From 057f9cca9c5a0a01d9fb1f3dc10af9fec741eecc Mon Sep 17 00:00:00 2001 From: Nathanael Lampe Date: Sun, 19 Jun 2022 22:02:02 +1000 Subject: [PATCH] add geometries for geant4 (#177) Co-authored-by: natl --- docs/source/examples.rst | 1 + .../generating-geometries-for-geant.ipynb | 30 +- .../generating-structures-for-geant.ipynb | 222 +++++++++++ fractaldna/structure_models/hilbert.py | 13 +- .../structure_models/random_placements.py | 7 +- fractaldna/structure_models/voxelisation.py | 56 +-- poetry.lock | 361 +++++++++--------- requirements-dev.txt | 65 ++-- requirements.txt | 6 +- 9 files changed, 494 insertions(+), 267 deletions(-) create mode 100644 docs/source/examples/generating-structures-for-geant.ipynb diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 3f07db7..1040bc9 100644 --- a/docs/source/examples.rst +++ b/docs/source/examples.rst @@ -11,4 +11,5 @@ Examples examples/multiple-solenoids examples/modifying-solenoids examples/generating-geometries-for-geant + examples/generating-structures-for-geant diff --git a/docs/source/examples/generating-geometries-for-geant.ipynb b/docs/source/examples/generating-geometries-for-geant.ipynb index 60cc7b1..c911800 100644 --- a/docs/source/examples/generating-geometries-for-geant.ipynb +++ b/docs/source/examples/generating-geometries-for-geant.ipynb @@ -64,13 +64,17 @@ " \"\".join(np.random.choice([\"G\", \"A\", \"T\", \"C\"], num_basepairs_turned))\n", ")\n", "\n", - "chain_straight.to_frame().to_csv(\"results/50nm_straight.csv\", sep=' ', index=False)\n", - "chain_turned.to_frame().to_csv(\"results/50nm_turn.csv\", sep=' ', index=False)\n", - "chain_turned_twisted.to_frame().to_csv(\"results/50nm_turn_twist.csv\", sep=' ', index=False)\n", + "chain_straight.to_frame().to_csv(\"results/50nm_straight.csv\", sep=\" \", index=False)\n", + "chain_turned.to_frame().to_csv(\"results/50nm_turn.csv\", sep=\" \", index=False)\n", + "chain_turned_twisted.to_frame().to_csv(\n", + " \"results/50nm_turn_twist.csv\", sep=\" \", index=False\n", + ")\n", "\n", - "chain_straight.to_plot().savefig(\"results/50nm_straight.png\", sep=' ', index=False)\n", - "chain_turned.to_plot().savefig(\"results/50nm_turn.png\", sep=' ', index=False)\n", - "chain_turned_twisted.to_plot().savefig(\"results/50nm_turn_twist.png\", sep=' ', index=False)" + "chain_straight.to_plot().savefig(\"results/50nm_straight.png\", sep=\" \", index=False)\n", + "chain_turned.to_plot().savefig(\"results/50nm_turn.png\", sep=\" \", index=False)\n", + "chain_turned_twisted.to_plot().savefig(\n", + " \"results/50nm_turn_twist.png\", sep=\" \", index=False\n", + ")" ] }, { @@ -119,7 +123,9 @@ "\n", "chain4_straight.to_frame().to_csv(\"results/50nm_4_straight.csv\", sep=\" \", index=False)\n", "chain4_turned.to_frame().to_csv(\"results/50nm_4_turn.csv\", sep=\" \", index=False)\n", - "chain4_turned_twisted.to_frame().to_csv(\"results/50nm_4_turn_twist.csv\", sep=\" \", index=False)\n", + "chain4_turned_twisted.to_frame().to_csv(\n", + " \"results/50nm_4_turn_twist.csv\", sep=\" \", index=False\n", + ")\n", "\n", "chain4_straight.to_plot().savefig(\"results/50nm_4_straight.png\")\n", "chain4_turned.to_plot().savefig(\"results/50nm_4_turn.png\")\n", @@ -168,7 +174,9 @@ "solenoid_turned.translate([0, 0, -side_length / 2.0])\n", "solenoid_turned_twisted.translate([0, 0, -side_length / 2.0])\n", "\n", - "solenoid_straight.to_frame().to_csv(\"results/solenoid_straight.csv\", sep=\" \", index=False)\n", + "solenoid_straight.to_frame().to_csv(\n", + " \"results/solenoid_straight.csv\", sep=\" \", index=False\n", + ")\n", "solenoid_turned.to_frame().to_csv(\"results/solenoid_turned.csv\", sep=\" \", index=False)\n", "solenoid_turned_twisted.to_frame().to_csv(\n", " \"results/solenoid_turned_twisted.csv\", sep=\" \", index=False\n", @@ -213,7 +221,7 @@ "source": [ "side_length = 1000 # angstrom\n", "radius_solenoid = 100 # angstrom\n", - "nhistones = 51 # histones\n", + "nhistones = 51 # histones\n", "separation = 250 # angstroms\n", "\n", "solenoid4_straight = dnachain.MultiSolenoidVolume(\n", @@ -251,7 +259,9 @@ "solenoid4_turned.translate([0, 0, -side_length / 2.0])\n", "solenoid4_turned_twisted.translate([0, 0, -side_length / 2.0])\n", "\n", - "solenoid4_straight.to_frame().to_csv(\"results/solenoid4_straight.csv\", sep=\" \", index=False)\n", + "solenoid4_straight.to_frame().to_csv(\n", + " \"results/solenoid4_straight.csv\", sep=\" \", index=False\n", + ")\n", "solenoid4_turned.to_frame().to_csv(\"results/solenoid4_turned.csv\", sep=\" \", index=False)\n", "solenoid4_turned_twisted.to_frame().to_csv(\n", " \"results/solenoid4_turned_twisted.csv\", sep=\" \", index=False\n", diff --git a/docs/source/examples/generating-structures-for-geant.ipynb b/docs/source/examples/generating-structures-for-geant.ipynb new file mode 100644 index 0000000..96b7743 --- /dev/null +++ b/docs/source/examples/generating-structures-for-geant.ipynb @@ -0,0 +1,222 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Making large scale structures in Geant4\n", + "\n", + "Geant4 simulations use a large scale structure " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "from pathlib import Path\n", + "\n", + "try:\n", + " # The voxelisation library produces the cubic voxelisation that\n", + " # can be used to build DNA\n", + " from fractaldna.structure_models import voxelisation as v\n", + "\n", + " # The hilbert module produces and handles L-Strings\n", + " from fractaldna.structure_models import hilbert as h\n", + "except (ImportError, ModuleNotFoundError):\n", + " sys.path.append(str(Path.cwd().parent.parent.parent))\n", + " from fractaldna.structure_models import voxelisation as v\n", + " from fractaldna.structure_models import hilbert as h\n", + "\n", + "import numpy as np\n", + "import pandas as pd\n", + "import matplotlib.pyplot as plt\n", + "from mpl_toolkits.mplot3d import Axes3D" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Fractal Cell Shapes\n", + "\n", + "### Generating a square shape" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Start with the initial L-String X for a Hilbert Curve\n", + "initial_string = \"X\"\n", + "# Iterate it as required (here, nn=3)\n", + "# for nn = 8, this takes about two hours on my 16GB RAM Mac\n", + "nn = 3\n", + "iterated_lstring = h.iterate_lstring(initial_string)\n", + "for _ in range(nn - 1):\n", + " iterated_lstring = h.iterate_lstring(iterated_lstring)\n", + "\n", + "vf = v.VoxelisedFractal.fromLString(iterated_lstring, pbar=True)\n", + "vf.center_fractal()\n", + "# fig = vf.to_plot()\n", + "# fig.savefig('results/fractal-X-3-centred.svg')\n", + "\n", + "# If you are saving a BIG fractal, try using the to_text() method instead\n", + "# as large dataframes are very slow to generate beyond 6 iterations.\n", + "# (Very slow as in multiple hours slow!)\n", + "# with open(f'results/fractal-X-{nn}-centred.csv', 'w') as ff:\n", + "# ff.write(vf.to_text())\n", + "vf.to_frame().to_csv(f\"results/fractal-X-{nn}-centred.csv\", index=False, sep=\" \")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Generating a Rectangular Shape\n", + "The seed `XFXFX` will generate a rectangular shape with aspect ratio 1:1:3" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Start with the initial L-String XFXFX for a Hilbert Curve\n", + "initial_string = \"XFXFX\"\n", + "# Iterate it as required (here, nn=4)\n", + "nn = 4\n", + "iterated_lstring = h.iterate_lstring(initial_string)\n", + "for _ in range(nn - 1):\n", + " iterated_lstring = h.iterate_lstring(iterated_lstring)\n", + "\n", + "vf = v.VoxelisedFractal.fromLString(iterated_lstring, pbar=True)\n", + "vf.center_fractal()\n", + "# fig = vf.to_plot()\n", + "# fig.savefig(f'results/fractal-XFXFX-{nn}-centred.svg')\n", + "\n", + "vf.to_frame().to_csv(f\"results/fractal-XFXFX-{nn}-centred.csv\", index=False, sep=\" \")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "*Note that the x-axis is compressed relative to the others in the below image*\n", + "\n", + "" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Importing a shape from a path\n", + "\n", + "The `voxelisation` model can convert the path of this curve to a voxelised representation, of straight\n", + "and curved boxes.