Mod: desc, docs, some fixes

anisotropy/__init__.py

@@ -7,7 +7,7 @@
 
 __license__ = "GPL3"
 __version__ = "1.1.0"
-__author__ = __maintainer = "George Kusayko"
+__author__ = __maintainer__ = "George Kusayko"
 __email__ = "gkusayko@gmail.com"
 
 ###

anisotropy/config/default.toml

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 [logger]
 name = "anisotropy"
 format = "[ %(levelname)s ] %(message)s"

anisotropy/core/__init__.py

@@ -0,0 +1,5 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
+

anisotropy/core/cli.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import click
 import ast
 
@@ -41,7 +45,6 @@ class KeyValueOption(click.Option):
             return self._convert(ctx, value)
 
         
-#pass_anisotropy = click.make_pass_decorator(Anisotropy)
 def version():
     msg = "Missed package anisotropy"
 
@@ -59,11 +62,34 @@ def version():
 def anisotropy():
     pass
 
-@anisotropy.command()
+@anisotropy.command(
-@click.option("-s", "--stage", "stage", type = click.Choice(["all", "mesh", "flow"]), default = "all")
+    help = """Computes cases by chain (mesh -> flow)
-@click.option("-p", "--param", "params", metavar = "key=value", multiple = True, cls = KeyValueOption)
+    
-def compute(stage, params):
+    Control parameters: type, direction, theta (each parameter affects on a queue)
+    """
+)
+@click.option(
+    "-s", "--stage", "stage", 
+    type = click.Choice(["all", "mesh", "flow"]), 
+    default = "all",
+    help = "Current computation stage"
+)
+@click.option(
+    "-P", "--parallel", "parallel",
+    type = click.INT,
+    default = 1,
+    help = "Count of parallel processes"
+)
+@click.option(
+    "-p", "--param", "params", 
+    metavar = "key=value", 
+    multiple = True, 
+    cls = KeyValueOption,
+    help = "Overwrite existing parameter (except control variables)"
+)
+def compute(stage, parallel, params):
     from anisotropy.core.main import Anisotropy, logger
+    from anisotropy.core.utils import timer
 
     args = dict()
 
@@ -82,6 +108,7 @@ def compute(stage, params):
 
     type, direction, theta = args["type"], args["direction"], args["theta"]
     
+    
     model.load(type, direction, theta)
     # TODO: merge cli params with db params here 
     model.evalParams()
@@ -90,17 +117,21 @@ def compute(stage, params):
     # TODO: single compute / queue
     
     if stage == "all" or stage == "mesh":
-        ((out, err, code), elapsed) = model.computeMesh(type, direction, theta)
+        ((out, err, code), elapsed) = timer(model.computeMesh)()
 
         if out: click.echo(out)
         if err: click.echo(err)
+
         if model.params.get("meshresult"):
             model.load(type, direction, theta)
             model.params["meshresult"]["calculationTime"] = elapsed
             model.update()
 
     if stage == "all" or stage == "flow":
-        ((out, err, code), elapsed) = model.computeFlow(type, direction, theta)
+        ((out, err, code), elapsed) = timer(model.computeFlow)()
+
+        if out: click.echo(out)
+        if err: click.echo(err)
 
         if model.params.get("flowresult"):
             model.load(type, direction, theta)
@@ -108,13 +139,15 @@ def compute(stage, params):
             model.update()
 
 
-@anisotropy.command()
+@anisotropy.command(
+    help = "! Not a user command"
+)
 @click.argument("root")
 @click.argument("type")
 @click.argument("direction")
 @click.argument("theta")
 def computemesh(root, type, direction, theta):
-    # ISSUE: can't hide command from help, hidden = True doesn't work
+    # ISSUE: can't hide command from help, 'hidden = True' doesn't work
     # [Salome Environment]
     
     ###

anisotropy/core/database.py

@@ -45,6 +45,11 @@ class Database(object):
 
 
     def isempty(self) -> bool:
+        """Checks DB for main table existence (Structure)
+
+        :return: True if exists
+        :rtype: bool
+        """
         query = Structure.select()
 
         return not query.exists()
@@ -96,6 +101,8 @@ class Database(object):
 
                     if flowresultsQuery.exists():
                         params["flowresult"] = flowresultsQuery.dicts().get()
+            else:
+                logger.error("Missed Structure table")
 
         return params
 

anisotropy/core/main.py

@@ -32,7 +32,7 @@ peeweeLogger.setLevel(logging.INFO)
 
