Add weldx file wrapper

.github/workflows/static_analysis.yml

@@ -16,7 +16,7 @@ jobs:
         with:
           python-version: ${{ matrix.py }}
       - name: pip installs
-        run: pip install pydocstyle==5.*
+        run: pip install pydocstyle
       - name: run pydocstyle
         run: |
           pydocstyle

CHANGELOG.md

@@ -7,6 +7,8 @@
 - added `asdf.util.get_schema_path` helper function [[#325]](https://github.com/BAMWelDX/weldx/pull/325)
 - added `util.compare_nested` to check equality of two nested data
   structures. [[#328]](https://github.com/BAMWelDX/weldx/pull/328)
+- added `WeldxFile` wrapper to handle asdf files with 
+  history and schemas more easily. [[#341]](https://github.com/BAMWelDX/weldx/pull/341).  
 
 ### changes
 

setup.cfg

@@ -52,6 +52,8 @@ install_requires =
     ipywidgets
     k3d
     meshio
+    attrdict
+
 include_package_data = True
 
 [options.extras_require]
@@ -86,12 +88,13 @@ exclude =
     doc/conf.py,
 
 [pydocstyle]
+# convention numpy is currently equivalent to ignoring 'D107', 'D203', 'D212', 'D213', 'D402', 'D413'
+convention = numpy
 match = (?!__)(?!_version)(?!conftest).*\.py
 match_dir = [^\.][^\docs].*
-ignore = D203,D213
 
 [tool:pytest]
-addopts = --tb=short --color=yes -rs --cov=weldx --cov-report=term-missing:skip-covered
+addopts = --tb=short --color=yes -rs --cov=weldx --cov-report=term-missing:skip-covered --doctest-modules
 #addopts = --tb=short --color=yes -rs -p no:cov
 # custom test markers, see https://docs.pytest.org/en/latest/example/markers.html#mark-examples
 markers =
@@ -100,6 +103,7 @@ asdf_schema_root = weldx/asdf/schemas
 #asdf_schema_tests_enabled = true
 asdf_schema_skip_tests =
     weldx.bam.de/weldx/datamodels/single_pass_weld-1.0.0.schema.yaml
+norecursedirs=doc
 
 [isort]
 profile = black

tutorials/GMAW_process.ipynb

@@ -20,10 +20,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import asdf\n",
     "import weldx\n",
     "from weldx import Q_\n",
-    "from weldx.asdf.extension import WeldxAsdfExtension, WeldxExtension\n",
     "from weldx.core import TimeSeries as TS\n",
     "from weldx.welding.processes import GmawProcess"
    ]
@@ -118,7 +116,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## using ASDF"
+    "## using ASDF\n",
+    "We write the dictionary containing our structured data to an ASDF file using the WeldxFile\n",
+    "class. We pass the tree as a named keyword argument.\n",
+    "The tree will be serialized to ASDF in memory, and we can have a look at the ASDF header."
    ]
   },
   {
@@ -136,17 +137,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "buffer = weldx.asdf.util._write_buffer(tree)\n",
-    "weldx.asdf.util.notebook_fileprinter(buffer)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data = weldx.asdf.util._read_buffer(buffer)"
+    "file = weldx.WeldxFile(tree=tree)\n",
+    "file.show_asdf_header()"
    ]
   },
   {

tutorials/custom_metadata.ipynb

@@ -57,7 +57,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now let's look at the ASDF file contents with our metadata:"
+    "Now let's look at the ASDF file contents with our metadata. We will find our data\n",
+    "at the very end after the ASDF header."
    ]
   },
   {
@@ -66,10 +67,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from weldx.asdf.util import _write_buffer, notebook_fileprinter\n",
-    "\n",
-    "buffer = _write_buffer({\"sensor\": HKS_sensor})\n",
-    "notebook_fileprinter(buffer)"
+    "from weldx import WeldxFile\n",
+    "file = WeldxFile(tree={\"sensor\": HKS_sensor})\n",
+    "file.show_asdf_header()"
    ]
   },
   {
@@ -92,9 +92,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from weldx.asdf.util import _read_buffer\n",
+    "data = WeldxFile(file.write_to())\n",
     "\n",
-    "data = _read_buffer(buffer)\n",
     "display(data[\"sensor\"].wx_metadata)\n",
     "display(data[\"sensor\"].wx_user)"
    ]

