FEAT: use 1D path for 3d

.devcontainer/Dockerfile

@@ -1,32 +1,31 @@
 FROM dolfinx/dolfinx:v0.6.0
 
-LABEL org.opencontainers.image.source https://github.com/equinor/warmth
-ARG DEBIAN_FRONTEND=noninteractive
 
 RUN DEBIAN_FRONTEND=noninteractive \
     && apt-get update \ 
-    && apt-get install -y build-essential --no-install-recommends make \
-        ca-certificates \
-        git \
-        libssl-dev \
-        zlib1g-dev \
-        libbz2-dev \
-        libreadline-dev \
-        libsqlite3-dev \
-        wget \
-        curl \
-        llvm \
-        libncurses5-dev \
-        xz-utils \
-        tk-dev \
-        libxml2-dev \
-        libxmlsec1-dev \
-        libffi-dev \
-        liblzma-dev
+    && apt-get install -y curl
+    # build-essential --no-install-recommends make \
+    #     ca-certificates \
+    #     git \
+    #     libssl-dev \
+    #     zlib1g-dev \
+    #     libbz2-dev \
+    #     libreadline-dev \
+    #     libsqlite3-dev \
+    #     wget \
+    #      \
+    #     llvm \
+    #     libncurses5-dev \
+    #     xz-utils \
+    #     tk-dev \
+    #     libxml2-dev \
+    #     libxmlsec1-dev \
+    #     libffi-dev \
+    #     liblzma-dev
 
-RUN useradd  -rm -d /home/vscode -s /bin/bash -g root -G sudo -u 1000 vscode -p ""
-USER vscode
-WORKDIR /home/vscode
-ENV HOME=/home/vscode
+# RUN useradd  -rm -d /home/vscode -s /bin/bash -g root -G sudo -u 1000 vscode -p ""
+# USER vscode
+# WORKDIR /home/vscode
+# ENV HOME=/home/vscode
 ENV PATH="/root/.local/bin:$HOME/.local/bin::$PATH"
 RUN curl -sSL https://install.python-poetry.org | python3 - 

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
 	"name": "warmth dolfinx poetry",
-	"image": "ghcr.io/equinor/warmth:latest",
+	"build": {"dockerfile": "Dockerfile"},
 
 	// 👇 Features to add to the Dev Container. More info: https://containers.dev/implementors/features.
 	// "features": {},
@@ -9,7 +9,7 @@
 	// "forwardPorts": [],
 
 	// 👇 Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "bash .devcontainer/postCreate.sh",
+	"postCreateCommand": "poetry config virtualenvs.create false && poetry env use system && poetry install --with dev --no-interaction",
 
 	// 👇 Configure tool-specific properties.
 	"customizations": {
@@ -27,8 +27,8 @@
 		"features": {
 			"ghcr.io/devcontainers/features/git-lfs:1": {},
 			"ghcr.io/devcontainers/features/docker-in-docker:2": {}
-		}
+		},
 
 	// 👇 Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
+	"remoteUser": "root"
 }

.gitignore

@@ -13,7 +13,7 @@ ehthumbs_vista.db
 
 # Recycle Bin used on file shares
 $RECYCLE.BIN/
-
+simout/
 # Windows Installer files
 *.cab
 *.msi

Dockerfile

@@ -1,32 +1,6 @@
 FROM dolfinx/dolfinx:v0.6.0
 
 LABEL org.opencontainers.image.source https://github.com/equinor/warmth
-ARG DEBIAN_FRONTEND=noninteractive
+WORKDIR /home/warmth
 
