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pyiron · Oct 3, 2024 · 307cc9b · 307cc9b
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diff --git a/.github/workflows/format_black.yml b/.github/workflows/format_black.yml
@@ -0,0 +1,33 @@
+# This workflow will checkout the branch of the PR, apply black formatting and commit the result to the PR. Does not work for forks.
+
+name: Format black
+
+on:
+  pull_request:
+    types: [labeled]
+
+jobs:
+  build:
+    if: contains(github.event.pull_request.labels.*.name, 'format_black' )
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
+        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+    - name: format black
+      uses: psf/black@stable
+      with:
+        options: ""
+        src: "./${{ github.event.repository.name }}"
+    - name: commit
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "pyiron-runner"
+        git commit -m "Format black" -a
+    - name: push
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
+        branch: ${{ github.event.pull_request.head.ref }}
diff --git a/.github/workflows/minimal.yml b/.github/workflows/minimal.yml
@@ -21,9 +21,6 @@ jobs:
         condarc-file: .condarc
         environment-file: .ci_support/environment-mini.yml
     - name: Test
-      shell: bash -l {0}
-      timeout-minutes: 5
-      run: |
-        pip install versioneer[toml]==0.29
+      pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
         python -m unittest discover tests
diff --git a/.github/workflows/pypicheck.yml b/.github/workflows/pypicheck.yml
@@ -0,0 +1,21 @@
+# This workflow is used to test, if the installation of the pypi package works
+
+name: Pip check
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Pip check
+      shell: bash -l {0}
+      run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        pip check
diff --git a/README.md b/README.md
@@ -0,0 +1,29 @@
+# Dataclasses for pyiron
+The `pyiron_dataclasses` module provides a series of [dataclasses](https://docs.python.org/3/library/dataclasses.html) 
+for the `pyiron` workflow framework. It can load HDF5 files created by `pyiron_atomistics` and read the content stored 
+in those files, without depending on `pyiron_atomistics`. Furthermore, it is not fixed to a single version of 
+`pyiron_atomistics` but rather matches multiple versions of `pyiron_atomistics` to the same API version of 
+`pyiron_dataclasses`. 
+
+## Usage 
+Using the `get_dataclass()` function of the built-in converter:
+```python
+from h5io_browser import read_dict_from_hdf
+from pyiron_dataclasses.v1.converter import get_dataclass
+
+job_classes = get_dataclass(
+    job_dict=read_dict_from_hdf(
+        file_name=job.project_hdf5.file_name,
+        h5_path="/",
+        recursive=True,
+        slash='ignore',
+    )[job.job_name]
+)
+job_classes
+```
+
+## Supported Versions 
+### Version 1 - `v1`
+Supported versions of `pyiron_atomistics`:
+* `0.6.13`
+* `0.6.12`
diff --git a/tests/convert.py → pyiron_dataclasses/v1/converter.py b/tests/convert.py → pyiron_dataclasses/v1/converter.py
@@ -61,15 +61,24 @@
 )
 
 
-def convert_sphinx_job_dict(job_dict: dict) -> SphinxJob:
+def get_dataclass(job_dict):
+    funct_dict = {
+        "<class 'pyiron_atomistics.lammps.lammps.Lammps'>": _convert_lammps_job_dict,
+        "<class 'pyiron_atomistics.sphinx.sphinx.Sphinx'>": _convert_sphinx_job_dict,
+        "<class 'pyiron_atomistics.vasp.vasp.Vasp'>": _convert_vasp_job_dict,
+    }
+    return funct_dict[job_dict["TYPE"]](job_dict=job_dict)
+
+
+def _convert_sphinx_job_dict(job_dict: dict) -> SphinxJob:
     ureg = UnitRegistry()
-    sphinx_input_parameter_dict = convert_datacontainer_to_dictionary(
+    sphinx_input_parameter_dict = _convert_datacontainer_to_dictionary(
         data_container_dict=job_dict["input"]["parameters"]
     )
-    generic_input_dict = convert_generic_parameters_to_dictionary(
+    generic_input_dict = _convert_generic_parameters_to_dictionary(
         generic_parameter_dict=job_dict["input"]["generic"],
     )
-    output_dict = convert_datacontainer_to_dictionary(
+    output_dict = _convert_datacontainer_to_dictionary(
         data_container_dict=job_dict["output"]["generic"]
     )
     if "ricQN" in sphinx_input_parameter_dict["sphinx"]["main"]:
@@ -461,9 +470,9 @@ def convert_sphinx_job_dict(job_dict: dict) -> SphinxJob:
     )
 