\n", + "\n", + "In this example we perform this on a text file with X/Y/Z columns:\n", + "```\n", + "X\tY\tZ\n", + "-22\t-106\t216\n", + "-22\t-107\t216\n", + "-22\t-107\t215\n", + "-22\t-108\t215\n", + "-22\t-108\t214\n", + "-23\t-108\t214\n", + "-23\t-109\t214\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%%capture\n", + "df = pd.read_csv(\"results/example-path.csv\", sep=\"\\t\")\n", + "fig = plt.figure()\n", + "ax = fig.add_subplot(111, projection=\"3d\")\n", + "ax.plot(df.X, df.Y, df.Z)\n", + "fig.savefig(\"example-path.svg\")\n", + "\n", + "vf = v.VoxelisedFractal.from_path(df.values)\n", + "fig_fractal = vf.to_plot()\n", + "fig_fractal.savefig(\"example-path-voxels.svg\")\n", + "\n", + "vf.to_frame().to_csv(\"results/example-path-voxels.csv\", sep=\" \")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Left: Source Plot, Right:Voxelised Plot\n", + "\n", + " \n", + "\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Generating Random Volumes\n", + "\n", + "It can be useful to generate randomised volumes for testing a simulation. \n", + "This was the subject of (this article)[https://doi.org/10.1016/j.ejmp.2018.02.011].\n", + "\n", + "To generate a randomised volume, the `fractaldna.structure_models.random_placements`\n", + "is available.\n", + "\n", + "In that paper, 200,000 non overlapping prisms were simulated in a r=3000nm \n", + "ball.\n", + "The prisms had dimensions 30x30x100nm" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from fractaldna.structure_models import random_placements as rp\n", + "\n", + "# Generating 200,000 prisms can take around 4-5 hours\n", + "prisms = rp.generate_non_overlapping_prisms(\n", + " n_prisms=200_000,\n", + " size=[30, 30, 100], # nanometres\n", + " rad=3000, # nanometres\n", + " early_exit=-1,\n", + " verbose=True,\n", + ")\n", + "\n", + "df = prisms.to_frame()\n", + "df.to_csv(\"results/prisms_200k_r3000.csv\", sep=\" \", index=False)" + ] + } + ], + "metadata": { + "language_info": { + "name": "python", + "pygments_lexer": "ipython3" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/fractaldna/structure_models/hilbert.py b/fractaldna/structure_models/hilbert.py index 82c3781..dcaeb0b 100644 --- a/fractaldna/structure_models/hilbert.py +++ b/fractaldna/structure_models/hilbert.py @@ -3,6 +3,7 @@ import matplotlib.pyplot as plt import numpy as np from mpl_toolkits.mplot3d import Axes3D # NOQA +from tqdm import tqdm # interpret F as DrawForward(1); # interpret + as Yaw(90); @@ -120,7 +121,11 @@ def iterate_lstring(inString: str): def generate_path( - lstring: str, n: int = 2, distance: float = 10.0, rounding: int = 0 + lstring: str, + n: int = 2, + distance: float = 10.0, + rounding: int = 0, + pbar: bool = False, ) -> List[np.array]: """ Generate a path from an l-string @@ -134,6 +139,7 @@ def generate_path( :param n: steps on path between forward movements :param distance: distance between points forward movements :param rounding: rounding to apply to each position + :param pbar: display a progress bar :return: list of XYZ points """ if distance < 10 ** (-1 * rounding): @@ -161,7 +167,10 @@ def forward(axis, n=n, distance=distance): r"|": lambda axis: np.dot(rotu(axis, np.pi), axis), } - for char in lstring: + pbar_lstring = tqdm( + lstring, total=len(lstring), disable=(not pbar), desc="Generating Path" + ) + for char in pbar_lstring: if char == r"F": lastpos = pos[len(pos) - 1] for point in forward(axis): diff --git a/fractaldna/structure_models/random_placements.py b/fractaldna/structure_models/random_placements.py index a369d2e..e9dd990 100644 --- a/fractaldna/structure_models/random_placements.py +++ b/fractaldna/structure_models/random_placements.py @@ -477,9 +477,6 @@ def new_prism(rad=rad): if verbose is True: pbar = tqdm(iterable=None, total=n_prisms) while n_prisms_placed < n_prisms: - if (n_prisms // 10000) * 10000 == n_prisms_placed: - sys.stderr.write(f"Generating prism {n_prisms_placed} of {n_prisms}") - if attempts >= early_exit and early_exit >= 0: sys.stderr.write( f"Too many failed prism placements, stopped after {n_prisms_placed} placements." @@ -494,8 +491,8 @@ def new_prism(rad=rad): n_prisms_placed += 1 else: attempts += 1 - - pbar.close() + if verbose is True: + pbar.close() return prisms diff --git a/fractaldna/structure_models/voxelisation.py b/fractaldna/structure_models/voxelisation.py index 1b59a24..8d683e2 100644 --- a/fractaldna/structure_models/voxelisation.py +++ b/fractaldna/structure_models/voxelisation.