-RUN DEBIAN_FRONTEND=noninteractive \
-    && apt-get update \ 
-    && apt-get install -y build-essential --no-install-recommends make \
-        ca-certificates \
-        git \
-        libssl-dev \
-        zlib1g-dev \
-        libbz2-dev \
-        libreadline-dev \
-        libsqlite3-dev \
-        wget \
-        curl \
-        llvm \
-        libncurses5-dev \
-        xz-utils \
-        tk-dev \
-        libxml2-dev \
-        libxmlsec1-dev \
-        libffi-dev \
-        liblzma-dev
-
-RUN useradd  -rm -d /home/vscode -s /bin/bash -g root -G sudo -u 1000 vscode -p ""
-USER vscode
-WORKDIR /home/vscode
-ENV HOME=/home/vscode
-ENV PATH="/root/.local/bin:$HOME/.local/bin::$PATH"
-RUN curl -sSL https://install.python-poetry.org | python3 - 
+ENTRYPOINT pip install . pytest==7.4.2 pytest-cov==4.1.0 && pytest --cov-report=term-missing --cov=warmth tests | tee pytest-coverage.txt 

tests/warmth3d/test_3d.py

@@ -52,14 +52,7 @@ def test_3d_compare():
 
 
 
-    try:
-        os.mkdir('mesh')
-    except FileExistsError:
-        pass
-    try:
-        os.mkdir('temp')
-    except FileExistsError:
-        pass
+
     mm2 = run_3d(model.builder,model.parameters,start_time=model.parameters.time_start,end_time=0, pad_num_nodes=2,writeout=False, base_flux=None)
 
 

warmth/mesh_model.py

@@ -600,8 +600,9 @@ def constructMesh(self):
             cell_data={"layer": [ (np.array(cell_data_layerID, dtype=np.float64)+3)*1e7 + np.array(node_index, dtype=np.float64) ] },
         )
 
-
-        fn = self.modelName+"_mesh.xdmf"
+        p = self._parameters.output_path/ 'mesh'
+        p.mkdir(parents=True, exist_ok=True)
+        fn = p/(self.modelName+"_mesh.xdmf")
 
         mesh.write( fn )
         logger.info(f"saved mesh to {fn}")             
@@ -1358,15 +1359,16 @@ def boundary(x):
 
 
 def run_3d( builder:Builder, parameters:Parameters,  start_time=182, end_time=0, pad_num_nodes=0,
-            out_dir = "out-mapA/",sedimentsOnly=False, writeout=True, base_flux=None):
+            sedimentsOnly=False, writeout=True, base_flux=None):
     builder=interpolate_all_nodes(builder)
     nums = 4
     dt = parameters.myr2s / nums # time step is 1/4 of 1Ma
     mms2 = []
     mms_tti = []
     tti = 0
     # base_flux = 0.0033
-
+    out_dir = parameters.output_path / 'results3d'/'layers'
+    out_dir.mkdir(parents=True, exist_ok=True)
     time_solve = 0.0    
     with Bar('Processing...',check_tty=False, max=(start_time-end_time)) as bar:
         for tti in range(start_time, end_time-1,-1): #start from oldest
@@ -1390,15 +1392,15 @@ def run_3d( builder:Builder, parameters:Parameters,  start_time=182, end_time=0,
                 mm2.useBaseFlux = False
                 mm2.setupSolverAndSolve(n_steps=40, time_step = 314712e8 * 2e2, skip_setup=False)   
                 time_solve = time_solve + toc(msg="setup solver and solve")
-            else:    
+            else:
                 mm2.useBaseFlux = (base_flux is not None)
                 tic()
                 mm2.setupSolverAndSolve( n_steps=nums, time_step=dt, skip_setup=(not rebuild_mesh))
                 time_solve = time_solve + toc(msg="setup solver and solve")
             if (writeout):
                 tic()
-                mm2.writeLayerIDFunction(out_dir+"LayerID-"+str(tti)+".xdmf", tti=tti)
-                mm2.writeTemperatureFunction(out_dir+"Temperature-"+str(tti)+".xdmf", tti=tti)
+                mm2.writeLayerIDFunction(out_dir/f"LayerID-{str(tti)}.xdmf", tti=tti)
+                mm2.writeTemperatureFunction(out_dir+f"Temperature-{str(tti)}.xdmf", tti=tti)
                 # mm2.writeOutputFunctions(out_dir+"test4-"+str(tti)+".xdmf", tti=tti)
                 toc(msg="write function")
 
