From 5b9548234f7102b69e57dfe75145f7dca7118d6f Mon Sep 17 00:00:00 2001
From: Fabian Zills <46721498+PythonFZ@users.noreply.github.com>
Date: Sun, 30 Oct 2022 12:48:55 +0100
Subject: [PATCH] add `znlib.atomistic.ase.FileToASE` (#1)

* add 'atomistic' extras

* add pylint; modify imports; code linting
---
 poetry.lock                       | 1513 ++++++++++++++++++++++++++++-
 pyproject.toml                    |    8 +
 tests/conftest.py                 |   24 +
 tests/test_atomistic.py           |   25 +
 znlib/__init__.py                 |    6 +
 znlib/atomistic/__init__.py       |    5 +
 znlib/atomistic/ase.py            |  170 ++++
 znlib/cli.py                      |   27 +-
 znlib/examples/__init__.py        |    1 +
 znlib/examples/mc_pi_estimator.py |    5 +-
 10 files changed, 1770 insertions(+), 14 deletions(-)
 create mode 100644 tests/test_atomistic.py
 create mode 100644 znlib/atomistic/__init__.py
 create mode 100644 znlib/atomistic/ase.py

diff --git a/poetry.lock b/poetry.lock
index a542c65..b4ef047 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -59,6 +59,23 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "anyio"
+version = "3.6.2"
+description = "High level compatibility layer for multiple asynchronous event loop implementations"
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+idna = ">=2.8"
+sniffio = ">=1.1"
+
+[package.extras]
+doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"]
+trio = ["trio (>=0.16,<0.22)"]
+
 [[package]]
 name = "appdirs"
 version = "1.4.4"
@@ -67,6 +84,92 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "appnope"
+version = "0.1.3"
+description = "Disable App Nap on macOS >= 10.9"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "argon2-cffi"
+version = "21.3.0"
+description = "The secure Argon2 password hashing algorithm."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+argon2-cffi-bindings = "*"
+
+[package.extras]
+dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"]
+docs = ["furo", "sphinx", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"]
+
+[[package]]
+name = "argon2-cffi-bindings"
+version = "21.2.0"
+description = "Low-level CFFI bindings for Argon2"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cffi = ">=1.0.1"
+
+[package.extras]
+dev = ["cogapp", "pre-commit", "pytest", "wheel"]
+tests = ["pytest"]
+
+[[package]]
+name = "ase"
+version = "3.22.1"
+description = "Atomic Simulation Environment"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+matplotlib = ">=3.1.0"
+numpy = ">=1.15.0"
+scipy = ">=1.1.0"
+
+[package.extras]
+docs = ["pillow", "sphinx", "sphinx-rtd-theme"]
+test = ["pytest (>=5.0.0)", "pytest-mock (>=3.3.0)", "pytest-xdist (>=1.30.0)"]
+
+[[package]]
+name = "astroid"
+version = "2.12.12"
+description = "An abstract syntax tree for Python with inference support."
+category = "dev"
+optional = false
+python-versions = ">=3.7.2"
+
+[package.dependencies]
+lazy-object-proxy = ">=1.4.0"
+typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""}
+wrapt = [
+    {version = ">=1.11,<2", markers = "python_version < \"3.11\""},
+    {version = ">=1.14,<2", markers = "python_version >= \"3.11\""},
+]
+
+[[package]]
+name = "asttokens"
+version = "2.0.8"
+description = "Annotate AST trees with source code positions"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+six = "*"
+
+[package.extras]
+test = ["astroid (<=2.5.3)", "pytest"]
+
 [[package]]
 name = "async-timeout"
 version = "4.0.2"
@@ -118,6 +221,40 @@ 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 = "2.10.3"
+description = "Internationalization utilities"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pytz = ">=2015.7"
+
+[[package]]
+name = "backcall"
+version = "0.2.0"
+description = "Specifications for callback functions passed in to an API"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "beautifulsoup4"
+version = "4.11.1"
+description = "Screen-scraping library"
+category = "dev"
+optional = false
+python-versions = ">=3.6.0"
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
 [[package]]
 name = "billiard"
 version = "3.6.4.0"
@@ -148,6 +285,22 @@ d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "bleach"
+version = "5.0.1"
+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,<1.2)"]
+dev = ["Sphinx (==4.3.2)", "black (==22.3.0)", "build (==0.8.0)", "flake8 (==4.0.1)", "hashin (==0.17.0)", "mypy (==0.961)", "pip-tools (==6.6.2)", "pytest (==7.1.2)", "tox (==3.25.0)", "twine (==4.0.1)", "wheel (==0.37.1)"]
+
 [[package]]
 name = "celery"
 version = "5.2.7"
@@ -372,6 +525,30 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "debugpy"
+version = "1.6.3"
+description = "An implementation of the Debug Adapter Protocol for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+description = "XML bomb protection for Python stdlib modules"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "dictdiffer"
 version = "0.9.0"
@@ -386,6 +563,17 @@ docs = ["Sphinx (>=3)", "sphinx-rtd-theme (>=0.2)"]
 numpy = ["numpy (>=1.13.0)", "numpy (>=1.15.0)", "numpy (>=1.18.0)", "numpy (>=1.20.0)"]
 tests = ["check-manifest (>=0.42)", "mock (>=1.3.0)", "pytest (==5.4.3)", "pytest (>=6)", "pytest-cov (>=2.10.1)", "pytest-isort (>=1.2.0)", "pytest-pycodestyle (>=2)", "pytest-pycodestyle (>=2.2.0)", "pytest-pydocstyle (>=2)", "pytest-pydocstyle (>=2.2.0)", "sphinx (>=3)", "tox (>=3.7.0)"]
 
