Asdf setup (#10)

asdf:
- add basic file/directory layout for asdf files
  - asdf schemas are located in `weldx/asdf/schemas/weldx.bam.de/weldx`
  - tag implementations are in `weldx/asdf/tags/weldx`
- implement support for pint quantities
- implement support for basic pandas time class
- implement base welding classes from AWS/NIST "A Welding Data Dictionary"
- add and implement ISO groove types (DIN EN ISO 9692-1:2013)
- add basic jinja templates and functions for adding simple dataclass objects
- setup package to include and install ASDF extensions and schemas (see setup.py, MANIFEST.in)
- add basic tests for writing/reading all ASDF classes (these only run code without any real checks!)

module:
- add and populate `__init__.py` files
- add setup.py package configuration for install
  - required packages
  - package metadata
  - asdf extension entry points
  - version support
- update pandas, scipy, xarray and pint minimum versions (in conda env and setup.py)
- add versioneer
- update options in setup.cfg
- update tool configurations
  - ignore `asdf`-module in deepsource run

CI:
- add local conda build workflow (no artifacts so far, testing only)
- add asdf schema test workflow with local package install (schemas are excluded from default pytest run)
- add debug isort workflow (can be used to check files that would be sorted, we can activate isort test with new options in release 5.0)

.codacy.yml

@@ -12,3 +12,6 @@ engines:
 exclude_paths:
   - 'docs/**'
   - '.vulture_whitelist.py'
+  - 'versioneer.py'
+  - 'weldx/_version.py'
+  - 'scripts/**'

.deepsource.toml

@@ -7,7 +7,10 @@ test_patterns = [
 
 exclude_patterns = [
   "docs/**",
-  ".vulture_whitelist.py"
+  ".vulture_whitelist.py",
+  "versioneer.py",
+  "weldx/_version.py",
+  "weldx/asdf/**"
 ]
 
 [[analyzers]]

.gitattributes

@@ -0,0 +1 @@
+weldx/_version.py export-subst

.github/workflows/conda_build.yml

@@ -0,0 +1,24 @@
+name: conda build
+on: [push]
+
+jobs:
+  test:
+    name: conda build (local)
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Include $CONDA in $PATH
+      run: echo ::add-path::$CONDA/bin
+    - name: Add conda-forge & print conda info
+      run: |
+        conda config --append channels conda-forge
+        conda info -a
+    - name: Create conda build environment
+      run: conda env create -f ./conda.recipe/build_env.yml
+    - name: Build from local conda recipe
+      run: |
+        source activate build_env
+        conda build .

.github/workflows/pytest_asdf.yml

@@ -0,0 +1,45 @@
+name: pytest asdf
+on: [push]
+
+jobs:
+#  pytest:
+#    name: pytest asdf
+#    runs-on: ${{ matrix.os }}
+#    strategy:
+#      matrix:
+#        os: [ubuntu-18.04]
+#    steps:
+#    - uses: actions/checkout@v1
+#    - name: Include $CONDA in $PATH
+#      run: echo ::add-path::$CONDA/bin
+#    - name: Print conda info
+#      run: conda info -a
+#    - name: Create conda environment
+#      run: conda env create -f ./environment.yml
+#    - name: Conda develop install of source package for ASDF Schema links
+#      run: |
+#        conda install conda-build -n weldx
+#    - name: Run tests with added asdf schema file location
+#      run: |
+#        source activate weldx
+#        python setup.py install --user
+#        pytest --asdf-tests --ignore=tests/
+  pytest:
+    name: pytest asdf
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        py: [ '3.7', '3.8' ]
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.py }}
+      - name: pip installs
+        run: |
+          pip install pytest pytest-cov
+          pip install .
+      - name: run pytest
+        run: |
+          pytest --asdf-tests --ignore=tests/

