Fix: digging for errors

anisotropy/cli/cli.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 import click
+import pathlib
 import os
 import logging
 
@@ -93,30 +94,33 @@ def init(path, verbose):
 def compute(path, configFile, nprocs, stage, overwrite, params, verbose, execution, pid, logfile):
     import anisotropy
     from anisotropy.core import UltimateRunner
-    from anisotropy.core import config
+    from anisotropy.core import config as core_config
     from anisotropy.core import utils as core_utils
     
     anisotropy.loadEnv()
 
     if path:
-        os.makedirs(os.path.abspath(path), exist_ok = True)
-        os.chdir(os.path.abspath(path))
-        os.environ["ANISOTROPY_CWD"] = path
+        path = pathlib.Path(path).resolve()
+
+        os.makedirs(path, exist_ok = True)
+        os.chdir(path)
+        os.environ["AP_CWD"] = str(path)
 
     core_utils.setupLogger(utils.verbose_level(verbose), logfile)
     logger = logging.getLogger(__name__)
     
-    conf = config.DefaultConfig() 
+    config = core_config.DefaultConfig() 
 
     if configFile:
-        filepath = os.path.abspath(configFile)
-        logger.info(f"Loading file from { filepath }")
+        configFile = pathlib.Path(configFile).resolve()
+
+        logger.info(f"Loading file from { configFile }")
 
         try:
-            conf.load(configFile)
+            config.load(configFile)
 
         except FileNotFoundError:
-            conf.dump(configFile)
+            config.dump(configFile)
 
     else:
         logger.info("Using default configuration")
@@ -129,19 +133,21 @@ def compute(path, configFile, nprocs, stage, overwrite, params, verbose, executi
 
     for k, v in args.items():
         if v is not None:
-            conf.update(**{ k: v })
+            config.update(**{ k: v })
 
     if pid:
-        pidpath = os.path.abspath(pid)
+        pid = pathlib.Path(pid).resolve()
 
-        with open(pidpath, "w") as io:
+        with open(pid, "w") as io:
             io.write(str(os.getpid()))
 
-    runner = UltimateRunner(config = conf, exec_id = execution)
-    runner.fill()
+    runner = UltimateRunner(config = config, exec_id = execution)
+    runner.prepare_queue()
     runner.start()
 
-    os.remove(pidpath)
+    if pid:
+        os.remove(pid)
+
     logger.info("Computation done. Exiting ...")
 
 

anisotropy/core/postprocess.py

@@ -1,22 +1,17 @@
 # -*- coding: utf-8 -*-
 
-from os import path
-import logging
+import pathlib
 
-logger = logging.getLogger(__name__)
-
-from anisotropy.openfoam import commands 
-from anisotropy.openfoam import conversion
+import anisotropy.openfoam as of
 
 
-class PostProcess(object):
-    def __init__(self, dirpath):
-        self.path = path.abspath(dirpath)
+def flowRate(patch: str, path: str = None):
+    func = f"patchFlowRate(patch={ patch })"
 
-    def flowRate(self, patch: str):
-        func = "patchFlowRate(patch={})".format(patch)
-        filepath = path.join(self.path, "postProcessing", func, "0", "surfaceFieldValue.dat")
-        commands.postProcess(func, cwd = self.path, logpath = path.join(self.path, "patchFlowRate.log"))
-        surfaceFieldValue = conversion.datReader(filepath)
+    path = pathlib.Path(path or "").resolve()
+    outfile = path / "postProcessing" / func / "0/surfaceFieldValue.dat"
 
-        return surfaceFieldValue["sum(phi)"][-1]
+    of.commands.postProcess(func, cwd = path, logpath = path / "patchFlowRate.log")
+    surfaceFieldValue = of.conversion.read_dat(outfile)["sum(phi)"][-1]
+
+    return surfaceFieldValue

anisotropy/core/runner.py

@@ -12,7 +12,7 @@ from anisotropy import shaping
 from anisotropy import meshing
 from anisotropy import solving
 
