pre-commit fix

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+---
+# Run basic tests for this app on the latest aiidalab-docker image.
+
+name: continuous-integration
+
+on: [push, pull_request]
+
+jobs:
+
+    pre-commit:
+    # Adapted from: https://github.com/CasperWA/voila-optimade-client
+
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Setup Python
+              uses: actions/setup-python@v2
+              with:
+                  python-version: 3.8
+
+            - name: Install dependencies
+              run: |
+                  python -m pip install pre-commit==2.11.1
+            - name: Run pre-commit
+              run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/release.yml

@@ -0,0 +1,23 @@
+---
+name: Release
+
+on:
+    push:
+        tags:
+            - v*
+        branches:
+            - release/*
+
+jobs:
+
+    publish:
+
+        runs-on: ubuntu-latest
+
+        steps:
+
+            - uses: softprops/action-gh-release@v0.1.14
+              name: Create release
+              if: startsWith(github.ref, 'refs/tags/v')
+              with:
+                  generate_release_notes: true

.gitignore

@@ -12,4 +12,4 @@
 build
 
 .vscode
-pseduos_json_demo/*
+pseduos_json_demo/*

.pre-commit-config.yaml

@@ -1,22 +1,45 @@
-# Install pre-commit hooks via:
-# pre-commit install
-
-# yapf = yet another python formatter
+---
 repos:
-- repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.30.0
-  hooks:
-  - id: yapf
-    name: yapf
-    args: ["-i"]
 
--   repo: https://github.com/PyCQA/pylint
-    rev: pylint-2.6.0
-    hooks:
-    -   id: pylint
-        language: system
-        exclude: &exclude_files >
-          (?x)^(
-              start.py|
-              tests/.*(?<!\.py)$
-          )$
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.1.0
+      hooks:
+          - id: check-json
+          - id: check-yaml
+          - id: end-of-file-fixer
+          - id: trailing-whitespace
+
+    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+      rev: 0.1.0
+      hooks:
+          - id: yamlfmt
+
+    - repo: https://github.com/psf/black
+      rev: 22.1.0
+      hooks:
+          - id: black
+            language_version: python3 # Should be a command that runs python3.6+
+
+    - repo: https://github.com/PyCQA/flake8
+      rev: 4.0.1
+      hooks:
+          - id: flake8
+            args: [--count, --show-source, --statistics]
+            additional_dependencies:
+                - flake8-bugbear==21.3.1
+
+    - repo: https://github.com/pycqa/isort
+      rev: 5.10.1
+      hooks:
+          - id: isort
+            args: [--profile, black, --filter-files]
+
+    - repo: https://github.com/asottile/setup-cfg-fmt
+      rev: v1.20.0
+      hooks:
+          - id: setup-cfg-fmt
+
+    - repo: https://github.com/sirosen/check-jsonschema
+      rev: 0.14.0
+      hooks:
+          - id: check-github-workflows

README.md

@@ -31,4 +31,4 @@ MIT
 
 ## Contact
 
-📧 email: jusong.yu@epfl.ch
+📧 email: jusong.yu@epfl.ch

aiidalab_sssp/plot.py

@@ -1,50 +1,55 @@
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+
 
 def delta_measure_hist(pseudos: dict, measure_type):
 
-    px = 1/plt.rcParams['figure.dpi']  # pixel in inches
-    fig, ax = plt.subplots(1, 1, figsize=(1024*px, 360*px))
-    cmap = plt.get_cmap('tab20')
+    px = 1 / plt.rcParams["figure.dpi"]  # pixel in inches
+    fig, ax = plt.subplots(1, 1, figsize=(1024 * px, 360 * px))
+    cmap = plt.get_cmap("tab20")
     NUM_COLOR = 20
-    structures = ['X', 'XO', 'X2O', 'XO3', 'X2O', 'X2O3', 'X2O5']
+    structures = ["X", "XO", "X2O", "XO3", "X2O", "X2O3", "X2O5"]
     num_structures = len(structures)
 
     # element
     try:
         v0 = list(pseudos.values())[0]
-        element = v0['pseudo_info']['element']
-    except:
+        element = v0["pseudo_info"]["element"]
+    except Exception:
         element = None
 