.github/workflows/static_analysis.yml

@@ -40,6 +40,28 @@ jobs:
         run: |
           flake8
 
+  isort:
+    name: isort
+    runs-on: ${{ matrix.os }}
+    continue-on-error: true
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        py: [ '3.7', '3.8' ]
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.py }}
+      - name: pip installs
+        run: pip install git+https://github.com/timothycrosley/isort.git
+      - name: show isort diff
+        run: |
+          isort ./weldx --diff
+      - name: run isort
+        run: |
+          isort ./weldx --check-only
+
   vulture:
     name: vulture
     runs-on: ${{ matrix.os }}
@@ -57,4 +79,4 @@ jobs:
         run: pip install vulture==1.4
       - name: run vulture
         run: |
-          vulture .
+          vulture . --exclude weldx/asdf/,versioneer.py,weldx/_version.py

.typo-ci.yml

@@ -7,24 +7,32 @@ excluded_files:
   - "docs*"
   - "environment.yml"
   - "tools*"
+  - "versioneer.py"
+  - "weldx/_version.py"
 
 excluded_words:
   - typoci
   # python packages -----------------------------
+  - asdf
   - numpy
   - pandas
   - xarray
   - scipy
   - pytest
   - pydocstyle
   - matplotlib
+  - versioneer
+  - isort
   - networkx
   # matplotlib ----------------------------------
   - pyplot
   - gca
   - plt
   # flake8 --------------------------------------
   - noqa
+  - addopts
+  # asdf ----------------------------------------
+  - yamlutil
   # numpy ---------------------------------------
   - arange
   - allclose
@@ -41,14 +49,21 @@ excluded_words:
   - vstack
   # pandas / xarray -----------------------------
   - bfill
+  - ffill
   - idxmax
   - idxmin
   - isel
+  - iloc
   - isin
   - isnan
   - ffill
   - fillna
   - sel
+  - dtypes
+  - timedelta
+  - timedeltaindex
+  - datetimeindex
+  - isoformat
   # jupyter notebooks ---------------------------
   - jupyter
   - nbformat
@@ -58,6 +73,11 @@ excluded_words:
   - ipython
   # scipy ---------------------------------------
   - Slerp
+  # welding -------------------------------------
+  - weldment
+  # conda ---------------------------------------
+  - conda
+  - noarch
   # other ---------------------------------------
   - addopts
   - csm
@@ -67,4 +87,7 @@ excluded_words:
   - interp
   - isort
   - linearization
+  - ureg
+  - Cagtay
+  - Fabry
   - xyz

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include weldx/asdf/schemas *.yaml
+include versioneer.py
+include weldx/_version.py

conda.recipe/build_env.yml

@@ -0,0 +1,8 @@
+name: build_env
+channels:
+  - defaults
+dependencies:
+  - python=3.7
+  - setuptools
+  - conda-build
+  - conda-verify

conda.recipe/meta.yaml

@@ -0,0 +1,32 @@
+{% set data = load_setup_py_data() %}
+
+package:
+    name: weldx
+    version: {{ data['version'] }}
+
+source:
+    path: ..
+
+build:
+  script: python setup.py install --single-version-externally-managed --record=record.txt
+  number: 0
+  noarch: python
+
+requirements:
+    build:
+        - python
+        - setuptools
+    run:
+        - python
+        # dependencies are defined in setup.py
+        {% for dep in data['install_requires'] %}
+        - {{ dep.lower() }}
+        {% endfor %}
+
+test:
+    imports:
+        - weldx
+
+about:
+    home: www.bam.de/weldx
+    license: BSD

environment.yml

@@ -6,15 +6,16 @@ channels:
 dependencies:
   - python=3.7
   - numpy>=1.18
-  - pandas>=0.25
-  - scipy
-  - xarray
-  - pint
+  - pandas>=1.0
+  - scipy>=1.4
+  - xarray>=0.15
+  - pint>=0.11
   - bottleneck
   - asdf=2.5.1
   - sphinx
   - recommonmark
   - openpyxl
+  - jinja2
   # graph packages
   - networkx
   # Code quality

