Update linters, switch black to ruff format (#225)

* Bump ruff to v0.1.1 * Enable ruff autofixes through pre-commit * Use ruff format instead of black * Add new hooks from pre-commit-hooks * Add badges to README * Add check for large files
ispg-group · Oct 22, 2023 · 8de5700 · 8de5700
1 parent 54081f8
commit 8de5700
Show file tree

Hide file tree

Showing 17 changed files with 84 additions and 78 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -9,24 +9,14 @@ on:
     tags:
       - "v*"
   pull_request:
-    branches:
-      - "*"
 
 jobs:
 
   pre-commit:
     runs-on: ubuntu-latest
     steps:
       - name: Check out app
-        uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-            python-version: "3.10"
-            cache: "pip"
-            cache-dependency-path: |
-              **/setup.cfg
-              **/pyproject.toml
+        uses: actions/checkout@v4
       - name: Run pre-commit
         uses: pre-commit/[email protected]
 
@@ -60,7 +50,7 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check out app
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v4

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,27 @@
+default_language_version:
+    # all hooks should run with python 3.6+
+    python: python3
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.6+
+      - id: no-commit-to-branch
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-added-large-files
+        args: ['--maxkb=500', '--enforce-all']
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: check-yaml
+      - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.270
+    rev: v0.1.1
     hooks:
     - id: ruff
-      args: [--show-source]
+      args: [--show-source, --fix]
+    - id: ruff-format
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1

diff --git a/README.md b/README.md
@@ -1,3 +1,7 @@
+[![CI](https://github.com/ispg-group/aiidalab-ispg/workflows/CI/badge.svg?branch=main&event=push)](https://github.com/ispg-group/aiidalab-ispg/actions?query=workflow%3ACI)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
 # AiiDAlab ISPG applications
 
 ATMOSPEC - ab initio workflow for UV/VIS spectroscopy of organic molecules.

diff --git a/aiidalab_ispg/app/experimental_spectra/acrolein.yaml b/aiidalab_ispg/app/experimental_spectra/acrolein.yaml
@@ -15,7 +15,7 @@ metadata:
       - "G.K. Moortgat"
       - "K. Wirtz"
     title: "A study of the photolysis and OH-initiated oxidation of acrolein and trans-crotonaldehyde"
-    journal:  "J. Phys. Chem. A" 
+    journal:  "J. Phys. Chem. A"
     issue: "106"
     pages: "2526-2537"
     year: "2002"

diff --git a/aiidalab_ispg/app/experimental_spectra/glycolaldehyde.yaml b/aiidalab_ispg/app/experimental_spectra/glycolaldehyde.yaml
@@ -1,5 +1,5 @@
 ---
-molecule: glycolaldehyde 
+molecule: glycolaldehyde
 smiles: "O=CCO"
 source_file: glycolaldehyde.txt
 metadata:
@@ -11,7 +11,7 @@ metadata:
       - "Tyndall, G.S."
       - "Orlando, J.J."
     title: "The Atmospheric Chemistry of Glycolaldehyde"
-    journal:  "J. Atmos. Chem." 
+    journal:  "J. Atmos. Chem."
     issue: "39"
     pages: "171-189"
     year: "2001"

diff --git a/aiidalab_ispg/app/experimental_spectra/methylhydroperoxide.yaml b/aiidalab_ispg/app/experimental_spectra/methylhydroperoxide.yaml
@@ -4,7 +4,7 @@ smiles: "COO"
 source_file: methylhydroperoxide.txt
 y_axis_scaling: 1e-20
 metadata:
-  description: 'H3OOH absorption spectrum from IUPAC97, originally from Vaghjiani and Ravishankara (1989)' 
+  description: 'H3OOH absorption spectrum from IUPAC97, originally from Vaghjiani and Ravishankara (1989)'
   license: '?'
   source:
     db_name: 'Andrew`s data'
diff --git a/aiidalab_ispg/app/qeapp/process.py b/aiidalab_ispg/app/qeapp/process.py
@@ -31,8 +31,8 @@ class WorkChainSelector(ipw.HBox):
 
     BASE_FMT_WORKCHAIN = "{wc.pk:6}{wc.ctime:>10}\t{wc.state:<16}"
 