-from . import config
+from . import config as core_config
 from . import postprocess
 from . import utils
 from . import ParallelRunner
@@ -22,10 +22,10 @@ logger = logging.getLogger(__name__)
 
 
 class UltimateRunner(object):
-    def __init__(self, conf = None, exec_id: int = None, typo: str = "master"):
+    def __init__(self, config = None, exec_id: int = None, typo: str = "master"):
 
         # Configuration file
-        self.config = conf or config.DefaultConfig()
+        self.config = config or core_config.DefaultConfig()
 
         # Database preparation
         self.database = Database(self.config["database"])
@@ -69,7 +69,7 @@ class UltimateRunner(object):
 
         if not flow:
             flow = tables.FlowOnephase(mesh_id = mesh.mesh_id, **self.config.params)
-            self.database.csave(mesh)
+            self.database.csave(flow)
 
     def prepare_queue(self):
         self.config.expand()
@@ -137,8 +137,8 @@ class UltimateRunner(object):
         
         generate_shape = {
             "simple": shaping.primitives.simple,
-            "bodyCentered": shaping.primitives.bodyCentered,
-            "faceCentered": shaping.primitives.faceCentered
+            "bodyCentered": shaping.primitives.body_centered,
+            "faceCentered": shaping.primitives.face_centered
         }[shapeParams.label]
 
         try:
@@ -151,12 +151,12 @@ class UltimateRunner(object):
             )
 
             #   export
-            self.casepath.mkdir(exist_ok = True)
+            self.casepath.mkdir(parents = True, exist_ok = True)
 
             shape.write(shapefile)
         
         except Exception as e:
-            logger.error(e)
+            logger.error(e, exc_info = True)
 
             shapeParams.shapeStatus = "failed"
 
@@ -207,27 +207,26 @@ class UltimateRunner(object):
             mesh.generate(parameters)
 
             #   export
-            self.casepath.mkdir(exist_ok = True)
+            self.casepath.mkdir(parents = True, exist_ok = True)
 
             mesh.write(meshfile)
             mesh.write(self.casepath / "mesh.msh")
 
         except Exception as e:
-            logger.error(e)
+            logger.error(e, exc_info = True)
 
             meshParams.meshStatus = "failed"
 
         else:
             meshParams.meshStatus = "done"
-            meshParams.edges = len(self.mesh.edges)
-            meshParams.faces = len(self.mesh.faces)
-            meshParams.volumes = len(self.mesh.volumes)
+            meshParams.faces = len(mesh.faces)
+            meshParams.volumes = len(mesh.volumes)
 
         #   commit parameters
         meshParams.meshExecutionTime = timer.elapsed()
         self.database.csave(meshParams)
 
-    def computeFlow(self):
+    def compute_flow(self):
         params = self.config.params
         query = (
             params["label"],
@@ -249,25 +248,24 @@ class UltimateRunner(object):
         #
         flowParamsDict = self.database.getFlowOnephase(*query, to_dict = True)
 
-        flow = solving.FlowOnephase(
-            direction = params["direction"], 
-            **flowParamsDict,
-            path = self.casepath
-        )
-
         try:
             #   load shape
             shapefile = self.casepath / "shape.step"
             shape = shaping.Shape().read(shapefile)
 
-            patches = shape.patches(group = True, shiftIndex = True, prefix = "patch")
+            #
+            flow = solving.FlowOnePhase(
+                path = self.casepath,
+                direction = params["direction"], 
+                patches = shape.patches(group = True, shiftIndex = True, prefix = "patch"),
+                **flowParamsDict
+            )
 
             #   generate solution
-            flow.createPatches(patches)
-            flow.build()
+            flow.generate()
 
         except Exception as e:
-            logger.error(e)
+            logger.error(e, exc_info = True)
 
             flowParams.flowStatus = "failed"
 