+[[package]]
+name = "dill"
+version = "0.3.6"
+description = "serialize all of python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+graph = ["objgraph (>=1.7.2)"]
+
 [[package]]
 name = "diskcache"
 version = "5.4.0"
@@ -632,6 +820,14 @@ tests = ["mypy (==0.981)", "pylint (==2.15.0)", "pylint-plugin-utils (>=0.6)", "
 tf = ["tensorflow"]
 xgb = ["xgboost"]
 
+[[package]]
+name = "entrypoints"
+version = "0.4"
+description = "Discover and load entry points from installed packages."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "exceptiongroup"
 version = "1.0.0"
@@ -643,6 +839,28 @@ python-versions = ">=3.7"
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "executing"
+version = "1.1.1"
+description = "Get the currently executing AST node of a frame, and other information"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+tests = ["asttokens", "littleutils", "pytest", "rich"]
+
+[[package]]
+name = "fastjsonschema"
+version = "2.16.2"
+description = "Fastest Python implementation of JSON schema"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+
 [[package]]
 name = "filelock"
 version = "3.8.0"
@@ -829,6 +1047,22 @@ category = "main"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "importlib-metadata"
+version = "5.0.0"
+description = "Read metadata from Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+perf = ["ipython"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "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 (>=0.9.2)"]
+
 [[package]]
 name = "importlib-resources"
 version = "5.10.0"
@@ -852,6 +1086,74 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "ipykernel"
+version = "6.16.2"
+description = "IPython Kernel for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+appnope = {version = "*", markers = "platform_system == \"Darwin\""}
+debugpy = ">=1.0"
+ipython = ">=7.23.1"
+jupyter-client = ">=6.1.12"
+matplotlib-inline = ">=0.1"
+nest-asyncio = "*"
+packaging = "*"
+psutil = "*"
+pyzmq = ">=17"
+tornado = ">=6.1"
+traitlets = ">=5.1.0"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "ipython"
+version = "8.5.0"
+description = "IPython: Productive Interactive Computing"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
+appnope = {version = "*", markers = "sys_platform == \"darwin\""}
+backcall = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+decorator = "*"
+jedi = ">=0.16"
+matplotlib-inline = "*"
+pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
+pickleshare = "*"
+prompt-toolkit = ">3.0.1,<3.1.0"
+pygments = ">=2.4.0"
+stack-data = "*"
+traitlets = ">=5"
+
+[package.extras]
+all = ["Sphinx (>=1.3)", "black", "curio", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "testpath", "trio"]
+black = ["black"]
+doc = ["Sphinx (>=1.3)"]
+kernel = ["ipykernel"]
+nbconvert = ["nbconvert"]
+nbformat = ["nbformat"]
+notebook = ["ipywidgets", "notebook"]
+parallel = ["ipyparallel"]
+qtconsole = ["qtconsole"]
+test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+
+[[package]]
+name = "ipython-genutils"
+version = "0.2.0"
+description = "Vestigial utilities from IPython"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "isort"
 version = "5.10.1"
@@ -885,6 +1187,184 @@ dev = ["mkdocs (==1.3.0)", "mkdocs-gen-files (==0.3.4)", "mkdocs-material (==8.2
 docs = ["mkdocs (==1.3.0)", "mkdocs-gen-files (==0.3.4)", "mkdocs-material (==8.2.11)", "mkdocs-section-index (==0.3.4)", "mkdocstrings-python (==0.6.6)"]
 tests = ["mypy (==0.942)", "pylint (==2.13.7)", "pytest (==7.1.2)", "pytest-cov (==3.0.0)", "pytest-mock (==3.7.0)", "pytest-sugar (==0.9.4)", "types-requests"]
 
+[[package]]
+name = "jedi"
+version = "0.18.1"
+description = "An autocompletion tool for Python that can be used for text editors."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+parso = ">=0.8.0,<0.9.0"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
+
+[[package]]
+name = "jinja2"
+version = "3.1.2"
+description = "A very fast and expressive template engine."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
+[[package]]
+name = "json5"
+version = "0.9.10"
+description = "A Python implementation of the JSON5 data format."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+dev = ["hypothesis"]
+
+[[package]]
+name = "jsonschema"
+version = "4.16.0"
+description = "An implementation of JSON Schema validation for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+attrs = ">=17.4.0"
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
+[[package]]
+name = "jupyter-client"
+version = "7.4.4"
+description = "Jupyter protocol implementation and client libraries"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+entrypoints = "*"
+jupyter-core = ">=4.9.2"
+nest-asyncio = ">=1.5.4"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=23.0"
+tornado = ">=6.2"
+traitlets = "*"
+
+[package.extras]
+doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
+test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "4.11.2"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+traitlets = "*"
+
+[package.extras]
+test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-server"
+version = "1.21.0"
+description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+anyio = ">=3.1.0,<4"
+argon2-cffi = "*"
+jinja2 = "*"
+jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.7.0"
+nbconvert = ">=6.4.4"
+nbformat = ">=5.2.0"
+packaging = "*"
+prometheus-client = "*"
+pywinpty = {version = "*", markers = "os_name == \"nt\""}
+pyzmq = ">=17"
+Send2Trash = "*"
+terminado = ">=0.8.3"
+tornado = ">=6.1.0"
+traitlets = ">=5.1"
+websocket-client = "*"
+
+[package.extras]
+test = ["coverage", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-mock", "pytest-timeout", "pytest-tornasync", "requests"]
+
+[[package]]
+name = "jupyterlab"
+version = "3.5.0"
+description = "JupyterLab computational environment"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+ipython = "*"
+jinja2 = ">=2.1"
+jupyter-core = "*"
+jupyter-server = ">=1.16.0,<3"
+jupyterlab-server = ">=2.10,<3.0"
+nbclassic = "*"
+notebook = "<7"
+packaging = "*"
+tomli = "*"
+tornado = ">=6.1.0"
+
+[package.extras]
+test = ["check-manifest", "coverage", "jupyterlab-server[test]", "pre-commit", "pytest (>=6.0)", "pytest-check-links (>=0.5)", "pytest-console-scripts", "pytest-cov", "requests", "requests-cache", "virtualenv"]
+ui-tests = ["build"]
+
+[[package]]
+name = "jupyterlab-pygments"
+version = "0.2.2"
+description = "Pygments theme using JupyterLab CSS variables"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "jupyterlab-server"
+version = "2.16.1"
+description = "A set of server components for JupyterLab and JupyterLab like applications."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+babel = "*"
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jinja2 = ">=3.0.3"
+json5 = "*"
+jsonschema = ">=3.0.1"
+jupyter-server = ">=1.8,<3"
+packaging = "*"
+requests = "*"
+
+[package.extras]
+docs = ["autodoc-traits", "docutils (<0.19)", "jinja2 (<3.1.0)", "mistune (<1)", "myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinxcontrib-openapi"]
+openapi = ["openapi-core (>=0.14.2)", "ruamel-yaml"]
+test = ["codecov", "ipykernel", "jupyter-server[test]", "openapi-core (>=0.14.2,<0.15.0)", "openapi-spec-validator (<0.5)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "ruamel-yaml", "strict-rfc3339"]
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.4"
@@ -921,6 +1401,22 @@ sqs = ["boto3 (>=1.9.12)", "pycurl (>=7.44.1,<7.45.0)", "urllib3 (>=1.26.7)"]
 yaml = ["PyYAML (>=3.10)"]
 zookeeper = ["kazoo (>=1.3.1)"]
 
