From 9ae558edf221c9577859f2bfd6a68a4c32985722 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:14:17 -0400 Subject: [PATCH 01/11] Fixed dependencies for Apple Silicone --- README.md | 21 +- poetry.lock | 916 +++++++++++++++++++++++++------------------------ pyproject.toml | 18 +- smps/io.py | 6 +- 4 files changed, 501 insertions(+), 460 deletions(-) diff --git a/README.md b/README.md index f68b595..0c3417c 100644 --- a/README.md +++ b/README.md @@ -8,15 +8,24 @@ Python library for the analysis and visualization of data from a Scanning Mobili ## Dependencies - * pandas - * numpy - * scipy - * seaborn - * statsmodels +The full list of dependencies can be found in the `pyproject.toml` file and are summarized below: + +```py +python = ">=3.8, <3.12" +statsmodels = "^0.13" +seaborn = "^0.10" +joblib = "^1.0" +requests = "^2.24" +scipy = "^1.9" +numpy = "^1.23.2" +pandas = "^1.4" +``` + +As of `v1.2.0a0`, the library should be compatible with Apple silicone (tested on both M1 and M2). ## Python Versions -Python3.7+ is supported. +Python3.8 through Python3.11 are currently supported. ## Installation diff --git a/poetry.lock b/poetry.lock index c3d8031..8c4b5fc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -8,7 +8,7 @@ python-versions = "*" [[package]] name = "atomicwrites" -version = "1.4.0" +version = "1.4.1" description = "Atomic file writes." category = "dev" optional = false @@ -16,36 +16,36 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.4.0" +version = "22.1.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.5" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] +tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] [[package]] -name = "babel" -version = "2.9.1" +name = "Babel" +version = "2.10.3" description = "Internationalization utilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.dependencies] pytz = ">=2015.7" [[package]] name = "beautifulsoup4" -version = "4.10.0" +version = "4.11.1" description = "Screen-scraping library" category = "dev" optional = false -python-versions = ">3.0.0" +python-versions = ">=3.6.0" [package.dependencies] soupsieve = ">1.2" @@ -56,26 +56,26 @@ lxml = ["lxml"] [[package]] name = "certifi" -version = "2021.10.8" +version = "2022.6.15" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "charset-normalizer" -version = "2.0.12" +version = "2.1.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=3.5.0" +python-versions = ">=3.6.0" [package.extras] unicode_backport = ["unicodedata2"] [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.5" description = "Cross-platform colored terminal text." category = "dev" optional = false @@ -113,24 +113,25 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "fonttools" -version = "4.29.1" +version = "4.37.1" description = "Tools to manipulate font files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] -interpolatable = ["scipy", "munkres"] +interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] pathops = ["skia-pathops (>=0.5.0)"] plot = ["matplotlib"] +repacker = ["uharfbuzz (>=0.23.0)"] symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] unicode = ["unicodedata2 (>=14.0.0)"] -woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"] +woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "furo" @@ -145,7 +146,7 @@ beautifulsoup4 = "*" sphinx = ">=3.0,<5.0" [package.extras] -doc = ["myst-parser", "sphinx-copybutton", "sphinx-inline-tabs", "docutils (!=0.17)"] +doc = ["docutils (!=0.17)", "myst-parser", "sphinx-copybutton", "sphinx-inline-tabs"] test = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] @@ -158,29 +159,12 @@ python-versions = ">=3.5" [[package]] name = "imagesize" -version = "1.3.0" +version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -[[package]] -name = "importlib-metadata" -version = "4.11.1" -description = "Read metadata from Python packages" -category = "dev" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} -zipp = ">=0.5" - -[package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] - [[package]] name = "iniconfig" version = "1.1.1" @@ -190,12 +174,12 @@ optional = false python-versions = "*" [[package]] -name = "jinja2" -version = "3.0.3" +name = "Jinja2" +version = "3.1.2" description = "A very fast and expressive template engine." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] MarkupSafe = ">=2.0" @@ -213,7 +197,7 @@ python-versions = ">=3.6" [[package]] name = "kiwisolver" -version = "1.3.2" +version = "1.4.4" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -221,29 +205,28 @@ python-versions = ">=3.7" [[package]] name = "markdown-it-py" -version = "2.0.1" +version = "2.1.0" description = "Python port of markdown-it. Markdown parsing, done right!" category = "dev" optional = false -python-versions = "~=3.6" +python-versions = ">=3.7" [package.dependencies] -attrs = ">=19,<22" mdurl = ">=0.1,<1.0" -typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} [package.extras] benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"] code_style = ["pre-commit (==2.6)"] -compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2.2,<3.3.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "mistune (>=0.8.4,<0.9.0)", "panflute (>=1.12,<2.0)"] +compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] plugins = ["mdit-py-plugins"] -rtd = ["myst-nb (==0.13.0a1)", "pyyaml", "sphinx (>=2,<4)", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-book-theme"] +profiling = ["gprof2dot"] +rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] [[package]] -name = "markupsafe" -version = "2.1.0" +name = "MarkupSafe" +version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." category = "dev" optional = false @@ -251,7 +234,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.5.1" +version = "3.5.3" description = "Python plotting package" category = "main" optional = false @@ -266,7 +249,7 @@ packaging = ">=20.0" pillow = ">=6.2.0" pyparsing = ">=2.2.1" python-dateutil = ">=2.7" -setuptools_scm = ">=4" +setuptools_scm = ">=4,<7" [[package]] name = "mdit-py-plugins" @@ -286,15 +269,15 @@ testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] [[package]] name = "mdurl" -version = "0.1.0" +version = "0.1.2" description = "Markdown URL utilities" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "myst-parser" -version = "0.17.0" +version = "0.17.2" description = "An extended commonmark compliant parser, with bridges to docutils & sphinx." category = "dev" optional = false @@ -312,20 +295,20 @@ typing-extensions = "*" [package.extras] code_style = ["pre-commit (>=2.12,<3.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] -rtd = ["ipython", "sphinx-book-theme (>=0.1.0,<0.2.0)", "sphinx-panels (>=0.5.2,<0.6.0)", "sphinxcontrib-bibtex (>=2.1,<3.0)", "sphinxext-rediraffe (>=0.2,<1.0)", "sphinxcontrib.mermaid (>=0.6.3,<0.7.0)", "sphinxext-opengraph (>=0.4.2,<0.5.0)"] -testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "pytest-param-files (>=0.3.4,<0.4.0)"] +rtd = ["ipython", "sphinx-book-theme", "sphinx-panels", "sphinxcontrib-bibtex (>=2.4,<3.0)", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"] +testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions"] [[package]] name = "numpy" -version = "1.21.1" +version = "1.23.2" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "numpydoc" -version = "1.2" +version = "1.4.0" description = "Sphinx extension to support docstrings in Numpy format" category = "dev" optional = false @@ -333,10 +316,10 @@ python-versions = ">=3.7" [package.dependencies] Jinja2 = ">=2.10" -sphinx = ">=1.8" +sphinx = ">=3.0" [package.extras] -testing = ["pytest", "pytest-cov", "matplotlib"] +testing = ["matplotlib", "pytest", "pytest-cov"] [[package]] name = "packaging" @@ -351,24 +334,24 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.3.5" +version = "1.4.4" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false -python-versions = ">=3.7.1" +python-versions = ">=3.8" [package.dependencies] numpy = [ - {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, + {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, ] -python-dateutil = ">=2.7.3" -pytz = ">=2017.3" +python-dateutil = ">=2.8.1" +pytz = ">=2020.1" [package.extras] -test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"] +test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "patsy" @@ -386,13 +369,17 @@ six = "*" test = ["pytest", "pytest-cov", "scipy"] [[package]] -name = "pillow" -version = "9.0.1" +name = "Pillow" +version = "9.2.0" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" +[package.extras] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] + [[package]] name = "pluggy" version = "1.0.0" @@ -401,9 +388,6 @@ category = "dev" optional = false python-versions = ">=3.6" -[package.dependencies] -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} - [package.extras] dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] @@ -417,20 +401,23 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] -name = "pygments" -version = "2.11.2" +name = "Pygments" +version = "2.13.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" + +[package.extras] +plugins = ["importlib-metadata"] [[package]] name = "pyparsing" -version = "3.0.7" -description = "Python parsing module" +version = "3.0.9" +description = "pyparsing module - Classes and methods to define and execute parsing grammars" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.6.8" [package.extras] diagrams = ["jinja2", "railroad-diagrams"] @@ -447,7 +434,6 @@ python-versions = ">=3.6" atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} -importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" @@ -470,7 +456,7 @@ coverage = {version = ">=5.2.1", extras = ["toml"]} pytest = ">=4.6" [package.extras] -testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] [[package]] name = "pytest-cover" @@ -507,14 +493,14 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2021.3" +version = "2022.2.1" description = "World timezone definitions, modern and historical" category = "main" optional = false python-versions = "*" [[package]] -name = "pyyaml" +name = "PyYAML" version = "6.0" description = "YAML parser and emitter for Python" category = "dev" @@ -523,32 +509,32 @@ python-versions = ">=3.6" [[package]] name = "requests" -version = "2.27.1" +version = "2.28.1" description = "Python HTTP for Humans." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7, <4" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""} -idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""} +charset-normalizer = ">=2,<3" +idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" [package.extras] -socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +socks = ["PySocks (>=1.5.6,!=1.5.7)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "scipy" -version = "1.6.1" +version = "1.9.1" description = "SciPy: Scientific Library for Python" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8,<3.12" [package.dependencies] -numpy = ">=1.16.5" +numpy = ">=1.18.5,<1.25.0" [[package]] name = "seaborn" @@ -564,6 +550,19 @@ numpy = ">=1.13.3" pandas = ">=0.22.0" scipy = ">=1.0.1" +[[package]] +name = "setuptools" +version = "65.3.0" +description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] + [[package]] name = "setuptools-scm" version = "6.4.2" @@ -574,6 +573,7 @@ python-versions = ">=3.6" [package.dependencies] packaging = ">=20.0" +setuptools = "*" tomli = ">=1.0.0" [package.extras] @@ -598,14 +598,14 @@ python-versions = "*" [[package]] name = "soupsieve" -version = "2.3.1" +version = "2.3.2.post1" description = "A modern CSS selector implementation for Beautiful Soup." category = "dev" optional = false python-versions = ">=3.6" [[package]] -name = "sphinx" +name = "Sphinx" version = "3.5.3" description = "Python documentation generator" category = "dev" @@ -622,6 +622,7 @@ Jinja2 = ">=2.3" packaging = "*" Pygments = ">=2.0" requests = ">=2.5.0" +setuptools = "*" snowballstemmer = ">=1.1" sphinxcontrib-applehelp = "*" sphinxcontrib-devhelp = "*" @@ -632,8 +633,8 @@ sphinxcontrib-serializinghtml = "*" [package.extras] docs = ["sphinxcontrib-websupport"] -lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.800)", "docutils-stubs"] -test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] +lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.800)"] +test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"] [[package]] name = "sphinx-copybutton" @@ -648,7 +649,7 @@ sphinx = ">=1.8" [package.extras] code_style = ["pre-commit (==2.12.1)"] -rtd = ["sphinx", "ipython", "myst-nb", "sphinx-book-theme"] +rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme"] [[package]] name = "sphinxcontrib-applehelp" @@ -659,7 +660,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -671,7 +672,7 @@ optional = false python-versions = ">=3.5" [package.extras] -lint = ["flake8", "mypy", "docutils-stubs"] +lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] [[package]] @@ -683,8 +684,8 @@ optional = false python-versions = ">=3.6" [package.extras] -lint = 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[tool.poetry.dependencies] -python = ">=3.7.1" -pandas = ">=1.2.4" -numpy = ">=1.19.1" -statsmodels = "^0.12.0" -seaborn = ">=0.10.1" -joblib = "^1.0.0" -requests = "^2.24.0" -scipy = ">=1.5.2" +python = ">=3.8, <3.12" +statsmodels = "^0.13" +seaborn = "^0.10" +joblib = "^1.0" +requests = "^2.24" +scipy = "^1.9" +numpy = "^1.23.2" +pandas = "^1.4" [tool.poetry.dev-dependencies] pytest = "^6.0.1" diff --git a/smps/io.py b/smps/io.py index e912f57..d66653e 100644 --- a/smps/io.py +++ b/smps/io.py @@ -57,8 +57,7 @@ def smps_from_txt(fpath, column=True, delimiter=',', delimiter=delimiter, header=None, encoding=encoding, - error_bad_lines=False, - warn_bad_lines=False, + on_bad_lines='warn', index_col=0 ).T.iloc[0,:].to_dict() @@ -120,8 +119,7 @@ def smps_from_txt(fpath, column=True, delimiter=',', skiprows=(meta_num_lines+4+nbins), delimiter=delimiter, header=None, - error_bad_lines=False, - warn_bad_lines=True, + on_bad_lines='warn', encoding=encoding).T # Rename the columns to the first row From 4cacf61ccfb521004cf0e8dcef46b1173a6eeb68 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:20:24 -0400 Subject: [PATCH 02/11] Updated reqs --- .github/ISSUE_TEMPLATE/bug_report.md | 8 +++----- .github/workflows/test-and-report.yml | 2 +- poetry.lock | 2 +- pyproject.toml | 1 + 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index dd84ea7..3492760 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -28,11 +28,9 @@ If applicable, add screenshots to help explain your problem. - Browser [e.g. chrome, safari] - Version [e.g. 22] -**Smartphone (please complete the following information):** - - Device: [e.g. iPhone6] - - OS: [e.g. iOS8.1] - - Browser [e.g. stock browser, safari] - - Version [e.g. 22] +**Python Environment (please complete the following information)** + +Please run `pip list` and `python -v` and post below. **Additional context** Add any other context about the problem here. diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index e15b8c6..e941065 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python: [3.7, 3.8, 3.9] + python: [3.8, 3.9, 3.10, 3.11] name: Python ${{ matrix.python }} steps: - name: Checkout branch diff --git a/poetry.lock b/poetry.lock index 8c4b5fc..28f2a10 100644 --- a/poetry.lock +++ b/poetry.lock @@ -782,7 +782,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [metadata] lock-version = "1.1" python-versions = ">=3.8, <3.12" -content-hash = "cc0c909f0ef558d0b6c3e3ee6bc19e0806d49b3cf5d362a7e6e65353b8f0afa2" +content-hash = "69471ce94b760fc4c2b315d4faae5bc4e086b6a9a4f0ef0bb8ab3a7c7485f3de" [metadata.files] alabaster = [ diff --git a/pyproject.toml b/pyproject.toml index 136a588..d17374a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ requests = "^2.24" scipy = "^1.9" numpy = "^1.23.2" pandas = "^1.4" +setuptools = "^65.3" [tool.poetry.dev-dependencies] pytest = "^6.0.1" From 1161a7aad0146698a337e389b85ba24191370694 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:23:47 -0400 Subject: [PATCH 03/11] update versions to test against --- .github/workflows/test-and-report.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index e941065..8d6d8ae 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python: [3.8, 3.9, 3.10, 3.11] + python: [3.8, 3.9, "3.10"] name: Python ${{ matrix.python }} steps: - name: Checkout branch From 25b7c2f89e14c6c041829a8070c820cf96951c51 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:30:10 -0400 Subject: [PATCH 04/11] Updated gh-actions --- .github/workflows/test-and-report.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index 8d6d8ae..6bf4e4a 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -11,21 +11,24 @@ jobs: - name: Checkout branch uses: actions/checkout@v2 - - name: Setup pyton ${{ matrix.python }} + - name: Setup python ${{ matrix.python }} uses: actions/setup-python@master with: python-version: ${{ matrix.python }} - name: Install poetry - uses: snok/install-poetry@v1.1.4 + uses: snok/install-poetry@v1.3 with: version: 1.1.4 virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true - name: Install dependencies - run: | - source $HOME/.poetry/env - poetry install + run: poetry install --no-interaction --no-root + + - name: Install library + run: poetry install --no-interaction - name: Run tests and generate coverage report run: | From 0fa13bd91230c73d59c27c332070384b2f672b62 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:34:49 -0400 Subject: [PATCH 05/11] Relax poetry req --- .github/workflows/test-and-report.