Adding Pre-commit and Ruff (#91)

* Adding Pre-commit and Ruff

* Readme Modification

.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.

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

@@ -3,7 +3,10 @@
 from aiidalab_qe_vibroscopy.app.result import Result
 from aiidalab_qe.common.panel import OutlinePanel
 
-from aiidalab_qe.common.widgets import QEAppComputationalResourcesWidget, PwCodeResourceSetupWidget
+from aiidalab_qe.common.widgets import (
+    QEAppComputationalResourcesWidget,
+    PwCodeResourceSetupWidget,
+)
 
 
 class Outline(OutlinePanel):
@@ -12,28 +15,28 @@ class Outline(OutlinePanel):
 
 
 PhononWorkChainPwCode = PwCodeResourceSetupWidget(
-    description="pw.x for phonons", #code for the PhononWorkChain workflow",
+    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",
+    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",
+    description="phonopy",  # code for the PhonopyCalculation calcjob",
     default_calc_job_plugin="phonopy.phonopy",
 )
 
 property = {
     "outline": Outline,
     "code": {
-        "phonon":PhononWorkChainPwCode,
+        "phonon": PhononWorkChainPwCode,
         "dielectric": DielectricWorkChainPwCode,
         "phonopy": PhonopyCalculationCode,
-        },
+    },
     "setting": Setting,
     "workchain": workchain_and_builder,
     "result": Result,

src/aiidalab_qe_vibroscopy/app/result.py

@@ -1,12 +1,11 @@
-"""Bands results view widgets
+"""Bands results view widgets"""
 
-"""
 from __future__ import annotations
 
 
 from aiidalab_qe.common.panel import ResultPanel
 from aiidalab_qe.common.bandpdoswidget import BandPdosPlotly
-
+from IPython.display import display
 import numpy as np
 
 from ..utils.raman.result import export_iramanworkchain_data
@@ -23,21 +22,6 @@
 
 from ..utils.raman.result import SpectrumPlotWidget, ActiveModesWidget
 
-def create_html_table(matrix):
-    """
-    Create an HTML table representation of a 3x3 matrix.
-
-    :param matrix: List of lists representing a 3x3 matrix
-    :return: HTML table string
-    """
-    html = '<table border="1" style="border-collapse: collapse;">'
-    for row in matrix:
-        html += '<tr>'
-        for cell in row:
-            html += f'<td style="padding: 5px; text-align: center;">{cell}</td>'
-        html += '</tr>'
-    html += '</table>'
-    return html
 
 class PhononBandPdosPlotly(BandPdosPlotly):
     def __init__(self, bands_data=None, pdos_data=None):
@@ -92,7 +76,6 @@ class Result(ResultPanel):
     children_result_widget = ()
 
     def _update_view(self):
-
         children_result_widget = ()
         tab_titles = []  # this is needed to name the sub panels
 
@@ -102,15 +85,14 @@ def _update_view(self):
         dielectric_data = export_dielectric_data(self.node)
 
         if phonon_data:
-
             phonon_children = ()
             if phonon_data["bands"] or phonon_data["pdos"]:
                 _bands_plot_view_class = PhononBandPdosPlotly(
                     bands_data=phonon_data["bands"][0],
                     pdos_data=phonon_data["pdos"][0],
                 )
 
-                # the data (bands and pdos) are the first element of the lists phonon_data["bands"] and phonon_data["pdos"]! 
+                # the data (bands and pdos) are the first element of the lists phonon_data["bands"] and phonon_data["pdos"]!
                 downloadBandsPdos_widget = DownloadBandsPdosWidget(
                     data=phonon_data,
                 )
@@ -120,10 +102,12 @@ def _update_view(self):
 
                 phonon_children += (
                     _bands_plot_view_class.bandspdosfigure,
-                    ipw.HBox(children=[
-                        downloadBandsPdos_widget,
-                        downloadYamlHdf5_widget,
-                        ]),
+                    ipw.HBox(
+                        children=[
+                            downloadBandsPdos_widget,
+                            downloadYamlHdf5_widget,
+                        ]
+                    ),
                 )
 
             if phonon_data["thermo"]:
@@ -157,9 +141,8 @@ def _update_view(self):
                 g.add_scatter(x=T, y=E, name=f"Entropy ({E_units})")
                 g.add_scatter(x=T, y=Cv, name=f"Specific Heat-V=const ({Cv_units})")
 