scripts/aws_run.py

@@ -0,0 +1,94 @@
+"""Run the AWS Data Dictionary debug example."""
+
+import asdf
+import pprint
+
+from weldx.constants import WELDX_QUANTITY as Q_
+
+from weldx.asdf.extension import WeldxExtension, WeldxAsdfExtension
+
+# welding process -----------------------------------------------------------------
+from weldx.asdf.tags.weldx.aws.process.gas_component import GasComponent
+from weldx.asdf.tags.weldx.aws.process.shielding_gas_type import ShieldingGasType
+from weldx.asdf.tags.weldx.aws.process.shielding_gas_for_procedure import (
+    ShieldingGasForProcedure,
+)
+from weldx.asdf.tags.weldx.aws.process.arc_welding_process import ArcWeldingProcess
+
+# weld design -----------------------------------------------------------------
+from weldx.asdf.tags.weldx.aws.design.joint_penetration import JointPenetration
+from weldx.asdf.tags.weldx.aws.design.weld_details import WeldDetails
+from weldx.asdf.tags.weldx.aws.design.connection import Connection
+from weldx.asdf.tags.weldx.aws.design.workpiece import Workpiece
+from weldx.asdf.tags.weldx.aws.design.sub_assembly import SubAssembly
+from weldx.asdf.tags.weldx.aws.design.weldment import Weldment
+from weldx.asdf.tags.weldx.aws.design.base_metal import BaseMetal
+from weldx.asdf.tags.weldx.core.iso_groove import get_groove
+
+
+# welding process -----------------------------------------------------------------
+gas_comp = [
+    GasComponent("argon", Q_(82, "percent")),
+    GasComponent("carbon dioxide", Q_(18, "percent")),
+]
+gas_type = ShieldingGasType(gas_component=gas_comp, common_name="SG")
+
+gas_for_procedure = ShieldingGasForProcedure(
+    use_torch_shielding_gas=True,
+    torch_shielding_gas=gas_type,
+    torch_shielding_gas_flowrate=Q_(20, "l / min"),
+)
+
+arc_welding_process = ArcWeldingProcess("GMAW")
+process = {
+    "arc_welding_process": arc_welding_process,
+    "shielding_gas": gas_for_procedure,
+}
+
+# weld design -----------------------------------------------------------------
+v_groove = get_groove(
+    groove_type="VGroove",
+    workpiece_thickness=Q_(9, "mm"),
+    groove_angle=Q_(50, "deg"),
+    root_face=Q_(4, "mm"),
+    root_gap=Q_(2, "mm"),
+)
+
+joint_penetration = JointPenetration(
+    complete_or_partial="completePenetration", root_penetration=Q_(1.0, "mm")
+)
+weld_details = WeldDetails(
+    joint_design=v_groove, weld_sizes=Q_(320, "mm"), number_of_passes=1
+)
+connection = Connection(
+    joint_type="butt_joint",
+    weld_type="singleVGroove",
+    joint_penetration=joint_penetration,
+    weld_details=weld_details,
+)
+workpieces = [Workpiece(geometry="V-Groove")]
+sub_assembly = [SubAssembly(workpiece=workpieces, connection=connection)]
+
+weldment = Weldment(sub_assembly)
+
+base_metal = BaseMetal("steel", "plate", Q_(10.3, "mm"))
+
+filename = "aws_demo.yaml"
+tree = dict(process=process, weldment=weldment, base_metal=base_metal)
+
+# Write the data to a new file
+with asdf.AsdfFile(
+    tree,
+    extensions=[WeldxExtension(), WeldxAsdfExtension()],
+    ignore_version_mismatch=False,
+) as ff:
+    ff.write_to(filename, all_array_storage="inline")
+
+# read back data from ASDF file
+with asdf.open(
+    filename, copy_arrays=True, extensions=[WeldxExtension(), WeldxAsdfExtension()]
+) as af:
+    data = af.tree
+    pprint.pprint(data["process"])
+    pprint.pprint(data["weldment"].__dict__)
+    pprint.pprint(data["base_metal"].__dict__)