@@ -291,10 +289,8 @@ class UltimateRunner(object):
             params["label"], params["direction"], params["alpha"]
         ))
 
-        postProcess = postprocess.PostProcess(self.casepath)
-
         if flowParams.flowStatus == "done":
-            flowParams.flowRate = postProcess.flowRate("outlet")
+            flowParams.flowRate = postprocess.flowRate("outlet", self.casepath)
 
         self.database.csave(flowParams)
         

anisotropy/meshing/mesh.py

@@ -154,7 +154,7 @@ class Mesh:
             self.cells += utils.collect_cells(volume_cells, 3, volume_indices)
 
             surface_cells, surface_indices = utils.extract_netgen_cells(mesh, 2)
-            cell_blocks = utils.collect_cells(surface_cells, 3, surface_indices)
+            cell_blocks = utils.collect_cells(surface_cells, 2, surface_indices)
 
             for cellBlock in cell_blocks:
                 cellBlock.is_boundary = True

anisotropy/openfoam/case.py

@@ -14,6 +14,7 @@ class FoamCase(object):
     def __init__(self, files: FoamFile | list[FoamFile] = None, path: str = None):
         
         self.path = path 
+        self._backpath = None
         self._files = []
         
         if files is not None:
@@ -34,12 +35,13 @@ class FoamCase(object):
             assert type(file) is FoamFile, "passed object is not a FoamFile"
             assert file.object is not None, "FoamFile object attribute is None"
 
-            for n, _file in enumerate(self._files):
-                if _file.object == file.object:
-                    self._files.pop(n)
-                    self._files.append(file)
-                    
-                    return self
+            idn = self.contains(file.object)
+
+            if idn is not None:
+                self._files.pop(idn)
+                self._files.append(file)
+                
+                return self
             
             self._files.append(file)
         
@@ -48,16 +50,23 @@ class FoamCase(object):
     def __add__(self, files: FoamFile | list[FoamFile]):
         return self.add(files)
 
+    def contains(self, name: str) -> int | None:
+        for n, file in enumerate(self._files):
+            if file.object == name:
+                return n
+
+        return None
+
     def write(self, path: str = None):
         path = pathlib.Path(path or self.path or "")
 
         for file in self._files:
-            path /= (
+            path_ = path / (
                 file.location + "/" + file.object 
                 if file.location else file.object
             )
 
-            file.write(path.resolve())
+            file.write(path_.resolve())
     
     def read(self, path: str = None):
         path = pathlib.Path(path or self.path or "")
@@ -108,3 +117,14 @@ class FoamCase(object):
 
                 if os.path.isfile(file):
                     os.remove(file)
+
+    def chdir(self, path: str = None):
+        path = pathlib.Path(path or self.path or "").resolve()
+        self._backpath = os.getcwd()
+        
+        os.chdir(path)
+    
+    def chback(self):
+        path = pathlib.Path(self._backpath or "").resolve()
+
+        os.chdir(path)

anisotropy/openfoam/file.py

@@ -68,7 +68,7 @@ class FoamFile(object):
 
     @property
     def location(self) -> str:
-        return self.header.get("location")
+        return self.header.get("location").replace('"', "")
 
     def __getitem__(self, key):
         return self.content[key]
@@ -136,6 +136,7 @@ class FoamFile(object):
             if self.location else self.object
         )
         path = pathlib.Path(filename).resolve()
+        path.parent.mkdir(parents = True, exist_ok = True)
         conversion.write_foamfile(self.header, self.content, path)
 
     def remove(self, filename: str = None):

anisotropy/solving/__init__.py

@@ -1,3 +1,8 @@
 # -*- coding: utf-8 -*-
 
-from .onephase import OnePhaseFlow
+from .onephase import FlowOnePhase
+
+
+__all__ = [
+    "FlowOnePhase"
+]

anisotropy/solving/onephase.py

@@ -1,19 +1,18 @@
 # -*- coding: utf-8 -*-
 
-import anisotropy.openfoam.presets as F
-import anisotropy.openfoam.runnerPresets as R
-from anisotropy.openfoam import FoamCase, uniform
-from numpy import array
-import logging
+import numpy as np
+
+import anisotropy.openfoam as of
+from anisotropy.openfoam import presets
+from anisotropy.openfoam import commands
 
