introduce pre-commit (#38)

* add pre-commit dep

* add ruff hook

* format calculations.py

* format all files

* remove static analysis CI

* remove fmt env and ruff feature

Author: ethan-shanahan

.github/workflows/ci.yml

@@ -6,23 +6,6 @@ on:
 
 jobs:
 
-  static-analysis:
-    name: Perform static analysis
-    runs-on: ubuntu-latest
-    timeout-minutes: 15
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.8.1
-        with:
-          pixi-version: v0.40.2
-          cache: false
-          environments: fmt
-          activate-environment: true
-      - name: Run formatter and linter
-        run: pixi run fmt
-
   docs:
     name: Generate documentation
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.12.0
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format

pyproject.toml

@@ -44,9 +44,6 @@ platforms = ["linux-64"]
 ### pixi: features
 [tool.pixi.feature.py3]
 dependencies = {python = "3.*"}
-[tool.pixi.feature.ruff]
-dependencies = {ruff = "*"}
-tasks = {fmt = "ruff check"}
 [tool.pixi.feature.build]
 pypi-dependencies = {build = "*"}
 tasks = {build-dist = "python -m build"}
@@ -63,12 +60,12 @@ dependencies = {fans = "0.4.*"}
 [tool.pixi.dependencies]
 aiida-core = "2.6.*"
 h5py = "*"
+pre-commit = "*"
 [tool.pixi.pypi-dependencies]
 aiida-fans = { path = ".", editable = true }
 
 ### pixi: environments
 [tool.pixi.environments]
-fmt  = { no-default-feature = true, features = ["py3", "ruff"] } # CI env
 dist = { no-default-feature = true, features = ["py3", "build"] } # CI env
 docs = { no-default-feature = true, features = ["py3", "sphinx"] } # CI env
 tutorial = { features = ["marimo", "fans"] }

src/aiida_fans/calculations.py

@@ -26,10 +26,7 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
         spec.inputs["metadata"]["label"].default = "FANS"
         ## Processing Power
         spec.inputs["metadata"]["options"]["withmpi"].default = True
-        spec.inputs["metadata"]["options"]["resources"].default = {
-            "num_machines": 1,
-            "num_mpiprocs_per_machine": 4
-        }
+        spec.inputs["metadata"]["options"]["resources"].default = {"num_machines": 1, "num_mpiprocs_per_machine": 4}
         ## Filenames
         spec.inputs["metadata"]["options"]["input_filename"].default = "input.json"
         spec.inputs["metadata"]["options"]["output_filename"].default = "output.h5"
@@ -72,14 +69,16 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         """Prepare the calculation for submission."""
         # Stashed Strategy:
         if self.options.stashed_microstructure:
-            ms_filepath: Path = Path(self.inputs.code.computer.get_workdir()) / \
-                                "stash/microstructures" / \
-                                self.inputs.microstructure.file.filename
+            ms_filepath: Path = (
+                Path(self.inputs.code.computer.get_workdir())
+                / "stash/microstructures"
+                / self.inputs.microstructure.file.filename
+            )
             # if microstructure does not exist in stash, make it
             if not ms_filepath.is_file():
                 ms_filepath.parent.mkdir(parents=True, exist_ok=True)
-                with self.inputs.microstructure.file.open(mode='rb') as source:
-                    with ms_filepath.open(mode='wb') as target:
+                with self.inputs.microstructure.file.open(mode="rb") as source:
+                    with ms_filepath.open(mode="wb") as target:
                         copyfileobj(source, target)
 
             # input.json as dict
@@ -90,11 +89,11 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
                 dump(input_dict, json, indent=4)
         # Fragmented Strategy:
         else:
-            datasetname : str = self.inputs.microstructure.datasetname.value
-            with folder.open("microstructure.h5","bw") as f_dest:
-                with h5File(f_dest,"w") as h5_dest:
+            datasetname: str = self.inputs.microstructure.datasetname.value
+            with folder.open("microstructure.h5", "bw") as f_dest:
+                with h5File(f_dest, "w") as h5_dest:
                     with self.inputs.microstructure.file.open(mode="rb") as f_src:
-                        with h5File(f_src,'r') as h5_src:
+                        with h5File(f_src, "r") as h5_src:
                             h5_src.copy(datasetname, h5_dest, name=datasetname)
 
             # input.json as dict
@@ -117,8 +116,6 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         calcinfo.local_copy_list = []
         calcinfo.remote_copy_list = []
         calcinfo.retrieve_list = [codeinfo.stdout_name, codeinfo.stderr_name]
-        calcinfo.retrieve_temporary_list = [
-            self.options.output_filename
-        ]
+        calcinfo.retrieve_temporary_list = [self.options.output_filename]
 
         return calcinfo

src/aiida_fans/helpers.py

@@ -11,9 +11,9 @@ def make_input_dict(job: CalcJob) -> dict[str, Any]:
     return {
         ## Microstructure Definition
         "microstructure": {
-            "filepath": None, # path to stashed microstructure, must be overwritten by impl
+            "filepath": None,  # path to stashed microstructure, must be overwritten by impl
             "datasetname": job.inputs.microstructure.datasetname.value,
-            "L": job.inputs.microstructure.L.get_list()
+            "L": job.inputs.microstructure.L.get_list(),
         },
         "results_prefix": job.inputs.metadata.options.results_prefix,
         ## Problem Type and Material Model
@@ -26,14 +26,15 @@ def make_input_dict(job: CalcJob) -> dict[str, Any]:
         "error_parameters": {
             "measure": job.inputs.error_parameters.measure.value,
             "type": job.inputs.error_parameters.type.value,
-            "tolerance": job.inputs.error_parameters.tolerance.value
+            "tolerance": job.inputs.error_parameters.tolerance.value,
         },
         ## Macroscale Loading Conditions
         "macroscale_loading": job.inputs.macroscale_loading.get_list(),
         ## Results Specification
-        "results": job.inputs.metadata.options.results
+        "results": job.inputs.metadata.options.results,
     }
 
+
 def arraydata_equal(first: dict[str, ndarray], second: dict[str, ndarray]) -> bool:
     """Return whether two dicts of arrays are roughly equal."""
     if first.keys() != second.keys():

src/aiida_fans/parsers.py

@@ -19,17 +19,15 @@ def __init__(self, node: CalcJobNode):
 
     def parse(self, **kwargs) -> ExitCode | None:
         """Parse outputs and store results as nodes."""
-        output_path: Path = Path(kwargs["retrieved_temporary_folder"]) / self.node.get_option("output_filename") # type: ignore
+        output_path: Path = Path(kwargs["retrieved_temporary_folder"]) / self.node.get_option("output_filename")  # type: ignore
         if output_path.is_file():
             self.out("output", node=SinglefileData(output_path))
         else:
             return self.exit_codes.ERROR_MISSING_OUTPUT
 
         with h5File(output_path) as h5:
             results = h5[
-                self.node.inputs.microstructure.datasetname.value + \
-                    "_results/" + \
-                        self.node.get_option('results_prefix')
+                self.node.inputs.microstructure.datasetname.value + "_results/" + self.node.get_option("results_prefix")
             ]
             results.visititems(self.parse_h5)
 

src/aiida_fans/utils.py

@@ -132,10 +132,7 @@ def compile_query(ins: dict[str, Any], qb: QueryBuilder) -> None:
             qb.append(cls=type(v), with_outgoing="calc", filters={"pk": v.pk})
 
 
-def execute_fans(
-    mode: Literal["Submit", "Run"],
-    inputs: dict[str, Any]
-):
+def execute_fans(mode: Literal["Submit", "Run"], inputs: dict[str, Any]):
     """This utility function simplifies the process of executing aiida-fans jobs.
 
     The only nodes you must provide are the `code` and `microstructure` inputs.
@@ -199,15 +196,11 @@ def execute_fans(
                 submit(calcjob, inputs)  # type: ignore
 
 
-def submit_fans(
-    inputs: dict[str, Any]
-):
+def submit_fans(inputs: dict[str, Any]):
     """See `execute_fans` for implementation and usage details."""
     execute_fans("Submit", inputs)
 
 
-def run_fans(
-    inputs: dict[str, Any]
-):
+def run_fans(inputs: dict[str, Any]):
     """See `execute_fans` for implementation and usage details."""
     execute_fans("Run", inputs)