+[[package]]
+name = "lazy-object-proxy"
+version = "1.8.0"
+description = "A fast and thorough lazy object proxy."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "markupsafe"
+version = "2.1.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "matplotlib"
 version = "3.6.1"
@@ -941,6 +1437,33 @@ pyparsing = ">=2.2.1"
 python-dateutil = ">=2.7"
 setuptools_scm = ">=7"
 
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.6"
+description = "Inline Matplotlib backend for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+traitlets = "*"
+
+[[package]]
+name = "mccabe"
+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "mistune"
+version = "2.0.4"
+description = "A sane Markdown parser with useful plugins and renderers"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "multidict"
 version = "6.0.2"
@@ -963,7 +1486,117 @@ version = "0.5.2"
 description = "nanotime python implementation"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = "*"
+
+[[package]]
+name = "nbclassic"
+version = "0.4.7"
+description = "A web-based notebook environment for interactive computing"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+argon2-cffi = "*"
+ipykernel = "*"
+ipython-genutils = "*"
+jinja2 = "*"
+jupyter-client = ">=6.1.1"
+jupyter-core = ">=4.6.1"
+jupyter-server = ">=1.8"
+nbconvert = ">=5"
+nbformat = "*"
+nest-asyncio = ">=1.5"
+notebook-shim = ">=0.1.0"
+prometheus-client = "*"
+pyzmq = ">=17"
+Send2Trash = ">=1.8.0"
+terminado = ">=0.8.3"
+tornado = ">=6.1"
+traitlets = ">=4.2.1"
+
+[package.extras]
+docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
+json-logging = ["json-logging"]
+test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-tornasync", "requests", "requests-unixsocket", "selenium (==4.1.5)", "testpath"]
+
+[[package]]
+name = "nbclient"
+version = "0.7.0"
+description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+category = "dev"
+optional = false
+python-versions = ">=3.7.0"
+
+[package.dependencies]
+jupyter-client = ">=6.1.5"
+nbformat = ">=5.0"
+nest-asyncio = "*"
+traitlets = ">=5.2.2"
+
+[package.extras]
+sphinx = ["Sphinx (>=1.7)", "autodoc-traits", "mock", "moto", "myst-parser", "sphinx-book-theme"]
+test = ["black", "check-manifest", "flake8", "ipykernel", "ipython", "ipywidgets", "mypy", "nbconvert", "pip (>=18.1)", "pre-commit", "pytest (>=4.1)", "pytest-asyncio", "pytest-cov (>=2.6.1)", "setuptools (>=60.0)", "testpath", "twine (>=1.11.0)", "xmltodict"]
+
+[[package]]
+name = "nbconvert"
+version = "7.2.3"
+description = "Converting Jupyter Notebooks"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+beautifulsoup4 = "*"
+bleach = "*"
+defusedxml = "*"
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
+jinja2 = ">=3.0"
+jupyter-core = ">=4.7"
+jupyterlab-pygments = "*"
+markupsafe = ">=2.0"
+mistune = ">=2.0.3,<3"
+nbclient = ">=0.5.0"
+nbformat = ">=5.1"
+packaging = "*"
+pandocfilters = ">=1.4.1"
+pygments = ">=2.4.1"
+tinycss2 = "*"
+traitlets = ">=5.0"
+
+[package.extras]
+all = ["ipykernel", "ipython", "ipywidgets (>=7)", "myst-parser", "nbsphinx (>=0.2.12)", "pre-commit", "pyppeteer (>=1,<1.1)", "pyqtwebengine (>=5.15)", "pytest", "pytest-cov", "pytest-dependency", "sphinx (==5.0.2)", "sphinx-rtd-theme", "tornado (>=6.1)"]
+docs = ["ipython", "myst-parser", "nbsphinx (>=0.2.12)", "sphinx (==5.0.2)", "sphinx-rtd-theme"]
+qtpdf = ["pyqtwebengine (>=5.15)"]
+qtpng = ["pyqtwebengine (>=5.15)"]
+serve = ["tornado (>=6.1)"]
+test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pyppeteer (>=1,<1.1)", "pytest", "pytest-cov", "pytest-dependency"]
+webpdf = ["pyppeteer (>=1,<1.1)"]
+
+[[package]]
+name = "nbformat"
+version = "5.7.0"
+description = "The Jupyter Notebook format"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+fastjsonschema = "*"
+jsonschema = ">=2.6"
+jupyter-core = "*"
+traitlets = ">=5.1"
+
+[package.extras]
+test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"]
+
+[[package]]
+name = "nest-asyncio"
+version = "1.5.6"
+description = "Patch asyncio to allow nested event loops"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
 