 
-def convert_lammps_job_dict(job_dict: dict) -> LammpsJob:
+def _convert_lammps_job_dict(job_dict: dict) -> LammpsJob:
     ureg = UnitRegistry()
-    generic_input_dict = convert_generic_parameters_to_dictionary(
+    generic_input_dict = _convert_generic_parameters_to_dictionary(
         generic_parameter_dict=job_dict["input"]["generic"],
     )
     return LammpsJob(
@@ -541,10 +550,10 @@ def convert_lammps_job_dict(job_dict: dict) -> LammpsJob:
                 species=job_dict["input"]["potential_inp"]["potential"]["Species"],
             ),
             input_files=LammpsInputFiles(
-                control_inp=convert_generic_parameters_to_string(
+                control_inp=_convert_generic_parameters_to_string(
                     generic_parameter_dict=job_dict["input"]["control_inp"]
                 ),
-                potential_inp=convert_generic_parameters_to_string(
+                potential_inp=_convert_generic_parameters_to_string(
                     generic_parameter_dict=job_dict["input"]["potential_inp"]
                 ),
             ),
@@ -609,9 +618,9 @@ def convert_lammps_job_dict(job_dict: dict) -> LammpsJob:
     )
 
 
-def convert_vasp_job_dict(job_dict):
+def _convert_vasp_job_dict(job_dict):
     ureg = UnitRegistry()
-    generic_input_dict = convert_generic_parameters_to_dictionary(
+    generic_input_dict = _convert_generic_parameters_to_dictionary(
         generic_parameter_dict=job_dict["input"]["generic"],
     )
     return VaspJob(
@@ -693,14 +702,14 @@ def convert_vasp_job_dict(job_dict):
                 fix_spin_constraint=generic_input_dict.get("fix_spin_constraint", None),
                 max_iter=generic_input_dict.get("max_iter", None),
             ),
-            incar=convert_generic_parameters_to_string(
+            incar=_convert_generic_parameters_to_string(
                 generic_parameter_dict=job_dict["input"]["incar"]
             ),
-            kpoints=convert_generic_parameters_to_string(
+            kpoints=_convert_generic_parameters_to_string(
                 generic_parameter_dict=job_dict["input"]["kpoints"]
             ),
             potcar=PotCar(
-                xc=convert_generic_parameters_to_dictionary(
+                xc=_convert_generic_parameters_to_dictionary(
                     generic_parameter_dict=job_dict["input"]["potcar"]
                 )["xc"]
             ),
@@ -915,16 +924,7 @@ def convert_vasp_job_dict(job_dict):
     )
 
 
-def convert(job_dict):
-    funct_dict = {
-        "<class 'pyiron_atomistics.lammps.lammps.Lammps'>": convert_lammps_job_dict,
-        "<class 'pyiron_atomistics.sphinx.sphinx.Sphinx'>": convert_sphinx_job_dict,
-        "<class 'pyiron_atomistics.vasp.vasp.Vasp'>": convert_vasp_job_dict,
-    }
-    return funct_dict[job_dict["TYPE"]](job_dict=job_dict)
-
-
-def convert_generic_parameters_to_string(generic_parameter_dict: dict) -> str:
+def _convert_generic_parameters_to_string(generic_parameter_dict: dict) -> str:
     output_str = ""
     for p, v in zip(
         generic_parameter_dict["data_dict"]["Parameter"],
@@ -934,7 +934,7 @@ def convert_generic_parameters_to_string(generic_parameter_dict: dict) -> str:
     return output_str[:-1]
 
 
-def convert_generic_parameters_to_dictionary(generic_parameter_dict: dict) -> dict:
+def _convert_generic_parameters_to_dictionary(generic_parameter_dict: dict) -> dict:
     return {
         p: v
         for p, v in zip(
@@ -976,7 +976,7 @@ def recursive_sort(input_value: dict) -> dict:
             else:
                 ind_dict[int(ind)] = key
                 content_dict[key] = recursive_sort(input_value=v)
-        elif k != "DICT_VERSION":
+        else:
             content_dict[k] = recursive_sort(input_value=v)
     if content_lst_flag:
         return [ind_dict[ind] for ind in sorted(list(ind_dict.keys()))]
@@ -991,14 +991,15 @@ def recursive_sort(input_value: dict) -> dict:
         raise KeyError(ind_dict, content_dict)
 
 
-def convert_datacontainer_to_dictionary(data_container_dict: dict) -> dict:
+def _convert_datacontainer_to_dictionary(data_container_dict: dict) -> dict:
     return _sort_dictionary_from_datacontainer(
         input_dict=_filter_dict(
             input_dict=data_container_dict,
             remove_keys_lst=[
                 "NAME",
                 "TYPE",
                 "OBJECT",
+                "DICT_VERSION",
                 "HDF_VERSION",
                 "READ_ONLY",
                 "VERSION",

diff --git a/tests/test_pyiron_atomistics_live.py b/tests/test_pyiron_atomistics_live.py
@@ -1,12 +1,9 @@
 import unittest
 
-from h5io_browser.base import read_dict_from_hdf
+from h5io_browser import read_dict_from_hdf
 from pint import UnitRegistry
 
