From 436bdc5a15df055a9290971ed312eccacbab9cd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20S=2E=20Soriano=20P=C3=A9rez?= Date: Mon, 13 Jun 2022 09:36:26 +0200 Subject: [PATCH 1/5] ci: Changed dependencies on pyproject.toml --- poetry.lock | 1123 +++++++++++++++++++++++++----------------------- pyproject.toml | 5 +- 2 files changed, 599 insertions(+), 529 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1e06c80..194f0e6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -30,33 +30,21 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.2.0" +version = "21.4.0" description = "Classes Without Boilerplate" category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [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"] +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"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] - -[[package]] -name = "backports.entry-points-selectable" -version = "1.1.0" -description = "Compatibility shim providing selectable entry points for older implementations" -category = "dev" -optional = false -python-versions = ">=2.7" - -[package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"] +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"] [[package]] name = "black" -version = "21.9b0" +version = "21.12b0" description = "The uncompromising code formatter." category = "main" optional = false @@ -67,7 +55,6 @@ click = ">=7.1.2" mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0,<1" platformdirs = ">=2" -regex = ">=2020.1.8" tomli = ">=0.2.6,<2.0.0" typing-extensions = [ {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, @@ -76,9 +63,9 @@ typing-extensions = [ [package.extras] colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.6.0)", "aiohttp-cors (>=0.4.0)"] +d = ["aiohttp (>=3.7.4)"] jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] -python2 = ["typed-ast (>=1.4.2)"] +python2 = ["typed-ast (>=1.4.3)"] uvloop = ["uvloop (>=0.15.2)"] [[package]] @@ -107,22 +94,22 @@ python-versions = ">=3.6.1" [[package]] name = "cftime" -version = "1.5.1" +version = "1.6.0" description = "Time-handling functionality from netcdf4-python" category = "main" optional = false python-versions = "*" [package.dependencies] -numpy = "*" +numpy = ">1.13.3" [[package]] name = "click" -version = "8.0.3" +version = "8.1.3" description = "Composable command line interface toolkit" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} @@ -137,11 +124,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "commitizen" -version = "2.20.0" +version = "2.27.1" description = "Python commitizen client tool" category = "dev" optional = false -python-versions = ">=3.6.1,<4.0.0" +python-versions = ">=3.6.2,<4.0.0" [package.dependencies] argcomplete = ">=1.12.1,<2.0.0" @@ -153,28 +140,26 @@ pyyaml = ">=3.08" questionary = ">=1.4.0,<2.0.0" termcolor = ">=1.1,<2.0" tomlkit = ">=0.5.3,<1.0.0" +typing-extensions = ">=4.0.1,<5.0.0" [[package]] name = "coverage" -version = "6.0.2" +version = "6.4.1" description = "Code coverage measurement for Python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] toml = ["tomli"] [[package]] name = "cycler" -version = "0.10.0" +version = "0.11.0" description = "Composable style cycles" category = "main" optional = false -python-versions = "*" - -[package.dependencies] -six = "*" +python-versions = ">=3.6" [[package]] name = "decli" @@ -197,7 +182,7 @@ pygments = ["Pygments (>=2.2.0)"] [[package]] name = "distlib" -version = "0.3.3" +version = "0.3.4" description = "Distribution utilities" category = "dev" optional = false @@ -224,11 +209,11 @@ docopt = "0.6.1" [[package]] name = "filelock" -version = "3.3.2" +version = "3.7.1" description = "A platform independent file lock." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"] @@ -247,9 +232,31 @@ mccabe = ">=0.6.0,<0.7.0" pycodestyle = ">=2.7.0,<2.8.0" pyflakes = ">=2.3.0,<2.4.0" +[[package]] +name = "fonttools" +version = "4.33.3" +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)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +graphite = ["lz4 (>=1.7.4.2)"] +interpolatable = ["scipy", "munkres"] +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)"] + [[package]] name = "ghp-import" -version = "2.0.2" +version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." category = "dev" optional = false @@ -261,32 +268,43 @@ python-dateutil = ">=2.8.1" [package.extras] dev = ["twine", "markdown", "flake8", "wheel"] +[[package]] +name = "h5py" +version = "3.7.0" +description = "Read and write HDF5 files from Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +numpy = ">=1.14.5" + [[package]] name = "identify" -version = "2.3.3" +version = "2.5.1" description = "File identification library for Python" category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.extras] -license = ["editdistance-s"] +license = ["ukkonen"] [[package]] name = "importlib-metadata" -version = "4.8.1" +version = "4.11.4" description = "Read metadata from Python packages" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] zipp = ">=0.5" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] perf = ["ipython"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +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" @@ -298,7 +316,7 @@ python-versions = "*" [[package]] name = "isort" -version = "5.9.3" +version = "5.10.1" description = "A Python utility / library to sort Python imports." category = "main" optional = false @@ -312,11 +330,11 @@ plugins = ["setuptools"] [[package]] name = "jinja2" -version = "3.0.2" +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" @@ -326,7 +344,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "kiwisolver" -version = "1.3.2" +version = "1.4.2" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -334,39 +352,44 @@ python-versions = ">=3.7" [[package]] name = "markdown" -version = "3.3.4" +version = "3.3.7" description = "Python implementation of Markdown." category = "dev" optional = false python-versions = ">=3.6" +[package.dependencies] +importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""} + [package.extras] testing = ["coverage", "pyyaml"] [[package]] name = "markupsafe" -version = "2.0.1" +version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "2.2.5" +version = "3.5.2" description = "Python plotting package" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" [package.dependencies] cycler = ">=0.10" +fonttools = ">=4.22.0" kiwisolver = ">=1.0.1" -numpy = ">=1.7.1" -pyparsing = ">=2.0.1,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6" -python-dateutil = ">=2.1" -pytz = "*" -six = ">=1.10" +numpy = ">=1.17" +packaging = ">=20.0" +pillow = ">=6.2.0" +pyparsing = ">=2.2.1" +python-dateutil = ">=2.7" +setuptools_scm = ">=4" [[package]] name = "mccabe" @@ -386,7 +409,7 @@ python-versions = ">=3.6" [[package]] name = "mkdocs" -version = "1.2.3" +version = "1.3.0" description = "Project documentation with Markdown." category = "dev" optional = false @@ -395,8 +418,8 @@ python-versions = ">=3.6" [package.dependencies] click = ">=3.3" ghp-import = ">=1.0" -importlib-metadata = ">=3.10" -Jinja2 = ">=2.10.1" +importlib-metadata = ">=4.3" +Jinja2 = ">=2.10.2" Markdown = ">=3.2.1" mergedeep = ">=1.3.4" packaging = ">=20.5" @@ -486,7 +509,7 @@ python-versions = "*" [[package]] name = "netcdf4" -version = "1.5.7" +version = "1.5.8" description = "Provides an object-oriented python interface to the netCDF version 