ENH: Add Ruff Formatter and Linter

.github/workflows/tap-cmp.yml → .github/workflows/code-checks.yml

@@ -1,5 +1,5 @@
-# This workflow will compare tapenade file.
-name: Tapenade Comparison
+# This workflow will check code (tapenade compare and ruff check)
+name: Code Checks
 
 on:
 
@@ -25,11 +25,26 @@ jobs:
 
         steps:
         - uses: actions/checkout@v3
+
+        - name: Set up Python
+          uses: actions/setup-python@v4
+          with:
+            python-version: "3.11"
+
         - name: Install dependencies
           run: |
             sudo apt-get update -y
             sudo apt-get install build-essential make openjdk-11-jre-headless
+            python -m venv test
+            . test/bin/activate
+            python -m pip install --upgrade pip
+            pip install ruff
 
-        - name: Compare
+        - name: Tapenade Compare
           run: |
             make tap-cmp
+
+        - name: Ruff Check
+          run: |
+            . test/bin/activate
+            make check

dependencies.py

@@ -65,13 +65,15 @@ def find_use_statement(f: pathlib.PosixPath) -> set[str]:
 
     Notes
     -----
-    An explanation of the pattern: r"^(?!\s*[!]).*?use\s+(\w+)"
+    An explanation of the pattern: r"^(?!\\s*[!]).*?use\\s+(\\w+)"
 
     - ^ : Matches the start of a line
-    - (?!\s*[!]) : Negative lookahead that excludes matches with ! after zero or more whitespace characters (\s)
-    - .*? : Lazy match of any character (.) zero or more times (*) until it encounters the next part of the pattern
-    - use\s+ : Matches the string "use" followed by one or more whitespace characters (\s)
-    - (\w+) : Captures one or more word characters (\w+) after "use" as a group
+    - (?!\\s*[!]) : Negative lookahead that excludes matches with ! after zero or more whitespace characters
+      (\\s)
+    - .*? : Lazy match of any character (.) zero or more times (*) until it encounters the next part of the
+      pattern
+    - use\\s+ : Matches the string "use" followed by one or more whitespace characters (\\s)
+    - (\\w+) : Captures one or more word characters (\\w+) after "use" as a group
 
     So this regex pattern looks for lines that start with "use" followed by one or more whitespace characters,
     but excludes lines that have a comment symbol (!) before the "use".
@@ -109,7 +111,7 @@ def get_dependencies(files: list[pathlib.PosixPath]) -> dict[list]:
     """
     ret = {}
 
-    for i, f in enumerate(files):
+    for f in files:
         deps = find_use_statement(f)
 
         ret.update({f.stem: deps})
@@ -131,7 +133,8 @@ def sort_by_dependencies(files: list[pathlib.PosixPath]):
     -----
     The sorting algorithm is applied sequentially for each module and there is the explanation for one:
     - We look first for it's dependencies and we move the module behind each dependency (Forward loop)
-    - We look for dependencies for the current module in other module and we move the current module above each dependency (Backward loop)
+    - We look for dependencies for the current module in other module and we move the current module above
+      each dependency (Backward loop)
     """
 
     # % Get dependencies dictionary
@@ -178,14 +181,13 @@ def sort_by_dependencies(files: list[pathlib.PosixPath]):
 if __name__ == "__main__":
     fcore_path = pathlib.Path("smash/fcore/")
 
-    # % The files are presorted to avoid the randomness that makes the order of dependencies change even if there are no new files.
+    # % The files are presorted to avoid the randomness that makes the order of dependencies change even if
+    # % there are no new files.
     # % There can be several ways to sort files by dependencies
-    c_files = sorted(list(fcore_path.glob("*/*.c")))
-    f77_files = sorted(list(fcore_path.glob("*/*.f")))
+    c_files = sorted(fcore_path.glob("*/*.c"))
+    f77_files = sorted(fcore_path.glob("*/*.f"))
     # % In case we have generated f90wrap files we must remove them
-    f90_files = sorted(
-        list(set(fcore_path.glob("*/*.f90")) - set(fcore_path.glob("f90wrap/*.f90")))
-    )
+    f90_files = sorted(set(fcore_path.glob("*/*.f90")) - set(fcore_path.glob("f90wrap/*.f90")))
 
     sort_by_dependencies(f90_files)
 

doc/gen_dataset.py

@@ -1,13 +1,12 @@
-import os
 import argparse
+import os
 
 DATASET = ["Cance", "France", "Lez"]
 DATASET_PATH = f"{os.path.dirname(os.path.realpath(__file__))}/../smash/factory/dataset"
 
 # TODO: Refactorize this when it gets more complicated. Pass to each dataset the files or directories
 # that we want to be uploaded and used in the documentation.
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser()
 
     parser.add_argument(
@@ -40,13 +39,12 @@
         os.system(f"cp -r {DATASET_PATH}/{ds}/pet {DATASET_PATH}/{ds}/prcp {ds_dir}/.")
 
         if ds == "Cance":
-            os.system(
-                f"cp -r {DATASET_PATH}/{ds}/qobs {DATASET_PATH}/{ds}/gauge_attributes.csv {ds_dir}/."
-            )
+            os.system(f"cp -r {DATASET_PATH}/{ds}/qobs {DATASET_PATH}/{ds}/gauge_attributes.csv {ds_dir}/.")
 