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd from mpl_toolkits.mplot3d import Axes3D # NOQA +from tqdm import tqdm from . import hilbert @@ -480,10 +481,13 @@ def fromSeed(cls, seed: str, iterations: int, distance: float = 1): return cls.fromLString(seed, distance=distance) @classmethod - def from_path(cls, path: Union[List[np.array], List[List], np.array]): + def from_path( + cls, path: Union[List[np.array], List[List], np.array], pbar: bool = False + ): """Convert a path (a list of xyz positions) to a voxelised representation :param path: path to convert + :param pbar: show a progress bar if true :returns: Voxelised Fractal representation """ @@ -529,7 +533,11 @@ def from_path(cls, path: Union[List[np.array], List[List], np.array]): vf.fractal = [cls._makeVoxel(zeroVoxel, first, second)] - for ii in range(1, len(path) - 1): + stop = len(path) - 1 + iters = tqdm( + range(1, stop), disable=(not pbar), total=stop - 1, desc="Building Voxels" + ) + for ii in iters: vf.fractal.append( cls._makeVoxel(vf.fractal[ii - 1], arrpath[ii], arrpath[ii + 1]) ) @@ -539,50 +547,14 @@ def from_path(cls, path: Union[List[np.array], List[List], np.array]): return vf @classmethod - def fromLString(cls, lstring): + def fromLString(cls, lstring: str, pbar: bool = False): """Convert an L-String into a VoxelisedFractal :param lstring: L-String to convert + :param pbar: Show a progress bar for generating path and voxels :returns: Voxelised Fractal representation """ - path = hilbert.generate_path(lstring, n=1, distance=1) - - return cls.from_path(path) - lastpos = 2 * path[len(path) - 1] - path[len(path) - 2] - path.append(lastpos) - - vf = cls() - - arrpath = np.array(path) - - mins = np.zeros(3) # array [xmin, ymin, zmin] - maxs = np.zeros(3) # array [xmax, ymax, zmax] - lens = np.zeros(3) + path = hilbert.generate_path(lstring, n=1, distance=1, pbar=pbar) - for ii in range(3): - mins[ii] = min(arrpath[:, ii]) - maxs[ii] = max(arrpath[:, ii]) - lens[ii] = maxs[ii] - mins[ii] - - first = arrpath[0] - second = arrpath[1] - zeroheading = second - first - zeroposition = first - distance * zeroheading - zeroprincipal = np.array([1, 0, 0]) - if (np.around(zeroheading, 8) == zeroprincipal).all(): - zeroprincipal = np.array([0, 1, 0]) - zeroVoxel = Voxel( - zeroposition, zeroheading, zeroprincipal, zeroheading, zeroprincipal - ) - - vf.fractal = [cls._makeVoxel(zeroVoxel, first, second)] - - for ii in range(1, len(path) - 1): - vf.fractal.append( - cls._makeVoxel(vf.fractal[ii - 1], arrpath[ii], arrpath[ii + 1]) - ) - # print np.around(arrpath[ii], 3) - # print "Path Length: ", len(vf.fractal) - - return vf + return cls.from_path(path, pbar=pbar) diff --git a/poetry.lock b/poetry.lock index 3e3fa0b..0f17401 100644 --- a/poetry.lock +++ b/poetry.lock @@ -47,7 +47,7 @@ tests = ["pytest"] [[package]] name = "astroid" -version = "2.11.5" +version = "2.11.6" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false @@ -96,7 +96,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "babel" -version = "2.10.1" +version = "2.10.3" description = "Internationalization utilities" category = "dev" optional = false @@ -187,7 +187,7 @@ dev = ["pip-tools (==6.5.1)", "pytest (==7.1.1)", "flake8 (==4.0.1)", "tox (==3. [[package]] name = "certifi" -version = "2022.5.18.1" +version = "2022.6.15" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false @@ -236,7 +236,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.5" description = "Cross-platform colored terminal text." category = "main" optional = false @@ -365,7 +365,7 @@ devel = ["colorama", "jsonschema", "json-spec", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.7.0" +version = "3.7.1" description = "A platform independent file lock." category = "dev" optional = false @@ -464,7 +464,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest- [[package]] name = "importlib-resources" -version = "5.7.1" +version = "5.8.0" description = "Read resources from Python packages" category = "dev" optional = false @@ -502,7 +502,7 @@ test = ["pytest", "pytest-cov", "nbval"] [[package]] name = "ipykernel" -version = "6.13.0" +version = "6.15.0" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -517,11 +517,12 @@ matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" psutil = "*" +pyzmq = ">=17" tornado = ">=6.1" traitlets = ">=5.1.0" [package.extras] -test = ["pytest (>=6.0)", "pytest-cov", "flaky", "ipyparallel", "pre-commit", "pytest-timeout"] +test = ["flaky", "ipyparallel", "pre-commit", "pytest-cov", "pytest-timeout", "pytest (>=6.0)"] [[package]] name = "ipython" @@ -634,7 +635,7 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" -version = "4.5.1" +version = "4.6.0" description = "An implementation of JSON Schema validation for Python" category = "dev" optional = false @@ -647,11 +648,11 @@ 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)"] +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 = "7.3.1" +version = "7.3.4" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false @@ -662,12 +663,12 @@ entrypoints = "*" jupyter-core = ">=4.9.2" nest-asyncio = ">=1.5.4" python-dateutil = ">=2.8.2" -pyzmq = ">=22.3" +pyzmq = ">=23.0" tornado = ">=6.0" traitlets = "*" [package.extras] -doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] +doc = ["ipykernel", "myst-parser", "sphinx-rtd-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt"] test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] [[package]] @@ -703,7 +704,7 @@ python-versions = ">=3.6" [[package]] name = "kiwisolver" -version = "1.4.2" +version = "1.4.3" description = "A fast implementation of the Cassowary constraint solver" category = "main" optional = false @@ -799,7 +800,7 @@ python-versions = "*" [[package]] name = "nbclient" -version = "0.6.3" +version = "0.6.4" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "dev" optional = false @@ -809,7 +810,7 @@ python-versions = ">=3.7.0" jupyter-client = ">=6.1.5" nbformat = ">=5.0" nest-asyncio = "*" -traitlets = ">=5.0.0" +traitlets = ">=5.2.2" [package.extras] sphinx = ["autodoc-traits", "mock", "moto", "myst-parser", "Sphinx (>=1.7)", "sphinx-book-theme"] @@ -867,7 +868,7 @@ test = ["check-manifest", "testpath", "pytest", "pre-commit"] [[package]] name = "nbsphinx" -version = "0.8.8" +version = "0.8.9" description = "Jupyter Notebook Tools for Sphinx" category = "dev" optional = false @@ -879,7 +880,7 @@ jinja2 = "*" nbconvert = "!=5.4" nbformat = "*" sphinx = ">=1.8" -traitlets = "*" +traitlets = ">=5" [[package]] name = "nest-asyncio" @@ -899,7 +900,7 @@ python-versions = "*" [[package]] name = "notebook" -version = "6.4.11" +version = "6.4.12" description = "A web-based notebook environment for interactive computing" category = "dev" optional = false @@ -1166,24 +1167,26 @@ python-versions 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"sha256:e8467f0ebac0c81366c2168d6ad9f888efdfb6d4e1d3d5b4a004f46fa444b5c3"}, diff --git a/requirements-dev.txt b/requirements-dev.txt index 7389509..4a373cc 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,74 +2,74 @@ alabaster==0.7.12; python_version >= "3.6" and python_full_version < "3.0.0" or appnope==0.1.3; platform_system == "Darwin" and python_version >= "3.8" and sys_platform == "darwin" argon2-cffi-bindings==21.2.0; python_version >= "3.7" argon2-cffi==21.3.0; python_version >= "3.7" -astroid==2.11.5; python_full_version >= "3.6.2" +astroid==2.11.6; python_full_version >= "3.7.2" asttokens==2.0.5; python_version >= "3.8" atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" attrs==21.4.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" -babel==2.10.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +babel==2.10.