-    BASE_FIELDS = [("pk", int), ("ctime", str), ("state", str)]
-    extra_fields: Optional[list] = None
+    _BASE_FIELDS = (("pk", int), ("ctime", str), ("state", str))
+    extra_fields: Optional[tuple] = None
 
     def __init__(self, process_label, **kwargs):
         self.process_label = process_label
@@ -48,7 +48,7 @@ def __init__(self, process_label, **kwargs):
         )
 
         if self.extra_fields is not None:
-            fmt_extra = "".join([f"{{wc.{field[0]}}}\t" for field in self.extra_fields])
+            fmt_extra = "\t".join(f"{{wc.{field[0]}}}" for field in self.extra_fields)
             self.fmt_workchain = self.BASE_FMT_WORKCHAIN + "\t" + fmt_extra
         else:
             self.fmt_workchain = self.BASE_FMT_WORKCHAIN
@@ -95,11 +95,11 @@ def find_work_chains(self):
                 pk = process_info["pk"]
                 extra_info = self.parse_extra_info(pk)
 
-                yield make_dataclass("WorkChain", self.BASE_FIELDS + self.extra_fields)(
-                    **process_info, **extra_info
-                )
+                yield make_dataclass(
+                    "WorkChain", self._BASE_FIELDS + self.extra_fields
+                )(**process_info, **extra_info)
             else:
-                yield make_dataclass("WorkChain", self.BASE_FIELDS)(**process_info)
+                yield make_dataclass("WorkChain", self._BASE_FIELDS)(**process_info)
 
     @tl.default("busy")
     def _default_busy(self):

diff --git a/aiidalab_ispg/app/qeapp/structures.py b/aiidalab_ispg/app/qeapp/structures.py
@@ -60,7 +60,7 @@ def __init__(self, manager, description=None, **kwargs):
                 self.message_area,
                 self.confirm_button,
             ],
-            **kwargs
+            **kwargs,
         )
 
     @traitlets.default("state")

diff --git a/aiidalab_ispg/app/spectrum.py b/aiidalab_ispg/app/spectrum.py
@@ -196,7 +196,7 @@ class SpectrumWidget(ipw.VBox):
     # https://docs.bokeh.org/en/latest/docs/user_guide/tools.html?highlight=tools#specifying-tools
     _TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
     # https://docs.bokeh.org/en/latest/docs/user_guide/tools.html?highlight#hovertool
-    _TOOLTIPS = [("(energy, cross_section)", "($x,$y)")]
+    _TOOLTIPS = (("(energy, cross_section)", "($x,$y)"),)
 
     def __init__(self, **kwargs):
         self.width_slider = ipw.FloatSlider(
@@ -279,7 +279,7 @@ def __init__(self, **kwargs):
             "width": 500,
         }
         self.figure = self._init_figure(
-            tools=self._TOOLS, tooltips=self._TOOLTIPS, **figure_size
+            tools=self._TOOLS, tooltips=list(self._TOOLTIPS), **figure_size
         )
         self.figure.layout = ipw.Layout(overflow="initial")
 

diff --git a/aiidalab_ispg/app/static/StandardActinicFluxes2.csv b/aiidalab_ispg/app/static/StandardActinicFluxes2.csv
@@ -468,4 +468,4 @@ WL,WU,wc,L90_500,M60_350,H0_200
 746,747,746.5,1.754E+14,5.176E+14,5.836E+14
 747,748,747.5,1.774E+14,5.213E+14,5.876E+14
 748,749,748.5,1.787E+14,5.222E+14,5.885E+14
-749,750,749.5,1.762E+14,5.116E+14,5.764E+14
+749,750,749.5,1.762E+14,5.116E+14,5.764E+14
diff --git a/aiidalab_ispg/app/widgets.py b/aiidalab_ispg/app/widgets.py
@@ -46,12 +46,12 @@
 
 
 class ISPGWorkChainSelector(WorkChainSelector):
-    extra_fields = [
+    extra_fields = (
         ("formula", str),
         ("method", str),
         ("label", str),
         ("description", str),
-    ]
+    )
 
     def __init__(self, process_label: str, **kwargs):
         super().__init__(process_label=process_label, **kwargs)
@@ -170,7 +170,8 @@ class TrajectoryDataViewer(StructureDataViewer):
     trajectory = traitlets.Instance(Node, allow_none=True)
     selected_structure_id = traitlets.Int(allow_none=True)
 
-    _structures: list[StructureData] = []
+    # TODO: Should probably be tuple instead
+    _structures: list[StructureData] = []  # noqa: RUF012
     _energies: Optional[np.ndarray] = None
     _boltzmann_weights: Optional[np.ndarray] = None
 