 [[package]]
 name = "networkx"
@@ -991,6 +1624,50 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*
 [package.dependencies]
 setuptools = "*"
 
+[[package]]
+name = "notebook"
+version = "6.4.12"
+description = "A web-based notebook environment for interactive computing"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+argon2-cffi = "*"
+ipykernel = "*"
+ipython-genutils = "*"
+jinja2 = "*"
+jupyter-client = ">=5.3.4"
+jupyter-core = ">=4.6.1"
+nbconvert = ">=5"
+nbformat = "*"
+nest-asyncio = ">=1.5"
+prometheus-client = "*"
+pyzmq = ">=17"
+Send2Trash = ">=1.8.0"
+terminado = ">=0.8.3"
+tornado = ">=6.1"
+traitlets = ">=4.2.1"
+
+[package.extras]
+docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
+json-logging = ["json-logging"]
+test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixsocket", "selenium", "testpath"]
+
+[[package]]
+name = "notebook-shim"
+version = "0.2.0"
+description = "A shim layer for notebook traits and config"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+jupyter-server = ">=1.8,<3"
+
+[package.extras]
+test = ["pytest", "pytest-console-scripts", "pytest-tornasync"]
+
 [[package]]
 name = "numpy"
 version = "1.23.4"
@@ -1032,8 +1709,8 @@ python-versions = ">=3.8"
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.20.3", markers = "python_version < \"3.10\""},
+    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
 ]
 python-dateutil = ">=2.8.1"
 pytz = ">=2020.1"
@@ -1041,6 +1718,26 @@ pytz = ">=2020.1"
 [package.extras]
 test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
+[[package]]
+name = "pandocfilters"
+version = "1.5.0"
+description = "Utilities for writing pandoc filters in python"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "parso"
+version = "0.8.3"
+description = "A Python Parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["docopt", "pytest (<6.0.0)"]
+
 [[package]]
 name = "pathspec"
 version = "0.9.0"
@@ -1049,6 +1746,25 @@ category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 
+[[package]]
+name = "pexpect"
+version = "4.8.0"
+description = "Pexpect allows easy control of interactive console applications."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ptyprocess = ">=0.5"
+
+[[package]]
+name = "pickleshare"
+version = "0.7.5"
+description = "Tiny 'shelve'-like database with concurrency support"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "pillow"
 version = "9.2.0"
@@ -1061,6 +1777,14 @@ python-versions = ">=3.7"
 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 = "pkgutil-resolve-name"
+version = "1.3.10"
+description = "Resolve a name to an object."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "platformdirs"
 version = "2.5.2"
@@ -1101,6 +1825,17 @@ pyyaml = ">=5.1"
 toml = "*"
 virtualenv = ">=20.0.8"
 
+[[package]]
+name = "prometheus-client"
+version = "0.15.0"
+description = "Python client for the Prometheus monitoring system."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+twisted = ["twisted"]
+
 [[package]]
 name = "prompt-toolkit"
 version = "3.0.31"
@@ -1123,6 +1858,33 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 [package.extras]
 test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pure-eval"
+version = "0.2.2"
+description = "Safely evaluate AST nodes without side effects"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+tests = ["pytest"]
+
+[[package]]
+name = "py"
+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.*, !=3.4.*"
+
 [[package]]
 name = "pycparser"
 version = "2.21"
@@ -1172,6 +1934,29 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pylint"
+version = "2.15.5"
+description = "python code static checker"
+category = "dev"
+optional = false
+python-versions = ">=3.7.2"
+
+[package.dependencies]
+astroid = ">=2.12.12,<=2.14.0-dev0"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+dill = ">=0.2"
+isort = ">=4.2.5,<6"
+mccabe = ">=0.6,<0.8"
+platformdirs = ">=2.2.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+tomlkit = ">=0.10.1"
+typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+spelling = ["pyenchant (>=3.2,<4.0)"]
+testutils = ["gitpython (>3)"]
+
 [[package]]
 name = "pyparsing"
 version = "3.0.9"
@@ -1183,6 +1968,14 @@ python-versions = ">=3.6.8"
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyrsistent"
+version = "0.18.1"
+description = "Persistent/Functional/Immutable data structures"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "pytest"
 version = "7.2.0"
@@ -1230,6 +2023,14 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pywinpty"
+version = "2.0.9"
+description = "Pseudo terminal support for Windows from Python."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -1238,6 +2039,18 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "pyzmq"
+version = "24.0.1"
+description = "Python bindings for 0MQ"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cffi = {version = "*", markers = "implementation_name == \"pypy\""}
+py = {version = "*", markers = "implementation_name == \"pypy\""}
+
 [[package]]
 name = "requests"
 version = "2.28.1"
@@ -1303,6 +2116,22 @@ category = "dev"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "scipy"
+version = "1.9.3"
+description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
+numpy = ">=1.18.5,<1.26.0"
+
+[package.extras]
+dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"]
+doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"]
+test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "scmrepo"
 version = "0.1.2"
@@ -1325,6 +2154,19 @@ pygtrie = ">=2.3.2"
 dev = ["mock (==4.0.3)", "mypy (==0.971)", "paramiko (==2.11.0)", "pylint (==2.15.0)", "pytest (==7.1.2)", "pytest-asyncio (==0.18.3)", "pytest-cov (==3.0.0)", "pytest-docker (==0.12.0)", "pytest-mock (==3.8.2)", "pytest-sugar (==0.9.5)", "pytest-test-utils (==0.0.8)", "types-certifi (==2021.10.8.3)", "types-mock (==4.0.15)", "types-paramiko (==2.11.6)"]
 tests = ["mock (==4.0.3)", "mypy (==0.971)", "paramiko (==2.11.0)", "pylint (==2.15.0)", "pytest (==7.1.2)", "pytest-asyncio (==0.18.3)", "pytest-cov (==3.0.0)", "pytest-docker (==0.12.0)", "pytest-mock (==3.8.2)", "pytest-sugar (==0.9.5)", "pytest-test-utils (==0.0.8)", "types-certifi (==2021.10.8.3)", "types-mock (==4.0.15)", "types-paramiko (==2.11.6)"]
 
