-1][-1]) == sum(x_mat[-1])
+        # test output 
+        assert np.count_nonzero(ext[0]) == k, "Values extended incorrectly at ext[0]"
+        assert ext.shape == (m * (R+1), k), "Output array does not have shape M(R+1) x K"
 
+        if R > k: # if extension factor is bigger than length of array to extend, the last row is all zeros
+            assert np.count_nonzero(ext[-1]) == 0, "Values incorrectly extended at ext[-1]" 
+        else:
+            # otherwise there should be R zeros in last row
+            assert np.count_nonzero(ext[-1]) + R == k, "Values incorrectly extended at ext[-1]" 
+            
 def create_emg_data(m=13, n=5, q=10):
     """
     Creates array (m, n) of arrays (1, q) with one empty subarray.

From ce5fdd8dc8869a3c55cc044105adebef975d503b Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 13:48:20 -0700
Subject: [PATCH 10/24] docs: minor docstring inconsistencies in
 extend_all_channels()

---
 src/emgdecompy/emgdecompy.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/emgdecompy/emgdecompy.py b/src/emgdecompy/emgdecompy.py
index b50658d..c3ceecd 100644
--- a/src/emgdecompy/emgdecompy.py
+++ b/src/emgdecompy/emgdecompy.py
@@ -91,9 +91,9 @@ def extend_all_channels(x_mat, R):
         
     Examples
     --------
-        >>> R = 5
+        >>> R = 3
         >>> x_mat = np.array([[1, 2, 3, 4,], [5, 6, 7, 8,]])
-        >>> extend_input_all_channels(x_mat, 3)
+        >>> extend_all_channels(x_mat, R)
         array([[1., 2., 3., 4.],
                [0., 1., 2., 3.],
                [0., 0., 1., 2.],

From 7a6c50b1ec4437934eec4282475b56f42bb2f86a Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 14:01:55 -0700
Subject: [PATCH 11/24] fix: rearrange functions so create_emg_data() defined
 before called in test functions

---
 tests/test_emgdecompy.py | 60 ++++++++++++++++++++--------------------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index b3e6050..b86cc6d 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -3,6 +3,36 @@
 import numpy as np
 from scipy import linalg
 
+def create_emg_data(m=13, n=5, q=10):
+    """
+    Creates array (m, n) of arrays (1, q) with one empty subarray.
+    
+    Parameters
+    ---------
+    m : int
+        Number of rows to set as outer array size. The default size is 13.
+    n : int
+        Number of entries for outer array to have in each row. The default size is 5. 
+    q : int
+        Number of entries for inner array to have in each row. The default size is 10; the default shape is (1, 10). 
+
+    Returns
+    -------
+    raw : numpy.ndarray
+    """
+    # intialize which subarray will be empty
+    empty_row = np.random.randint(0, m)
+    empty_col = np.random.randint(0, n)
+
+    fake_data = np.zeros([m, n], dtype=object)
+
+    for i in range(0, m):
+        fake_data[i, :] = [np.random.randn(1,q)] # same sequence for each row in array
+
+    fake_data[empty_row, empty_col] = np.array([])
+    
+    return fake_data
+
 def test_extend_input_by_R():
     """
     Run unit tests on extend_input_by_R function from EMGdecomPy.
@@ -75,36 +105,6 @@ def test_extend_all_channels():
         else:
             # otherwise there should be R zeros in last row
             assert np.count_nonzero(ext[-1]) + R == k, "Values incorrectly extended at ext[-1]" 
-            
-def create_emg_data(m=13, n=5, q=10):
-    """
-    Creates array (m, n) of arrays (1, q) with one empty subarray.
-    
-    Parameters
-    ---------
-    m : int
-        Number of rows to set as outer array size. The default size is 13.
-    n : int
-        Number of entries for outer array to have in each row. The default size is 5. 
-    q : int
-        Number of entries for inner array to have in each row. The default size is 10; the default shape is (1, 10). 
-
-    Returns
-    -------
-    raw : numpy.ndarray
-    """
-    # intialize which subarray will be empty
-    empty_row = np.random.randint(0, m)
-    empty_col = np.random.randint(0, n)
-
-    fake_data = np.zeros([m, n], dtype=object)
-
-    for i in range(0, m):
-        fake_data[i, :] = [np.random.randn(1,q)] # same sequence for each row in array
-
-    fake_data[empty_row, empty_col] = np.array([])
-    
-    return fake_data
 
 def test_flatten_signal():
     """

From fe93f12b76edff9cf58cb68020c45659268cef6e Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 14:11:40 -0700
Subject: [PATCH 12/24] fix: incorrectly called create_emg_data()

---
 tests/test_emgdecompy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index b86cc6d..c006948 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -74,7 +74,7 @@ def test_extend_all_channels():
         z = np.random.randint(2, 1000) 
 