@@ -285,9 +286,7 @@ def _update_trajectory(self, change):
     def _update_structure_viewer(self, change):
         """Update the view if displayed_structure trait was modified."""
         with self.hold_trait_notifications():
-            for (
-                comp_id
-            ) in self._viewer._ngl_component_ids:  # pylint: disable=protected-access
+            for comp_id in self._viewer._ngl_component_ids:  # pylint: disable=protected-access
                 self._viewer.remove_component(comp_id)
             self.selection = []
             if change["new"] is not None:
@@ -316,7 +315,7 @@ def _prepare_payload(self, file_format=None):
 # NOTE: TrajectoryManagerWidget will hopefully note be necessary once
 # the trajectory viewer is merged to AWB
 class TrajectoryManagerWidget(StructureManagerWidget):
-    SUPPORTED_DATA_FORMATS = {
+    SUPPORTED_DATA_FORMATS = {  # noqa: RUF012
         "CifData": "core.cif",
         "StructureData": "core.structure",
         "TrajectoryData": "core.array.trajectory",
@@ -398,9 +397,7 @@ def _convert_to_structure_node(self, structure):
         """Convert structure of any type to the StructureNode object."""
         if structure is None:
             return None
-        structure_node_type = DataFactory(
-            self.SUPPORTED_DATA_FORMATS[self.node_class]
-        )  # pylint: disable=invalid-name
+        structure_node_type = DataFactory(self.SUPPORTED_DATA_FORMATS[self.node_class])  # pylint: disable=invalid-name
 
         # If the input_structure trait is set to Atoms object, structure node must be created from it.
         if isinstance(structure, Atoms):

diff --git a/aiidalab_ispg/workflows/utils.py b/aiidalab_ispg/workflows/utils.py
@@ -118,7 +118,7 @@ def extract_trajectory_arrays(**orca_output_parameters) -> ArrayData:
     en0 = min(gibbs_energies)
     relative_gibbs_energies_kj = AUtoKJ * (gibbs_energies - en0)
 
-    temperature = list(orca_output_parameters.values())[0]["temperature"]
+    temperature = next(iter(orca_output_parameters.values()))["temperature"]
 
     boltzmann_weights = calc_boltzmann_weights(relative_gibbs_energies_kj, temperature)
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -8,31 +8,35 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.ruff]
-# Enable pyflakes and pyf-builtins, pyflakes, f=bugbear 
+line-length = 88
+# TODO: Enable ruff for notebooks
+src = ["aiidalab_ispg", "tests"]
+target-version = "py39"
+
+# Enable pyflakes and pyf-builtins, pyflakes, f=bugbear
 select = [
-    "A", # flake8-builtins
-    "B", # flake8-bugbear
-    "E", # pycodestyle
-    "F", # pyflakes
-    "C90", # McCabe code complexity
-    "UP", # pyupgrade
-    "S", # bandit
-    "C4", # comprehensiosn 
-    "EM", # errormsg
-    "ISC", # implicit concatenation
-    "ICN", # import convention
-    "INP", # no implicite namespace package
-    "PIE", # 
-    "PT", # pytest style
+    "A",    # flake8-builtins
+    "B",    # flake8-bugbear
+    "E",    # pycodestyle
+    "F",    # pyflakes
+    "C90",  # McCabe code complexity
+    "UP",   # pyupgrade
+    "S",    # bandit
+    "C4",   # comprehensions
+    "EM",   # errormsg
+    "ISC",  # implicit concatenation
+    "ICN",  # import convention
+    "INP",  # no implicite namespace package
+    "PIE",  #
+    "PT",   # pytest style
     "PTH",
-    # "PL", # pylint, for now disabled
+    "PLC",
+    "PLE",
+    "PLW",
+    "RUF",
+    # "PL",  # pylint, disabled for now
     # "PLR", # pylint refactor
-    "PLC", "PLE", "PLW",
-    "RUF", # ruff
 ]
-line-length = 120
-src = ["aiidalab_ispg", "tests"]
-target-version = "py39"
 
 # Never enforce `E501` (line length violations).
 # TODO: Remove all asserts from the codebase and enable this rule

diff --git a/tests/app/test_app.py b/tests/app/test_app.py
diff --git a/tests/wigner/wigner_test/freq_g09.molden b/tests/wigner/wigner_test/freq_g09.molden
@@ -15,7 +15,7 @@ scf-first    1 THROUGH   12
    -108.933430
 [GEOMETRIES] XYZ
     7
- 
+
  C    -1.115872    -0.220612     0.023971
  O     0.021884     0.600791    -0.024280
  O     1.147735    -0.274299    -0.097254