-from convert import (
-    convert_sphinx_job_dict,
-    convert_lammps_job_dict,
-)
+from pyiron_dataclasses.v1.converter import get_dataclass
 
 try:
     from pyiron_atomistics import Project
@@ -45,7 +42,7 @@ def test_sphinx_calc_minimize(self):
             recursive=True,
             slash='ignore',
         )
-        job_sphinx = convert_sphinx_job_dict(job_dict[job.job_name])
+        job_sphinx = get_dataclass(job_dict[job.job_name])
         self.assertEqual(job_sphinx.calculation_output.generic.energy_tot[-1], -228.78315943905295 * ureg.eV)
 
     def test_sphinx_calc_static(self):
@@ -59,7 +56,7 @@ def test_sphinx_calc_static(self):
             recursive=True,
             slash='ignore',
         )
-        job_sphinx = convert_sphinx_job_dict(job_dict[job.job_name])
+        job_sphinx = get_dataclass(job_dict[job.job_name])
         self.assertEqual(job_sphinx.calculation_output.generic.energy_tot[-1], -228.78315953829286 * ureg.eV)
 
     def test_lammps_calc_static(self):
@@ -74,7 +71,7 @@ def test_lammps_calc_static(self):
             recursive=True,
             slash='ignore',
         )
-        job_lammps = convert_lammps_job_dict(job_dict[job.job_name])
+        job_lammps = get_dataclass(job_dict[job.job_name])
         self.assertEqual(job_lammps.calculation_output.generic.energy_tot[-1], -13.4486826111902 * ureg.eV)
 
     def test_lammps_calc_md(self):
@@ -89,7 +86,7 @@ def test_lammps_calc_md(self):
             recursive=True,
             slash='ignore',
         )
-        job_lammps = convert_lammps_job_dict(job_dict[job.job_name])
+        job_lammps = get_dataclass(job_dict[job.job_name])
         self.assertEqual(len(job_lammps.calculation_output.generic.energy_tot), 11)
 
     def test_lammps_calc_minimize(self):
@@ -104,5 +101,5 @@ def test_lammps_calc_minimize(self):
             recursive=True,
             slash='ignore',
         )
-        job_lammps = convert_lammps_job_dict(job_dict[job.job_name])
+        job_lammps = get_dataclass(job_dict[job.job_name])
         self.assertEqual(job_lammps.calculation_output.generic.energy_tot[-1], -13.4486826111902 * ureg.eV)
diff --git a/tests/test_pyiron_atomistics_static.py b/tests/test_pyiron_atomistics_static.py
@@ -1,51 +1,15 @@
 import os
 from unittest import TestCase
 
-from h5io_browser.base import read_dict_from_hdf
+from h5io_browser import read_dict_from_hdf
 from pint import UnitRegistry
 
-from convert import (
-    convert,
-    convert_sphinx_job_dict,
-    convert_lammps_job_dict,
-    convert_vasp_job_dict,
+from pyiron_dataclasses.v1.converter import (
+    get_dataclass,
 )
 
 
 class TestPyironAtomisticsStatic(TestCase):
-    def test_sphinx(self):
-        ureg = UnitRegistry()
-        job_dict = read_dict_from_hdf(
-            file_name=os.path.join(os.path.dirname(__file__), "pyiron_atomistics_0_6_13", "sx.h5"),
-            h5_path="/sx",
-            recursive=True,
-            slash='ignore',
-        )
-        job_sphinx = convert_sphinx_job_dict(job_dict=job_dict)
-        self.assertEqual(job_sphinx.calculation_output.generic.energy_tot[-1], -228.7831594379917 * ureg.eV)
-
-    def test_lammps(self):
-        ureg = UnitRegistry()
-        job_dict = read_dict_from_hdf(
-            file_name=os.path.join(os.path.dirname(__file__), "pyiron_atomistics_0_6_13", "lmp.h5"),
-            h5_path="/lmp",
-            recursive=True,
-            slash='ignore',
-        )
-        job_lammps = convert_lammps_job_dict(job_dict=job_dict)
-        self.assertEqual(job_lammps.calculation_output.generic.energy_tot[-1], -9428.45286561574 * ureg.eV)
-
-    def test_vasp(self):
-        ureg = UnitRegistry()
-        job_dict = read_dict_from_hdf(
-            file_name=os.path.join(os.path.dirname(__file__), "pyiron_atomistics_0_6_13", "vasp.h5"),
-            h5_path="/vasp",
-            recursive=True,
-            slash='ignore',
-        )
-        job_vasp = convert_vasp_job_dict(job_dict=job_dict)
-        self.assertEqual(job_vasp.calculation_output.generic.energy_tot[-1], -14.7459202 * ureg.eV)
-
     def test_all(self):
         ureg = UnitRegistry()
         static_folder = os.path.join(os.path.dirname(__file__), "pyiron_atomistics_0_6_13")
@@ -62,6 +26,6 @@ def test_all(self):
                 slash='ignore',
             )[hdf5_file.split(".")[0]]
             self.assertEqual(
-                convert(job_dict=job_dict).calculation_output.generic.energy_tot[-1],
+                get_dataclass(job_dict=job_dict).calculation_output.generic.energy_tot[-1],
                 energy_dict[hdf5_file]
             )