Merge pull request #2 from BAMresearch/v0.2_annika

V0.2 annika

.github/workflows/usecase.yml

@@ -0,0 +1,80 @@
+# This workflow will install the environment, run the usecase param_wall
+name: tests
+
+on:
+  push:
+    branches-ignore:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  CACHE_NUMBER: 1 # increase to reset cache manually
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            activate-environment: amworkflow
+            use-mamba: true
+
+      - name: Set cache date
+        run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
+
+      - uses: actions/cache@v2
+        with:
+          path: "/usr/share/miniconda3/envs/amworkflow"
+          key: conda-${{ hashFiles('environment.yaml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
+        id: cache
+
+      - name: Update environment
+        run: mamba env update -n amworkflow -f environment.yaml
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Install package
+        run: git clone https://github.com/tpaviot/pythonocc-utils.git && pip install ./pythonocc-utils
+
+      - name: Run param_wall
+        shell: bash -l {0} #new shell
+        run: |
+          python usecases/param_wall/param_wall.py
+
+
+
+
+#name: Test
+#
+#on: [push]
+#
+#jobs:
+#  # Run tests
+#  test_model:
+#    name: Run tests
+#    runs-on: ${{ matrix.operating-system }}
+#    strategy:
+#      matrix:
+#        operating-system: [ubuntu-latest]
+#    steps:
+#    - uses: actions/checkout@v2
+#    - uses: conda-incubator/setup-miniconda@v2
+#      with:
+#        channels: conda-forge
+#        channel-priority: strict
+#        auto-update-conda: true
+#        environment-file: environment.yaml
+#
+#    - name: Install package
+#      run: git clone https://github.com/tpaviot/pythonocc-utils.git && pip install ./pythonocc-utils
+#
+#    - name: Run param_wall
+#      shell: bash -l {0} #new shell
+#      run: |
+#        python usecases/param_wall/param_wall.py

amworkflow/src/constants/data_model.py

@@ -1,8 +1,8 @@
 from pydantic import BaseModel, ValidationError, NegativeInt, PositiveInt, conint, conlist, constr, PositiveFloat, validator
 from typing import Optional
 from polyfactory.factories.pydantic_factory import ModelFactory
-from src.utils.parser import yaml_parser
-from src.constants.enums import Directory as D
+from amworkflow.src.utils.parser import yaml_parser
+from amworkflow.src.constants.enums import Directory as D
 class BatchParameter(BaseModel):
     isbatch: bool
 

amworkflow/src/core/workflow.py

@@ -1,18 +1,18 @@
 from OCC.Core.TopoDS import TopoDS_Shape
 import yaml
-from src.constants.enums import Directory as D
-from src.constants.data_model import WallParam, DB_WallGeometryFile, DB_XdmfFile, DB_H5File
-from src.utils.parser import yaml_parser
+from amworkflow.src.constants.enums import Directory as D
+from amworkflow.src.constants.data_model import WallParam, DB_WallGeometryFile, DB_XdmfFile, DB_H5File
+from amworkflow.src.utils.parser import yaml_parser
 import gmsh
-from src.infrastructure.database.models.model import XdmfFile, H5File, FEResult, SliceFile, GCode
-from src.infrastructure.database.cruds.crud import insert_data
-from src.geometries.mesher import mesher, get_geom_pointer
-from src.utils.writer import mesh_writer
-from src.utils.permutator import simple_permutator
-from src.utils.writer import namer, stl_writer, batch_num_creator
-from tests.test import dimension_check
+from amworkflow.src.infrastructure.database.models.model import XdmfFile, H5File, FEResult, SliceFile, GCode
+from amworkflow.src.infrastructure.database.cruds.crud import insert_data
+from amworkflow.src.geometries.mesher import mesher, get_geom_pointer
+from amworkflow.src.utils.writer import mesh_writer
+from amworkflow.src.utils.permutator import simple_permutator
+from amworkflow.src.utils.writer import namer, stl_writer, batch_num_creator
+from amworkflow.tests.test import dimension_check
 import numpy as np
-from src.utils.download import downloader
+from amworkflow.src.utils.download import downloader
 import copy
 
