Merge branch 'main' into fix/number_of_supercells

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout the repository
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      # Set up Python environment
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      # Install pre-commit
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      # Run pre-commit on all files
+      - name: Run pre-commit
+        run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -8,7 +8,12 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 24.4.2
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.1
     hooks:
-    -   id: black
+    -   id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+    -   id: ruff-format
+        types_or: [python, pyi, jupyter]

LICENSE.txt

@@ -5,4 +5,4 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
 
 The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -6,7 +6,7 @@ Plugin to compute vibrational properties of materials via the aiida-vibroscopy A
 Once cloned the repository, `cd` into it and:
 
 ```shell
-pip install -e 
+pip install --user .
 ```
 
 If you want to easily set up phonopy, use the CLI of this package (inspect it via `aiidalab-qe-vibroscopy --help`):

pyproject.toml

@@ -27,6 +27,9 @@ dependencies = [
     "kaleido",
 ]
 
+[tool.ruff.lint]
+ignore = ["E501", "E402", "TRY003", "RUF012", "N806"]
+
 [project.urls]
 Source = "https://github.com/mikibonacci/aiidalab-qe-vibroscopy"
 
@@ -37,4 +40,4 @@ Source = "https://github.com/mikibonacci/aiidalab-qe-vibroscopy"
 "vibronic" = "aiidalab_qe_vibroscopy.app:property"
 
 [project.scripts]
-"aiidalab-qe-vibroscopy" = "aiidalab_qe_vibroscopy.__main__:cli"
+"aiidalab-qe-vibroscopy" = "aiidalab_qe_vibroscopy.__main__:cli"

src/aiidalab_qe_vibroscopy/__init__.py

@@ -1 +1 @@
-"""AiiDAlab Qe plugin for vibrational spectoscopy."""
+"""AiiDAlab Qe plugin for vibrational spectoscopy."""

src/aiidalab_qe_vibroscopy/__main__.py

@@ -12,13 +12,13 @@
 So we only setup in AiiDA.
 """
 
+
 @click.group()
 def cli():
     pass
 
-@cli.command(
-    help="Setup phonopy@localhost in the current AiiDA database."
-)
+
+@cli.command(help="Setup phonopy@localhost in the current AiiDA database.")
 def setup_phonopy():
     load_profile()
     try:
@@ -27,10 +27,12 @@ def setup_phonopy():
         # Use shutil.which to find the path of the phonopy executable
         phonopy_path = shutil.which("phonopy")
         if not phonopy_path:
-            raise FileNotFoundError("Phonopy code is not found in PATH.  \
+            raise FileNotFoundError(
+                "Phonopy code is not found in PATH.  \
                                     You should update your PATH. If you have not phonopy in , \
                                     your environment, install the code via \
-                                    `pip install phonopy --user`.")
+                                    `pip install phonopy --user`."
+            )
         # Construct the command as a list of arguments
         command = [
             "verdi",
@@ -53,5 +55,6 @@ def setup_phonopy():
     else:
         print("Code phonopy@localhost is already installed! Nothing to do here.")
 
+
 if __name__ == "__main__":
-    cli()
+    cli()

src/aiidalab_qe_vibroscopy/app/__init__.py

@@ -3,22 +3,40 @@
 from aiidalab_qe_vibroscopy.app.result import Result
 from aiidalab_qe.common.panel import OutlinePanel
 
-from aiidalab_qe.common.widgets import QEAppComputationalResourcesWidget
+from aiidalab_qe.common.widgets import (
+    QEAppComputationalResourcesWidget,
+    PwCodeResourceSetupWidget,
+)
 
 
 class Outline(OutlinePanel):
     title = "Vibrational properties"
     # description = "IR and Raman spectra; you may also select phononic and dielectric properties"
 
 
-phonopy_code = QEAppComputationalResourcesWidget(
-    description="phonopy",
+PhononWorkChainPwCode = PwCodeResourceSetupWidget(
+    description="pw.x for phonons",  # code for the PhononWorkChain workflow",
+    default_calc_job_plugin="quantumespresso.pw",
+)
+
+# The finite electric field does not support npools (does not work with npools>1), so we just set it as QEAppComputationalResourcesWidget
+DielectricWorkChainPwCode = QEAppComputationalResourcesWidget(
+    description="pw.x for dielectric",  # code for the DielectricWorChain workflow",
+    default_calc_job_plugin="quantumespresso.pw",
+)
+
+PhonopyCalculationCode = QEAppComputationalResourcesWidget(
+    description="phonopy",  # code for the PhonopyCalculation calcjob",
     default_calc_job_plugin="phonopy.phonopy",
 )
 
 property = {
     "outline": Outline,
-    "code": {"phonopy": phonopy_code},
+    "code": {
+        "phonon": PhononWorkChainPwCode,
+        "dielectric": DielectricWorkChainPwCode,
+        "phonopy": PhonopyCalculationCode,
+    },
     "setting": Setting,
     "workchain": workchain_and_builder,
     "result": Result,