Rudimentary version for symlinks

benchcab/benchcab.py

@@ -28,7 +28,7 @@
 from benchcab.utils.pbs import render_job_script
 from benchcab.utils.repo import create_repo
 from benchcab.utils.subprocess import SubprocessWrapper, SubprocessWrapperInterface
-from benchcab.workdir import setup_fluxsite_directory_tree
+from benchcab.workdir import clean_directory_tree, clean_cwd_logfiles, setup_fluxsite_directory_tree
 
 
 class Benchcab:
@@ -308,6 +308,11 @@ def fluxsite(self, config_path: str, no_submit: bool, skip: list[str]):
         else:
             self.fluxsite_submit_job(config_path, skip)
 
+    def clean(self, config_path: str):
+        """Endpoint for cleaning runs uirectory ig."""
+        clean_directory_tree()
+        clean_cwd_logfiles()
+
     def spatial(self, config_path: str):
         """Endpoint for `benchcab spatial`."""
 

benchcab/cli.py

@@ -199,4 +199,15 @@ def generate_parser(app: Benchcab) -> argparse.ArgumentParser:
     )
     parser_spatial.set_defaults(func=app.spatial)
 
+    # subcommand: 'benchcab clean'
+    parser_spatial = subparsers.add_parser(
+        "clean",
+        parents=[args_help, args_subcommand],
+        help="Cleanup files created by running benchcab.",
+        description="""Removes src/ and runs/ directories, along with log files in the 
+        project root directory.""",
+        add_help=False,
+    )
+    parser_spatial.set_defaults(func=app.clean)
+
     return main_parser

benchcab/data/config-schema.yml

@@ -24,7 +24,7 @@ realisations:
         schema:
           git:
             type: "dict"
-            excludes: "svn"
+            excludes: ["svn", "local"]
             schema:
               branch:
                 type: "string"
@@ -37,13 +37,20 @@ realisations:
                 required: false
           svn:
             type: "dict"
-            excludes: "git"
+            excludes: ["git", "local"]
             schema:
               branch_path:
                 type: "string"
                 required: true
               revision:
                 type: "integer"
+          local:
+            type: "dict"
+            excludes: ["git", "svn"]
+            schema:
+              local_path:
+                type: "string"
+                required: true
       name:
         nullable: true
         type: "string"

benchcab/model.py

@@ -14,7 +14,7 @@
 from benchcab.environment_modules import EnvironmentModules, EnvironmentModulesInterface
 from benchcab.utils import get_logger
 from benchcab.utils.fs import chdir, copy2, rename
-from benchcab.utils.repo import GitRepo, Repo
+from benchcab.utils.repo import GitRepo, LocalRepo, Repo
 from benchcab.utils.subprocess import SubprocessWrapper, SubprocessWrapperInterface
 
 
@@ -62,7 +62,7 @@ def __init__(
         # TODO(Sean) we should not have to know whether `repo` is a `GitRepo` or
         # `SVNRepo`, we should only be working with the `Repo` interface.
         # See issue https://github.com/CABLE-LSM/benchcab/issues/210
-        if isinstance(repo, GitRepo):
+        if isinstance(repo, (GitRepo, LocalRepo)):
             self.src_dir = Path("src")
 
     @property

benchcab/utils/repo.py

@@ -46,6 +46,49 @@ def get_branch_name(self) -> str:
         """
 
 
+class LocalRepo(Repo):
+    """Concrete implementation of the `Repo` class using local path backend."""
+
+    def __init__(self, local_path: str, path: str) -> None:
+        """Return a LocalRepo instance.
+
+        Parameters
+        ----------
+        path : str
+            Path of local CABLE branch
+        """        
+        self.name = Path(local_path).name
+        self.local_path = local_path
+        self.path = path / self.name if path.is_dir() else path
+        self.logger = get_logger()
+
+    def checkout(self):
+        """Checkout the source code."""
+        self.path.symlink_to(self.local_path)
+        self.logger.info(f"Created symlink from to {self.path} named {self.name}")
+
+    def get_revision(self) -> str:
+        """Return the latest revision of the source code.
+
+        Returns
+        -------
+        str
+            Human readable string describing the latest revision.
+
+        """
+        return f"Using local CABLE branch: {self.name}"
+
+    def get_branch_name(self) -> str:
+        """Return the branch name of the source code.
+
+        Returns
+        -------
+        str
+            Branch name of the source code.
+
+        """
+        return Path(self.path).absolute()
+
 class GitRepo(Repo):
     """A concrete implementation of the `Repo` class using a Git backend.
 
@@ -236,4 +279,6 @@ def create_repo(spec: dict, path: Path) -> Repo:
         return GitRepo(path=path, **spec["git"])
     if "svn" in spec:
         return SVNRepo(svn_root=internal.CABLE_SVN_ROOT, path=path, **spec["svn"])
+    if "local" in spec:
+        return LocalRepo(path=path, **spec["local"])
     raise RepoSpecError

benchcab/workdir.py

@@ -8,15 +8,23 @@
 from benchcab import internal
 from benchcab.utils.fs import mkdir
 
-
 def clean_directory_tree():
-    """Remove pre-existing directories in current working directory."""
+    """Remove pre-existing directories and log files in current working directory."""
     if internal.SRC_DIR.exists():
+        for realisation in internal.SRC_DIR.iterdir():
+            if realisation.is_symlink():
+                realisation.unlink()
         shutil.rmtree(internal.SRC_DIR)
 
     if internal.RUN_DIR.exists():
         shutil.rmtree(internal.RUN_DIR)
+
+def clean_cwd_logfiles():
+    for rev_log_file in internal.CWD.glob("rev_number-*.log"):
+        rev_log_file.unlink()
 
+    for pbs_job_file in internal.CWD.glob("benchcab_cable_qsub.sh*"):
+        pbs_job_file.unlink()
 
 def setup_fluxsite_directory_tree():
     """Generate the directory structure used by `benchcab`."""

tests/test_workdir.py

@@ -6,11 +6,13 @@
 """
 
 from pathlib import Path
+from benchcab import internal
 
 import pytest
 
 from benchcab.workdir import (
     clean_directory_tree,
+    clean_cwd_logfiles,
     setup_fluxsite_directory_tree,
 )
 
@@ -37,12 +39,22 @@ def test_directory_structure_generated(self, fluxsite_directory_list):
             assert path.exists()
 
 
-class TestCleanDirectoryTree:
-    """Tests for `clean_directory_tree()`."""
+class TestCleanFiles:
+    """Tests for `clean_directory_tree()` and `clean_cwd_logfiles)."""
 
     @pytest.mark.parametrize("test_path", [Path("runs"), Path("src")])
     def test_clean_directory_tree(self, test_path):
         """Success case: directory tree does not exist after clean."""
         test_path.mkdir()
         clean_directory_tree()
         assert not test_path.exists()
+
+    @pytest.mark.parametrize("test_path", [Path("rev_number-200.log"), Path("benchcab_cable_qsub.sh.o21871")])
+    def test_clean_directory_tree(self, test_path: Path, monkeypatch):
+        """Success case: log files in project root directory do not exist after clean."""
+        monkeypatch.setattr(internal, "CWD", Path.cwd())
+        test_path.touch()
+        clean_cwd_logfiles()
+
+        assert not test_path.exists()
+