 class BaseWorkflow(object):

amworkflow/src/geometries/mesher.py

@@ -1,8 +1,8 @@
 import gmsh
 import math as m
 from OCC.Core.TopoDS import TopoDS_Shape
-from src.geometries.operator import split
-from src.geometries.operator import get_occ_bounding_box
+from amworkflow.src.geometries.operator import split
+from amworkflow.src.geometries.operator import get_occ_bounding_box
 import logging
 
 def get_geom_pointer(model: gmsh.model, shape: TopoDS_Shape) -> None:

amworkflow/src/geometries/operator.py

@@ -9,7 +9,7 @@
 from OCCUtils.Topology  import Topo
 from OCCUtils.Construct import make_face
 from OCCUtils.Construct import vec_to_dir
-from src.geometries.builder import geometry_builder
+from amworkflow.src.geometries.builder import geometry_builder
 from OCC.Core.BRepBndLib import brepbndlib_Add
 from OCC.Core.Bnd import Bnd_Box
 

amworkflow/src/geometries/simple_geometry.py

@@ -3,8 +3,8 @@
 from OCC.Core.gp import gp_Pnt, gp_Vec, gp_Ax2, gp_Dir
 from OCC.Core.BRepBuilderAPI import BRepBuilderAPI_MakeEdge, BRepBuilderAPI_MakeWire, BRepBuilderAPI_MakeFace, BRepBuilderAPI_Sewing, BRepBuilderAPI_MakeSolid, BRepBuilderAPI_MakeShell, brepbuilderapi_Precision
 from OCC.Core.BRepPrimAPI import BRepPrimAPI_MakePrism, BRepPrimAPI_MakeCylinder
-from src.geometries.operator import geom_copy, translate, reverse
-from src.geometries.builder import geometry_builder
+from amworkflow.src.geometries.operator import geom_copy, translate, reverse
+from amworkflow.src.geometries.builder import geometry_builder
 
 from OCC.Core.GC import GC_MakeArcOfCircle
 import math as m

amworkflow/src/infrastructure/database/Engine/engine.py

@@ -1,4 +1,4 @@
-from src.infrastructure.database.models.model import engine, Base
+from amworkflow.src.infrastructure.database.models.model import engine, Base
 from sqlalchemy.orm import Session
 
 Base.metadata.create_all(engine)

amworkflow/src/infrastructure/database/cruds/crud.py

@@ -1,5 +1,5 @@
 from uuid import uuid4
-from src.infrastructure.database.Engine.engine import session
+from amworkflow.src.infrastructure.database.Engine.engine import session
 from sqlalchemy import insert
 from sqlalchemy.sql.expression import select
 

amworkflow/src/infrastructure/database/models/model.py

@@ -1,13 +1,13 @@
 from sqlalchemy import create_engine
-from src.constants.enums import Directory as D
+from amworkflow.src.constants.enums import Directory as D
 engine = create_engine("sqlite+pysqlite:////" + D.DATABASE_FILE_PATH.value + r'amworkflow.db', echo=True)
 
 from typing import List
 from typing import Optional
 from sqlalchemy import ForeignKey
 from sqlalchemy import String
 from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
-from src.constants.enums import Timestamp as T
+from amworkflow.src.constants.enums import Timestamp as T
 from datetime import datetime
 class Base(DeclarativeBase):
     pass

amworkflow/src/interface/main_window.py

@@ -3,7 +3,7 @@
 from PyQt5.QtGui import QFont, QIcon
 from OCC.Display.backend import load_backend
 load_backend('qt-pyqt5')
-from src.geometries.simple_geometry import create_box, create_prism
+from amworkflow.src.geometries.simple_geometry import create_box, create_prism
 from OCC.Display.qtDisplay import qtViewer3d
 from OCC.Core.AIS import AIS_Shape, AIS_InteractiveObject
 

