diff --git a/anisotropy/core/cli.py b/anisotropy/core/cli.py index 7763db3..548d052 100644 --- a/anisotropy/core/cli.py +++ b/anisotropy/core/cli.py @@ -194,7 +194,7 @@ def compute(path, configFile, nprocs, stage, overwrite, params, verbose, executi for k, v in args.items(): if v is not None: config.update(**{ k: v }) - + if pid: pidpath = os.path.abspath(pid) @@ -206,6 +206,7 @@ def compute(path, configFile, nprocs, stage, overwrite, params, verbose, executi runner.start() os.remove(pidpath) + logger.info("Computation done. Exiting ...") @anisotropy.command() @click.option( diff --git a/anisotropy/core/config.py b/anisotropy/core/config.py index 3535789..106130c 100644 --- a/anisotropy/core/config.py +++ b/anisotropy/core/config.py @@ -104,18 +104,18 @@ class DefaultConfig(Config): def __init__(self): Config.__init__(self) + self.options = { + "nprocs": 1, + "stage": "all", + "overwrite": False, + "database": "anisotropy.db", + "build": "build", + "logs": "logs" + } + self.content = { - "options": { - "nprocs": 1, - "stage": "all", - "overwrite": False, - "database": "anisotropy.db", - "build": "build", - "logs": "logs" - }, "structures": [] } - self.options = deepcopy(self.content["options"]) labels = ["simple", "bodyCentered", "faceCentered"] alphas = [[0.01, 0.28], [0.01, 0.17], [0.01, 0.13]] diff --git a/anisotropy/core/runner.py b/anisotropy/core/runner.py index 988d6fc..33c8a3a 100644 --- a/anisotropy/core/runner.py +++ b/anisotropy/core/runner.py @@ -37,10 +37,13 @@ class UltimateRunner(object): if exec_id: if self.database.getExecution(exec_id): self.exec_id = exec_id + + else: + logger.warning(f"Execution id '{ exec_id }' not found. Creating new.") if not self.exec_id: with self.database: - self.exec_id = T.Execution.create(date=datetime.now()) + self.exec_id = T.Execution.create(date = datetime.now()) # Parameters self.shape = None @@ -50,23 +53,33 @@ class UltimateRunner(object): self.queue = [] + def dispose(self): + self.shape = None + self.mesh = None + self.flow = None + def createRow(self): # create a row in each table for the current case with self.database: shape = self.database.getShape(execution = self.exec_id, **self.config.params) - if not shape: - shape = T.Shape.create(exec_id = self.exec_id, **self.config.params) + if not shape: + shape = T.Shape(exec_id = self.exec_id, **self.config.params) + self.database.csave(shape) + with self.database: mesh = self.database.getMesh(execution = self.exec_id, **self.config.params) - if not mesh: - mesh = T.Mesh.create(shape_id = shape) + if not mesh: + mesh = T.Mesh(shape_id = shape.shape_id) + self.database.csave(mesh) + with self.database: flow = self.database.getFlowOnephase(execution = self.exec_id, **self.config.params) - if not flow: - flow = T.FlowOnephase.create(mesh_id = mesh, **self.config.params) + if not flow: + flow = T.FlowOnephase(mesh_id = mesh.mesh_id, **self.config.params) + self.database.csave(mesh) def fill(self): self.config.expand() @@ -156,9 +169,11 @@ class UltimateRunner(object): logger.error(err) shapeParams.shapeStatus = "failed" - with self.database: - shapeParams.shapeExecutionTime = timer.elapsed() - shapeParams.save() + #with self.database: + shapeParams.shapeExecutionTime = timer.elapsed() + #shapeParams.save() + self.database.csave(shapeParams) + self.dispose() def computeMesh(self): out, err, returncode = "", "", 0 @@ -177,8 +192,8 @@ class UltimateRunner(object): timer = Timer() if not self.shape: - filename = "shape.step" - filepath = path.join(self.casepath(), filename) + shapefile = "shape.step" + filepath = path.join(self.casepath(), shapefile) if not path.exists(filepath) and not path.isfile(filepath): err = f"File not found: { filepath }" @@ -215,7 +230,8 @@ class UltimateRunner(object): with self.database: meshParams.meshExecutionTime = timer.elapsed() meshParams.save() - + self.dispose() + def computeFlow(self): params = self.config.params query = ( @@ -301,6 +317,8 @@ class UltimateRunner(object): with self.database: flowParams.save() + + self.dispose() def pipeline(self, stage: str = None): stage = stage or self.config["stage"] diff --git a/anisotropy/database/db.py b/anisotropy/database/db.py index 6f04d95..d8b9a07 100644 --- a/anisotropy/database/db.py +++ b/anisotropy/database/db.py @@ -3,7 +3,7 @@ # License: GNU GPL version 3, see the file "LICENSE" for details. import os -from peewee import SqliteDatabase, JOIN +from peewee import SqliteDatabase, JOIN, OperationalError from . import models class Database(SqliteDatabase): @@ -42,6 +42,23 @@ class Database(SqliteDatabase): with self: self.create_tables(self.tables) + def csave(self, table, tries: int = 100): + while tries >= 0: + if self.is_closed(): + self.connect() + + try: + table.save() + + except OperationalError as e: + logger.debug(e) + tries -= 1 + time.sleep(1) + + else: + self.close() + break + def getExecution(self, idn): query = models.Execution.select().where(models.Execution.exec_id == idn) diff --git a/anisotropy/gui/runner.py b/anisotropy/gui/runner.py index 68da305..7aa1bea 100644 --- a/anisotropy/gui/runner.py +++ b/anisotropy/gui/runner.py @@ -32,6 +32,9 @@ layout = html.Div([ # Runner html.H2("Runner"), html.Hr(), + html.P("Execution (leave zero for the latest)"), + dcc.Input(id = "execution", type = "number", value = 0, min = 0, style = minWidth), + html.Br(), dbc.Button("Start", id = "start", color = "success", style = minWidth), dbc.Button("Stop", id = "stop", color = "danger", disabled = True, style = minWidth), @@ -56,21 +59,25 @@ layout = html.Div([ @app.callback( Output("start", "active"), [ Input("start", "n_clicks") ], + [ State("execution", "value") ], prevent_initial_call = True ) -def runnerStart(clicks): +def runnerStart(clicks, execution): import subprocess command = [ "anisotropy", "compute", "-v", - "--path", "/tmp/anisotropy", - "--conf", "anisotropy.toml", + "--path", os.environ["ANISOTROPY_CWD"], + "--conf", os.environ["ANISOTROPY_CONF_FILE"], "--pid", "anisotropy.pid", - "--logfile", "anisotropy.log" + "--logfile", os.environ["ANISOTROPY_LOG_FILE"], ] + if execution > 0: + command.extend([ "--exec-id", str(execution) ]) + subprocess.run( command, start_new_session = True, @@ -87,7 +94,7 @@ def runnerStop(clicks): import psutil import signal - pidpath = "/tmp/anisotropy/anisotropy.pid" + pidpath = os.path.join(os.environ["ANISOTROPY_CWD"], "anisotropy.pid") try: pid = int(open(pidpath, "r").read()) @@ -115,7 +122,7 @@ def runnerStop(clicks): def monitorUpdate(intervals): import psutil - pidpath = "/tmp/anisotropy/anisotropy.pid" + pidpath = os.path.join(os.environ["ANISOTROPY_CWD"], "anisotropy.pid") processes = [] try: @@ -146,7 +153,7 @@ def monitorUpdate(intervals): [ Input("interval", "n_intervals") ] ) def logUpdate(intervals): - logpath = "/tmp/anisotropy/anisotropy.log" + logpath = os.path.join(os.environ["ANISOTROPY_CWD"], "anisotropy.log") if os.path.exists(logpath): with open(logpath, "r") as io: @@ -160,10 +167,11 @@ def logUpdate(intervals): @app.callback( Output("delete", "active"), - [ Input("delete", "n_clicks") ] + [ Input("delete", "n_clicks") ], + prevent_initial_call = True ) def logDelete(clicks): - logpath = "/tmp/anisotropy/anisotropy.log" + logpath = os.path.join(os.environ["ANISOTROPY_CWD"], "anisotropy.log") if os.path.exists(logpath): os.remove(logpath) diff --git a/anisotropy/meshing/mesh.py b/anisotropy/meshing/mesh.py index c20a37b..47492dc 100644 --- a/anisotropy/meshing/mesh.py +++ b/anisotropy/meshing/mesh.py @@ -67,7 +67,7 @@ class Mesh(object): self.mesh.Export(filename, "Neutral Format") else: - raise NotImplementedError(f"{ ext } is not supported") + raise NotImplementedError(f"Mesh format '{ ext }' is not supported") except NotImplementedError as e: err = e diff --git a/anisotropy/shaping/shape.py b/anisotropy/shaping/shape.py index 963ace0..0c0a2d2 100644 --- a/anisotropy/shaping/shape.py +++ b/anisotropy/shaping/shape.py @@ -55,7 +55,7 @@ class Shape(object): self.shape = OCCGeometry(filename).shape else: - raise NotImplementedError(f"{ext} is not supported") + raise NotImplementedError(f"Shape format '{ext}' is not supported") def normal(self, face: FACE) -> numpy.array: """ diff --git a/poetry.lock b/poetry.lock index 4a61dd9..847e38d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -24,17 +24,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.2.0" +version = "21.4.0" description = "Classes Without Boilerplate" category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] [[package]] name = "babel" @@ -47,6 +47,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [package.dependencies] pytz = ">=2015.7" +[[package]] +name = "brotli" +version = "1.0.9" +description = "Python bindings for the Brotli compression library" +category = "main" +optional = true +python-versions = "*" + [[package]] name = "certifi" version = "2021.10.8" @@ -57,7 +65,7 @@ python-versions = "*" [[package]] name = "charset-normalizer" -version = "2.0.7" +version = "2.0.10" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = true @@ -107,6 +115,64 @@ category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "dash" +version = "2.0.0" +description = "A Python framework for building reactive web-apps. Developed by Plotly." +category = "main" +optional = true +python-versions = ">=3.6" + +[package.dependencies] +dash-core-components = "2.0.0" +dash-html-components = "2.0.0" +dash-table = "5.0.0" +Flask = ">=1.0.4" +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)"] + +[[package]] +name = "dash-bootstrap-components" +version = "1.0.2" +description = "Bootstrap themed components for use in Plotly Dash" +category = "main" +optional = true +python-versions = ">=3.6, <4" + +[package.dependencies] +dash = ">=2.0.0" + +[package.extras] +pandas = ["numpy", "pandas"] + +[[package]] +name = "dash-core-components" +version = "2.0.0" +description = "Core component suite for Dash" +category = "main" +optional = true +python-versions = "*" + +[[package]] +name = "dash-html-components" +version = "2.0.0" +description = "Vanilla HTML components for Dash" +category = "main" +optional = true +python-versions = "*" + +[[package]] +name = "dash-table" +version = "5.0.0" +description = "Dash table" +category = "main" +optional = true +python-versions = "*" + [[package]] name = "dill" version = "0.3.4" @@ -147,9 +213,40 @@ mccabe = ">=0.6.0,<0.7.0" pycodestyle = ">=2.8.0,<2.9.0" pyflakes = ">=2.4.0,<2.5.0" +[[package]] +name = "flask" +version = "1.1.2" +description = "A simple framework for building complex web applications." +category = "main" +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[package.dependencies] +click = ">=5.1" +itsdangerous = ">=0.24" +Jinja2 = ">=2.10.1" +Werkzeug = ">=0.15" + +[package.extras] +dev = ["pytest", "coverage", "tox", "sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] +docs = ["sphinx", "pallets-sphinx-themes", "sphinxcontrib-log-cabinet", "sphinx-issues"] +dotenv = ["python-dotenv"] + +[[package]] +name = "flask-compress" +version = "1.10.1" +description = "Compress responses in your Flask app with gzip, deflate or brotli." +category = "main" +optional = true +python-versions = "*" + +[package.dependencies] +brotli = "*" +flask = "*" + [[package]] name = "fonttools" -version = "4.28.1" +version = "4.28.5" description = "Tools to manipulate font files" category = "main" optional = false @@ -205,11 +302,19 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "itsdangerous" +version = "2.0.1" +description = "Safely pass data to untrusted environments and back." +category = "main" +optional = true +python-versions = ">=3.6" + [[package]] name = "jinja2" version = "2.11.3" description = "A very fast and expressive template engine." -category = "dev" +category = "main" optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" @@ -231,13 +336,13 @@ python-versions = ">=3.7" name = "markupsafe" version = "2.0.