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" backcall==0.2.0; python_version >= "3.8" bandit==1.7.4; python_version >= "3.7" beautifulsoup4==4.11.1; python_full_version >= "3.6.0" and python_version >= "3.7" black==22.3.0; python_full_version >= "3.6.2" bleach==5.0.0; python_version >= "3.7" -certifi==2022.5.18.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" +certifi==2022.6.15; python_version >= "3.7" and python_version < "4" cffi==1.15.0; implementation_name == "pypy" and python_version >= "3.7" cfgv==3.3.1; python_full_version >= "3.6.1" and python_version >= "3.7" -charset-normalizer==2.0.12; python_full_version >= "3.6.0" and python_version >= "3.5" +charset-normalizer==2.0.12; python_version >= "3.7" and python_version < "4" and python_full_version >= "3.5.0" click==8.1.3; python_version >= "3.7" and python_full_version >= "3.6.2" -colorama==0.4.4; sys_platform == "win32" and python_full_version >= "3.6.2" and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0") and (python_version >= "3.7" and python_full_version < "3.0.0" and platform_system == "Windows" or platform_system == "Windows" and python_version >= "3.7" and python_full_version >= "3.5.0") and python_version < "4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.5.0") and (python_version >= "3.8" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.8" and python_full_version >= "3.5.0") +colorama==0.4.5; sys_platform == "win32" and python_full_version >= "3.7.2" and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0") and (python_version >= "3.7" and python_full_version < "3.0.0" and platform_system == "Windows" or platform_system == "Windows" and python_version >= "3.7" and python_full_version >= "3.5.0") and python_version < "4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.5.0") and (python_version >= "3.8" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.8" and python_full_version >= "3.5.0") commonmark==0.9.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0" cycler==0.11.0; python_version >= "3.7" darglint==1.8.1; python_version >= "3.6" and python_version < "4.0" debugpy==1.6.0; python_version >= "3.7" decorator==5.1.1; python_version >= "3.8" defusedxml==0.7.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" -dill==0.3.5.1; python_full_version >= "3.7.0" +dill==0.3.5.1; python_full_version >= "3.7.2" distlib==0.3.4; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" docutils==0.17.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6" dparse==0.5.1; python_version >= "3.5" entrypoints==0.4; python_version >= "3.7" executing==0.8.3; python_version >= "3.8" fastjsonschema==2.15.3; python_version >= "3.7" -filelock==3.7.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" +filelock==3.7.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" fonttools==4.33.3; python_version >= "3.7" gitdb==4.0.9; python_version >= "3.7" gitpython==3.1.27; python_version >= "3.7" identify==2.5.1; python_version >= "3.7" -idna==3.3; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.5" +idna==3.3; python_version >= "3.7" and python_version < "4" imagesize==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" importlib-metadata==4.11.4; python_version >= "3.7" -importlib-resources==5.7.1; python_version < "3.9" and python_version >= "3.7" +importlib-resources==5.8.0; python_version < "3.9" and python_version >= "3.7" iniconfig==1.1.1; python_version >= "3.6" ipyevents==2.0.1 -ipykernel==6.13.0; python_version >= "3.7" +ipykernel==6.15.0; python_version >= "3.7" ipython-genutils==0.2.0; python_version >= "3.7" ipython==8.4.0; python_version >= "3.8" ipywidgets==7.7.0 isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0" jedi==0.18.1; python_version >= "3.8" jinja2==3.1.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7" -jsonschema==4.5.1; python_version >= "3.7" -jupyter-client==7.3.1; python_full_version >= "3.7.0" and python_version >= "3.7" +jsonschema==4.6.0; python_version >= "3.7" +jupyter-client==7.3.4; python_full_version >= "3.7.0" and python_version >= "3.7" jupyter-core==4.10.0; python_version >= "3.7" jupyterlab-pygments==0.2.2; python_version >= "3.7" jupyterlab-widgets==1.1.0; python_version >= "3.6" -kiwisolver==1.4.2; python_version >= "3.7" -lazy-object-proxy==1.7.1; python_version >= "3.6" and python_full_version >= "3.6.2" +kiwisolver==1.4.3; python_version >= "3.7" +lazy-object-proxy==1.7.1; python_version >= "3.6" and python_full_version >= "3.7.2" markupsafe==2.1.1; python_version >= "3.7" matplotlib-inline==0.1.3; python_version >= "3.8" matplotlib==3.5.2; python_version >= "3.7" -mccabe==0.7.0; python_version >= "3.6" and python_full_version >= "3.6.2" +mccabe==0.7.0; python_version >= "3.6" and python_full_version >= "3.7.2" mistune==0.8.4 mypy-extensions==0.4.3 -mypy==0.931; python_version >= "3.6" -nbclient==0.6.3; python_full_version >= "3.7.0" and python_version >= "3.7" +mypy==0.960; python_version >= "3.6" +nbclient==0.6.4; python_full_version >= "3.7.0" and python_version >= "3.7" nbconvert==6.5.0; python_version >= "3.7" nbformat==5.4.0; python_full_version >= "3.7.0" and python_version >= "3.7" -nbsphinx==0.8.8; python_version >= "3.6" +nbsphinx==0.8.9; python_version >= "3.6" nest-asyncio==1.5.5; python_full_version >= "3.7.0" and python_version >= "3.7" nodeenv==1.6.0; python_version >= "3.7" -notebook==6.4.11; python_version >= "3.7" +notebook==6.4.12; python_version >= "3.7" numpy==1.22.4; python_version >= "3.8" packaging==21.3; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7" pandas==1.4.2; python_version >= "3.8" @@ -80,7 +80,7 @@ pbr==5.9.0; python_version >= "3.7" pexpect==4.8.0; sys_platform != "win32" and python_version >= "3.8" pickleshare==0.7.5; python_version >= "3.8" pillow==9.1.1; python_version >= "3.7" -platformdirs==2.5.2; python_version >= "3.7" and python_full_version >= "3.6.2" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7") +platformdirs==2.5.2; python_version >= "3.7" and python_full_version >= "3.7.2" and (python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7") pluggy==1.0.0; python_version >= "3.6" pre-commit==2.19.0; python_version >= "3.7" prometheus-client==0.14.1; python_version >= "3.7" @@ -92,19 +92,19 @@ py==1.11.0; python_version >= "3.7" and python_full_version < "3.0.0" and implem pycparser==2.21; python_version >= "3.7" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.7" and python_full_version >= "3.4.0" pydocstyle==6.1.1; python_version >= "3.6" pygments==2.12.0; python_full_version >= "3.6.3" and python_full_version < "4.0.0" and python_version >= "3.8" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") -pylint==2.13.9; python_full_version >= "3.6.2" +pylint==2.14.2; python_full_version >= "3.7.2" pyparsing==3.0.9; python_full_version >= "3.6.8" and python_version >= "3.7" pyrsistent==0.18.1; python_version >= "3.7" pytest==6.2.5; python_version >= "3.6" python-dateutil==2.8.2; python_version >= "3.8" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.8" pytz==2022.1; python_version >= "3.8" -pyupgrade==2.32.1; python_version >= "3.7" +pyupgrade==2.34.0; python_version >= "3.7" pywin32==304; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.7" pywinpty==2.0.5; os_name == "nt" and python_version >= "3.7" pyyaml==6.0; python_version >= "3.7" -pyzmq==23.0.0; python_version >= "3.7" -requests==2.27.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" -rich==12.4.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0" +pyzmq==23.1.0; python_version >= "3.7" +requests==2.28.0; python_version >= "3.7" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") +rich==12.4.4; python_full_version >= "3.6.3" and python_full_version < "4.0.0" safety==1.10.3; python_version >= "3.5" scipy==1.8.1; python_version >= "3.8" and python_version < "3.11" send2trash==1.8.0; python_version >= "3.7" @@ -114,7 +114,7 @@ six==1.16.0; python_version >= "3.8" and python_full_version < "3.0.0" or python smmap==5.0.0; python_version >= "3.7" snowballstemmer==2.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" soupsieve==2.3.2.post1; python_full_version >= "3.6.0" and python_version >= "3.7" -sphinx-autodoc-typehints==1.18.1; python_version >= "3.7" +sphinx-autodoc-typehints==1.18.3; python_version >= "3.7" sphinx-rtd-theme==1.0.