 
-logger = logging.getLogger(__name__)
-
-
-class OnePhaseFlow(FoamCase):
+class FlowOnePhase:
     def __init__(
         self,
+        path: str = None,
         direction: list[float] = None,
+        patches: dict = None,
         pressureInlet: float = None,
         pressureOutlet: float = None,
         pressureInternal: float = None,
@@ -22,12 +21,15 @@ class OnePhaseFlow(FoamCase):
         velocityInternal: float = None,
         density: float = None,
         viscosityKinematic: float = None,
-        path: str = None,
         **kwargs
     ):
-        FoamCase.__init__(self, path = path)
-
+        
         self.direction = direction 
+        self.patches = patches
+        self.path = path
+        self.case = None
+        self.boundaryNames = ["inlet", "outlet", "symetry", "wall"]
+
         self.pressureInlet = pressureInlet 
         self.pressureOutlet = pressureOutlet 
         self.pressureInternal = pressureInternal 
@@ -37,23 +39,30 @@ class OnePhaseFlow(FoamCase):
         self.density = density 
         self.viscosityKinematic = viscosityKinematic
 
-        controlDict = F.ControlDict()
-        controlDict.update(
+    def controlDict(self) -> of.FoamFile:
+        ff = presets.controlDict()
+        ff.update(
             startFrom = "latestTime",
             endTime = 5000,
             writeInterval = 100,
             runTimeModifiable = "true"
         )
 
-        fvSchemes = F.FvSchemes()
-        
-        fvSolution = F.FvSolution()
-        fvSolution["solvers"]["U"].update(
+        return ff
+
+    def fvSchemes(self) -> of.FoamFile:
+        ff = presets.fvSchemes()
+
+        return ff
+    
+    def fvSolution(self) -> of.FoamFile:    
+        ff = presets.fvSolution()
+        ff["solvers"]["U"].update(
             nSweeps = 2,
             tolerance = 1e-08,
             smoother = "GaussSeidel"
         )
-        fvSolution["solvers"]["Phi"] = dict(
+        ff["solvers"]["Phi"] = dict(
             solver = "GAMG",
             smoother = "DIC",
             cacheAgglomeration = "yes",
@@ -63,87 +72,122 @@ class OnePhaseFlow(FoamCase):
             tolerance = 1e-06,
             relTol = 0.01
         )
-        fvSolution["potentialFlow"] = dict(
+        ff["potentialFlow"] = dict(
             nNonOrthogonalCorrectors = 13,
             PhiRefCell = 0,
             PhiRefPoint = 0,
             PhiRefValue = 0,
             Phi = 0
         )
-        fvSolution["cache"] = { "grad(U)": None }
-        fvSolution["SIMPLE"].update(
+        ff["cache"] = { "grad(U)": None }
+        ff["SIMPLE"].update(
             nNonOrthogonalCorrectors = 6,
             residualControl = dict(
                 p = 1e-05,
                 U = 1e-05
             )
         )
-        fvSolution["relaxationFactors"]["equations"]["U"] = 0.5
+        ff["relaxationFactors"]["equations"]["U"] = 0.5
 
-        transportProperties = F.TransportProperties()
-        transportProperties.update(
+        return ff
+
+    def transportProperties(self) -> of.FoamFile:
+        ff = presets.transportProperties()
+        ff.update(
             nu = self.viscosityKinematic
         )
+
+        return ff
         