+[[package]]
+name = "send2trash"
+version = "1.8.0"
+description = "Send file to trash natively under Mac OS X, Windows and Linux."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+nativelib = ["pyobjc-framework-Cocoa", "pywin32"]
+objc = ["pyobjc-framework-Cocoa"]
+win32 = ["pywin32"]
+
 [[package]]
 name = "setuptools"
 version = "65.5.0"
@@ -1388,6 +2230,38 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "sniffio"
+version = "1.3.0"
+description = "Sniff out which async library your code is running under"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "soupsieve"
+version = "2.3.2.post1"
+description = "A modern CSS selector implementation for Beautiful Soup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "stack-data"
+version = "0.5.1"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+asttokens = "*"
+executing = "*"
+pure-eval = "*"
+
+[package.extras]
+tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
+
 [[package]]
 name = "tabulate"
 version = "0.9.0"
@@ -1399,6 +2273,38 @@ python-versions = ">=3.7"
 [package.extras]
 widechars = ["wcwidth"]
 
+[[package]]
+name = "terminado"
+version = "0.17.0"
+description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+ptyprocess = {version = "*", markers = "os_name != \"nt\""}
+pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""}
+tornado = ">=6.1.0"
+
+[package.extras]
+docs = ["pydata-sphinx-theme", "sphinx"]
+test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
+
+[[package]]
+name = "tinycss2"
+version = "1.2.1"
+description = "A tiny CSS parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+webencodings = ">=0.4"
+
+[package.extras]
+doc = ["sphinx", "sphinx_rtd_theme"]
+test = ["flake8", "isort", "pytest"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -1423,6 +2329,14 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "tornado"
+version = "6.2"
+description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+category = "dev"
+optional = false
+python-versions = ">= 3.7"
+
 [[package]]
 name = "tqdm"
 version = "4.64.1"
@@ -1440,6 +2354,18 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
+[[package]]
+name = "traitlets"
+version = "5.5.0"
+description = ""
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["pre-commit", "pytest"]
+
 [[package]]
 name = "typing-extensions"
 version = "4.4.0"
@@ -1502,6 +2428,35 @@ category = "main"
 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 = "websocket-client"
+version = "1.4.1"
+description = "WebSocket client for Python with low level API options"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+optional = ["python-socks", "wsaccel"]
+test = ["websockets"]
+
+[[package]]
+name = "wrapt"
+version = "1.14.1"
+description = "Module for decorators, wrappers and monkey patching."
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
 [[package]]
 name = "yarl"
 version = "1.8.1"
@@ -1575,12 +2530,13 @@ zninit = ">=0.1.1"
 znjson = ">=0.2.1,<0.3.0"
 
 [extras]
+atomistic = ["ase", "zntrack"]
 zntrack = ["zntrack", "matplotlib"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.8,<4.0.0"
-content-hash = "37f62ddad76b76789e176fdf53ff4421b3b56fb7ef8a9bac65cca29adb225d86"
+content-hash = "1b048bca5a02d530589e3e61e21657a978f34bb842794b6eba18f3694f04ede7"
 