-    if measure_type == 'delta':
-        keyname = 'delta'
-        ylabel = 'Δ -factor'
-    elif measure_type == 'nv_delta':
-        keyname = 'rel_errors_vec_length'
-        ylabel = 'νΔ -factor'
+    if measure_type == "delta":
+        keyname = "delta"
+        ylabel = "Δ -factor"
+    elif measure_type == "nv_delta":
+        keyname = "rel_errors_vec_length"
+        ylabel = "νΔ -factor"
 
     for i, (label, output) in enumerate(pseudos.items()):
         N = len(structures)
-        idx = np.arange(N) # the x locations for the groups
-        width = 0.1       # the width of the bars
+        idx = np.arange(N)  # the x locations for the groups
+        width = 0.1  # the width of the bars
 
         y_delta = []
         for structure in structures:
             try:
-                res = output['delta_factor']['output_delta_analyze'][f'output_{structure}']
+                res = output["delta_factor"]["output_delta_analyze"][
+                    f"output_{structure}"
+                ]
                 y_delta.append(res[keyname])
-            except:
+            except Exception:
                 y_delta.append(-1)
 
-        _, pp_family, pp_z, pp_type, pp_version = label.split('/')
-        out_label = f'{pp_z}/{pp_type}({pp_family}-{pp_version})'
+        _, pp_family, pp_z, pp_type, pp_version = label.split("/")
+        out_label = f"{pp_z}/{pp_type}({pp_family}-{pp_version})"
 
-        ax.bar(idx+width*i, y_delta, width, color=cmap(i/NUM_COLOR), label=out_label)
+        ax.bar(
+            idx + width * i, y_delta, width, color=cmap(i / NUM_COLOR), label=out_label
+        )
         ax.legend()
-        ax.set_title(f'X={element}')
-        
-    ax.axhline(y=1.0, linestyle='--', color='gray')
+        ax.set_title(f"X={element}")
+
+    ax.axhline(y=1.0, linestyle="--", color="gray")
     ax.set_ylabel(ylabel)
     ax.set_ylim([0, 10])
     ax.set_yticks(np.arange(10))
@@ -53,64 +58,79 @@ def delta_measure_hist(pseudos: dict, measure_type):
 
     return fig
 
+
 def convergence(pseudos: dict, wf_name, measure_name, ylabel, threshold=None):
-
-    px = 1/plt.rcParams['figure.dpi']
-    fig, (ax1, ax2) = plt.subplots(1, 2, gridspec_kw={'width_ratios': [2, 1]}, figsize=(1024*px, 360*px))
-    cmap = plt.get_cmap('tab20')
+
+    px = 1 / plt.rcParams["figure.dpi"]
+    fig, (ax1, ax2) = plt.subplots(
+        1, 2, gridspec_kw={"width_ratios": [2, 1]}, figsize=(1024 * px, 360 * px)
+    )
+    cmap = plt.get_cmap("tab20")
     NUM_COLOR = 20
-
 
     for i, (label, output) in enumerate(pseudos.items()):
         # Calculate the avg delta measure value
-        structures = ['X', 'XO', 'X2O', 'XO3', 'X2O', 'X2O3', 'X2O5']
+        structures = ["X", "XO", "X2O", "XO3", "X2O", "X2O3", "X2O5"]
         lst = []
         for structure in structures:
             try:
-                res = output['delta_factor']['output_delta_analyze'][f'output_{structure}']
-                lst.append(res['rel_errors_vec_length'])
-            except:
+                res = output["delta_factor"]["output_delta_analyze"][
+                    f"output_{structure}"
+                ]
+                lst.append(res["rel_errors_vec_length"])
+            except Exception:
                 pass
 
         avg_delta = sum(lst) / len(lst)
 