         # create test data + flatten
-        fake = emg.create_emg_data(x, y, z)
+        fake = create_emg_data(x, y, z)
         flat = emg.flatten_signal(fake)
 
         # input array must be two dimensional 

From 4fb93e4ca5c89734669412efe59a90f1675a3f63 Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 15:26:06 -0700
Subject: [PATCH 13/24] test: add more robust tests for
 test_extend_input_by_R()

---
 tests/test_emgdecompy.py | 39 +++++++++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 14 deletions(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index c006948..746fc5a 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -35,32 +35,43 @@ def create_emg_data(m=13, n=5, q=10):
 
 def test_extend_input_by_R():
     """
-    Run unit tests on extend_input_by_R function from EMGdecomPy.
+    Run unit tests on extend_input_by_R function from emg-decomPy
     """
 
     for i in range(0, 15): 
-        R = np.random.randint(1, 100) # to extend 
-        
-        assert R % 1 == 0, "Value of R is not an integer."  
-        assert R > 0 , "Value of R must be greater than zero."
+        # extension factor
+        R = np.random.randint(1, 100)
 
         # length of input array 
-        if R == 1:
-            q = 1 
+        q = np.random.randint(1, 100)
 
-        else: 
-            q = np.random.randint(1, R)
+        # create input array
+        x = np.random.rand(q) 
+
+        # check input parameters
+        assert R % 1 == 0, "Value of R must be an integer."  
+        assert R > 0 , "Value of R must be greater than zero."
+        assert sum(x.shape) == x.shape[0], f"Input array must be one-dimensional eg. ({k},)"
 
-        middle = round(q/2)    
-        x = np.random.rand(q) # create input array
+        k = x.shape[0]
 
         testing = emg.extend_input_by_R(x, R)
 
-        assert testing[1][0] == 0, "Array not extended properly." # check first value 
-        assert testing[middle][middle] == x[0] # check middle value 
-        assert testing[q-1][q-1] == x[0], "Array not extended properly." # check end value 
+        # check values are properly extended
+        assert testing[1][0] == 0, "Array not extended properly." # first extended array 
         assert testing.shape == (R+1, x.shape[0]), "Shape of extended array incorrect"
 
+        if R >= k:
+
+            # if R >=k, last few arrays will be all zeroes
+            assert testing[k-1][-1] == x[0], "Array not extended properly."
+            assert np.count_nonzero(testing[k]) == 0, f"Extended array should contain all zeros at testing[{k}]"
+            assert np.count_nonzero(testing[-1]) == 0, "Extended array should contain all zeros in last row"
+
+        else: 
+            assert testing[R][R] == x[0], "Array not extended not properly."
+            assert np.count_nonzero(testing[-1]) + R == k, "Array not extended not properly."
+
 
 def test_extend_all_channels():
     """

From f3022da9f77a3d282607c887396845625684c6a6 Mon Sep 17 00:00:00 2001
From: Jasmine Ortega <jorteg01@ubc.ca>
Date: Wed, 18 May 2022 15:28:50 -0700
Subject: [PATCH 14/24] docs: update package name in test_extend_input_by_R

---
 tests/test_emgdecompy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_emgdecompy.py b/tests/test_emgdecompy.py
index 746fc5a..7e6afc7 100644
--- a/tests/test_emgdecompy.py
+++ b/tests/test_emgdecompy.py
@@ -35,7 +35,7 @@ def create_emg_data(m=13, n=5, q=10):
 
 def test_extend_input_by_R():
     """
-    Run unit tests on extend_input_by_R function from emg-decomPy
+    Run unit tests on extend_input_by_R function from EMGdecomPy.
     """
 
     for i in range(0, 15): 

From 233aac0bd2dceaa03af9385dd60960e9f7ceb767 Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 16:09:05 -0700
Subject: [PATCH 15/24] fix: correct package name

---
 .github/workflows/ci-cd.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index dcccd2c..0c4f122 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -84,7 +84,7 @@ jobs:
           pip install \
           --index-url https://test.pypi.org/simple/ \
           --extra-index-url https://pypi.org/simple \
-          emg-decompy
+          emgdecompy
 
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

From 3fb899c946f959409e86efdc45ce5208adb53edf Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 16:14:38 -0700
Subject: [PATCH 16/24] build: Change PSR token

---
 .github/workflows/ci-cd.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index 0c4f122..c10bbe4 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -56,6 +56,7 @@ jobs:
       uses: actions/checkout@v2
       with:
         fetch-depth: 0
+        token: PSR_PUSH_TOKEN
 
     - name: Install poetry
       uses: snok/install-poetry@v1
@@ -66,7 +67,7 @@ jobs:
     - name: Use Python Semantic Release to prepare release
       env:
         # This token is created automatically by GH Actions
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GH_TOKEN: ${{ secrets.PSR_PUSH_TOKEN }}
       run: |
           git config user.name github-actions
           git config user.email github-actions@github.com