-        turbulenceProperties = F.TurbulenceProperties()
-        turbulenceProperties.content = dict(
+    def turbulenceProperties(self) -> of.FoamFile:
+        ff = presets.turbulenceProperties()
+        ff.content = dict(
             simulationType = "laminar"
         )
 
-        boundaries = ["inlet", "outlet", "symetry", "wall"]
-        p = F.P()
-        p["boundaryField"] = {}
-        u = F.U()
-        u["boundaryField"] = {}
+        return ff
 
-        for boundary in boundaries:
+    def p(self) -> of.FoamFile:
+        ff = presets.p()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
             if boundary == "inlet":
-                p["boundaryField"][boundary] = dict(
+                ff["boundaryField"][boundary] = dict(
                     type = "fixedValue",
-                    value = uniform(self.pressureInlet / self.density)
-                )
-                u["boundaryField"][boundary] = dict(
-                    type = "fixedValue",
-                    value = uniform(array(self.direction) * -6e-5)
+                    value = of.utils.uniform(self.pressureInlet / self.density)
                 )
 
             elif boundary == "outlet":
-                p["boundaryField"][boundary] = dict(
+                ff["boundaryField"][boundary] = dict(
                     type = "fixedValue",
-                    value = uniform(self.pressureOutlet / self.density)
+                    value = of.utils.uniform(self.pressureOutlet / self.density)
                 )
-                u["boundaryField"][boundary] = dict(
+
+            else:
+                ff["boundaryField"][boundary] = dict(
+                    type = "zeroGradient"
+                )
+ 
+        return ff
+
+    def U_approx(self) -> of.FoamFile:
+        ff = presets.U()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
+            if boundary == "inlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform(np.array(self.direction) * -6e-5)
+                )
+
+            elif boundary == "outlet":
+                ff["boundaryField"][boundary] = dict(
                     type = "zeroGradient",
                 )
 
             else:
-                p["boundaryField"][boundary] = dict(
-                    type = "zeroGradient"
-                )
-                u["boundaryField"][boundary] = dict(
+                ff["boundaryField"][boundary] = dict(
                     type = "fixedValue",
-                    value = uniform([0, 0, 0])
+                    value = of.utils.uniform([0., 0., 0.])
                 ) 
 
-        self.extend([
-            controlDict, 
-            fvSchemes, 
-            fvSolution,
-            transportProperties, 
-            turbulenceProperties,
-            p, 
-            u
-        ])
-    
-    def createPatches(self, patches: dict):
+        return ff
+
+    def U(self) -> of.FoamFile:
+        ff = presets.U()
+        ff["boundaryField"] = {}
+
+        for boundary in self.boundaryNames:
+            if boundary == "inlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "pressureInletVelocity",
+                    value = of.utils.uniform(self.velocityInlet)
+                )
+
+            elif boundary == "outlet":
+                ff["boundaryField"][boundary] = dict(
+                    type = "zeroGradient",
+                )
+
+            else:
+                ff["boundaryField"][boundary] = dict(
+                    type = "fixedValue",
+                    value = of.utils.uniform([0., 0., 0.])
+                ) 
+
+        return ff
+
+    def createPatchDict(self) -> of.FoamFile:
         # initial 43 unnamed patches ->
-        # 6 named patches (inlet, outlet, wall, symetry0 - 3/5) ->
+        # 6 named patches (inlet, outlet, wall, symetry 0 to 3 or 5) ->
         # 4 inGroups (inlet, outlet, wall, symetry)
 
-        createPatchDict = F.CreatePatchDict()
-        createPatchDict["patches"] = []
+        ff = presets.createPatchDict()
+        ff["patches"] = []
 
-        for name in patches.keys():
+        for name in self.patches.keys():
             if name == "inlet":
                 patchGroup = "inlet"
                 patchType = "patch"
@@ -160,39 +204,60 @@ class OnePhaseFlow(FoamCase):
                 patchGroup = "symetry"
                 patchType = "symetryPlane"
 