amworkflow/src/utils/db_calib.py

@@ -1,8 +1,8 @@
 import os
-from src.infrastructure.database.cruds.crud import query_multi_data, delete_data
-from src.infrastructure.database.models import model
+from amworkflow.src.infrastructure.database.cruds.crud import query_multi_data, delete_data
+from amworkflow.src.infrastructure.database.models import model
 import inspect
-from src.constants.enums import InputFormat, Directory
+from amworkflow.src.constants.enums import InputFormat, Directory
 
 def db_calib():
     tables = [model.GeometryFile]

amworkflow/src/utils/download.py

@@ -1,6 +1,6 @@
-from src.infrastructure.database.cruds.crud import _query_data, query_multi_data
-from src.infrastructure.database.models.model import GeometryFile, XdmfFile, H5File
-from src.constants.enums import Directory as D
+from amworkflow.src.infrastructure.database.cruds.crud import _query_data, query_multi_data
+from amworkflow.src.infrastructure.database.models.model import GeometryFile, XdmfFile, H5File
+from amworkflow.src.constants.enums import Directory as D
 import shutil
 import os
 

amworkflow/src/utils/parser.py

@@ -1,7 +1,7 @@
 import yaml
 import os
 import logging
-from src.constants.enums import Directory as D
+from amworkflow.src.constants.enums import Directory as D
 import numpy as np
 import flatdict
 import ruamel.yaml

amworkflow/src/utils/sanity_check.py

@@ -1,10 +1,10 @@
-from src.constants.enums import Mapper as M
-from src.constants.exceptions import DimensionViolationException
+from amworkflow.src.constants.enums import Mapper as M
+from amworkflow.src.constants.exceptions import DimensionViolationException
 import numpy as np
 
 def import_freecad_check():
     import sys
-    from src.constants.enums import Directory
+    from amworkflow.src.constants.enums import Directory
     freecad_path = Directory.SYS_PATH.value + Directory.FREECAD_PATH.value
     sys.path.append(freecad_path)
     try:

amworkflow/src/utils/writer.py

@@ -5,10 +5,10 @@
 import copy
 from OCC.Core.StlAPI import StlAPI_Writer
 from OCC.Extend.DataExchange import write_stl_file, write_step_file, read_stl_file
-from tests.test import path_append_check
+from amworkflow.tests.test import path_append_check
 path_append_check()
-from src.constants.enums import Directory
-from src.constants.enums import Timestamp as T
+from amworkflow.src.constants.enums import Directory
+from amworkflow.src.constants.enums import Timestamp as T
 from datetime import datetime
 import numpy as np
 import gmsh

amworkflow/tests/test.py

@@ -1,4 +1,4 @@
-from src.constants.exceptions import DimensionViolationException
+from amworkflow.src.constants.exceptions import DimensionViolationException
 
 
 def dimension_check(dm_list: list):

dodo.py

@@ -1,7 +1,7 @@
 from doit.action import CmdAction
-import amworkflow.src.core.create_geometry as cg
-import amworkflow.src.constants.enums as e
-from amworkflow.src.utils.db_calib import db_calib
+import amworkflow.amworkflow.src.core.create_geometry as cg
+import amworkflow.amworkflow.src.constants.enums as e
+from amworkflow.amworkflow.src.utils.db_calib import db_calib
 # Define actions here
 def environment_init() -> bool:
     import  sys, os

environment.yaml

@@ -330,6 +330,8 @@ dependencies:
   - zipp=3.15.0=pyhd8ed1ab_0
   - zlib=1.2.13=h166bdaf_4
   - zstd=1.5.2=h3eb15da_6
+  - pydantic
+  - pyyaml
   - pip:
     - anyio==3.7.0
     - argon2-cffi==21.3.0
@@ -371,7 +373,6 @@ dependencies:
     - nest-asyncio==1.5.6
     - notebook==6.5.4
     - notebook-shim==0.2.3
-    - occutils==0.1.dev0
     - overrides==7.3.1
     - pandocfilters==1.5.0
     - plotly==5.15.0
@@ -381,7 +382,6 @@ dependencies:
     - pydantic==1.10.9
     - pyrsistent==0.19.3
     - python-json-logger==2.0.7
-    - pyyaml==6.0
     - pyzmq==25.1.0
     - rfc3339-validator==0.1.4
     - rfc3986-validator==0.1.1
@@ -398,4 +398,5 @@ dependencies:
     - webencodings==0.5.1
     - websocket-client==1.6.1
     - widgetsnbextension==3.6.4
-prefix: /home/yhe/anaconda3/envs/amworkflow
+    - polyfactory
+    - -e .