-
         try:
             res = output[wf_name]
-            x_wfc = res['output_parameters_wfc_test']['ecutwfc']
-            y_wfc = res['output_parameters_wfc_test'][measure_name]
-
-            x_rho = res['output_parameters_rho_test']['ecutrho']
-            y_rho = res['output_parameters_rho_test'][measure_name]
-
-            wfc_cutoff = res['final_output_parameters']['wfc_cutoff']
-
-            _, pp_family, pp_z, pp_type, pp_version = label.split('/')
-            out_label = f'{pp_z}/{pp_type}(νΔ={avg_delta:.2f})({pp_family}-{pp_version})'
-
-            ax1.plot(x_wfc, y_wfc, marker='o', color=cmap(i/NUM_COLOR), label=out_label)
-            ax2.plot(x_rho, y_rho, marker='o', color=cmap(i/NUM_COLOR), label=f'cutoff wfc = {wfc_cutoff} Ry')
-        except:
+            x_wfc = res["output_parameters_wfc_test"]["ecutwfc"]
+            y_wfc = res["output_parameters_wfc_test"][measure_name]
+
+            x_rho = res["output_parameters_rho_test"]["ecutrho"]
+            y_rho = res["output_parameters_rho_test"][measure_name]
+
+            wfc_cutoff = res["final_output_parameters"]["wfc_cutoff"]
+
+            _, pp_family, pp_z, pp_type, pp_version = label.split("/")
+            out_label = (
+                f"{pp_z}/{pp_type}(νΔ={avg_delta:.2f})({pp_family}-{pp_version})"
+            )
+
+            ax1.plot(
+                x_wfc, y_wfc, marker="o", color=cmap(i / NUM_COLOR), label=out_label
+            )
+            ax2.plot(
+                x_rho,
+                y_rho,
+                marker="o",
+                color=cmap(i / NUM_COLOR),
+                label=f"cutoff wfc = {wfc_cutoff} Ry",
+            )
+        except Exception:
             pass
 
     ax1.set_ylabel(ylabel)
-    ax1.set_xlabel('Wavefuntion cutoff (Ry)')
-    ax1.set_title('Fixed rho cutoff at 200 * dual (dual=4 for NC and dual=8 for non-NC)')
+    ax1.set_xlabel("Wavefuntion cutoff (Ry)")
+    ax1.set_title(
+        "Fixed rho cutoff at 200 * dual (dual=4 for NC and dual=8 for non-NC)"
+    )
 
     # ax2.legend(loc='upper left', bbox_to_anchor=(1, 1.0))
     ax1.legend()
 
-    ax2.set_xlabel('Charge density cudoff (Ry)')
-    ax2.set_title('Convergence test at fixed wavefunction cutoff')
+    ax2.set_xlabel("Charge density cudoff (Ry)")
+    ax2.set_title("Convergence test at fixed wavefunction cutoff")
     ax2.legend()
 
     if threshold:
-        ax1.axhline(y=threshold, color='r', linestyle='--')
-        ax2.axhline(y=threshold, color='r', linestyle='--')
+        ax1.axhline(y=threshold, color="r", linestyle="--")
+        ax2.axhline(y=threshold, color="r", linestyle="--")
 
-        ax1.set_ylim(-0.5 * threshold, 10*threshold)
-        ax2.set_ylim(-0.5 * threshold, 10*threshold)
+        ax1.set_ylim(-0.5 * threshold, 10 * threshold)
+        ax2.set_ylim(-0.5 * threshold, 10 * threshold)
 
     plt.tight_layout()
 
-    return fig
+    return fig

aiidalab_sssp/setup_codes.py

@@ -2,10 +2,10 @@
 from pathlib import Path
 from shutil import which
 from subprocess import CalledProcessError, run
-from threading import Thread, Event
+from threading import Event, Thread
 from time import time
-import ipywidgets as ipw
 
+import ipywidgets as ipw
 import traitlets
 from aiida.common.exceptions import NotExistent
 from aiida.orm import load_code
@@ -295,6 +295,7 @@ def _trigger_reinstall(self, _=None):
         FN_DO_NOT_SETUP.unlink()
         self.refresh()
 
+
 class ProgressBar(ipw.HBox):
     class AnimationRate(float):
         pass
@@ -371,4 +372,4 @@ def _observe_value(self, change):
             self._animation_rate = change["new"]
         else:
             self._animation_rate = 0
-            self._progress_bar.value = change["new"]
+            self._progress_bar.value = change["new"]