-                downloadThermo_widget = DownloadThermoWidget(
-                    T,F,E,Cv)
-
+                downloadThermo_widget = DownloadThermoWidget(T, F, E, Cv)
+
                 phonon_children += (
                     g,
                     downloadThermo_widget,
@@ -179,16 +162,14 @@ def _update_view(self):
         if ins_data:
             intensity_maps = EuphonicSuperWidget(fc=ins_data["fc"])
             children_result_widget += (intensity_maps,)
-            tab_titles.append(f"Inelastic Neutrons")
+            tab_titles.append("Inelastic Neutrons")
 
         if spectra_data:
-
             # Here we should provide the possibility to have both IR and Raman,
             # as the new logic can provide both at the same time.
             # We are gonna use the same widget, providing the correct spectrum_type: "Raman" or "Ir".
             children_spectra = ()
             for spectrum, data in spectra_data.items():
-
                 if not data:
                     continue
 
@@ -223,29 +204,23 @@ def _update_view(self):
                     ),
                 ),
             )
-            tab_titles.append(f"Raman/IR spectra")
-
-            #create and VBox
-            my_VBox = ipw.VBox(children=children_spectra, layout=ipw.Layout(width="100%"))
+            tab_titles.append("Raman/IR spectra")
 
         if dielectric_data:
-
             dielectric_results = DielectricResults(dielectric_data)
             children_result_widget += (dielectric_results,)
             tab_titles.append("Dielectric properties")
 
-
-
         self.result_tabs = ipw.Tab(children=children_result_widget)
 
         for title_index in range(len(tab_titles)):
             self.result_tabs.set_title(title_index, tab_titles[title_index])
 
         self.children = [self.result_tabs]
 
+
 class DownloadBandsPdosWidget(ipw.HBox):
     def __init__(self, data, **kwargs):
-
         self.download_button = ipw.Button(
             description="Download phonon bands and pdos data",
             icon="pencil",
@@ -268,6 +243,7 @@ def download_data(self, _=None):
         import json
         from monty.json import jsanitize
         import base64
+
         file_name_bands = "phonon_bands_data.json"
         file_name_pdos = "phonon_dos_data.json"
         if self.bands_data[0]:
@@ -298,16 +274,13 @@ def _download(payload, filename):
             document.body.appendChild(link);
             link.click();
             document.body.removeChild(link);
-            """.format(
-                payload=payload, filename=filename
-            )
+            """.format(payload=payload, filename=filename)
         )
         display(javas)
-
-class DownloadThermoWidget(ipw.HBox):
-
-    def __init__(self, T,F,E,Cv, **kwargs):
 
+
+class DownloadThermoWidget(ipw.HBox):
+    def __init__(self, T, F, E, Cv, **kwargs):
         self.download_button = ipw.Button(
             description="Download thermal properties data",
             icon="pencil",
@@ -316,7 +289,7 @@ def __init__(self, T,F,E,Cv, **kwargs):
             layout=ipw.Layout(width="auto"),
         )
         self.download_button.on_click(self.download_data)
-        
+
         self.temperature = T
         self.free_E = F
         self.entropy = E
@@ -331,14 +304,19 @@ def __init__(self, T,F,E,Cv, **kwargs):
     def download_data(self, _=None):
         """Function to download the phonon data."""
         import json
-        from monty.json import jsanitize
         import base64
+
         file_name = "phonon_thermo_data.json"
         data_export = {}
         for key, value in zip(
-            ["Temperature (K)","Helmoltz Free Energy (kJ/mol)",
-             "Entropy (J/K/mol)","Specific Heat-V=const (J/K/mol)"],
-            [self.temperature, self.free_E,self.entropy, self.Cv]):
+            [
+                "Temperature (K)",
+                "Helmoltz Free Energy (kJ/mol)",
+                "Entropy (J/K/mol)",
+                "Specific Heat-V=const (J/K/mol)",
+            ],
+            [self.temperature, self.free_E, self.entropy, self.Cv],
+        ):
             if isinstance(value, np.ndarray):
                 data_export[key] = value.tolist()
             else:
@@ -347,7 +325,6 @@ def download_data(self, _=None):
         json_str = json.dumps(data_export)
         b64_str = base64.b64encode(json_str.encode()).decode()
         self._download(payload=b64_str, filename=file_name)
-
 
     @staticmethod
     def _download(payload, filename):
@@ -361,8 +338,6 @@ def _download(payload, filename):
             document.body.appendChild(link);
             link.click();
             document.body.removeChild(link);
-            """.format(
-                payload=payload, filename=filename
-            )
+            """.format(payload=payload, filename=filename)
         )
-        display(javas)
+        display(javas)