pyproject.toml

@@ -0,0 +1,28 @@
+[project]
+name = "amworkflow"
+version = "0.2"
+authors = [
+    {name = "Annika Robens-Radermacher", email = "[email protected]"},
+]
+
+description = "Automatic workflows for AM concrete appplications"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+]
+license = {file = "LICENSE"}
+keywords = ["AM concrete", "workflow", "CAD"]
+dependencies = [
+  "fenics-dolfinx",
+  "gmsh",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/BAMresearch/amworkflow"
+"Bug Tracker" = "https://github.com/BAMresearch/amworkflow/issues"
+
+[build-system]
+requires = ["setuptools", "wheel"]

setup.py

@@ -0,0 +1,12 @@
+from setuptools import setup
+
+setup(
+    name='amworkflow',
+    version='',
+    packages=['amworkflow.src', 'amworkflow.tests'],
+    url='',
+    license='MIT',
+    author='Yuxiang He',
+    author_email='',
+    description=''
+)

usecases/param_wall/dodo.py

@@ -1,6 +1,6 @@
 from param_wall import ParamWallWorkflow
-from amworkflow.src.constants.data_model import WallGeometryParameter, DB_WallGeometryFile
-from amworkflow.src.infrastructure.database.models.model import GeometryFile
+from amworkflow.amworkflow.src.constants.data_model import WallGeometryParameter, DB_WallGeometryFile
+from amworkflow.amworkflow.src.infrastructure.database.models.model import GeometryFile
 
 def create_param_wall(yaml_dir: str, 
                       filename: str,

usecases/param_wall/param_wall.py

@@ -1,11 +1,12 @@
 import sys
 import os
-sys.path.append("/home/yhe/Documents/amworkflow/amworkflow")
+import pathlib
+#sys.path.append("/home/yhe/Documents/amworkflow/amworkflow")
 from OCC.Core.TopoDS import TopoDS_Shape
-from src.core.workflow import BaseWorkflow
-from src.constants.data_model import WallParam, DB_WallGeometryFile
-from src.infrastructure.database.models.model import GeometryFile
-from src.geometries.simple_geometry import create_box
+from amworkflow.src.core.workflow import BaseWorkflow
+from amworkflow.src.constants.data_model import WallParam, DB_WallGeometryFile
+from amworkflow.src.infrastructure.database.models.model import GeometryFile
+from amworkflow.src.geometries.simple_geometry import create_box
 
 class ParamWallWorkflow(BaseWorkflow):
     def __init__(self, yaml_dir: str, filename: str, data_model: callable, geom_db_model: callable = None, geom_db_data_model: callable = None):
@@ -37,10 +38,10 @@ def geom_process(self, ind: int, param: list, name_type: str):
         model.stl_hashname = hash_name
         self.db_data_collection["geometry"].append(model.dict())
 
-yaml_dir = r"//home/yhe/Documents/amworkflow/usecases/param_wall/"
+yaml_dir = pathlib.Path(__file__).parent
 yaml_filename = "test1.yaml"
 
-p_wall = ParamWallWorkflow(yaml_dir=yaml_dir,
+p_wall = ParamWallWorkflow(yaml_dir=str(yaml_dir),
                          filename=yaml_filename,
                          data_model= WallParam, 
                          geom_db_model= GeometryFile,

usecases/param_wall/test1.yaml

@@ -4,7 +4,7 @@ geometry_parameter:
   length:
     length: 100
     endpoint: 180
-    num: 1
+    num: 2
   height:
     length: 4.3
     endpoint: 6.6