-            createPatchDict["patches"].append({
+            ff["patches"].append({
                 "name": name,
                 "patchInfo": {
                     "type": patchType,
                     "inGroups": [patchGroup]
                 },
                 "constructFrom": "patches",
-                "patches": patches[name]
+                "patches": self.patches[name]
             })
 
-        self.append(createPatchDict)
+        return ff
 
-    def build(self) -> tuple[str, str, int]:
-        with self:
-            self.write()
+    def generate(self, approximation: bool = False, meshfile: str = "mesh.mesh"):
 
-            R.netgenNeutralToFoam("mesh.mesh")
-            R.createPatch()
-            R.checkMesh()
-            R.transformPoints({
-                "scale": [1e-5, 1e-5, 1e-5]
-            })
-            R.renumberMesh()
-            # R.potentialFoam()
+        self.case = of.FoamCase(
+            path = self.path,
+            files = [
+                self.controlDict(),
+                self.fvSchemes(),
+                self.fvSolution(),
+                self.transportProperties(), 
+                self.turbulenceProperties(),
+                self.p()
+            ]
+        )
 
-            self.read()
+        if self.patches is not None:
+            self.case += self.createPatchDict()
+        
+        self.case += self.U_approx() if approximation else self.U()
+        
+        self.case.write(self.path)
 
-            self.U["boundaryField"]["inlet"] = dict(
-                type = "pressureInletVelocity",
-                value = uniform(self.velocityInlet)
-            )
-            self.write()
+        self.case.chdir()
 
-            R.simpleFoam()
+        commands.netgenNeutralToFoam(meshfile)
 
-        return "", "", 0
+        # TODO: contain
+        if self.case.contains("createPatchDict"):
+            commands.createPatch()
+
+        commands.checkMesh()
+        commands.transformPoints({
+            "scale": [1e-5, 1e-5, 1e-5]
+        })
+        commands.renumberMesh()
+
+        if approximation:
+            commands.potentialFoam()
+
+            #   replace velocity for the main simulation
+            self.case += self.U()
+            self.case.write(self.path)
+        
+        commands.simpleFoam()
+
+        self.case.chback()

poetry.lock

@@ -104,7 +104,7 @@ python-versions = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.10"
+version = "2.0.11"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -145,11 +145,11 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
 
 [[package]]
 name = "coverage"
-version = "6.2"
+version = "6.3.1"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
@@ -167,7 +167,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "dash"
-version = "2.0.0"
+version = "2.1.0"
 description = "A Python framework for building reactive web-apps. Developed by Plotly."
 category = "main"
 optional = true
@@ -182,12 +182,15 @@ flask-compress = "*"
 plotly = ">=5.0.0"
 