 
 class Anisotropy(object):
-    """Ultimate class that organize whole working process"""
+    """Ultimate class that organizes whole working process"""
 
     def __init__(self):
         """Constructor method"""
@@ -43,10 +43,18 @@ class Anisotropy(object):
 
 
     def load(self, structure_type: str, structure_direction: list, structure_theta: float):
+        """Shortcut for `Database.setup` and `Database.load`. 
+
+        See :class:`anisotropy.core.database.Database` for more details.
+        """
         self.db.setup()
         self.params = self.db.load(structure_type, structure_direction, structure_theta)
 
     def update(self, params: dict = None):
+        """Shortcut for `Database.setup` and `Database.update`. 
+
+        See :class:`anisotropy.core.database.Database` for more details.
+        """
         self.db.setup()
         self.db.update(self.params if not params else params)
 
@@ -124,7 +132,7 @@ class Anisotropy(object):
                         "flowapprox": deepcopy(entry["flowapprox"])
                     }
 
-                    # For type = fixedValue only
+                    # For `type = fixedValue` only
                     _velocity = entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"]
                     entryNew["flowapprox"]["velocity"]["boundaryField"]["inlet"]["value"] = [ 
                         val * _velocity for val in entryNew["structure"]["direction"] 
@@ -190,7 +198,6 @@ class Anisotropy(object):
             fillets = delta - Cf * (radius - r0)
 
         self.params["structure"].update(
-            #**structure,
             L = L,
             r0 = r0,
             radius = radius,
@@ -198,7 +205,7 @@ class Anisotropy(object):
         )
 
     def getCasePath(self) -> str:
-        """Constructs case path from main control parameters
+        """Constructs case path from control parameters
         
         :return: Absolute path to case
         :rtype: str
@@ -217,20 +224,31 @@ class Anisotropy(object):
         )
 
 
-    @timer
+    def computeMesh(self):
-    def computeMesh(self, type, direction, theta):
+        """Computes a mesh on shape via Salome
+
+        :return: Process output, error messages and returncode
+        :rtype: tuple(str, str, int)
+        """
         scriptpath = os.path.join(self.env["ROOT"], "anisotropy/core/cli.py")
         port = 2900
 
+        p = self.params["structure"]
+
         return salomepl.utils.runSalome(
             self.env["salome_port"], 
             scriptpath, 
             self.env["ROOT"],
-            "computemesh", type, direction, theta,
+            "computemesh", 
+            p["type"], p["direction"], p["theta"],
             logpath = os.path.join(self.env["LOG"], "salome.log")
         )
 
     def genmesh(self):
+        """Computes a mesh on shape
+
+        Warning: Working only inside Salome Environment
+        """
         # ISSUE: double logger output
 
         import salome 
@@ -309,7 +327,12 @@ class Anisotropy(object):
 
 
         self.update()
-        returncode, errors = mesh.compute()
+        out, err, returncode = mesh.compute()
+
+        ###
+        #   Results
+        ##
+        p["meshresult"] = dict()
 
         if not returncode:
             mesh.removePyramids()
@@ -320,7 +343,8 @@ class Anisotropy(object):
             mesh.exportUNV(os.path.join(casePath, "mesh.unv"))
 
             meshStats = mesh.stats()
-            p["meshresult"] = dict(
+            p["meshresult"].update(
+                status = "Done",
                 surfaceArea = surfaceArea,
                 volume = volume,
                 **meshStats
@@ -334,7 +358,8 @@ class Anisotropy(object):
         else:
             logger.error(errors)
 
-            p["meshresult"] = dict(
+            p["meshresult"].update(
+                status = "Failed",
                 surfaceArea = surfaceArea,
                 volume = volume
             )
@@ -342,8 +367,13 @@ class Anisotropy(object):
 
         salome.salome_close()
 
-    @timer
+
-    def computeFlow(self, type, direction, theta):
+    def computeFlow(self):
+        """Computes a flow on mesh via OpenFOAM
+
+        :return: Process output, error messages and returncode
+        :rtype: tuple(str, str, int)
+        """
         ###
         #   Case preparation
         ##
@@ -468,20 +498,29 @@ class Anisotropy(object):
             logger.info(out)
 
         ###
-        #   Check results
+        #   Results
         ##
+        self.params["flowresult"] = dict()
 
-        if returncode == 0:
+        if not returncode:
             postProcessing = "postProcessing/flowRatePatch(name=outlet)/0/surfaceFieldValue.dat"
 
             with open(os.path.join(casePath, postProcessing), "r") as io:
                 lastLine = io.readlines()[-1]
                 flowRate = float(lastLine.replace(" ", "").replace("\n", "").split("\t")[1])
                 