From e0f10683c9d52e4d4ca115005b60f8f762a71c07 Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 16:19:21 -0700
Subject: [PATCH 17/24] build: get rid of token under check-out repository

---
 .github/workflows/ci-cd.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index c10bbe4..e8d6c0b 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -56,7 +56,6 @@ jobs:
       uses: actions/checkout@v2
       with:
         fetch-depth: 0
-        token: PSR_PUSH_TOKEN
 
     - name: Install poetry
       uses: snok/install-poetry@v1

From 5fbbab7cca0b9ab48f4882a8fd7ad96036b33f2c Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 16:35:40 -0700
Subject: [PATCH 18/24] build: change PSR token back to GITHUB_TOKEN

---
 .github/workflows/ci-cd.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
index e8d6c0b..0c4f122 100644
--- a/.github/workflows/ci-cd.yml
+++ b/.github/workflows/ci-cd.yml
@@ -66,7 +66,7 @@ jobs:
     - name: Use Python Semantic Release to prepare release
       env:
         # This token is created automatically by GH Actions
-        GH_TOKEN: ${{ secrets.PSR_PUSH_TOKEN }}
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
           git config user.name github-actions
           git config user.email github-actions@github.com

From a778710bea0a1c3fd8129241aec38fe6924e0042 Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 16:36:24 -0700
Subject: [PATCH 19/24] docs: add codecov badge

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 288eca6..e100be3 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 # emgdecompy
 [![ci-cd](https://github.com/UBC-SPL-MDS/emg-decomPy/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/UBC-SPL-MDS/emg-decomPy/actions/workflows/ci-cd.yml)
+[![codecov](https://codecov.io/gh/UBC-SPL-MDS/EMGdecomPy/branch/main/graph/badge.svg?token=78ZU40UEOE)](https://codecov.io/gh/UBC-SPL-MDS/EMGdecomPy)
+
 
 A package for decomposing raw EMG signals into individual motor unit activity.
 

From 703b8dc433fe1c6d4e25a2d7bb80eae02650ac3c Mon Sep 17 00:00:00 2001
From: Daniel King <dnlkng13@gmail.com>
Date: Wed, 18 May 2022 18:31:05 -0700
Subject: [PATCH 20/24] build: add sklearn dependency

---
 poetry.lock    | 80 +++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |  1 +
 2 files changed, 80 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index f42a550..6239556 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -477,6 +477,14 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "joblib"
+version = "1.1.0"
+description = "Lightweight pipelining with Python functions"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "jsonschema"
 version = "4.5.1"
@@ -1114,6 +1122,26 @@ python-versions = ">=3.7"
 [package.extras]
 idna2008 = ["idna"]
 
+[[package]]
+name = "scikit-learn"
+version = "1.1.0"
+description = "A set of python modules for machine learning and data mining"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
+joblib = ">=1.0.0"
+numpy = ">=1.17.3"
+scipy = ">=1.3.2"
+threadpoolctl = ">=2.0.0"
+
+[package.extras]
+benchmark = ["matplotlib (>=3.1.2)", "pandas (>=1.0.5)", "memory-profiler (>=0.57.0)"]
+docs = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=4.0.1)", "sphinx-gallery (>=0.7.0)", "numpydoc (>=1.2.0)", "Pillow (>=7.1.2)", "sphinx-prompt (>=1.3.0)", "sphinxext-opengraph (>=0.4.2)"]
+examples = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "seaborn (>=0.9.0)"]
+tests = ["matplotlib (>=3.1.2)", "scikit-image (>=0.14.5)", "pandas (>=1.0.5)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "flake8 (>=3.8.2)", "black (>=22.3.0)", "mypy (>=0.770)", "pyamg (>=4.0.0)", "numpydoc (>=1.2.0)"]
+
 [[package]]
 name = "scipy"
 version = "1.8.0"
@@ -1169,6 +1197,17 @@ category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "sklearn"
+version = "0.0"
+description = "A set of python modules for machine learning and data mining"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+scikit-learn = "*"
+
 [[package]]
 name = "smmap"
 version = "5.0.0"
@@ -1397,6 +1436,14 @@ python-versions = "*"
 [package.extras]
 widechars = ["wcwidth"]
 
+[[package]]
+name = "threadpoolctl"
+version = "3.1.0"
+description = "threadpoolctl"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -1545,7 +1592,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.9, <3.11"
-content-hash = "8613b3abc288fa9a243ab25e3ebd1c6d6ba25ad9c8f3bc5a9cdc27c396ae743c"
+content-hash = "8a3d9d1719812425200d838857223227855dc2040addba212ee506a747577183"
 