 [package.extras]
-dev = ["dash-flow-example (==0.0.5)", "dash-dangerously-set-inner-html", "mock (==4.0.3)", "flake8 (==3.9.2)", "PyYAML (==5.4.1)", "pylint (==2.10.2)", "black (==21.6b0)", "fire (==0.4.0)", "coloredlogs (==15.0.1)", "flask-talisman (==0.8.1)", "isort (==4.3.21)", "orjson (==3.3.1)", "orjson (==3.6.1)"]
-testing = ["pytest (>=6.0.2)", "pytest-sugar (>=0.9.4)", "pytest-mock (>=3.2.0)", "lxml (>=4.6.2)", "selenium (>=3.141.0)", "percy (>=2.0.2)", "requests[security] (>=2.21.0)", "beautifulsoup4 (>=4.8.2)", "waitress (>=1.4.4)", "diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "redis (>=3.5.3)", "psutil (>=5.8.0)", "celery[redis] (>=5.1.2)", "flaky (>=3.7.0)", "cryptography (<3.4)"]
+celery = ["redis (>=3.5.3)", "celery[redis] (>=5.1.2)"]
+ci = ["black (==21.6b0)", "dash-flow-example (==0.0.5)", "dash-dangerously-set-inner-html", "flake8 (==3.9.2)", "flaky (==3.7.0)", "flask-talisman (==0.8.1)", "mimesis", "mock (==4.0.3)", "numpy", "preconditions", "pylint (==2.10.2)", "pytest-mock (==3.2.0)", "pytest-sugar (==0.9.4)", "isort (==4.3.21)", "orjson (==3.5.4)", "pyarrow (<3)", "pandas (==1.1.5)", "xlrd (<2)", "orjson (==3.6.3)", "pyarrow", "openpyxl", "pandas (>=1.4.0)", "xlrd (>=2.0.1)"]
+dev = ["coloredlogs (>=15.0.1)", "fire (>=0.4.0)", "PyYAML (>=5.4.1)"]
+diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"]
+testing = ["beautifulsoup4 (>=4.8.2)", "lxml (>=4.6.2)", "percy (>=2.0.2)", "pytest (>=6.0.2)", "requests[security] (>=2.21.0)", "selenium (>=3.141.0)", "waitress (>=1.4.4)", "webdriver-manager (>=3.5.1)", "cryptography (<3.4)"]
 
 [[package]]
 name = "dash-bootstrap-components"
-version = "1.0.2"
+version = "1.0.3"
 description = "Bootstrap themed components for use in Plotly Dash"
 category = "main"
 optional = true
@@ -308,14 +311,14 @@ flask = "*"
 
 [[package]]
 name = "fonttools"
-version = "4.28.5"
+version = "4.29.1"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=13.0.0)", "xattr"]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"]
 graphite = ["lz4 (>=1.7.4.2)"]
 interpolatable = ["scipy", "munkres"]
 lxml = ["lxml (>=4.0,<5)"]
@@ -324,16 +327,16 @@ plot = ["matplotlib"]
 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=13.0.0)"]
+unicode = ["unicodedata2 (>=14.0.0)"]
 woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
 
 [[package]]
 name = "frozenlist"
-version = "1.2.0"
+version = "1.3.0"
 description = "A list-like structure which implements collections.abc.MutableSequence"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "graphviz"
@@ -364,6 +367,22 @@ category = "dev"
 optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "importlib-metadata"
+version = "4.10.1"
+description = "Read metadata from Python packages"
+category = "dev"
+optional = true
+python-versions = ">=3.7"
+
+[package.dependencies]
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+perf = ["ipython"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+
 [[package]]
 name = "iniconfig"
 version = "1.1.1"
@@ -439,7 +458,7 @@ python-versions = "*"
 
 [[package]]
 name = "meshio"
-version = "5.2.2"
+version = "5.3.0"
 description = "I/O for many mesh formats"
 category = "main"
 optional = false
@@ -454,15 +473,15 @@ all = ["netcdf4", "h5py"]
 
 [[package]]
 name = "multidict"
-version = "5.2.0"
+version = "6.0.2"
 description = "multidict implementation"
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [[package]]
 name = "numpy"
-version = "1.22.0"
+version = "1.22.2"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -481,24 +500,24 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "pandas"
-version = "1.3.5"
+version = "1.4.0"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
-python-versions = ">=3.7.1"
+python-versions = ">=3.8"
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
+    {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
     {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""},
     {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""},
     {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
 ]
-python-dateutil = ">=2.7.3"
-pytz = ">=2017.3"
+python-dateutil = ">=2.8.1"
+pytz = ">=2020.1"
 
 [package.extras]
-test = ["hypothesis (>=3.58)", "pytest (>=6.0)", "pytest-xdist"]
+test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "pathtools"
@@ -536,7 +555,7 @@ live-view = ["PySide2 (>=5.13,<6.0)"]
 
