diff --git a/README.md b/README.md index f240731d..45d0b0c1 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ Documentation Status -PyPI +PyPI

Summit is a set of tools for optimising chemical processes. We’ve started by targeting reactions. Go through a tutorial [here](https://colab.research.google.com/drive/1E_KVm-aZMqMm3memvesn3FIzGiXKHwJz#scrollTo=Wxg4TiHLV0Kd&uniqifier=2)! diff --git a/poetry.lock b/poetry.lock index b7fedce4..cd9cb8ef 100644 --- a/poetry.lock +++ b/poetry.lock @@ -214,20 +214,20 @@ python-versions = "*" [[package]] name = "boto3" -version = "1.17.72" +version = "1.17.95" description = "The AWS SDK for Python" category = "main" optional = true python-versions = ">= 2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [package.dependencies] -botocore = ">=1.20.72,<1.21.0" +botocore = ">=1.20.95,<1.21.0" jmespath = ">=0.7.1,<1.0.0" s3transfer = ">=0.4.0,<0.5.0" [[package]] name = "botocore" -version = "1.20.72" +version = "1.20.95" description = "Low-level, data-driven core of boto 3." category = "main" optional = true @@ -243,21 +243,21 @@ crt = ["awscrt (==0.11.15)"] [[package]] name = "botorch" -version = "0.3.3" +version = "0.4.0" description = "Bayesian Optimization in PyTorch" category = "main" optional = false python-versions = ">=3.7" [package.dependencies] -gpytorch = ">=1.3" +gpytorch = ">=1.4" scipy = "*" -torch = ">=1.7" +torch = ">=1.7.1" [package.extras] dev = ["pytest", "pytest-cov", "black", "flake8", "sphinx", "sphinx-autodoc-typehints"] test = ["pytest", "pytest-cov"] -tutorials = ["jupyter", "matplotlib", "cma", "torchvision"] +tutorials = ["ax-platform", "cma", "jupyter", "matplotlib", "memory-profiler", "pykeops", "torchvision"] [[package]] name = "bravado" @@ -327,7 +327,7 @@ python-versions = "~=3.5" [[package]] name = "certifi" -version = "2020.12.5" +version = "2021.5.30" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = true @@ -354,7 +354,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "click" -version = "8.0.0" +version = "8.0.1" description = "Composable command line interface toolkit" category = "main" optional = false @@ -362,6 +362,7 @@ python-versions = ">=3.6" [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "cma" @@ -419,7 +420,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "decorator" -version = "5.0.7" +version = "5.0.9" description = "Decorators for Humans" category = "main" optional = false @@ -481,26 +482,25 @@ python-versions = ">=3.6" [[package]] name = "flask" -version = "1.1.2" +version = "2.0.1" description = "A simple framework for building complex web applications." category = "main" optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [package.dependencies] -click = ">=5.1" -itsdangerous = ">=0.24" -Jinja2 = ">=2.10.1" -Werkzeug = ">=0.15" +click = ">=7.1.2" +itsdangerous = ">=2.0" +Jinja2 = ">=3.0" +Werkzeug = ">=2.0" [package.extras] -dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] -docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] +async = ["asgiref (>=3.2)"] dotenv = ["python-dotenv"] [[package]] name = "flask-compress" -version = "1.9.0" +version = "1.10.1" description = "Compress responses in your Flask app with gzip, deflate or brotli." category = "main" optional = true @@ -531,7 +531,7 @@ smmap = ">=3.0.1,<5" [[package]] name = "gitpython" -version = "3.1.16" +version = "3.1.17" description = "Python Git Library" category = "main" optional = true @@ -581,12 +581,17 @@ optimizer = ["direct", "cma", "pydoe", "sobol-seq", "emcee"] [[package]] name = "gpytorch" -version = "1.3.0" +version = "1.4.2" description = "An implementation of Gaussian Processes in Pytorch" category = "main" optional = false python-versions = ">=3.6" +[package.dependencies] +scikit-learn = "*" +scipy = "*" +torch = ">=1.7" + [package.extras] dev = ["black", "twine", "pre-commit"] docs = ["ipython", "ipykernel", "sphinx (<3.0.0)", "sphinx-rtd-theme", "nbsphinx", "m2r"] @@ -613,7 +618,7 @@ numpy = [ [[package]] name = "hiplot" -version = "0.1.24" +version = "0.1.25" description = "High dimensional Interactive Plotting tool" category = "main" optional = true @@ -646,7 +651,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.0.1" +version = "4.5.0" description = "Read metadata from Python packages" category = "main" optional = false @@ -662,15 +667,14 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytes [[package]] name = "ipdb" -version = "0.13.7" +version = "0.13.4" description = "IPython-enabled pdb" category = "dev" optional = false python-versions = ">=2.7" [package.dependencies] -ipython = {version = ">=7.17.0", markers = "python_version > \"3.6\""} -toml = {version = ">=0.10.2", markers = "python_version > \"3.6\""} +ipython = {version = ">=5.1.0", markers = "python_version >= \"3.4\""} [[package]] name = "ipykernel" @@ -692,7 +696,7 @@ test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "nose", "jedi (<=0.17.2)"] [[package]] name = "ipython" -version = "7.23.1" +version = "7.24.1" description = "IPython: Productive Interactive Computing" category = "main" optional = false @@ -712,7 +716,7 @@ pygments = "*" traitlets = ">=4.2" [package.extras] -all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.16)", "pygments", "qtconsole", "requests", "testpath"] +all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.17)", "pygments", "qtconsole", "requests", "testpath"] doc = ["Sphinx (>=1.3)"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] @@ -720,7 +724,7 @@ nbformat = ["nbformat"] notebook = ["notebook", "ipywidgets"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] -test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.16)"] +test = ["nose (>=0.10.1)", "requests", "testpath", "pygments", "nbformat", "ipykernel", "numpy (>=1.17)"] [[package]] name = "ipython-genutils" @@ -751,7 +755,7 @@ test = ["pytest (>=3.6.0)", "pytest-cov", "mock"] [[package]] name = "itsdangerous" -version = "2.0.0" +version = "2.0.1" description = "Safely pass data to untrusted environments and back." category = "main" optional = true @@ -774,17 +778,17 @@ testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<6.0.0)"] [[package]] name = "jinja2" -version = "2.11.3" +version = "3.0.1" description = "A very fast and expressive template engine." category = "main" optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [package.dependencies] -MarkupSafe = ">=0.23" +MarkupSafe = ">=2.0" [package.extras] -i18n = ["Babel (>=0.8)"] +i18n = ["Babel (>=2.7)"] [[package]] name = "jmespath" @@ -926,7 +930,7 @@ python-versions = ">=3.6" [[package]] name = "markupsafe" -version = "2.0.0" +version = "2.0.1" description = "Safely add untrusted strings to HTML/XML markup." category = "main" optional = true @@ -977,7 +981,7 @@ python-versions = "*" [[package]] name = "more-itertools" -version = "8.7.0" +version = "8.8.0" description = "More routines for operating on iterables, beyond itertools" category = "main" optional = false @@ -1069,7 +1073,7 @@ test = ["check-manifest", "fastjsonschema", "testpath", "pytest", "pytest-cov"] [[package]] name = "nbsphinx" -version = "0.8.5" +version = "0.8.6" description = "Jupyter Notebook Tools for Sphinx" category = "main" optional = true @@ -1077,7 +1081,7 @@ python-versions = ">=3.6" [package.dependencies] docutils = "*" -jinja2 = ">=2.11,<3.0" +jinja2 = "*" nbconvert = "!