-            self.params["flowresult"] = dict(
+            self.params["flowresult"].update(
+                status = "Done",
                 flowRate = flowRate
             )
 
+        else:
+            self.params["flowresult"].update(
+                status = "Failed",
+                flowRate = flowRate
+            )
+
+
         self.update()
 
         os.chdir(self.env["ROOT"])
@@ -489,10 +528,3 @@ class Anisotropy(object):
         return out, err, returncode
 
     
-    def _queue(self):
-        pass
-
-    def computeAll(self):
-        pass
-
-

anisotropy/core/models.py

@@ -139,6 +139,7 @@ class MeshResult(BaseModel):
     prisms = IntegerField(null = True)
     pyramids = IntegerField(null = True)
 
+    status = TextField(null = True, default = "Idle")
     calculationTime = TimeField(null = True)
 
 class Flow(BaseModel):
@@ -164,4 +165,6 @@ class FlowResult(BaseModel):
     flow_id = ForeignKeyField(Flow, backref = "flowresults")
 
     flowRate = FloatField(null = True)
+
+    status = TextField(null = True, default = "Idle")
     calculationTime = TimeField(null = True)

anisotropy/core/utils.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import logging
 
 from multiprocessing import Queue, Process, cpu_count

anisotropy/openfoam/__init__.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 
 from .meshConversion import ideasUnvToFoam
 from .meshManipulation import createPatch, transformPoints, checkMesh, renumberMesh

anisotropy/openfoam/application.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import os, sys
 import subprocess
 

anisotropy/openfoam/meshConversion.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from .application import application
 
 def ideasUnvToFoam(mesh: str, case: str = None) -> (str, int):

anisotropy/openfoam/meshManipulation.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from .application import application
 
 import re

anisotropy/openfoam/miscellaneous.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from .application import application
 
 def foamDictionary(filepath: str, entry: str, value: str = None, case: str = None):

anisotropy/openfoam/parallelProcessing.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from .application import application
 
 def decomposePar(case: str = None):

anisotropy/openfoam/solvers.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from .application import application
 
 import re 

anisotropy/openfoam/utils.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import os
 import shutil
 

anisotropy/salomepl/__init__.py

@@ -1,4 +1,5 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
 
 

anisotropy/salomepl/geometry.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import logging
 
 logger = logging.getLogger("anisotropy")

anisotropy/salomepl/mesh.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 import logging
 
 logger = logging.getLogger("anisotropy")
@@ -113,9 +117,9 @@ class Mesh(object):
     def compute(self):
         isDone = self.mesh.Compute()
         returncode = int(not isDone)
-        errors = self.mesh.GetComputeErrors()
+        err = self.mesh.GetComputeErrors()
 
-        return returncode, errors
+        return "", err, returncode
 
     def stats(self):
         return {

anisotropy/salomepl/utils.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 #import salome
 import subprocess
 import logging

anisotropy/samples/__init__.py

@@ -1,5 +1,6 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
 
 from anisotropy.samples.simple import Simple
 from anisotropy.samples.bodyCentered import BodyCentered

anisotropy/samples/bodyCentered.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from math import pi, sqrt
 from anisotropy.salomepl import geometry
 

anisotropy/samples/faceCentered.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from math import pi, sqrt
 from anisotropy.salomepl import geometry
 

anisotropy/samples/simple.py

@@ -1,3 +1,7 @@
+# -*- coding: utf-8 -*-
+# This file is part of anisotropy.
+# License: GNU GPL version 3, see the file "LICENSE" for details.
+
 from math import pi, sqrt
 from anisotropy.salomepl import geometry
 

docs/source/anisotropy.core.rst

@@ -12,6 +12,14 @@ anisotropy.core.cli module
    :undoc-members:
    :show-inheritance:
 
+anisotropy.core.database module
+-------------------------------
+
+.. automodule:: anisotropy.core.database
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 anisotropy.core.main module
 ---------------------------
 

docs/source/modules.rst

@@ -6,3 +6,4 @@ anisotropy
 
    anisotropy
    setup
+   tests

docs/source/tests.rst

@@ -0,0 +1,29 @@
+tests package
+=============
+
+Submodules
+----------
+
+tests.anisotropy\-cli module
+----------------------------
+
+.. automodule:: tests.anisotropy-cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tests.test\_anisotropy module
+-----------------------------
+
+.. automodule:: tests.test_anisotropy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tests
+   :members:
+   :undoc-members:
+   :show-inheritance: