Fix: missed viscosity value

Fix: postProcess incorrect log path
Mod: flake8 poetry deps

anisotropy/core/postProcess.py

@@ -16,10 +16,9 @@ class PostProcess(object):
         self.path = path.abspath(dirpath)
 
     def flowRate(self, patch: str):
-        # TODO: fix wrong log path
         func = "patchFlowRate(patch={})".format(patch)
         filepath = path.join(self.path, "postProcessing", func, "0", "surfaceFieldValue.dat")
-        postProcess(func, cwd = self.path)
+        postProcess(func, cwd = self.path, logpath = self.path)
         surfaceFieldValue = datReader(filepath)
 
         return surfaceFieldValue["sum(phi)"][-1]

anisotropy/core/runner.py

@@ -217,12 +217,13 @@ class UltimateRunner(object):
         
     def computeFlow(self):
         params = self.config.params
-        flowParams = self.database.getFlowOnephase(
+        query = (
             params["label"],
             params["direction"],
             params["alpha"],
             self.exec_id
         )
+        flowParams = self.database.getFlowOnephase(*query)
 
         logger.info("Computing flow for {} with direction = {} and alpha = {}".format(
             params["label"], params["direction"], params["alpha"]
@@ -234,9 +235,11 @@ class UltimateRunner(object):
         with self.database:
             flowParams.save()
             
+
+        with self.database:
             self.flow = OnePhaseFlow(
                 direction = params["direction"], 
-                **flowParams.select().dicts().get(), 
+                **self.database.getFlowOnephase(*query, to_dict = True),
                 path = self.casepath()
             )
 

anisotropy/database/db.py

@@ -97,7 +97,7 @@ class Database(SqliteDatabase):
 
         return table
 
-    def getFlowOnephase(self, label = None, direction = None, alpha = None, execution = None, **kwargs):
+    def getFlowOnephase(self, label = None, direction = None, alpha = None, execution = None, to_dict = False, **kwargs):
         execution = execution or self.getLatest()
         query = (
             models.FlowOnephase
@@ -114,6 +114,10 @@ class Database(SqliteDatabase):
         )
 
         with self:
+            if to_dict:
+                table = query.dicts().get() if query.exists() else None
+            
+            else:
                 table = query.get() if query.exists() else None
 
         return table

anisotropy/openfoam/runner.py

@@ -51,6 +51,8 @@ class FoamRunner(object):
             if self.logpath:
                 with proc, open(self.logpath, "w") as io:
                     while True:
+
+
                         output = proc.stdout.read(1)
 
                         if output == "" and proc.poll() is not None:
@@ -59,7 +61,12 @@ class FoamRunner(object):
                         if not output == "":
                             io.write(output)
 
-            self.output, self.error = proc.communicate()
+                    error = proc.stderr.read()
+
+                    if not error == "":
+                        self.error = error
+                        io.write(error)
+
             self.returncode = proc.returncode
 
             if self.logpath and self.error:

poetry.lock

@@ -134,6 +134,19 @@ category = "dev"
 optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[[package]]
+name = "flake8"
+version = "4.0.1"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+mccabe = ">=0.6.0,<0.7.0"
+pycodestyle = ">=2.8.0,<2.9.0"
+pyflakes = ">=2.4.0,<2.5.0"
+
 [[package]]
 name = "fonttools"
 version = "4.28.1"
@@ -241,6 +254,14 @@ pyparsing = ">=2.2.1"
 python-dateutil = ">=2.7"
 setuptools_scm = ">=4"
 
+[[package]]
+name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
+category = "main"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "numpy"
 version = "1.21.4"
@@ -346,7 +367,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 name = "pycodestyle"
 version = "2.8.0"
 description = "Python style guide checker"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
@@ -361,6 +382,14 @@ python-versions = "*"
 [package.dependencies]
 stdlib-list = "*"
 
+[[package]]
+name = "pyflakes"
+version = "2.4.0"
+description = "passive checker of Python programs"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
 [[package]]
 name = "pyfoam"
 version = "2021.6"
@@ -739,7 +768,7 @@ docs = []
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.9,<3.11"
-content-hash = "2c64a48e55f744606cbe36145764db1d47f9c6f48118a961ddc4a8918ef4d78e"
+content-hash = "47b4c70e61dfa848eff69c0edcaaf59db6eac989a4635994ee02ec96a9f05754"
 
 [metadata.files]
 alabaster = [
@@ -842,6 +871,10 @@ docutils = [
     {file = "docutils-0.17.1-py2.py3-none-any.whl", hash = "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61"},
     {file = "docutils-0.17.1.tar.gz", hash = "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125"},
 ]
+flake8 = [
+    {file = "flake8-4.0.1-py2.py3-none-any.whl", hash = "sha256:479b1304f72536a55948cb40a32dce8bb0ffe3501e26eaf292c7e60eb5e0428d"},
+    {file = "flake8-4.0.1.tar.gz", hash = "sha256:806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d"},
+]
 fonttools = [
     {file = "fonttools-4.28.1-py3-none-any.whl", hash = "sha256:68071406009e7ef6a5fdcd85d95975cd6963867bb226f2b786bfffe15d1959ef"},
     {file = "fonttools-4.28.1.zip", hash = "sha256:8c8f84131bf04f3b1dcf99b9763cec35c347164ab6ad006e18d2f99fcab05529"},
@@ -1020,6 +1053,10 @@ matplotlib = [
     {file = "matplotlib-3.5.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:a0ea10faa3bab0714d3a19c7e0921279a68d57552414d6eceaea99f97d7735db"},
     {file = "matplotlib-3.5.0.tar.gz", hash = "sha256:38892a254420d95594285077276162a5e9e9c30b6da08bdc2a4d53331ad9a6fa"},
 ]
+mccabe = [
+    {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
+    {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
+]
 numpy = [
     {file = "numpy-1.21.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8890b3360f345e8360133bc078d2dacc2843b6ee6059b568781b15b97acbe39f"},
     {file = "numpy-1.21.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:69077388c5a4b997442b843dbdc3a85b420fb693ec8e33020bb24d647c164fa5"},
@@ -1151,6 +1188,10 @@ pydeps = [
     {file = "pydeps-1.10.12-py3-none-any.whl", hash = "sha256:32659da82b220a0e4f8f7b2a618d3d590dc6525850df86d10427cc1be0dbe55d"},
     {file = "pydeps-1.10.12.tar.gz", hash = "sha256:712a44a211f47b9b5a1ff6e98e2765ed3fbaf926c194ea6081d4893786c576ec"},
 ]
+pyflakes = [
+    {file = "pyflakes-2.4.0-py2.py3-none-any.whl", hash = "sha256:3bb3a3f256f4b7968c9c788781e4ff07dce46bdf12339dcda61053375426ee2e"},
+    {file = "pyflakes-2.4.0.tar.gz", hash = "sha256:05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c"},
+]
 pyfoam = [
     {file = "PyFoam-2021.6-py2.py3-none-any.whl", hash = "sha256:2f1e3461f03c480060ae6dfba81bbeb5e21d33c64b825666ad4d94cdbd11e674"},
     {file = "PyFoam-2021.6.tar.gz", hash = "sha256:e0513d122b09a32427e817f1a8c14d74db1376bf942a13b505dd029f16cab44e"},

pyproject.toml

@@ -37,9 +37,9 @@ dill = "^0.3.4"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.5"
+flake8 = "^4.0.1"
 vulture = "^2.3"
 pytest-cov = "^3.0.0"
-pycodestyle = "^2.8.0"
 pydeps = {version = "^1.10.12", optional = true}
 peewee-erd = {version = "^0.1.3", optional = true}
 Sphinx = {version = "^4.3.0", optional = true}