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index 6bf4e4a..301f2ad 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python: [3.8, 3.9, "3.10"] + python: ["3.8", "3.9", "3.10"] name: Python ${{ matrix.python }} steps: - name: Checkout branch @@ -17,9 +17,8 @@ jobs: python-version: ${{ matrix.python }} - name: Install poetry - uses: snok/install-poetry@v1.3 + uses: snok/install-poetry@v1 with: - version: 1.1.4 virtualenvs-create: true virtualenvs-in-project: true installer-parallel: true @@ -27,9 +26,6 @@ jobs: - name: Install dependencies run: poetry install --no-interaction --no-root - - name: Install library - run: poetry install --no-interaction - - name: Run tests and generate coverage report run: | poetry run pytest tests/ --ignore=tests/datafiles --cov=./ --cov-report=xml From adf2f479803842fbc03fe3d86a18643c678667b1 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:42:01 -0400 Subject: [PATCH 06/11] update actions --- .github/workflows/test-and-report.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index 301f2ad..cfe1005 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -28,6 +28,7 @@ jobs: - name: Run tests and generate coverage report run: | + source .venv/bin/activate poetry run pytest tests/ --ignore=tests/datafiles --cov=./ --cov-report=xml - name: Upload coverage report to Codecov From 8f82557f17b7940c34f7291592f9bb1e9966667f Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:50:30 -0400 Subject: [PATCH 07/11] Updated actions --- .github/workflows/test-and-report.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index cfe1005..435543d 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -17,18 +17,16 @@ jobs: python-version: ${{ matrix.python }} - name: Install poetry - uses: snok/install-poetry@v1 + uses: snok/install-poetry@v1.1.2 with: + version: 1.1.5 virtualenvs-create: true - virtualenvs-in-project: true - installer-parallel: true - name: Install dependencies - run: poetry install --no-interaction --no-root + run: poetry install --no-interaction - name: Run tests and generate coverage report run: | - source .venv/bin/activate poetry run pytest tests/ --ignore=tests/datafiles --cov=./ --cov-report=xml - name: Upload coverage report to Codecov From 9dd4845a6ad7ff528546f198341abfb8025fc1ed Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:53:46 -0400 Subject: [PATCH 08/11] Updated once again --- .github/workflows/test-and-report.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index 435543d..5fdba61 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -17,9 +17,9 @@ jobs: python-version: ${{ matrix.python }} - name: Install poetry - uses: snok/install-poetry@v1.1.2 + uses: snok/install-poetry@v1 with: - version: 1.1.5 + version: 1.1.7 virtualenvs-create: true - name: Install dependencies From 3accfd42aafb3b5d790245ec2983409bdc4c5a70 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:55:43 -0400 Subject: [PATCH 09/11] gh-actions --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 28f2a10..69fb3fd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -782,7 +782,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [metadata] lock-version = "1.1" python-versions = ">=3.8, <3.12" -content-hash = "69471ce94b760fc4c2b315d4faae5bc4e086b6a9a4f0ef0bb8ab3a7c7485f3de" +content-hash = "e5c56522bd221f918041faa0446aa493b06c72fa83daf7a305314aa9e4c3efc3" [metadata.files] alabaster = [ From 5fa0676914474cd0d83fb55837384a4fdb8330d7 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 12:59:45 -0400 Subject: [PATCH 10/11] Updated action --- .github/workflows/test-and-report.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index 5fdba61..db18461 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -19,7 +19,7 @@ jobs: - name: Install poetry uses: snok/install-poetry@v1 with: - version: 1.1.7 + version: 1.2 virtualenvs-create: true - name: Install dependencies From 49ec754b4ce09cec27d9b788f4448c4354188b6d Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 4 Sep 2022 13:00:50 -0400 Subject: [PATCH 11/11] no specifiying poetry version --- .github/workflows/test-and-report.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/test-and-report.yml b/.github/workflows/test-and-report.yml index db18461..3ba6f63 100644 --- a/.github/workflows/test-and-report.yml +++ b/.github/workflows/test-and-report.yml @@ -19,7 +19,6 @@ jobs: - name: Install poetry uses: snok/install-poetry@v1 with: - version: 1.2 virtualenvs-create: true - name: Install dependencies