=5.4" nbformat = "*" sphinx = ">=1.8" @@ -1116,7 +1120,7 @@ python-versions = ">=3.5" [[package]] name = "notebook" -version = "6.3.0" +version = "6.4.0" description = "A web-based notebook environment for interactive computing" category = "main" optional = true @@ -1139,7 +1143,7 @@ tornado = ">=6.1" traitlets = ">=4.2.1" [package.extras] -docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt", "sphinx-rtd-theme"] +docs = ["sphinx", "nbsphinx", "sphinxcontrib-github-alt", "sphinx-rtd-theme", "myst-parser"] json-logging = ["json-logging"] test = ["pytest", "coverage", "requests", "nbval", "selenium", "pytest-cov", "requests-unixsocket"] @@ -1165,20 +1169,20 @@ python-versions = ">=3.7" [[package]] name = "oauthlib" -version = "3.1.0" +version = "3.1.1" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" category = "main" optional = true -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.extras] -rsa = ["cryptography"] -signals = ["blinker"] -signedtoken = ["cryptography", "pyjwt (>=1.0.0)"] +rsa = ["cryptography (>=3.0.0,<4)"] +signals = ["blinker (>=1.4.0)"] +signedtoken = ["cryptography (>=3.0.0,<4)", "pyjwt (>=2.0.0,<3)"] [[package]] name = "opencv-python" -version = "4.5.2.52" +version = "4.5.2.54" description = "Wrapper package for OpenCV python bindings." category = "main" optional = true @@ -1323,7 +1327,7 @@ dev = ["pre-commit", "tox"] [[package]] name = "prometheus-client" -version = "0.10.1" +version = "0.11.0" description = "Python client for the Prometheus monitoring system." category = "main" optional = true @@ -1345,7 +1349,7 @@ wcwidth = "*" [[package]] name = "protobuf" -version = "3.17.0" +version = "3.17.3" description = "Protocol Buffers" category = "main" optional = true @@ -1372,7 +1376,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pyarrow" -version = "4.0.0" +version = "4.0.1" description = "Python library for Apache Arrow" category = "main" optional = true @@ -1544,7 +1548,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "300" +version = "301" description = "Python for Window Extensions" category = "main" optional = true @@ -1552,11 +1556,11 @@ python-versions = "*" [[package]] name = "pywinpty" -version = "0.5.7" -description = "Python bindings for the winpty library" +version = "1.1.2" +description = "Pseudo terminal support for Windows from Python." category = "main" optional = true -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "pyyaml" @@ -1568,7 +1572,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" [[package]] name = "pyzmq" -version = "22.0.3" +version = "22.1.0" description = "Python bindings for 0MQ" category = "main" optional = true @@ -1833,11 +1837,11 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "1.0.3" +version = "2.0.0" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "main" optional = true -python-versions = ">=3.5" +python-versions = ">=3.6" [package.extras] lint = ["flake8", "mypy", "docutils-stubs"] @@ -1868,7 +1872,7 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.4" +version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." category = "main" optional = true @@ -1968,7 +1972,7 @@ widechars = ["wcwidth"] [[package]] name = "terminado" -version = "0.9.5" +version = "0.10.1" description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library." category = "main" optional = true @@ -1976,7 +1980,7 @@ python-versions = ">=3.6" [package.dependencies] ptyprocess = {version = "*", markers = "os_name != \"nt\""} -pywinpty = {version = ">=0.5,<1", markers = "os_name == \"nt\""} +pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""} tornado = ">=4" [package.extras] @@ -1984,14 +1988,14 @@ test = ["pytest"] [[package]] name = "testpath" -version = "0.4.4" +version = "0.5.0" description = "Test utilities for code working with files and commands" category = "main" optional = true -python-versions = "*" +python-versions = ">= 3.5" [package.extras] -test = ["pathlib2"] +test = ["pytest", "pathlib2"] [[package]] name = "threadpoolctl" @@ -2019,14 +2023,13 @@ python-versions = ">=3.5" [[package]] name = "torch" -version = "1.8.1" +version = "1.9.0" description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration" category = "main" optional = false python-versions = ">=3.6.2" [package.dependencies] -numpy = "*" typing-extensions = "*" [[package]] @@ -2039,7 +2042,7 @@ python-versions = ">= 3.5" [[package]] name = "tqdm" -version = "4.60.0" +version = "4.61.1" description = "Fast, Extensible Progress Meter" category = "main" optional = false @@ -2093,16 +2096,16 @@ pytz = "*" [[package]] name = "urllib3" -version = "1.26.4" +version = "1.26.5" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" [package.extras] +brotli = ["brotlipy (>=0.6.0)"] secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] -brotli = ["brotlipy (>=0.6.0)"] [[package]] name = "validators" @@ -2121,7 +2124,7 @@ test = ["pytest (>=2.2.3)", "flake8 (>=2.4.0)", "isort (>=4.2.2)"] [[package]] name = "watchdog" -version = "2.1.1" +version = "2.1.2" description = "Filesystem events monitoring" category = "main" optional = true @@ -2156,18 +2159,15 @@ python-versions = "*" [[package]] name = "websocket-client" -version = "0.59.0" +version = "1.1.0" description = "WebSocket client for Python with low level API options" category = "main" optional = true -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[package.dependencies] -six = "*" +python-versions = ">=3.6" [[package]] name = "werkzeug" -version = "2.0.0" +version = "2.0.1" description = "The comprehensive WSGI web application library." category = "main" optional = true @@ -2216,7 +2216,7 @@ experiments = ["neptune-client", "hiplot", "paramiko", "pyrecorder", "xlrd", "st [metadata] lock-version = "1.1" python-versions = "^3.7" -content-hash = "4124f8be241179b92e51b3b0b0578fe9bd0244a4f6a406193e2538ddedf7cb1d" +content-hash = "8521c79e5cb0f649983b7ff6b3f37c68dc785b0b9173e877b93a4a6db7e6c997" [metadata.files] alabaster = [ @@ -2310,16 +2310,16 @@ blinker = [ {file = "blinker-1.4.tar.gz", hash = "sha256:471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6"}, ] boto3 = [ - {file = "boto3-1.17.72-py2.py3-none-any.whl", hash = "sha256:ee3317fd79b443ef102469fac393a1ffb650ea51ac4fc27464013872c5e1ce31"}, - {file = "boto3-1.17.72.tar.gz", hash = "sha256:3317722a1e9acbfc0d30cdf273d1708c823ceb19309e9cd91cac8a3604762341"}, + {file = "boto3-1.17.95-py2.py3-none-any.whl", hash = "sha256:8e5af9c7ea16ce1c35b7c3220d073dea9735bb1790107820d475462500ae1eff"}, + {file = "boto3-1.17.95.tar.gz", hash = "sha256:e61607211816c194dbe2701db48dcddc87cf19372e6f57a9ebe4dfe93dfe177c"}, ] botocore = [ - {file = "botocore-1.20.72-py2.py3-none-any.whl", hash = "sha256:2aaf439e3683e4ac7e0a4f5fc3cd6779418456f3bd6f40b3e474cb151bbceab9"}, - {file = "botocore-1.20.72.tar.gz", hash = "sha256:0fa93a2e2daad5791c63ee526ada66896cc483d04cb2d32bfcadfeb881203453"}, + {file = "botocore-1.20.95-py2.py3-none-any.whl", hash = "sha256:240a9ef007292e986a4e11662f9038435d9d4fd242e083db160c86eb5c24af30"}, + {file = "botocore-1.20.95.tar.gz", hash = "sha256:dc215f59735a3abde6c66a61f43f10d95bc18754d310da4e2037b3b8c4d8aa2d"}, ] botorch = [ - {file = "botorch-0.3.3-py3-none-any.whl", hash = "sha256:d8883101dcf37051223bec5913c3f0600995f76d90e655edca4ecab6aa669ed4"}, - {file = "botorch-0.3.3.tar.gz", hash = "sha256:ed25e5eef10539cc41a17457adf2dbc3c1fe1964cb5515a241b3825e1d260765"}, + {file = "botorch-0.4.0-py3-none-any.whl", hash = "sha256:4de6ec904707b17bc304dbd6d9f3657b3e3688d4e2bf8338c263ecfa908133ee"}, + {file = "botorch-0.4.0.tar.gz", hash = "sha256:d98dd303294207b955a794b12433cc5ac2331e36cebf1b94f75c5f5162be861b"}, ] bravado = [ {file = "bravado-11.0.3-py2.py3-none-any.whl", hash = "sha256:8ac8bbb645e49607917a5c07808116c708521f51e80d9c29bc4a168ff4dd22c6"}, @@ -2367,8 +2367,8 @@ cachetools = [ {file = "cachetools-4.2.2.tar.gz", hash = "sha256:61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff"}, ] certifi = [ - {file = "certifi-2020.12.5-py2.py3-none-any.whl", hash = "sha256:719a74fb9e33b9bd44cc7f3a8d94bc35e4049deebe19ba7d8e108280cfd59830"}, - {file = "certifi-2020.12.5.tar.gz", hash = "sha256:1a4995114262bffbc2413b159f2a1a480c969de6e6eb13ee966d470af86af59c"}, + {file = "certifi-2021.5.30-py2.py3-none-any.whl", hash = "sha256:50b1e4f8446b06f41be7dd6338db18e0990601dce795c2b1686458aa7e8fa7d8"}, + {file = "certifi-2021.5.30.tar.gz", hash = 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