 [metadata.files]
 aiohttp = [
@@ -1687,10 +2643,57 @@ amqp = [
 antlr4-python3-runtime = [
     {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
 ]
+anyio = [
+    {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"},
+    {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"},
+]
 appdirs = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
 ]
+appnope = [
+    {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+]
+argon2-cffi = [
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@@ -2650,10 +3908,37 @@ pygments = [
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+    {file = "wrapt-1.14.1-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:ee6acae74a2b91865910eef5e7de37dc6895ad96fa23603d1d27ea69df545015"},
+    {file = "wrapt-1.14.1-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:2b39d38039a1fdad98c87279b48bc5dce2c0ca0d73483b12cb72aa9609278e8a"},
+    {file = "wrapt-1.14.1-cp37-cp37m-win32.whl", hash = "sha256:60db23fa423575eeb65ea430cee741acb7c26a1365d103f7b0f6ec412b893853"},
+    {file = "wrapt-1.14.1-cp37-cp37m-win_amd64.whl", hash = "sha256:709fe01086a55cf79d20f741f39325018f4df051ef39fe921b1ebe780a66184c"},
+    {file = "wrapt-1.14.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:8c0ce1e99116d5ab21355d8ebe53d9460366704ea38ae4d9f6933188f327b456"},
+    {file = "wrapt-1.14.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:e3fb1677c720409d5f671e39bac6c9e0e422584e5f518bfd50aa4cbbea02433f"},
+    {file = "wrapt-1.14.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:642c2e7a804fcf18c222e1060df25fc210b9c58db7c91416fb055897fc27e8cc"},
+    {file = "wrapt-1.14.1-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7b7c050ae976e286906dd3f26009e117eb000fb2cf3533398c5ad9ccc86867b1"},
+    {file = "wrapt-1.14.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ef3f72c9666bba2bab70d2a8b79f2c6d2c1a42a7f7e2b0ec83bb2f9e383950af"},
+    {file = "wrapt-1.14.1-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:01c205616a89d09827986bc4e859bcabd64f5a0662a7fe95e0d359424e0e071b"},
+    {file = "wrapt-1.14.1-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:5a0f54ce2c092aaf439813735584b9537cad479575a09892b8352fea5e988dc0"},
+    {file = "wrapt-1.14.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:2cf71233a0ed05ccdabe209c606fe0bac7379fdcf687f39b944420d2a09fdb57"},
+    {file = "wrapt-1.14.1-cp38-cp38-win32.whl", hash = "sha256:aa31fdcc33fef9eb2552cbcbfee7773d5a6792c137b359e82879c101e98584c5"},
+    {file = "wrapt-1.14.1-cp38-cp38-win_amd64.whl", hash = "sha256:d1967f46ea8f2db647c786e78d8cc7e4313dbd1b0aca360592d8027b8508e24d"},
+    {file = "wrapt-1.14.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3232822c7d98d23895ccc443bbdf57c7412c5a65996c30442ebe6ed3df335383"},
+    {file = "wrapt-1.14.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:988635d122aaf2bdcef9e795435662bcd65b02f4f4c1ae37fbee7401c440b3a7"},
+    {file = "wrapt-1.14.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9cca3c2cdadb362116235fdbd411735de4328c61425b0aa9f872fd76d02c4e86"},
+    {file = "wrapt-1.14.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:d52a25136894c63de15a35bc0bdc5adb4b0e173b9c0d07a2be9d3ca64a332735"},
+    {file = "wrapt-1.14.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:40e7bc81c9e2b2734ea4bc1aceb8a8f0ceaac7c5299bc5d69e37c44d9081d43b"},
+    {file = "wrapt-1.14.1-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:b9b7a708dd92306328117d8c4b62e2194d00c365f18eff11a9b53c6f923b01e3"},
+    {file = "wrapt-1.14.1-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:6a9a25751acb379b466ff6be78a315e2b439d4c94c1e99cb7266d40a537995d3"},
+    {file = "wrapt-1.14.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:34aa51c45f28ba7f12accd624225e2b1e5a3a45206aa191f6f9aac931d9d56fe"},
+    {file = "wrapt-1.14.1-cp39-cp39-win32.whl", hash = "sha256:dee0ce50c6a2dd9056c20db781e9c1cfd33e77d2d569f5d1d9321c641bb903d5"},
+    {file = "wrapt-1.14.1-cp39-cp39-win_amd64.whl", hash = "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb"},
+    {file = "wrapt-1.14.1.tar.gz", hash = "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"},
+]
 yarl = [
     {file = "yarl-1.8.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:abc06b97407868ef38f3d172762f4069323de52f2b70d133d096a48d72215d28"},
     {file = "yarl-1.8.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:07b21e274de4c637f3e3b7104694e53260b5fc10d51fb3ec5fed1da8e0f754e3"},
diff --git a/pyproject.toml b/pyproject.toml
index 286e2b3..03c9609 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,10 +11,12 @@ python = ">=3.8,<4.0.0"
 colorama = "^0.4.5"
 zntrack = { version = "^0.4.3", optional = true }
 matplotlib = { version = "^3.6.1", optional = true }
+ase = { version = "^3.22.1", optional = true }
 
 
 [tool.poetry.extras]
 zntrack = ["zntrack", "matplotlib"]
+atomistic = ["ase", "zntrack"]
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"
@@ -23,12 +25,18 @@ black = "^22.10.0"
 isort = "^5.10.1"
 coverage = "^6.5.0"
 pre-commit = "^2.20.0"
+jupyterlab = "^3.5.0"
+pylint = "^2.15.5"
 
 
 [tool.poetry.group.zntrack.dependencies]
 zntrack = "^0.4.3"
 matplotlib = "^3.6.1"
 
+
+[tool.poetry.group.atomistic.dependencies]
+ase = "^3.22.1"
+
 [tool.poetry.urls]
 repository = "https://github.com/zincware/znlib"
 
diff --git a/tests/conftest.py b/tests/conftest.py
index ab681e5..d99045f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,9 +5,11 @@
 """
 import os
 import pathlib
+import random
 import shutil
 import subprocess
 
+import ase.io
 import pytest
 
 
@@ -31,3 +33,25 @@ def proj_path(tmp_path, request) -> pathlib.Path:
     subprocess.check_call(["git", "commit", "-m", "initial commit"])
 
     return tmp_path
+
+
+@pytest.fixture
+def tetraeder_test_traj(tmp_path_factory) -> str:
+    """Generate n atoms objects of random shifts of a CH4 tetraeder."""
+    # different tetraeder
+
+    tetraeder = ase.Atoms(
+        "CH4",
+        positions=[(1, 1, 1), (0, 0, 0), (0, 2, 2), (2, 2, 0), (2, 0, 2)],
+        cell=(2, 2, 2),
+    )
+
+    random.seed(42)
+
+    atoms = [tetraeder.copy() for _ in range(20)]
+    [x.rattle(stdev=0.5, seed=random.randint(1, int(1e6))) for x in atoms]
+
+    temporary_path = tmp_path_factory.getbasetemp()
+    file = temporary_path / "tetraeder.extxyz"
+    ase.io.write(file, atoms)
+    return file.resolve().as_posix()
diff --git a/tests/test_atomistic.py b/tests/test_atomistic.py
new file mode 100644
index 0000000..b3c5288
--- /dev/null
+++ b/tests/test_atomistic.py
@@ -0,0 +1,25 @@
+import pathlib
+import shutil
+import subprocess
+
+import ase
+
+import znlib
+
+
+def test_AddData(proj_path, tetraeder_test_traj):
+    traj_file = pathlib.Path(tetraeder_test_traj)
+    shutil.copy(traj_file, ".")
+
+    subprocess.check_call(["dvc", "add", traj_file.name])
+    data = znlib.atomistic.FileToASE(file=traj_file.name)
+    data.run_and_save()
+
+    loaded_data = znlib.atomistic.FileToASE.load()
+
+    assert isinstance(loaded_data.atoms, znlib.atomistic.ase.LazyAtomsSequence)
+    assert isinstance(loaded_data.atoms[0], ase.Atoms)
+    assert loaded_data.atoms.__dict__["atoms"] == {0: loaded_data.atoms[0]}
+    assert isinstance(loaded_data.atoms[[0, 1]], list)
+    assert isinstance(loaded_data.atoms[:], list)
+    assert isinstance(loaded_data.atoms.tolist(), list)
diff --git a/znlib/__init__.py b/znlib/__init__.py
index 63c0e4b..f66d8d2 100644
--- a/znlib/__init__.py
+++ b/znlib/__init__.py
@@ -1,3 +1,4 @@
+"""The znlib package"""
 import importlib.metadata
 import importlib.util
 
@@ -9,3 +10,8 @@
     from znlib import examples  # noqa: F401
 
     __all__.append("examples")
+
+if importlib.util.find_spec("ase") is not None:
+    from znlib import atomistic  # noqa: F401
+
+    __all__.append("ase")
diff --git a/znlib/atomistic/__init__.py b/znlib/atomistic/__init__.py
new file mode 100644
index 0000000..62169ce
--- /dev/null
+++ b/znlib/atomistic/__init__.py
@@ -0,0 +1,5 @@
+"""The znlib atomistic interface"""
+from znlib.atomistic import ase
+from znlib.atomistic.ase import FileToASE
+
+__all__ = ["ase", "FileToASE"]
diff --git a/znlib/atomistic/ase.py b/znlib/atomistic/ase.py
new file mode 100644
index 0000000..b25f437
--- /dev/null
+++ b/znlib/atomistic/ase.py
@@ -0,0 +1,170 @@
+"""Atomic Simulation Environment interface for znlib / ZnTrack """
+import collections.abc
+import logging
+import pathlib
+import typing
+
+import ase.db
+import ase.io
+import tqdm
+from zntrack import Node, dvc, utils, zn
+from zntrack.core import ZnTrackOption
+
+log = logging.getLogger(__name__)
+
+AtomsList = typing.List[ase.Atoms]
+
+
+class LazyAtomsSequence(collections.abc.Sequence):
+    """Sequence that loads atoms objects from ase Database only when accessed
+
+    This sequence does not support modifications but only reading values from it.
+    """
+
+    def __init__(self, database: str, threshold: int = 100):
+        """Default __init__
+
+        Parameters
+        ----------
+        database: file
+            The database to read from
+        threshold: int
+            Minimum number of atoms to read at once to print tqdm loading bars
+        """
+        self._database = database
+        self._threshold = threshold
+        self.__dict__["atoms"]: typing.Dict[int, ase.Atoms] = {}
+        self._len = None
+
+    def _update_state_from_db(self, indices: list):
+        """Load requested atoms into memory
+
+        If the atoms are not present in __dict__ they will be read from db
+
+        Parameters
+        ----------
+        indices: list
+            The indices of the atoms. Indices are 0based and will be converted to 1 based
+            when reading from the ase db.
+        """
+        indices = [x for x in indices if x not in self.__dict__["atoms"]]
+
+        with ase.db.connect(self._database) as database:
+            for key in tqdm.tqdm(
+                indices,
+                disable=len(indices) < self._threshold,
+                ncols=120,
+                desc=f"Loading atoms from {self._database}",
+            ):
+                self.__dict__["atoms"][key] = database[key + 1].toatoms()
+
+    def __iter__(self):
+        """Enable iterating over the sequence. This will load all data at once"""
+        self._update_state_from_db(list(range(len(self))))
+        for idx in range(len(self)):
+            yield self[idx]
+
+    def __getitem__(self, item) -> typing.Union[ase.Atoms, AtomsList]:
+        """Get atoms
+
+        Parameters
+        ----------
+        item: int | list | slice
+            The identifier of the requested atoms to return
+
+        Returns
+        -------
+        Atoms | list[Atoms]
+
+        """
+        if isinstance(item, int):
+            # The most simple case
+            try:
+                return self.__dict__["atoms"][item]
+            except KeyError:
+                self._update_state_from_db([item])
+                return self.__dict__["atoms"][item]
+        # everything with lists
+        if isinstance(item, slice):
+            item = list(range(len(self)))[item]
+
+        try:
+            return [self.__dict__["atoms"][x] for x in item]
+        except KeyError:
+            self._update_state_from_db(item)
+            return [self.__dict__["atoms"][x] for x in item]
+
+    def __len__(self):
+        """Get the len based on the db. This value is cached because
+        the db is not expected to change during the lifetime of this class
+        """
+        if self._len is None:
+            with ase.db.connect(self._database) as db:
+                self._len = len(db)
+        return self._len
+
+    def __repr__(self):
+        return f"{self.__class__.__name__}(db={self._database})"
+
+    def tolist(self) -> AtomsList:
+        """Convert sequence to a list of atoms objects"""
+        return list(self)
+
+
+class ZnAtoms(ZnTrackOption):
+    """Store list[ase.Atoms] in an ASE database."""
+
+    dvc_option = "outs"
+    zn_type = utils.ZnTypes.RESULTS
+
+    def get_filename(self, instance) -> pathlib.Path:
+        """Overwrite filename to csv"""
+        return pathlib.Path("nodes", instance.node_name, f"{self.name}.db")
+
+    def save(self, instance):
+        """Save value with ase.db.connect"""
+        atoms: AtomsList = getattr(instance, self.name)
+        file = self.get_filename(instance)
+        # file.parent.mkdir(exist_ok=True, parents=True)
+        with ase.db.connect(file, append=False) as db:
+            for atom in tqdm.tqdm(atoms, desc=f"Writing atoms to {file}"):
+                db.write(atom, group=instance.node_name)
+
+    def get_data_from_files(self, instance) -> LazyAtomsSequence:
+        """Load value with ase.db.connect"""
+        return LazyAtomsSequence(
+            database=self.get_filename(instance).resolve().as_posix()
+        )
+
+
+class FileToASE(Node):
+    """Read a ASE compatible file and make it available as list of atoms objects
+
+    The atoms object is a LazyAtomsSequence
+    """
+
+    file: typing.Union[str, pathlib.Path] = dvc.deps()
+    frames_to_read: int = zn.params(None)
+
+    atoms: AtomsList = ZnAtoms()
+
+    def post_init(self):
+        if not self.is_loaded:
+            self.file = pathlib.Path(self.file)
+            dvc_file = pathlib.Path(self.file.name + ".dvc")
+            if not dvc_file.exists():
+                log.warning(
+                    "The File you are adding as a dependency does not seem to be tracked"
+                    f" by DVC. Please run 'dvc add {self.file}' to avoid tracking the"
+                    " file directly with GIT."
+                )
+
+    def run(self):
+        self.atoms = []
+        for config, atom in enumerate(
+            tqdm.tqdm(ase.io.iread(self.file), desc="Reading File")
+        ):
+            if self.frames_to_read is not None:
+                if config >= self.frames_to_read:
+                    break
+            self.atoms.append(atom)
diff --git a/znlib/cli.py b/znlib/cli.py
index afb57a3..85f48cb 100644
--- a/znlib/cli.py
+++ b/znlib/cli.py
@@ -1,3 +1,4 @@
+"""Command Line Interface"""
 import dataclasses
 import importlib.metadata
 from importlib.util import find_spec
@@ -33,13 +34,19 @@ def znlib_status():
     """All zincware packages that should be listed"""
     print(f"Available {Fore.LIGHTBLUE_EX}zincware{Style.RESET_ALL} packages:")
 