4 library." category = "main" optional = false @@ -506,43 +529,43 @@ python-versions = "*" [[package]] name = "numpy" -version = "1.21.1" +version = "1.22.4" 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 = "packaging" -version = "21.0" +version = "21.3" description = "Core utilities for Python packages" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -pyparsing = ">=2.0.2" +pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.3.4" +version = "1.4.2" 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 = "pathspec" @@ -552,17 +575,29 @@ category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +[[package]] +name = "pillow" +version = "9.1.1" +description = "Python Imaging Library (Fork)" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinx-rtd-theme (>=1.0)", "sphinxext-opengraph"] +tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] + [[package]] name = "platformdirs" -version = "2.4.0" +version = "2.5.2" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] -test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] +docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"] +test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"] [[package]] name = "pluggy" @@ -578,11 +613,11 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" -version = "2.15.0" +version = "2.19.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] cfgv = ">=2.0.0" @@ -594,7 +629,7 @@ virtualenv = ">=20.0.8" [[package]] name = "prompt-toolkit" -version = "3.0.21" +version = "3.0.29" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false @@ -605,11 +640,11 @@ wcwidth = "*" [[package]] name = "py" -version = "1.10.0" +version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pycodestyle" @@ -621,8 +656,8 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.8.2" -description = "Data validation and settings management using python 3.6 type hinting" +version = "1.9.1" +description = "Data validation and settings management using python type hints" category = "main" optional = false python-versions = ">=3.6.1" @@ -644,11 +679,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.10.0" +version = "2.12.0" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [[package]] name = "pymdown-extensions" @@ -663,14 +698,14 @@ Markdown = ">=3.2" [[package]] name = "pyparsing" -version = "3.0.1" -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"] +diagrams = ["railroad-diagrams", "jinja2"] [[package]] name = "pypiwin32" @@ -747,7 +782,7 @@ numpy-style = ["docstring_parser (>=0.7.3,<0.8.0)"] [[package]] name = "pytz" -version = "2021.3" +version = "2022.1" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -794,14 +829,6 @@ prompt_toolkit = ">=2.0,<4.0" [package.extras] docs = ["Sphinx (>=3.3,<4.0)", "sphinx-rtd-theme (>=0.5.0,<0.6.0)", "sphinx-autobuild (>=2020.9.1,<2021.0.0)", "sphinx-copybutton (>=0.3.1,<0.4.0)", "sphinx-autodoc-typehints (>=1.11.1,<2.0.0)"] -[[package]] -name = "regex" -version = "2021.10.23" -description = "Alternative regular expression module, to replace re." -category = "main" -optional = false -python-versions = "*" - [[package]] name = "scipy" version = "1.6.1" @@ -813,6 +840,22 @@ python-versions = ">=3.7" [package.dependencies] numpy = ">=1.16.5" +[[package]] +name = "setuptools-scm" +version = "6.4.2" +description = "the blessed package to manage your versions by scm tags" +category = "main" +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" @@ -839,7 +882,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "tomli" -version = "1.2.2" +version = "1.2.3" description = "A lil' TOML parser" category = "main" optional = false @@ -847,15 +890,15 @@ python-versions = ">=3.6" [[package]] name = "tomlkit" -version = "0.7.2" +version = "0.11.0" description = "Style preserving TOML library" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6,<4.0" [[package]] name = "tqdm" -version = "4.62.3" +version = "4.64.0" description = "Fast, Extensible Progress Meter" category = "main" optional = false @@ -867,26 +910,26 @@ 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 = "typing-extensions" -version = "3.10.0.2" -description = "Backported and Experimental Type Hints for Python 3.5+" +version = "4.2.0" +description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "virtualenv" -version = "20.10.0" +version = "20.14.1" description = "Virtual Python Environment builder" category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [package.dependencies] -"backports.entry-points-selectable" = ">=1.0.4" distlib = ">=0.3.1,<1" filelock = ">=3.2,<4" platformdirs = ">=2,<3" @@ -898,7 +941,7 @@ testing = ["coverage (>=4)", "coverage-enable-subprocess (>=1)", "flaky (>=3)", [[package]] name = "watchdog" -version = "2.1.6" +version = "2.1.9" description = "Filesystem events monitoring" category = "dev" optional = false @@ -917,20 +960,20 @@ python-versions = "*" [[package]] name = "zipp" -version = "3.6.0" +version = "3.8.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"] +docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "1.1" python-versions = "^3.8" -content-hash = "f74b8a551bfe6ea97dee4d7a79819d9b49adc0f31c5b0597a904ae1e8afcdbd6" +content-hash = "b69ff997b0cbefb8d58caf0d058810e3d40ae20f622962463f894b717e216b99" [metadata.files] argcomplete = [ @@ -946,16 +989,12 @@ atomicwrites = [ {file = 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explicit installation of netcdf4 --- .github/workflows/ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ea79165..2238414 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -39,6 +39,9 @@ jobs: poetry config virtualenvs.in-project false poetry config virtualenvs.path ~/.virtualenvs + - name: Install netcdf4 + run: poetry run pip install netcdf4 + - name: Install Dependencies run: poetry install if: steps.cache.outputs.cache-hit != 'true' From 1d04c95d7d698da231d1775d5536768c392a2b98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20S=2E=20Soriano=20P=C3=A9rez?= Date: Mon, 13 Jun 2022 10:23:17 +0200 Subject: [PATCH 3/5] ci: Moved black and isort to dev-dependencies --- poetry.lock | 53 +++++++++++++++++++++++++++++++++----------------- pyproject.toml | 4 ++-- 2 files changed, 37 insertions(+), 20 deletions(-) diff --git a/poetry.lock b/poetry.lock index 194f0e6..b7a3188 100644 --- a/poetry.lock +++ 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= "win32"} @@ -39,6 +37,8 @@ mypy = "^0.910" devtools = "^0.6.1" commitizen = "^2.20.0" pre-commit = "^2.15.0" +click = "^8.1.3" +isort = "^5.10.1" [tool.commitizen] name = "cz_conventional_commits" From 52013f265123c3d3118cefd11daacd2113ae1dd9 Mon Sep 17 00:00:00 2001 From: Carsopre Date: Mon, 13 Jun 2022 08:27:01 +0000 Subject: [PATCH 4/5] autoformat: isort & black --- .../coral/bio_process/dislodgment.py | 4 ++-- src/biota_models/coral/bio_process/flow.py | 8 ++++---- src/biota_models/coral/bio_process/light.py | 4 ++-- src/biota_models/coral/bio_process/morphology.py | 2 +- .../coral/bio_process/photosynthesis.py | 6 +++--- .../coral/bio_process/population_states.py | 2 +- .../coral/bio_process/recruitment.py | 2 +- src/biota_models/coral/model/coral_model.py | 16 ++++++++-------- src/core/hydrodynamics/reef_1d.py | 4 ++-- 9 files changed, 24 insertions(+), 24 deletions(-) diff --git a/src/biota_models/coral/bio_process/dislodgment.py b/src/biota_models/coral/bio_process/dislodgment.py index 6d3b299..6bca81d 100644 --- a/src/biota_models/coral/bio_process/dislodgment.py +++ b/src/biota_models/coral/bio_process/dislodgment.py @@ -93,7 +93,7 @@ def dmt_formula(constants, flow_velocity): :param flow_velocity: depth-averaged flow velocity :type flow_velocity: float, numpy.ndarray """ - return constants.sigma_t / (constants.rho_w * constants.Cd * flow_velocity ** 2) + return constants.sigma_t / (constants.rho_w * constants.Cd * flow_velocity**2) def colony_shape_factor(self, coral: Coral): """ @@ -134,4 +134,4 @@ def csf_formula(dc, hc, bc, tc): # integral integral = arm_top * area_top + arm_bottom * area_bottom # colony shape factor - return 16.0 / (np.pi * bc ** 3) * integral + return 16.0 / (np.pi * bc**3) * integral diff --git a/src/biota_models/coral/bio_process/flow.py b/src/biota_models/coral/bio_process/flow.py index 3a7fa7a..62045d1 100644 --- a/src/biota_models/coral/bio_process/flow.py +++ b/src/biota_models/coral/bio_process/flow.py @@ -159,7 +159,7 @@ def derivative(beta): shear = ( (1.0 - beta) ** 2 / abs(1.0 - beta) - abs(1.0 - beta) ) / shear_length - drag = (beta ** 2 / abs(beta) + beta) / drag_length + drag = (beta**2 / abs(beta) + beta) / drag_length inertia = 1j * (constants.Cm * lambda_planar) / (1.0 - lambda_planar) # combined df = 1j + (8.0 * above_motion) / (3.0 * np.pi) * (-shear + drag) + inertia @@ -188,12 +188,12 @@ def current_wac(): # # parameter definitions # geometric parameters - planar_area = 0.25 * np.pi * diameter ** 2 + planar_area = 0.25 * np.pi * diameter**2 frontal_area = diameter * height - total_area = 0.5 * distance ** 2 + total_area = 0.5 * distance**2 lambda_planar = planar_area / total_area lambda_frontal = frontal_area / total_area - shear_length = height / (constants.Cs ** 2) + shear_length = height / (constants.Cs**2) # # calculations wac = 1.0 if depth <= height: diff --git a/src/biota_models/coral/bio_process/light.py b/src/biota_models/coral/bio_process/light.py index db2dd5e..9f82d42 100644 --- a/src/biota_models/coral/bio_process/light.py +++ b/src/biota_models/coral/bio_process/light.py @@ -47,7 +47,7 @@ def rep_light(self, coral): top = ( 0.25 * np.pi - * coral.dc_matrix ** 2 + * coral.dc_matrix**2 * self.I0 * np.exp(-self.Kd * (self.h - coral.hc_matrix)) ) @@ -93,7 +93,7 @@ def biomass(self, coral): """ base_section = self.base_light(coral) coral.light_bc = np.pi * ( - 0.25 * coral.dc_matrix ** 2 + 0.25 * coral.dc_matrix**2 + coral.dc_matrix * coral.tc_matrix + coral.bc_matrix * base_section ) diff --git a/src/biota_models/coral/bio_process/morphology.py b/src/biota_models/coral/bio_process/morphology.py index b65f78a..011b1f2 100644 --- a/src/biota_models/coral/bio_process/morphology.py +++ b/src/biota_models/coral/bio_process/morphology.py @@ -168,7 +168,7 @@ def delta_volume(self, coral): """ self.vol_increase = ( 0.5 - * coral.ac ** 2 + * coral.ac**2 * self.calc_sum * self.dt_year / self.constants.rho_c diff --git a/src/biota_models/coral/bio_process/photosynthesis.py b/src/biota_models/coral/bio_process/photosynthesis.py index 4a2a44c..3e48aea 100644 --- a/src/biota_models/coral/bio_process/photosynthesis.py +++ b/src/biota_models/coral/bio_process/photosynthesis.py @@ -169,7 +169,7 @@ def spec(): return 4e-4 * np.exp(-0.33 * (delta_temp - 10)) response = -(coral.temp - coral.Tlo) * ( - (coral.temp - coral.Tlo) ** 2 - delta_temp ** 2 + (coral.temp - coral.Tlo) ** 2 - delta_temp**2 ) temp_cr = coral.Tlo - (1 / np.sqrt(3)) * delta_temp try: @@ -179,11 +179,11 @@ def spec(): ) else: response[coral.temp <= temp_cr] = -( - (2 / (3 * np.sqrt(3))) * delta_temp ** 3 + (2 / (3 * np.sqrt(3))) * delta_temp**3 ) except TypeError: if coral.temp <= temp_cr: - response = (2 / (3 * np.sqrt(3))) * delta_temp ** 3 + response = (2 / (3 * np.sqrt(3))) * delta_temp**3 return response * spec() diff --git a/src/biota_models/coral/bio_process/population_states.py b/src/biota_models/coral/bio_process/population_states.py index e24d9b4..ba22598 100644 --- a/src/biota_models/coral/bio_process/population_states.py +++ b/src/biota_models/coral/bio_process/population_states.py @@ -95,7 +95,7 @@ def pop_states_xy(self, coral: Coral, ps): * coral.Csp * p[ps > 0.0, 1] ) - p[ps > 0.0, 0] = (-b + np.sqrt(b ** 2 - 4.0 * a * c)) / (2.0 * a) + p[ps > 0.0, 0] = (-b + np.sqrt(b**2 - 4.0 * a * c)) / (2.0 * a) # bleaching conditions # > healthy pop. diff --git a/src/biota_models/coral/bio_process/recruitment.py b/src/biota_models/coral/bio_process/recruitment.py index a2d4088..029bf35 100644 --- a/src/biota_models/coral/bio_process/recruitment.py +++ b/src/biota_models/coral/bio_process/recruitment.py @@ -40,7 +40,7 @@ def spawning(self, coral: Coral, param): potential = ( self.constants.prob_settle * self.constants.no_larvae - * self.constants.d_larvae ** power + * self.constants.d_larvae**power ) # recruitment averaged_healthy_pop = coral.pop_states[:, -1, 0].mean() diff --git a/src/biota_models/coral/model/coral_model.py b/src/biota_models/coral/model/coral_model.py index 0450b85..03827e4 100644 --- a/src/biota_models/coral/model/coral_model.py +++ b/src/biota_models/coral/model/coral_model.py @@ -95,7 +95,7 @@ def rs(self): def volume(self): """Coral volume.""" coral_volume = ( - 0.25 * np.pi * ((self.hc - self.tc) * self.bc ** 2 + self.tc * self.dc ** 2) + 0.25 * np.pi * ((self.hc - self.tc) * self.bc**2 + self.tc * self.dc**2) ) return coral_volume @@ -134,7 +134,7 @@ def as_vegetation_density(self): """Translation from coral morphology to (vegetation) density.""" def function(dc_rep, ac): - return (2 * dc_rep) / (ac ** 2) + return (2 * dc_rep) / (ac**2) return CoralOnly().in_space( coral=self, function=function, args=(self.dc_rep, self.ac) @@ -241,7 +241,7 @@ def update_coral_morphology( def vc2dc(coral_volume, rf, rp): """Coral volume to coral plate diameter.""" - dc = ((4.0 * coral_volume) / (np.pi * rf * rp * (1.0 + rp - rp ** 2))) ** ( + dc = ((4.0 * coral_volume) / (np.pi * rf * rp * (1.0 + rp - rp**2))) ** ( 1.0 / 3.0 ) return dc @@ -249,29 +249,29 @@ def vc2dc(coral_volume, rf, rp): def vc2hc(coral_volume, rf, rp): """Coral volume to coral height.""" hc = ( - (4.0 * coral_volume * rf ** 2) / (np.pi * rp * (1.0 + rp - rp ** 2)) + (4.0 * coral_volume * rf**2) / (np.pi * rp * (1.0 + rp - rp**2)) ) ** (1.0 / 3.0) return hc def vc2bc(coral_volume, rf, rp): """Coral volume > diameter of the base.""" bc = ( - (4.0 * coral_volume * rp ** 2) / (np.pi * rf * (1.0 + rp - rp ** 2)) + (4.0 * coral_volume * rp**2) / (np.pi * rf * (1.0 + rp - rp**2)) ) ** (1.0 / 3.0) return bc def vc2tc(coral_volume, rf, rp): """Coral volume > thickness of the plate.""" tc = ( - (4.0 * coral_volume * rf ** 2 * rp ** 2) - / (np.pi * (1.0 + rp - rp ** 2)) + (4.0 * coral_volume * rf**2 * rp**2) + / (np.pi * (1.0 + rp - rp**2)) ) ** (1.0 / 3.0) return tc def vc2ac(coral_volume, rf, rp, rs): """Coral volume > axial distance.""" ac = (1.0 / rs) * ( - (4.0 * coral_volume) / (np.pi * rf * rp * (1.0 + rp - rp ** 2)) + (4.0 * coral_volume) / (np.pi * rf * rp * (1.0 + rp - rp**2)) ) ** (1.0 / 3.0) return ac diff --git a/src/core/hydrodynamics/reef_1d.py b/src/core/hydrodynamics/reef_1d.py index 26903cd..9e5da92 100644 --- a/src/core/hydrodynamics/reef_1d.py +++ b/src/core/hydrodynamics/reef_1d.py @@ -118,7 +118,7 @@ def dispersion(wave_length, wave_period, depth, grav_acc): """Dispersion relation to determine the wave length based on the wave period. """ - func = wave_length - ((grav_acc * wave_period ** 2) / (2 * np.pi)) * np.tanh( + func = wave_length - ((grav_acc * wave_period**2) / (2 * np.pi)) * np.tanh( 2 * np.pi * depth / wave_length ) return func @@ -126,7 +126,7 @@ def dispersion(wave_length, wave_period, depth, grav_acc): @property def wave_length(self): """Solve the dispersion relation to retrieve the wave length.""" - L0 = 9.81 * self.per_wav ** 2 + L0 = 9.81 * self.per_wav**2 L = np.zeros(len(self.depth)) for i, h in enumerate(self.depth): if h > 0: From bc11ec3750e1a6dc8a818c6d5e8b7521290b716b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Carles=20S=2E=20Soriano=20P=C3=A9rez?= Date: Mon, 13 Jun 2022 11:49:35 +0200 Subject: [PATCH 5/5] docs: Extended current documentation with new quick steps --- README.md | 21 +++++++++++++++++++++ docs/guides/contribute.md | 12 ++++++++++++ 2 files changed, 33 insertions(+) diff --git a/README.md b/README.md index 9e7469a..89a193e 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,27 @@ # Official Documentation. Check our official GitHub pages documentation at [https://deltares.github.io/NBSDynamics/](https://deltares.github.io/NBSDynamics/). +# Quickguide +Thanks to the latest version of Pypi you can get all setup by just installing the package in the edit mode, so we offer the following options: + +* Contributing to the project: + * [Full guide](https://deltares.github.io/NBSDynamics/guides/contribute/) + * Quick installation (without poetry) __for development__: + * Navigate to the checked-out directory. + * Update your 'pip' to the latest version. + * Install the package in edit mode: + ```cli + pip install -e . + ``` +* Using the package as an external library: + ```cli + pip install git+https://github.com/Deltares/NBSDynamics.git + ``` + | We recommend installing the latest available release at the time instead of from 'master'. For that just add @branch_name at the end of the previous pip call. + +### Potential Errors +We found out that packages such as `netcdf4` or `pypiwin32` / `pywin32` might give problems. In case you run against said problems while installing the package we recommend installing them beforehand. + # Current supported models. Currently we support the Vegetation and Coral models. More details of how to run them can be found at their respective documentation pages. In addition, quick links on how to run models in this package: diff --git a/docs/guides/contribute.md b/docs/guides/contribute.md index e7a9a0c..6713a7e 100644 --- a/docs/guides/contribute.md +++ b/docs/guides/contribute.md @@ -26,6 +26,18 @@ After installation, make sure it's available on your `PATH` and run it in the HY To install the package (by default in editable mode) run `poetry install`. We advise using `virtualenv`s, Poetry will create one for you. If you need to use an already existing Python installation, you can activate it and run `poetry env use system` before `poetry install`. +#### Pip +Latest versions of `pip` support installing packages from a .toml file. This streamlines the process so that you do not need to use poetry (although we highly recommend it in order to add packages that are compliant with the rest of the repository). + +You can easily develop your own features using the pip edit mode from the root of the NBSDynamics checked out repository: + +``` +pip install -e . +``` + +#### Known issues +We found out that packages such as `netcdf4` or `pypiwin32` / `pywin32` might give problems. In case you run against said problems while installing the package we recommend installing them beforehand. + ### 1.2. Code convention / Linters This project uses both black and isort as an autoformatter. It is recommended following the rules defined in pyproject.toml to avoid conflicts before a merge.