Remove dependence on root directory

This change forces paths to be relative to the CWD throughout the code
base unless absolute paths are required.

Improves code readability and the logging to standard output.

Fixes #162

benchcab/benchcab.py

@@ -33,7 +33,6 @@
 class Benchcab:
     """A class that represents the `benchcab` application."""
 
-    root_dir: Path = internal.CWD
     subprocess_handler: SubprocessWrapperInterface = SubprocessWrapper()
     modules_handler: EnvironmentModulesInterface = EnvironmentModules()
 
@@ -143,10 +142,10 @@ def fluxsite_submit_job(
             msg = "Path to benchcab executable is undefined."
             raise RuntimeError(msg)
 
-        job_script_path = self.root_dir / internal.QSUB_FNAME
+        job_script_path = Path(internal.QSUB_FNAME)
         print(
             "Creating PBS job script to run fluxsite tasks on compute "
-            f"nodes: {job_script_path.relative_to(self.root_dir)}"
+            f"nodes: {job_script_path}"
         )
         with job_script_path.open("w", encoding="utf-8") as file:
             contents = render_job_script(
@@ -202,12 +201,8 @@ def checkout(self, config_path: str, verbose: bool):
         )
         cable_aux_repo.checkout(verbose=verbose)
 
-        rev_number_log_path = self.root_dir / next_path(
-            self.root_dir, "rev_number-*.log"
-        )
-        print(
-            f"Writing revision number info to {rev_number_log_path.relative_to(self.root_dir)}"
-        )
+        rev_number_log_path = next_path("rev_number-*.log")
+        print(f"Writing revision number info to {rev_number_log_path}")
         with rev_number_log_path.open("w", encoding="utf-8") as file:
             file.write(rev_number_log)
 

benchcab/comparison.py

@@ -16,7 +16,6 @@
 class ComparisonTask:
     """A class used to represent a single bitwise comparison task."""
 
-    root_dir: Path = internal.CWD
     subprocess_handler: SubprocessWrapperInterface = SubprocessWrapper()
 
     def __init__(
@@ -42,9 +41,7 @@ def run(self, verbose=False) -> None:
             print(f"Success: files {file_a.name} {file_b.name} are identical")
         except CalledProcessError as exc:
             output_file = (
-                self.root_dir
-                / internal.FLUXSITE_DIRS["BITWISE_CMP"]
-                / f"{self.task_name}.txt"
+                internal.FLUXSITE_DIRS["BITWISE_CMP"] / f"{self.task_name}.txt"
             )
             with output_file.open("w", encoding="utf-8") as file:
                 file.write(exc.stdout)

benchcab/fluxsite.py

@@ -93,7 +93,6 @@ class CableError(Exception):
 class Task:
     """A class used to represent a single fluxsite task."""
 
-    root_dir: Path = internal.CWD
     subprocess_handler: SubprocessWrapperInterface = SubprocessWrapper()
 
     def __init__(
@@ -147,10 +146,7 @@ def setup_task(self, verbose=False):
         self.fetch_files(verbose=verbose)
 
         nml_path = (
-            self.root_dir
-            / internal.FLUXSITE_DIRS["TASKS"]
-            / self.get_task_name()
-            / internal.CABLE_NML
+            internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name() / internal.CABLE_NML
         )
 