         elif ds == "Lez":
             os.system(
-                f"cp -r {DATASET_PATH}/{ds}/qobs {DATASET_PATH}/{ds}/gauge_attributes.csv {DATASET_PATH}/{ds}/descriptor {ds_dir}/."
+                f"cp -r {DATASET_PATH}/{ds}/qobs {DATASET_PATH}/{ds}/gauge_attributes.csv "
+                f"{DATASET_PATH}/{ds}/descriptor {ds_dir}/."
             )
 
         if args.tar:

doc/source/_ext/custom_options_directive.py

@@ -1,3 +1,5 @@
+# ruff: noqa
+
 import pydoc
 import sphinx
 import inspect
@@ -52,9 +54,7 @@ class SmashModelOptimize(PythonDomain):
     def __init__(self, *a, **kw):
         super().__init__(*a, **kw)
         self.directives = dict(self.directives)
-        self.directives["function"] = wrap_mangling_directive(
-            self.directives["function"]
-        )
+        self.directives["function"] = wrap_mangling_directive(self.directives["function"])
 
 
 class SmashNetAdd(PythonDomain):
@@ -63,9 +63,7 @@ class SmashNetAdd(PythonDomain):
     def __init__(self, *a, **kw):
         super().__init__(*a, **kw)
         self.directives = dict(self.directives)
-        self.directives["function"] = wrap_mangling_directive(
-            self.directives["function"]
-        )
+        self.directives["function"] = wrap_mangling_directive(self.directives["function"])
 
 
 class SmashNetCompile(PythonDomain):
@@ -74,9 +72,7 @@ class SmashNetCompile(PythonDomain):
     def __init__(self, *a, **kw):
         super().__init__(*a, **kw)
         self.directives = dict(self.directives)
-        self.directives["function"] = wrap_mangling_directive(
-            self.directives["function"]
-        )
+        self.directives["function"] = wrap_mangling_directive(self.directives["function"])
 
 
 BLURB = """
@@ -107,9 +103,7 @@ def run(self):
             # Format signature taking implementation into account
             args = list(args)
 
-            if (
-                defaults is not None
-            ):  # only remove args and set default if defaults is not None
+            if defaults is not None:  # only remove args and set default if defaults is not None
                 defaults = list(defaults)
 
                 def set_default(arg, value):
@@ -134,9 +128,7 @@ def remove_arg(arg):
                         options.append(
                             (
                                 opt_name,
-                                impl_defaults[
-                                    len(impl_defaults) - (len(impl_args) - j)
-                                ],
+                                impl_defaults[len(impl_defaults) - (len(impl_args) - j)],
                             )
                         )
                     else:
@@ -167,10 +159,7 @@ def remove_arg(arg):
                 for parameters in signature.parameters.values():
                     if parameters.name == "self":
                         continue
-                    elif (
-                        parameters.name == "mapping"
-                        and self.options["alg"] == "l-bfgs-b"
-                    ):
+                    elif parameters.name == "mapping" and self.options["alg"] == "l-bfgs-b":
                         default = "'distributed'"
                     elif parameters.name == "optimizer":
                         default = f"'{self.options['opt']}'"

doc/source/conf.py

@@ -10,11 +10,11 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import inspect
 import os
+import pathlib
 import sys
 import warnings
-import inspect
-import pathlib
 
 import smash
 

doc/source/contributor_guide/development_process_details.rst

@@ -84,6 +84,16 @@ of each command, please look directly at the makefile.
     and an hdf5 file storing the new baseline (``new_baseline.hdf5``). Once you have ensured that all tests are successfully passed,
     rename the ``new_baseline.hdf5`` file to ``baseline.hdf5`` and remove the previous version.
 
+- ``format``
+    Format Python and Fortran files. Python files are formatted with `Ruff <https://docs.astral.sh/ruff/formatter/>`__
+    and Fortran files are formatted with `Fprettify <https://github.com/pseewald/fprettify/>`__.
+    Ruff formatter and fprettify options can be found, respectively, in the ``pyproject.toml`` file and ``makefile``
+
+- ``check``
+    Check Python files. Pythons files are checked with `Ruff <https://docs.astral.sh/ruff/linter/>`__.
+    Ruff linters rules can be found in the ``pyproject.toml`` file. This checks are also run in the continuous
+    integration service (``CI``).
+
 Fortran guideline
 -----------------
 

doc/source/gen_rst.py

@@ -1,5 +1,5 @@
-import sys
 import pathlib
+import sys
 
 if __name__ == "__main__":
     if len(sys.argv) < 2:
@@ -13,20 +13,14 @@
         exists_input = input("Overwrite existing file ([y]/n) ? ")
 
         if exists_input.lower() not in ["", "y", "yes"]:
-            exit(0)
+            sys.exit(0)
 
     file_path.parent.mkdir(exist_ok=True)
 
     if file_path.stem == "index":
         rst_label = ".. _" + str(file_path.parent).replace("/", ".") + ":"
     else:
-        rst_label = (
-            ".. _"
-            + str(file_path.parent).replace("/", ".")
-            + "."
-            + file_path.stem
-            + ":"
-        )
+        rst_label = ".. _" + str(file_path.parent).replace("/", ".") + "." + file_path.stem + ":"
 
     rst_main_title = " ".join(word.capitalize() for word in file_path.stem.split("_"))
     len_rst_main_title = len(rst_main_title)

environment-dev.yml

@@ -37,5 +37,5 @@ dependencies:
     - pytest-cov
 
     # format
-    - black
+    - ruff
     - fprettify