 [[package]]
 name = "pillow"
-version = "9.0.0"
+version = "9.0.1"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
@@ -544,7 +563,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "plotly"
-version = "5.5.0"
+version = "5.6.0"
 description = "An open-source, interactive data visualization library for Python"
 category = "main"
 optional = true
@@ -633,7 +652,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "pyparsing"
-version = "3.0.6"
+version = "3.0.7"
 description = "Python parsing module"
 category = "main"
 optional = false
@@ -748,7 +767,7 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
 [[package]]
 name = "rich"
-version = "11.0.0"
+version = "11.2.0"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 category = "main"
 optional = false
@@ -764,7 +783,7 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
 
 [[package]]
 name = "setuptools-scm"
-version = "6.3.2"
+version = "6.4.2"
 description = "the blessed package to manage your versions by scm tags"
 category = "main"
 optional = false
@@ -775,7 +794,8 @@ packaging = ">=20.0"
 tomli = ">=1.0.0"
 
 [package.extras]
-toml = ["setuptools (>=42)", "tomli (>=1.0.0)"]
+test = ["pytest (>=6.2)", "virtualenv (>20)"]
+toml = ["setuptools (>=42)"]
 
 [[package]]
 name = "six"
@@ -795,7 +815,7 @@ python-versions = "*"
 
 [[package]]
 name = "sphinx"
-version = "4.3.2"
+version = "4.4.0"
 description = "Python documentation generator"
 category = "dev"
 optional = true
@@ -807,6 +827,7 @@ babel = ">=1.3"
 colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
 docutils = ">=0.14,<0.18"
 imagesize = "*"
+importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.3"
 packaging = "*"
 Pygments = ">=2.0"
@@ -821,7 +842,7 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.920)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"]
+lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "docutils-stubs", "types-typed-ast", "types-requests"]
 test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 
 [[package]]
@@ -942,7 +963,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "tomli"
-version = "2.0.0"
+version = "2.0.1"
 description = "A lil' TOML parser"
 category = "main"
 optional = false
@@ -1002,7 +1023,7 @@ PyYAML = ">=3.10"
 
 [[package]]
 name = "werkzeug"
-version = "2.0.2"
+version = "2.0.3"
 description = "The comprehensive WSGI web application library."
 category = "main"
 optional = true
@@ -1013,7 +1034,7 @@ watchdog = ["watchdog"]
 
 [[package]]
 name = "wslink"
-version = "1.3.1"
+version = "1.4.1"
 description = "Python/JavaScript library for communicating over WebSocket"
 category = "main"
 optional = false
@@ -1034,15 +1055,27 @@ python-versions = ">=3.6"
 idna = ">=2.0"
 multidict = ">=4.0"
 
+[[package]]
+name = "zipp"
+version = "3.7.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "dev"
+optional = true
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [extras]
 analyze = []
 doc = []
-gui = ["dash", "dash-bootstrap-components"]
+gui = ["dash", "dash-bootstrap-components", "dash-vtk"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.9,<3.11"
-content-hash = "d690dac4b444af4dcd5d1c5001ecb445a47d545c93bc91b5a6fd7f88a4a8d994"
+content-hash = "9d38bd5da0ffac15f137cbbb7d4fbb7448aaf88ec77370f5361fa0b1a2e8ae68"
 
 [metadata.files]
 aiohttp = [
@@ -1201,8 +1234,8 @@ certifi = [
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 charset-normalizer = [
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+    {file = "charset-normalizer-2.0.11.tar.gz", hash = "sha256:98398a9d69ee80548c762ba991a4728bfc3836768ed226b3945908d1a688371c"},
+    {file = "charset_normalizer-2.0.11-py3-none-any.whl", hash = "sha256:2842d8f5e82a1f6aa437380934d5e1cd4fcf2003b06fed6940769c164a480a45"},
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@@ -1217,65 +1250,59 @@ commonmark = [
     {file = "commonmark-0.9.1.tar.gz", hash = "sha256:452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60"},
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