         if verbose:
@@ -162,25 +158,26 @@ def setup_task(self, verbose=False):
                     "filename": {
                         "met": str(internal.MET_DIR / self.met_forcing_file),
                         "out": str(
-                            self.root_dir
-                            / internal.FLUXSITE_DIRS["OUTPUT"]
-                            / self.get_output_filename()
+                            (
+                                internal.FLUXSITE_DIRS["OUTPUT"]
+                                / self.get_output_filename()
+                            ).resolve()
                         ),
                         "log": str(
-                            self.root_dir
-                            / internal.FLUXSITE_DIRS["LOG"]
-                            / self.get_log_filename()
+                            (
+                                internal.FLUXSITE_DIRS["LOG"] / self.get_log_filename()
+                            ).resolve()
                         ),
                         "restart_out": " ",
-                        "type": str(self.root_dir / internal.GRID_FILE),
+                        "type": str(internal.GRID_FILE.resolve()),
                     },
                     "output": {
                         "restart": False,
                     },
                     "fixedCO2": internal.CABLE_FIXED_CO2_CONC,
                     "casafile": {
-                        "phen": str(self.root_dir / internal.PHEN_FILE),
-                        "cnpbiome": str(self.root_dir / internal.CNPBIOME_FILE),
+                        "phen": str(internal.PHEN_FILE.resolve()),
+                        "cnpbiome": str(internal.CNPBIOME_FILE.resolve()),
                     },
                     "spinup": False,
                 }
@@ -210,9 +207,7 @@ def clean_task(self, verbose=False):
         if verbose:
             print("  Cleaning task")
 
-        task_dir = (
-            self.root_dir / internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name()
-        )
+        task_dir = internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name()
 
         cable_exe = task_dir / internal.CABLE_EXE
         if cable_exe.exists():
@@ -230,17 +225,11 @@ def clean_task(self, verbose=False):
         if cable_soil_nml.exists():
             cable_soil_nml.unlink()
 
-        output_file = (
-            self.root_dir
-            / internal.FLUXSITE_DIRS["OUTPUT"]
-            / self.get_output_filename()
-        )
+        output_file = internal.FLUXSITE_DIRS["OUTPUT"] / self.get_output_filename()
         if output_file.exists():
             output_file.unlink()
 
-        log_file = (
-            self.root_dir / internal.FLUXSITE_DIRS["LOG"] / self.get_log_filename()
-        )
+        log_file = internal.FLUXSITE_DIRS["LOG"] / self.get_log_filename()
         if log_file.exists():
             log_file.unlink()
 
@@ -253,19 +242,14 @@ def fetch_files(self, verbose=False):
         - copies contents of 'namelists' directory to 'runs/fluxsite/tasks/<task_name>' directory.
         - copies cable executable from source to 'runs/fluxsite/tasks/<task_name>' directory.
         """
-        task_dir = (
-            self.root_dir / internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name()
-        )
+        task_dir = internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name()
 
         if verbose:
             print(
-                f"  Copying namelist files from {self.root_dir / internal.NAMELIST_DIR} "
-                f"to {task_dir}"
+                f"  Copying namelist files from {internal.NAMELIST_DIR} to {task_dir}"
             )
 
-        shutil.copytree(
-            self.root_dir / internal.NAMELIST_DIR, task_dir, dirs_exist_ok=True
-        )
+        shutil.copytree(internal.NAMELIST_DIR, task_dir, dirs_exist_ok=True)
 
         exe_src = self.model.get_exe_path()
         exe_dest = task_dir / internal.CABLE_EXE
@@ -280,7 +264,7 @@ def fetch_files(self, verbose=False):
     def run(self, verbose=False):
         """Runs a single fluxsite task."""
         task_name = self.get_task_name()
-        task_dir = self.root_dir / internal.FLUXSITE_DIRS["TASKS"] / task_name
+        task_dir = internal.FLUXSITE_DIRS["TASKS"] / task_name
         if verbose:
             print(
                 f"Running task {task_name}... CABLE standard output "
@@ -303,14 +287,14 @@ def run_cable(self, verbose=False):
         Raises `CableError` when CABLE returns a non-zero exit code.
         """
         task_name = self.get_task_name()
-        task_dir = self.root_dir / internal.FLUXSITE_DIRS["TASKS"] / task_name
+        task_dir = internal.FLUXSITE_DIRS["TASKS"] / task_name
         stdout_path = task_dir / internal.CABLE_STDOUT_FILENAME
 
