Merge pull request #1521 from pyiron/tests

Add usecases to the tests

.github/workflows/usecase_ADIS.yml

@@ -0,0 +1,36 @@
+name: Usecase ADIS
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Merge Notebook environment
+      run: |
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 tests/usecases/ADIS/environment.yml >> environment.yml
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.11"
+        miniforge-variant: Mambaforge
+        channels: conda-forge
+        channel-priority: strict
+        activate-environment: my-env
+        environment-file: environment.yml
+        use-mamba: true
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        bash .ci_support/pip_install.sh
+        conda install -c conda-forge jupyter papermill
+        cd tests/usecases/ADIS
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        papermill notebook.ipynb notebook-out.ipynb -k "python3"

.github/workflows/usecase_NFDI4ING.yml

@@ -0,0 +1,35 @@
+name: Usecase NFDI4Ing
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Merge Notebook environment
+      run: |
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 tests/usecases/NFDI4ING/environment.yml >> environment.yml
+    - name: Setup Mambaforge
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: '3.11'
+        miniforge-variant: Mambaforge
+        channels: conda-forge
+        channel-priority: strict
+        activate-environment: my-env
+        environment-file: environment.yml
+        use-mamba: true
+    - name: Test
+      shell: bash -l {0}
+      timeout-minutes: 60
+      run: |
+        bash .ci_support/pip_install.sh
+        conda install -y papermill jupyter
+        sudo apt-get install -y $(cat tests/usecases/NFDI4ING/apt.txt)
+        cd tests/usecases/NFDI4ING
+        papermill notebook.ipynb notebook.ipynb -k "python3"

tests/usecases/ADIS/adis_tools/parsers.py

@@ -0,0 +1,70 @@
+import numpy
+
+from xmlschema import XMLSchema
+from qe_tools import CONSTANTS
+
+from ase import Atoms
+from importlib.resources import files
+
+from . import schemas
+
+
+def parse_pw(xml_file):
+    """Parse a Quantum Espresso XML output file."""
+
+    xml_dict = XMLSchema(str(files(schemas) / "qes_230310.xsd")).to_dict(xml_file)
+
+    parsed_results = {}
+
+    try:
+        cell = (
+            numpy.array(
+                [v for v in xml_dict["output"]["atomic_structure"]["cell"].values()]
+            )
+            * CONSTANTS.bohr_to_ang
+        )
+        symbols = [
+            el["@name"]
+            for el in xml_dict["output"]["atomic_structure"]["atomic_positions"]["atom"]
+        ]
+        positions = (
+            numpy.array(
+                [
+                    el["$"]
+                    for el in xml_dict["output"]["atomic_structure"][
+                        "atomic_positions"
+                    ]["atom"]
+                ]
+            )
+            * CONSTANTS.bohr_to_ang
+        )
+
+        parsed_results["ase_structure"] = Atoms(
+            cell=cell,
+            positions=positions,
+            symbols=symbols,
+            pbc=True,
+        )
+    except KeyError:
+        pass
+
+    try:
+        parsed_results["energy"] = (
+            xml_dict["output"]["total_energy"]["etot"] * CONSTANTS.ry_to_ev
+        )
+    except KeyError:
+        pass
+
+    try:
+        parsed_results["forces"] = (
+            numpy.array(xml_dict["output"]["forces"]["$"]).reshape(
+                xml_dict["output"]["forces"]["@dims"]
+            )
+            * 2
+            * CONSTANTS.ry_to_ev
+            / CONSTANTS.bohr_to_ang
+        )
+    except KeyError:
+        pass
+
+    return parsed_results