 [metadata.files]
 alabaster = [
@@ -1884,6 +1931,10 @@ jinja2 = [
     {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
     {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
 ]
+joblib = [
+    {file = "joblib-1.1.0-py2.py3-none-any.whl", hash = "sha256:f21f109b3c7ff9d95f8387f752d0d9c34a02aa2f7060c2135f465da0e5160ff6"},
+    {file = "joblib-1.1.0.tar.gz", hash = "sha256:4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35"},
+]
 jsonschema = [
     {file = "jsonschema-4.5.1-py3-none-any.whl", hash = "sha256:71b5e39324422543546572954ce71c67728922c104902cb7ce252e522235b33f"},
     {file = "jsonschema-4.5.1.tar.gz", hash = "sha256:7c6d882619340c3347a1bf7315e147e6d3dae439033ae6383d6acb908c101dfc"},
@@ -2323,6 +2374,26 @@ rfc3986 = [
     {file = "rfc3986-2.0.0-py2.py3-none-any.whl", hash = "sha256:50b1502b60e289cb37883f3dfd34532b8873c7de9f49bb546641ce9cbd256ebd"},
     {file = "rfc3986-2.0.0.tar.gz", hash = "sha256:97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c"},
 ]
+scikit-learn = [
+    {file = "scikit-learn-1.1.0.tar.gz", hash = "sha256:80f9904f5b1356adfc32406725dd94c8cc9c8d265047d98390033a6c238cbb29"},
+    {file = "scikit_learn-1.1.0-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:47c31f7e9a5689c3a2cbdf72e78570b33fa9abb42a1ca10d787516de9c4e37a4"},
+    {file = "scikit_learn-1.1.0-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:892be17fc261dff4097c061880586226d47ccd0426d9283091e2ca65da36e645"},
+    {file = "scikit_learn-1.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9d8e83d24df9595d4ccca961a2038e331aa7e17534af0b5b15d28e6d65723d1d"},
+    {file = "scikit_learn-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:068ee35f08681079a9aece49236f40837dbffebe047b0813bf71873fa976b132"},
+    {file = "scikit_learn-1.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:e4d41245915d0fc6fea26029349ff187b2992ef6588863e8570fc95a24697fd0"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-macosx_10_13_x86_64.whl", hash = "sha256:502865e025d3222530e350783a59cc37538effde64767721d830ceaae8bb3d42"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-macosx_12_0_arm64.whl", hash = "sha256:18aabbb26cbc1cf52583c1f1ecf6b5ff540d334f173e23122db43f97adbe0b2b"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:292525a17645bff043d33d427e93db8cec8d66b5022ead7971ce8bfdf7553feb"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ff60f63f1584d7daebfc93e69addd39760de49ae4325db5638c324cfde41c6c7"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-win32.whl", hash = "sha256:c10cd62443a9968c71fb9f1c7844f3f28189666f789d5a204dbad7463169b172"},
+    {file = "scikit_learn-1.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:cab8a8bef603f0fced7b245f7c4f77826602fd94f7c54ccb09b36b177dde246d"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-macosx_10_13_x86_64.whl", hash = "sha256:dc6681e2f99a4a5bc0682dc4e87192daeb0e9e64da36b35e672b56156e0cc867"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:05f9f004afe1b415922b2ff9453a191e3082acf1065aa0f0b238250f9e147606"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c819d2820b783f390dda2136508483d6f4302dfba98fc974ce759e55b2247d80"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2318fc717c9ff7eb3834bbb2c3be63768e97bb3221bbf70c01537e34e4fb8a1c"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-win32.whl", hash = "sha256:25b8d471169711dee7667969e7db3d33c372c13701cd2ab6783d0e85b2aab300"},
+    {file = "scikit_learn-1.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:1ef67ac0d44d9ecb36bc33ccc421f683aaeb42bdd72d8a97601eaded3b43f2e4"},
+]
 scipy = [
     {file = "scipy-1.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:87b01c7d5761e8a266a0fbdb9d88dcba0910d63c1c671bdb4d99d29f469e9e03"},
     {file = "scipy-1.8.0-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:ae3e327da323d82e918e593460e23babdce40d7ab21490ddf9fc06dec6b91a18"},
@@ -2364,6 +2435,9 @@ six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
+sklearn = [
+    {file = "sklearn-0.0.tar.gz", hash = "sha256:e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31"},
+]
 smmap = [
     {file = "smmap-5.0.0-py3-none-any.whl", hash = "sha256:2aba19d6a040e78d8b09de5c57e96207b09ed71d8e55ce0959eeee6c8e190d94"},
     {file = "smmap-5.0.0.tar.gz", hash = "sha256:c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936"},
@@ -2458,6 +2532,10 @@ tabulate = [
     {file = "tabulate-0.8.9-py3-none-any.whl", hash = "sha256:d7c013fe7abbc5e491394e10fa845f8f32fe54f8dc60c6622c6cf482d25d47e4"},
     {file = "tabulate-0.8.9.tar.gz", hash = "sha256:eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7"},
 ]
+threadpoolctl = [
+    {file = "threadpoolctl-3.1.0-py3-none-any.whl", hash = "sha256:8b99adda265feb6773280df41eece7b2e6561b772d21ffd52e372f999024907b"},
+    {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"},
+]
 tomli = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
diff --git a/pyproject.toml b/pyproject.toml
index 970b554..0eccf0e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,7 @@ pandas = "^1.4.2"
 altair = "^4.2.0"
 numpy = "^1.22.3"
 altair-data-server = "^0.4.1"
+sklearn = "^0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"