         try:
             with chdir(task_dir):
                 self.subprocess_handler.run_cmd(
                     f"./{internal.CABLE_EXE} {internal.CABLE_NML}",
-                    output_file=stdout_path,
+                    output_file=stdout_path.relative_to(task_dir),
                     verbose=verbose,
                 )
         except CalledProcessError as exc:
@@ -323,16 +307,9 @@ def add_provenance_info(self, verbose=False):
         Attributes include branch url, branch revision number and key value pairs in
         the namelist file used to run cable.
         """
-        nc_output_path = (
-            self.root_dir
-            / internal.FLUXSITE_DIRS["OUTPUT"]
-            / self.get_output_filename()
-        )
+        nc_output_path = internal.FLUXSITE_DIRS["OUTPUT"] / self.get_output_filename()
         nml = f90nml.read(
-            self.root_dir
-            / internal.FLUXSITE_DIRS["TASKS"]
-            / self.get_task_name()
-            / internal.CABLE_NML
+            internal.FLUXSITE_DIRS["TASKS"] / self.get_task_name() / internal.CABLE_NML
         )
         if verbose:
             print(f"Adding attributes to output file: {nc_output_path}")
@@ -389,16 +366,14 @@ def run_tasks_in_parallel(
         pool.map(run_task, tasks, chunksize=1)
 
 
-def get_fluxsite_comparisons(
-    tasks: list[Task], root_dir=internal.CWD
-) -> list[ComparisonTask]:
+def get_fluxsite_comparisons(tasks: list[Task]) -> list[ComparisonTask]:
     """Returns a list of `ComparisonTask` objects to run comparisons with.
 
     Pairs should be matching in science configurations and meteorological
     forcing, but differ in realisations. When multiple realisations are
     specified, return all pair wise combinations between all realisations.
     """
-    output_dir = root_dir / internal.FLUXSITE_DIRS["OUTPUT"]
+    output_dir = internal.FLUXSITE_DIRS["OUTPUT"]
     return [
         ComparisonTask(
             files=(

benchcab/internal.py

@@ -61,7 +61,8 @@
 )
 
 # Fluxsite directory tree
-FLUXSITE_DIRS = {}
+FLUXSITE_DIRS: dict[str, Path] = {}
+
 # Relative path to root directory for CABLE fluxsite runs
 FLUXSITE_DIRS["RUN"] = RUN_DIR / "fluxsite"
 

benchcab/model.py

@@ -20,7 +20,6 @@
 class Model:
     """A class used to represent a CABLE model version."""
 
-    root_dir: Path = internal.CWD
     subprocess_handler: SubprocessWrapperInterface = SubprocessWrapper()
     modules_handler: EnvironmentModulesInterface = EnvironmentModules()
 
@@ -61,19 +60,12 @@ def model_id(self, value: int):
     def get_exe_path(self) -> Path:
         """Return the path to the built executable."""
         return (
-            self.root_dir
-            / internal.SRC_DIR
-            / self.name
-            / self.src_dir
-            / "offline"
-            / internal.CABLE_EXE
+            internal.SRC_DIR / self.name / self.src_dir / "offline" / internal.CABLE_EXE
         )
 
     def custom_build(self, modules: list[str], verbose=False):
         """Build CABLE using a custom build script."""
-        build_script_path = (
-            self.root_dir / internal.SRC_DIR / self.name / self.build_script
-        )
+        build_script_path = internal.SRC_DIR / self.name / self.build_script
 
         if not build_script_path.is_file():
             msg = (
@@ -85,6 +77,7 @@ def custom_build(self, modules: list[str], verbose=False):
 
         tmp_script_path = build_script_path.parent / "tmp-build.sh"
 
+        # TODO(Sean) should this be a utility function?
         if verbose:
             print(f"Copying {build_script_path} to {tmp_script_path}")
         shutil.copy(build_script_path, tmp_script_path)
@@ -110,50 +103,40 @@ def custom_build(self, modules: list[str], verbose=False):
 
     def pre_build(self, verbose=False):
         """Runs CABLE pre-build steps."""
-        path_to_repo = self.root_dir / internal.SRC_DIR / self.name
+        path_to_repo = internal.SRC_DIR / self.name
         tmp_dir = path_to_repo / self.src_dir / "offline" / ".tmp"
         if not tmp_dir.exists():
             if verbose:
-                print(f"mkdir {tmp_dir.relative_to(self.root_dir)}")
+                print(f"mkdir {tmp_dir}")
             tmp_dir.mkdir()
 
         for pattern in internal.OFFLINE_SOURCE_FILES:
             for path in (path_to_repo / self.src_dir).glob(pattern):
                 if not path.is_file():
                     continue
-                copy2(
-                    path.relative_to(self.root_dir),
-                    tmp_dir.relative_to(self.root_dir),
-                    verbose=verbose,
-                )
+                copy2(path, tmp_dir, verbose=verbose)
 
         copy2(
-            (path_to_repo / self.src_dir / "offline" / "Makefile").relative_to(
-                self.root_dir
-            ),
-            tmp_dir.relative_to(self.root_dir),
+            (path_to_repo / self.src_dir / "offline" / "Makefile"),
+            tmp_dir,
             verbose=verbose,
         )
 
         copy2(
-            (path_to_repo / self.src_dir / "offline" / "parallel_cable").relative_to(
-                self.root_dir
-            ),
-            tmp_dir.relative_to(self.root_dir),
+            (path_to_repo / self.src_dir / "offline" / "parallel_cable"),
+            tmp_dir,
             verbose=verbose,
         )
 
         copy2(
-            (path_to_repo / self.src_dir / "offline" / "serial_cable").relative_to(
-                self.root_dir
-            ),
-            tmp_dir.relative_to(self.root_dir),
+            (path_to_repo / self.src_dir / "offline" / "serial_cable"),
+            tmp_dir,
             verbose=verbose,
         )
 
     def run_build(self, modules: list[str], verbose=False):
         """Runs CABLE build scripts."""
-        path_to_repo = self.root_dir / internal.SRC_DIR / self.name
+        path_to_repo = internal.SRC_DIR / self.name
         tmp_dir = path_to_repo / self.src_dir / "offline" / ".tmp"
 
         with chdir(tmp_dir), self.modules_handler.load(modules, verbose=verbose):
@@ -177,14 +160,12 @@ def run_build(self, modules: list[str], verbose=False):
 
     def post_build(self, verbose=False):
         """Runs CABLE post-build steps."""
-        path_to_repo = self.root_dir / internal.SRC_DIR / self.name
+        path_to_repo = internal.SRC_DIR / self.name
         tmp_dir = path_to_repo / self.src_dir / "offline" / ".tmp"
 
         rename(
-            (tmp_dir / internal.CABLE_EXE).relative_to(self.root_dir),
-            (path_to_repo / self.src_dir / "offline" / internal.CABLE_EXE).relative_to(
-                self.root_dir
-            ),
+            (tmp_dir / internal.CABLE_EXE),
+            (path_to_repo / self.src_dir / "offline" / internal.CABLE_EXE),
             verbose=verbose,
         )
 

benchcab/utils/fs.py

@@ -34,7 +34,7 @@ def copy2(src: Path, dest: Path, verbose=False):
     shutil.copy2(src, dest)
 
 
-def next_path(path: Path, path_pattern: str, sep: str = "-"):
+def next_path(path_pattern: str, path: Path = Path(), sep: str = "-") -> Path:
     """Finds the next free path in a sequentially named list of
     files with the following pattern in the `path` directory:
 
@@ -54,7 +54,7 @@ def next_path(path: Path, path_pattern: str, sep: str = "-"):
         common_filename, last_file_index = pattern_files_sorted[-1].stem.split(sep)
         new_file_index = int(last_file_index) + 1
 
-    return f"{common_filename}{sep}{new_file_index}{loc_pattern.suffix}"
+    return Path(f"{common_filename}{sep}{new_file_index}{loc_pattern.suffix}")
 
 
 def mkdir(new_path: Path, verbose=False, **kwargs):