tutorials/geometry_02_geometry.ipynb

@@ -481,7 +481,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.2"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

tutorials/groove_types_01.ipynb

@@ -189,9 +189,10 @@
    "source": [
     "## using ASDF\n",
     "\n",
-    "All groove types can be save to _ASDF_-files with the included schemas and _ASDF_-extension from the weldx-package.\n",
-    "\n",
-    "Writing the asdf file into a buffer:"
+    "All groove types can be saved to _ASDF_-files with the included schemas and _ASDF_-extension from the weldx-package.\n",
+    "Note that these schemas and extensions are being handled automatically and you do not have\n",
+    "to worry about these.\n",
+    "Here we demonstrate the writing of the groove data into a buffer (in-memory file):"
    ]
   },
   {
@@ -201,7 +202,7 @@
    "outputs": [],
    "source": [
     "tree = dict(test_v_groove=v_groove)\n",
-    "buffer = weldx.asdf.util._write_buffer(tree)"
+    "file = weldx.WeldxFile(tree=tree)"
    ]
   },
   {
@@ -217,14 +218,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "weldx.asdf.util.notebook_fileprinter(buffer)"
+    "file.show_asdf_header()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Reading the file contents again and validating the extracted groove:"
+    "Now we are taking a copy of the first file by calling `WeldxFile.write_to`.\n",
+    "Then we read the file contents again and validating the extracted groove:"
    ]
   },
   {
@@ -233,7 +235,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = weldx.asdf.util._read_buffer(buffer)\n",
+    "file_copy = file.write_to()\n",
+    "data = weldx.WeldxFile(file_copy)\n",
     "data[\"test_v_groove\"]"
    ]
   },
@@ -249,7 +252,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [],
    "source": [
     "# generate test grooves\n",
@@ -262,13 +269,6 @@
     "for k, v in groove_dict.items():\n",
     "    v[0].plot(line_style=\"-\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

tutorials/measurement_example.ipynb

@@ -460,25 +460,20 @@
     "    # \"data_sources\": sources,\n",
     "    # \"data_processors\": processors,\n",
     "}\n",
-    "buffer = weldx.asdf.util._write_buffer(tree)"
+    "file = weldx.WeldxFile(tree=tree)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "weldx.asdf.util.notebook_fileprinter(buffer)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
    "outputs": [],
    "source": [
-    "data = weldx.asdf.util._read_buffer(buffer)"
+    "file.show_asdf_header()"
    ]
   }
  ],

tutorials/welding_example_01_basics.ipynb

@@ -544,7 +544,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## using ASDF"
+    "## using ASDF\n",
+    "Now we write all of our structured data to an ASDF file and have a look at the ASDF header."
    ]
   },
   {
@@ -562,7 +563,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "buffer = weldx.asdf.util._write_buffer(tree)"
+    "file = weldx.WeldxFile(tree=tree)"
    ]
   },
   {
@@ -571,7 +572,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "weldx.asdf.util.notebook_fileprinter(buffer)"
+    "file.show_asdf_header()"
    ]
   }
  ],

weldx/__init__.py

@@ -22,6 +22,7 @@
 
 # asdf extensions and tags
 import weldx.asdf
+from weldx.asdf.file import WeldxFile
 
 # class imports to weldx namespace
 from weldx.constants import WELDX_QUANTITY as Q_
@@ -55,6 +56,7 @@
     "Shape",
     "SpatialData",
     "Trace",
+    "WeldxFile",
     "asdf",
     "core",
     "geometry",