@@ -1408,7 +1410,9 @@ def run_3d( builder:Builder, parameters:Parameters,  start_time=182, end_time=0,
             bar.next()
     print("total time solve: " , time_solve)
     if (writeout):
-        EPCfilename = mm2.write_hexa_mesh_resqml("temp/")
+        resqml_path= parameters.output_path / 'results3d'/'mesh'
+        resqml_path.mkdir(parents=True, exist_ok=True)
+        EPCfilename = mm2.write_hexa_mesh_resqml(resqml_path)
         print("RESQML model written to: " , EPCfilename)
         read_mesh_resqml_hexa(EPCfilename)  # test reading of the .epc file
     return mm2

warmth/parameters.py

@@ -46,6 +46,7 @@ def __init__(self) -> None:
         self.starting_beta: float = 1.1
         self.positive_down = True
         self.name:str = "model"
+        self.output_path:Path=Path('./simout')
         pass
 
     @property

warmth/simulator.py

@@ -5,6 +5,7 @@
 
 import time
 import numpy as np
+from warmth.parameters import Parameters
 from warmth.postprocessing import Results_interpolator
 from warmth.utils import load_pickle
 from .logging import logger
@@ -23,8 +24,7 @@ def __init__(self, args) -> None:
         self.parameter_path:Path = args[0]
         self.node_path:Path = args[1]
         self.node=load_node(self.node_path)
-        self.parameters = load_pickle(self.parameter_path)
-        self.out_path=args[2]
+        self.parameters:Parameters = load_pickle(self.parameter_path)
         pass
 
     def _pad_sediments(self):
@@ -39,7 +39,7 @@ def _pad_sediments(self):
 
     def _save_results(self) -> Path:
         filename = self.node._name+"_results"
-        filepath = self.out_path / NODES_DIR/filename
+        filepath = self.parameters.output_path / NODES_DIR/filename
         self.node._dump(filepath)
         return filepath
 
@@ -88,19 +88,19 @@ def __init__(self, builder: Builder) -> None:
         self.process = 2
         self.cpu=self.process
         self.simulate_every = 1
-        self.out_path:Path=Path('./simout')
+        self._builder.parameters.output_path:Path=self._builder.parameters.output_path
         pass
 
     @property
     def _nodes_path(self):
-        return self.out_path / NODES_DIR
+        return self._builder.parameters.output_path / NODES_DIR
 
     @property
     def _parameters_path(self):
-        return self.out_path / PARAMETER_FILE
+        return self._builder.parameters.output_path / PARAMETER_FILE
     @property
     def _grid_path(self):
-        return self.out_path / GRID_FILE
+        return self._builder.parameters.output_path / GRID_FILE
 
 
 
@@ -121,17 +121,17 @@ def dump_input_data(self):
             futures = [th.submit(self.dump_input_nodes,  i)
                        for i in self._builder.iter_node() if i is not False]
             for future in concurrent.futures.as_completed(futures):
-                p.append([parameter_data_path, future.result(),self.out_path])
+                p.append([parameter_data_path, future.result()])
         return p
 
     def setup_directory(self, purge=False):
-        if self.out_path.exists():
+        if self._builder.parameters.output_path.exists():
             if purge:
                 from shutil import rmtree
-                rmtree(self.out_path)
+                rmtree(self._builder.parameters.output_path)
             else:
                 raise Exception(
-                    f'Output directory {self.out_path} already exist. Use purge=True to delete existing data')
+                    f'Output directory {self._builder.parameters.output_path} already exist. Use purge=True to delete existing data')
         self._nodes_path.mkdir(parents=True, exist_ok=True)
         return
 
@@ -206,7 +206,7 @@ def _parellel_run(self, save,purge):
                 logger.warning(f"No result file for node X:{n.X}, Y:{n.Y}")
         if save==False:
             from shutil import rmtree
-            rmtree(self.out_path)
+            rmtree(self._builder.parameters.output_path)
         if filtered >0:
             logger.info(f"Interpolating results back to {filtered} partial simulated nodes")
             interp_res= Results_interpolator(self._builder,len(p)-filtered)