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") sphinx==4.5.0; python_version >= "3.6" sphinxcontrib-applehelp==1.0.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" @@ -123,22 +123,23 @@ sphinxcontrib-htmlhelp==2.0.0; python_version >= "3.6" and python_full_version < sphinxcontrib-jsmath==1.0.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" sphinxcontrib-qthelp==1.0.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" sphinxcontrib-serializinghtml==1.1.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" -stack-data==0.2.0; python_version >= "3.8" +stack-data==0.3.0; python_version >= "3.8" stevedore==3.5.0; python_version >= "3.7" terminado==0.15.0; python_version >= "3.7" tinycss2==1.1.1; python_version >= "3.7" tokenize-rt==4.2.1; python_full_version >= "3.6.1" and python_version >= "3.7" toml==0.10.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7" -tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.6.2" and python_version >= "3.7" +tomli==2.0.1; python_version < "3.11" and python_full_version >= "3.7.2" and python_version >= "3.7" +tomlkit==0.11.0; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.7.2" tornado==6.1; python_version >= "3.7" tqdm==4.64.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") -traitlets==5.2.1.post0; python_full_version >= "3.7.0" and python_version >= "3.8" +traitlets==5.3.0; python_full_version >= "3.7.0" and python_version >= "3.8" typer==0.4.1; python_version >= "3.6" -typing-extensions==4.2.0; python_full_version >= "3.6.3" and python_full_version < "4.0.0" and python_version < "3.9" and python_version >= "3.7" -urllib3==1.26.9; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.5" +typing-extensions==4.2.0; python_full_version >= "3.7.2" and python_full_version < "4.0.0" and python_version < "3.9" and python_version >= "3.7" +urllib3==1.26.9; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.7" virtualenv==20.14.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7" wcwidth==0.2.5; python_full_version >= "3.6.2" and python_version >= "3.8" webencodings==0.5.1; python_version >= "3.7" widgetsnbextension==3.6.0 -wrapt==1.14.1; python_full_version >= "3.6.2" +wrapt==1.14.1; python_full_version >= "3.7.2" zipp==3.8.0; python_version < "3.9" and python_version >= "3.7" diff --git a/requirements.txt b/requirements.txt index 9aef60e..eecb9f5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,13 +1,13 @@ atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" attrs==21.4.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6" click==8.1.3; python_version >= "3.7" -colorama==0.4.4; python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" and platform_system == "Windows" or python_version >= "3.7" and python_full_version >= "3.5.0" and sys_platform == "win32" and platform_system == "Windows" +colorama==0.4.5; python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" and platform_system == "Windows" or python_version >= "3.7" and python_full_version >= "3.5.0" and sys_platform == "win32" and platform_system == "Windows" commonmark==0.9.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0" cycler==0.11.0; python_version >= "3.7" fonttools==4.33.3; python_version >= "3.7" importlib-metadata==4.11.4; python_version >= "3.7" iniconfig==1.1.1; python_version >= "3.6" -kiwisolver==1.4.2; python_version >= "3.7" +kiwisolver==1.4.3; python_version >= "3.7" matplotlib==3.5.2; python_version >= "3.7" mistune==0.8.4 numpy==1.22.4; python_version >= "3.8" @@ -21,7 +21,7 @@ pyparsing==3.0.9; python_full_version >= "3.6.8" and python_version >= "3.7" pytest==6.2.5; python_version >= "3.6" python-dateutil==2.8.2; python_version >= "3.8" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.8" pytz==2022.1; python_version >= "3.8" -rich==12.4.1; python_full_version >= "3.6.3" and python_full_version < "4.0.0" +rich==12.4.4; python_full_version >= "3.6.3" and python_full_version < "4.0.0" scipy==1.8.1; python_version >= "3.8" and python_version < "3.11" setuptools-scm==6.4.2; python_version >= "3.7" shellingham==1.4.0; python_version >= "3.6"