-    ZnModules(name="znlib")
-    ZnModules(name="zntrack")
-    ZnModules(name="mdsuite")
-    ZnModules(name="znjson")
-    ZnModules(name="zninit")
-    ZnModules(name="dot4dict")
-    ZnModules(name="znipy")
-    ZnModules(name="supercharge")
-    ZnModules(name="znvis")
-    ZnModules(name="symdet")
+    packages = sorted(
+        [
+            "znlib",
+            "zntrack",
+            "mdsuite",
+            "znjson",
+            "zninit",
+            "dot4dict",
+            "znipy",
+            "supercharge",
+            "znvis",
+            "symdet",
+        ]
+    )
+    for package in packages:
+        ZnModules(package)
diff --git a/znlib/examples/__init__.py b/znlib/examples/__init__.py
index b5dabb5..b67bc07 100644
--- a/znlib/examples/__init__.py
+++ b/znlib/examples/__init__.py
@@ -1,3 +1,4 @@
+"""znlib / ZnTrack examples"""
 from znlib.examples.general import (
     AddInputs,
     InputToMetric,
diff --git a/znlib/examples/mc_pi_estimator.py b/znlib/examples/mc_pi_estimator.py
index 0291460..83eab07 100644
--- a/znlib/examples/mc_pi_estimator.py
+++ b/znlib/examples/mc_pi_estimator.py
@@ -6,6 +6,7 @@
 
 
 def plot_sampling(ax, coordinates, n_points, estimate):
+    """Plot a quarter of a circle with the sampled points"""
     circle = plt.Circle((0, 0), 1, fill=False, linewidth=3, edgecolor="k", zorder=10)
 
     ax.set_xlim(-0.0, 1.0)
@@ -20,7 +21,7 @@ def plot_sampling(ax, coordinates, n_points, estimate):
     inner_points = np.array(list(filter(lambda x: np.linalg.norm(x) <= 1, coordinates)))
     ax.plot(inner_points[:, 0], inner_points[:, 1], "r.")
     ax.add_patch(circle)
-    ax.set_title(f"N: {n_points} ; $\pi$ = {estimate}")
+    ax.set_title(rf"N: {n_points} ; $\pi$ = {estimate}")
     ax.set_aspect("equal")
 
 
@@ -34,6 +35,7 @@ class MonteCarloPiEstimator(Node):
     estimate: float = zn.metrics()
 
     def run(self):
+        """Compute pi using MC"""
         np.random.seed(self.seed)
         self.coordinates = np.random.random(size=(self.n_points, 2))
         radial_values = np.linalg.norm(self.coordinates, axis=1)
@@ -41,6 +43,7 @@ def run(self):
         self.estimate = 4 * n_circle_points / self.n_points
 
     def plot(self, ax):
+        """Create a plot of the sampled coordinates"""
         plot_sampling(
             ax,
             coordinates=self.coordinates,