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "dev" +category = "main" optional = true python-versions = ">=3.6" [[package]] name = "matplotlib" -version = "3.5.0" +version = "3.5.1" description = "Python plotting package" category = "main" optional = false @@ -264,26 +369,26 @@ python-versions = "*" [[package]] name = "numpy" -version = "1.21.4" +version = "1.22.0" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false -python-versions = ">=3.7,<3.11" +python-versions = ">=3.8" [[package]] name = "packaging" -version = "21.2" +version = "21.3" description = "Core utilities for Python packages" category = "main" optional = false python-versions = ">=3.6" [package.dependencies] -pyparsing = ">=2.0.2,<3" +pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.3.4" +version = "1.3.5" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -338,22 +443,35 @@ live-view = ["PySide2 (>=5.13,<6.0)"] [[package]] name = "pillow" -version = "8.4.0" +version = "9.0.0" description = "Python Imaging Library (Fork)" category = "main" optional = false +python-versions = ">=3.7" + +[[package]] +name = "plotly" +version = "5.5.0" +description = "An open-source, interactive data visualization library for Python" +category = "main" +optional = true python-versions = ">=3.6" +[package.dependencies] +six = "*" +tenacity = ">=6.2.0" + [[package]] name = "pluggy" -version = "0.13.1" +version = "1.0.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=3.6" [package.extras] dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "psutil" @@ -414,7 +532,7 @@ numpy = "*" [[package]] name = "pygments" -version = "2.10.0" +version = "2.11.2" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = true @@ -422,11 +540,14 @@ python-versions = ">=3.5" [[package]] name = "pyparsing" -version = "2.4.7" +version = "3.0.6" description = "Python parsing module" category = "main" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +python-versions = ">=3.6" + +[package.extras] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" @@ -516,7 +637,7 @@ python-versions = ">=3.6" [[package]] name = "requests" -version = "2.26.0" +version = "2.27.1" description = "Python HTTP for Humans." category = "dev" optional = true @@ -565,7 +686,7 @@ python-versions = "*" [[package]] name = "sphinx" -version = "4.3.0" +version = "4.3.2" description = "Python documentation generator" category = "dev" optional = true @@ -591,7 +712,7 @@ sphinxcontrib-serializinghtml = ">=1.1.5" [package.extras] docs = ["sphinxcontrib-websupport"] -lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.900)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"] +lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.920)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"] test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] [[package]] @@ -691,6 +812,17 @@ python-versions = "*" [package.extras] develop = ["sphinx"] +[[package]] +name = "tenacity" +version = "8.0.1" +description = "Retry code until it succeeds" +category = "main" +optional = true +python-versions = ">=3.6" + +[package.extras] +doc = ["reno", "sphinx", "tornado (>=4.5)"] + [[package]] name = "toml" version = "0.10.2" @@ -701,15 +833,15 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" [[package]] name = "tomli" -version = "1.2.2" +version = "2.0.0" description = "A lil' TOML parser" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [[package]] name = "urllib3" -version = "1.26.7" +version = "1.26.8" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" optional = true @@ -744,15 +876,26 @@ argh = ">=0.24.1" pathtools = ">=0.1.1" PyYAML = ">=3.10" +[[package]] +name = "werkzeug" +version = "2.0.2" +description = "The comprehensive WSGI web application library." +category = "main" +optional = true +python-versions = ">=3.6" + +[package.extras] +watchdog = ["watchdog"] + [extras] analyze = [] doc = [] -gui 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optional = true, extras = ["gui"]} +dash-bootstrap-components = {version = "^1.0.2", optional = true, extras = ["gui"]} [tool.poetry.dev-dependencies] pytest = "^6.2.5"