From 83d517454b7615f1b7e4cdc4580799643b87b3c6 Mon Sep 17 00:00:00 2001
From: Daniel King <dnlkng13@gmail.com>
Date: Wed, 18 May 2022 18:31:24 -0700
Subject: [PATCH 21/24] feat: add refinement function draft

---
 src/emgdecompy/emgdecompy.py | 62 +++++++++++++++++++++++++++++++++++-
 1 file changed, 61 insertions(+), 1 deletion(-)

diff --git a/src/emgdecompy/emgdecompy.py b/src/emgdecompy/emgdecompy.py
index c3ceecd..e1f490d 100644
--- a/src/emgdecompy/emgdecompy.py
+++ b/src/emgdecompy/emgdecompy.py
@@ -3,7 +3,10 @@
 import pandas as pd
 import altair as alt
 import numpy as np
-
+from scipy.signal import find_peaks
+from sklearn.cluster import KMeans
+from sklearn.metrics import silhouette_score
+from scipy.stats import variation
 
 def flatten_signal(raw):
     """
@@ -190,3 +193,60 @@ def whiten(x):
     wzca = np.dot(np.dot(np.dot(v, diagw), v.T), x_cent)
 
     return wzca
+
+def refinement(w_i, z):
+    # Initialize inter-spike interval coefficient of variations for n and n-1 as random numbers
+    cv_curr, cv_prev = np.random.ranf(), np.random.ranf()
+
+    if cv_curr > cv_prev:
+        cv_curr, cv_prev = cv_prev, cv_curr 
+
+    n = 0
+
+    while cv_curr < cv_prev:
+        
+        # a. Estimate the i-th source 
+        s_i = np.dot(w_i, z) # w_i and w_i.T are equal as far as I know
+        
+        # Estimate pulse train pt_n with peak detection applied to the square of the source vector
+        
+        s_i = np.square(s_i)
+        
+        peak_indices, _ = find_peaks(s_i, distance=41) #41 samples is ~equiv to 20 ms at a 2048 Hz sampling rate
+        
+        # b. Use KMeans to separate large peaks from relatively small peaks, which are discarded
+        kmeans = KMeans(n_clusters=2)
+        kmeans.fit(peak_indices)
+        clust_a = np.argmax(kmeans.cluster_centers_)
+        peak_a = ~kmeans.labels_.astype(bool) # Determine which peaks are large
+        
+        if clust_a == 1:
+            peak_a = ~peak_a
+        
+        peak_a = peak_indices[peak_a]
+        
+        # Create pulse train, where values are 0 except for when MU fires, which have values of 1
+        pt_n = np.zeros_like(s_i)
+        pt_n[peak_a] = 1
+        
+        # c. Update inter-spike interval coefficients of variation
+        isi = np.diff(peak_a) #inter-spike intervals
+        cv_prev = cv_curr
+        cv_curr = variation(isi)
+        
+        # d. Update separation vector
+        j = len(peak_a)
+        
+        w_i =  (1 / j) * z[:, peak_a].sum(axis=1)
+        
+        n += 1
+        
+    # Add way to save pulse train
+
+    # If silhouette score is greater than threshold, accept estimated source and add w_i to B   
+    sil = silhouette_score(peak_indices, kmeans.labels_) # Definition is slightly different than in paper, may change
+
+    if sil < th_sil:
+        w_i = np.zeros_like(w_i)
+
+    return w_i # May change implementation to update B here 
\ No newline at end of file

From 42f581e52c90a2e0f7d8c5ca2d11ddfe91132105 Mon Sep 17 00:00:00 2001
From: Daniel King <63321764+danfke@users.noreply.github.com>
Date: Wed, 18 May 2022 22:11:29 -0700
Subject: [PATCH 22/24] docs: update creator names

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e100be3..005c1a2 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ Interested in contributing? Check out the contributing guidelines. Please note t
 
 ## License
 
-`emgdecompy` was created by Daniel King. It is licensed under the terms of the MIT license.
+`emgdecompy` was created by Daniel King, Jasmine Ortega, Rada Rudyak, and Rowan Sivanandam. It is licensed under the terms of the MIT license.
 
 ## Credits
 

From d45b1d05af8ed5a43cf71bd07d886a5a12dbe30e Mon Sep 17 00:00:00 2001
From: semantic-release <semantic-release>
Date: Thu, 19 May 2022 05:15:34 +0000
Subject: [PATCH 23/24] 0.2.0

Automatically generated by python-semantic-release
---
 CHANGELOG.md   | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml |  2 +-
 2 files changed, 84 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 50be865..c79fe83 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,89 @@
 
 <!--next-version-placeholder-->
 
+## v0.2.0 (2022-05-19)
+### Feature
+* Add whiten function to emg-decompy.py ([`3682a09`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/3682a0977e1eca8268e109d5dea808963674d1a7))
+* Create functions script, debug extension functions, write docstrings ([`af7e346`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/af7e3469e4abea67eb44884cf423f1fb1fe2a0e7))
+
+### Fix
+* Correct package name ([`233aac0`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/233aac0bd2dceaa03af9385dd60960e9f7ceb767))
+* Incorrectly called create_emg_data() ([`fe93f12`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/fe93f12b76edff9cf58cb68020c45659268cef6e))
+* Rearrange functions so create_emg_data() defined before called in test functions ([`7a6c50b`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/7a6c50b1ec4437934eec4282475b56f42bb2f86a))
+* Tweak create_emg_data to use np.empty so that shape is consistent with real data ([`97d67c9`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/97d67c9ef6c663e4aab3c31167dd6775a1a313c1))
+* Tweak test_flatten_signal to test for empty arrays pre-flatten ([`a7c0da4`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/a7c0da45dd6f07dc81c05a7409505e6723cbbac1))
+* Small change to create_emg_data() function to not allow 1 dimensional arrays to be created ([`e744a7c`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/e744a7c704cfdfba43fd37003d47f0bae9de231c))
+* Change output dimensions so there are no 'channels' ([`3cacf69`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/3cacf69dc747bbabbe75505822f78e208dba72ce))
+* Add reg factor to whiten but leave commented out ([`7491d10`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/7491d10378f6ea6f23f9604273fd04d2368d90c9))
+* Fix transpose error ([`265592e`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/265592e5a45324e62f48190f4e44cd8c286dbb1d))
+* Correct test name for extend_all_channels ([`8f787ec`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/8f787eceb08468705dc07ea0c8cfb540ce9a4aef))
+* Import linalg from scipy ([`0ad2d15`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/0ad2d152557c656add1bf44e603d0a2d3bab4c19))
+* Properly call center_matrix function ([`db209b3`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/db209b3b47062d3c38a0f4abc604ae3b53d8b01e))
+* Output correct dimensions for extend_all_channels() ([`deba7a4`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/deba7a4b0f2d5ae8e14026607c3ec774f9ce6d25))
+* Get rid of codecov because repo is private ([`dd2bb66`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/dd2bb66954bed78714abe962e1bac58e769e74c6))
+* Extend() function now outputs what we agreed upon ([`98cfa16`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/98cfa16bc36207cd5d7f89aa4263d202ef750d61))
+* Figures were all showing weird, adding fig.pos='h' fixed it ([`db47734`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/db477347e20d5fd1b098a968664c3f2cb4454d27))
+* Correct package name ([`f4bf67f`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/f4bf67f01b7e27d1c169e8f7668644eaaed161a8))
+* Correct package name ([`76ae9fb`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/76ae9fbd31c14dd3c16d75eed39750f4bf4b9336))
+* Import packages, reference package name in functions ([`62d839a`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/62d839ad84c9ddd6d66d49ec141cf240dfbce419))
+* Remove packages line ([`1d0a6be`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/1d0a6be7eeb5bc9c7f363f893e966a1034bc7c24))
+* Correct package name ([`0163446`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/0163446f8afebdbb52cd22c379a35ea622d80e89))
+* Fix merge conflict and import emgdecompy ([`0005d9f`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/0005d9fb573367ece1a3f7eb5616bd349d7daefa))
+* Changing file name to new package ([`a8c18d5`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/a8c18d585c1a1f6d31324208f5e0cbc70a9c611d))
+* Changing package name in all documents ([`22f3129`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/22f3129ce2d37fd585a38c66dd78fd19fd43d4c0))
+* Put vector extension tests within functions ([`9b2fd18`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/9b2fd187c6821ff2f8733a6847a085a65157343f))
+
+### Documentation
+* Update creator names ([`42f581e`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/42f581e52c90a2e0f7d8c5ca2d11ddfe91132105))
+* Add codecov badge ([`a778710`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/a778710bea0a1c3fd8129241aec38fe6924e0042))
+* Update package name in test_extend_input_by_R ([`f3022da`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/f3022da9f77a3d282607c887396845625684c6a6))
+* Minor docstring inconsistencies in extend_all_channels() ([`ce5fdd8`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/ce5fdd8dc8869a3c55cc044105adebef975d503b))
+* Add clarification comment to test_flatten() according to Jasmine's feedback ([`bcc735c`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/bcc735cbed770547beacf584a1579ab481e3ba00))
+* Fix doc string for test_extend_by_R() ([`79490f4`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/79490f462fa946c123b747b38187e2cc919c0fc7))
+* Fix reference on page 2 ([`ee57a46`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/ee57a467b95ee92df39bc3dcf252146a7c31c590))
+* Make docstrings simpler and improve code commenting ([`5b397c0`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/5b397c0607d72df06b16160fa71c7e07dd0c2434))
+* Correct format of examples in center_matrix and make it simpler ([`200bd66`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/200bd6655a663221907b8776865d511fbf17bf85))
+* Correct docstring for extend_input_by_R ([`3e8e9df`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/3e8e9df975228029caa32f3e6eb9bad2301d4a58))
+* Fix grammar in docstrings ([`1190161`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/1190161f5c5e63e5af1c5774a561a303d25a0226))
+* Correct examples line in docstrings ([`9a4441a`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/9a4441af7f5e0282a6301b3e6a693bf31fa83556))
+* Correct spelling of fibre in summary ([`ea95835`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/ea95835c487ab4beaec90a2be9c2a71cbdce73b6))
+* Bold figure cross-references' ([`45a361f`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/45a361ff13ad7e677d474db1907d0a0250c014ff))
+* Made corrections to wordings, citations, figure locations ([`9c48f68`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/9c48f689152b73261b8974571f43dfa86bd9884d))
+* Replace emg hardware image ([`dc33fae`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/dc33faee41497ed10d001c978f48cac759f5d739))
+* Replace ot screenshot with higher quality one ([`ab702a6`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/ab702a68a9f1387c77d77b555cd4bae50d8e725d))
+* Replace ot screenshot with higher quality one ([`80cfd4b`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/80cfd4bbc13703eae55d96db9f7412f3b6dd9b7a))
+* Add visual of algorithm ([`e88f15d`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/e88f15d4c8b78f6c999ac41bb4be93b34531610a))
+* Edit Timeline ([`c4b210b`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/c4b210b1a0ef511902ce8c0c94307018821094d0))
+* Add more citations and figures ([`80de991`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/80de99168ac46dc829d178f74830edd9a3cf14d1))
+* Update timeline ([`afd53d2`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/afd53d2492b52a2d432bb6a812ca6182ef841ab6))
+* Add raw EMG image ([`b638e46`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/b638e46fb9bf4d91d84f21e2461b21625ac78c5f))
+* Fix Tools sections based on Alexi's feedback ([`6f64943`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/6f64943da4338915c61a88798acfd7098b6a8a26))
+* Fix package name ([`eb2b26a`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/eb2b26ae30761a5e78eff405be74ebcf958f81a1))
+* Add Alexi's corrections ([`5317c70`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/5317c7048ddb7b0c6f4bf65a70f396f75542c0cb))
+* Fix badge formatting ([`f4aa37d`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/f4aa37d84bdfb08e17e90e52b2d165a43688c183))
+* Add ci-cd badge ([`1d3cbf9`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/1d3cbf9c74c6608a1b7d03234e903818bd68e10a))
+* Change package description ([`16bf912`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/16bf91282eb532923487b43bfb0bb91bde34b0b7))
+* Bottleneck is spelled with an e lol ([`9fb41bc`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/9fb41bcf3982791ea1a7ad82f3384277fe336210))
+* Improve docstring based on Daniel's advice ([`7848f49`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/7848f49e0b35078a93e28ba28024fdd13a13b72c))
+* Add proposal section to README ([`89618b6`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/89618b66b3de0ced78df0435a48067308cbf998a))
+* Create layout of proposal and render to pdf ([`423d6b3`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/423d6b314338de95b8ac827adfd83dd07b9e632c))
+* Make corrections ([`adaa064`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/adaa0648e5959313c804fbc46abfec7684378cb1))
+* Add bibtex references ([`b299959`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/b299959789f45c7f26b01ba5e87cb2d65519a5d2))
+* Fix section on the interactive learning component ([`e8fc753`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/e8fc753f0d41f4ff9baa13415d3b96c641239ec6))
+* Make some edits and add bibtex ([`6b79ea7`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/6b79ea709d32ff665abe282748ad4f200bb5e3cd))
+* Remove obsolete citations file ([`1483e64`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/1483e6409ce389084dfe50d9a358d9574722bbc2))
+* Fix line breaks ([`a1707a6`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/a1707a6cd0a4698fb40cab04b3ea23cfc8f82761))
+* Make corrections to techniques section and add bibtex ([`d4af629`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/d4af629aaf795aa95645cd632a34e0030de27c03))
+* Remove html output ([`9107441`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/9107441ee64cafee5a7b3e3ed80f0b417ad103a5))
+* Move titles from child docs to parent doc ([`0abf1d6`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/0abf1d6696fc18037fe94e7978d535510948457b))
+* Create bibtex file ([`f5c6920`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/f5c692040951357e3cf3ef6643723771d22e8f1c))
+* Add title to data science technique section ([`f3ff884`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/f3ff884aa0cc0a1dbe5c6cb65dc4d17910099dce))
+* Add yaml metadata ([`0a625c1`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/0a625c1cff2f5028070b4aeb7735e39e263af122))
+* Add proposal intro rmd ([`472635a`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/472635a024c725f713f995a6b904d857b7c32e86))
+* Rewrite tools section to use sentenses instead of bullet points ([`503a4c2`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/503a4c2bdf83500a0750d02998eb90314e09c387))
+* Create proposal folder and components ([`042a808`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/042a8086c45bbc27bb9a76a1fcfba0a845f81f48))
+* Create teamwork contract ([`272638c`](https://github.com/UBC-SPL-MDS/EMGdecomPy/commit/272638c07cc0bf64372c88c4ccb4ec13de913c12))
+
 ## v0.1.0 (03/05/2022)
 
 - First release of `emgdecompy`!
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 970b554..210fa76 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "emgdecompy"
-version = "0.1.0"
+version = "0.2.0"
 description = "A package for decomposing raw EMG signals into individual motor unit activity."
 authors = ["Daniel King"]
 license = "MIT"

From 9fd71c50aea805995066c2bb4eb231d13c718ba7 Mon Sep 17 00:00:00 2001
From: Daniel King <dnlkng13@gmail.com>
Date: Thu, 19 May 2022 17:29:25 -0700
Subject: [PATCH 24/24] feat: add pulse train save functionality and made code
 clearer

---
 src/emgdecompy/emgdecompy.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/emgdecompy/emgdecompy.py b/src/emgdecompy/emgdecompy.py
index e1f490d..bd35aa9 100644
--- a/src/emgdecompy/emgdecompy.py
+++ b/src/emgdecompy/emgdecompy.py
@@ -194,7 +194,7 @@ def whiten(x):
 
     return wzca
 
-def refinement(w_i, z):
+def refinement(w_i, z, i, max_iter, th_sil, name=""):
     # Initialize inter-spike interval coefficient of variations for n and n-1 as random numbers
     cv_curr, cv_prev = np.random.ranf(), np.random.ranf()
 
@@ -209,7 +209,6 @@ def refinement(w_i, z):
         s_i = np.dot(w_i, z) # w_i and w_i.T are equal as far as I know
         
         # Estimate pulse train pt_n with peak detection applied to the square of the source vector
-        
         s_i = np.square(s_i)
         
         peak_indices, _ = find_peaks(s_i, distance=41) #41 samples is ~equiv to 20 ms at a 2048 Hz sampling rate
@@ -217,13 +216,13 @@ def refinement(w_i, z):
         # b. Use KMeans to separate large peaks from relatively small peaks, which are discarded
         kmeans = KMeans(n_clusters=2)
         kmeans.fit(peak_indices)
-        clust_a = np.argmax(kmeans.cluster_centers_)
-        peak_a = ~kmeans.labels_.astype(bool) # Determine which peaks are large
+        centroid_a = np.argmax(kmeans.cluster_centers_) # Determine which cluster contains large peaks
+        peak_a = ~kmeans.labels_.astype(bool) # Determine which peaks are large (part of cluster a)
         
-        if clust_a == 1:
+        if centroid_a == 1:
             peak_a = ~peak_a
         
-        peak_a = peak_indices[peak_a]
+        peak_a = peak_indices[peak_a] # Get the indices of the peaks in cluster a
         
         # Create pulse train, where values are 0 except for when MU fires, which have values of 1
         pt_n = np.zeros_like(s_i)
@@ -241,12 +240,13 @@ def refinement(w_i, z):
         
         n += 1
         
-    # Add way to save pulse train
+    # Save pulse train
+    pd.DataFrame(pt_n, columns=["pulse_train"]).rename_axis("sample").to_csv(f"{name}_PT_{i}")
 
     # If silhouette score is greater than threshold, accept estimated source and add w_i to B   
     sil = silhouette_score(peak_indices, kmeans.labels_) # Definition is slightly different than in paper, may change
 
     if sil < th_sil:
-        w_i = np.zeros_like(w_i)
+        return # If below threshold, reject estimated source and return nothing
 
     return w_i # May change implementation to update B here 
\ No newline at end of file