From 1701fdfec6bd917e6afe649f4269c9a501ba842d Mon Sep 17 00:00:00 2001
From: Claire Carouge <claire.carouge@anu.edu.au>
Date: Thu, 5 Oct 2023 11:58:59 +1100
Subject: [PATCH 1/2]  #149- Move next_path() to fs.py

---
 benchcab/benchcab.py                  |  2 +-
 benchcab/utils/fs.py                  | 23 +++++++++++++++++++++++
 benchcab/utils/logging.py             | 26 --------------------------
 tests/{test_logging.py => test_fs.py} |  4 ++--
 4 files changed, 26 insertions(+), 29 deletions(-)
 delete mode 100644 benchcab/utils/logging.py
 rename tests/{test_logging.py => test_fs.py} (85%)

diff --git a/benchcab/benchcab.py b/benchcab/benchcab.py
index c6fc1fcd..25c4bf73 100644
--- a/benchcab/benchcab.py
+++ b/benchcab/benchcab.py
@@ -25,7 +25,7 @@
 from benchcab.environment_modules import EnvironmentModules, EnvironmentModulesInterface
 from benchcab.utils.subprocess import SubprocessWrapper, SubprocessWrapperInterface
 from benchcab.utils.pbs import render_job_script
-from benchcab.utils.logging import next_path
+from benchcab.utils.fs import next_path
 
 
 class Benchcab:
diff --git a/benchcab/utils/fs.py b/benchcab/utils/fs.py
index 36027efe..300377e4 100644
--- a/benchcab/utils/fs.py
+++ b/benchcab/utils/fs.py
@@ -29,3 +29,26 @@ def copy2(src: Path, dest: Path, verbose=False):
     if verbose:
         print(f"cp -p {src} {dest}")
     shutil.copy2(src, dest)
+
+
+def next_path(path: Path, path_pattern: str, sep: str = "-"):
+    """Finds the next free path in a sequentially named list of
+    files with the following pattern in the `path` directory:
+
+    path_pattern = 'file{sep}*.suf':
+
+    file-1.txt
+    file-2.txt
+    file-3.txt
+    """
+
+    loc_pattern = Path(path_pattern)
+    new_file_index = 1
+    common_filename, _ = loc_pattern.stem.split(sep)
+
+    pattern_files_sorted = sorted(path.glob(path_pattern))
+    if pattern_files_sorted != []:
+        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}"
diff --git a/benchcab/utils/logging.py b/benchcab/utils/logging.py
deleted file mode 100644
index 06200a5c..00000000
--- a/benchcab/utils/logging.py
+++ /dev/null
@@ -1,26 +0,0 @@
-"""Contains helper functions for logging."""
-
-from pathlib import Path
-
-
-def next_path(path: Path, path_pattern: str, sep: str = "-"):
-    """Finds the next free path in a sequentially named list of
-    files with the following pattern in the `path` directory:
-
-    path_pattern = 'file{sep}*.suf':
-
-    file-1.txt
-    file-2.txt
-    file-3.txt
-    """
-
-    loc_pattern = Path(path_pattern)
-    new_file_index = 1
-    common_filename, _ = loc_pattern.stem.split(sep)
-
-    pattern_files_sorted = sorted(path.glob(path_pattern))
-    if pattern_files_sorted != []:
-        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}"
diff --git a/tests/test_logging.py b/tests/test_fs.py
similarity index 85%
rename from tests/test_logging.py
rename to tests/test_fs.py
index 8af56e01..1b1634da 100644
--- a/tests/test_logging.py
+++ b/tests/test_fs.py
@@ -1,6 +1,6 @@
-"""`pytest` tests for utils/logging.py"""
+"""`pytest` tests for utils/fs.py"""
 
-from benchcab.utils.logging import next_path
+from benchcab.utils.fs import next_path
 from .common import MOCK_CWD
 
 

From d3cd1a1229533ab17c55058a1c2496a407591e9b Mon Sep 17 00:00:00 2001
From: Claire Carouge <claire.carouge@anu.edu.au>
Date: Thu, 5 Oct 2023 12:12:17 +1100
Subject: [PATCH 2/2]  #149- Change `assert all()` to individual asserts

---
 tests/test_repository.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tests/test_repository.py b/tests/test_repository.py
index a578665e..2067d9cf 100644
--- a/tests/test_repository.py
+++ b/tests/test_repository.py
@@ -158,6 +158,15 @@ def test_run_build():
     mock_modules = ["foo", "bar"]
     (MOCK_CWD / internal.SRC_DIR / "trunk" / "offline" / ".tmp").mkdir(parents=True)
 
+    environment_vars = {
+        "NCDIR": f"{mock_netcdf_root}/lib/Intel",
+        "NCMOD": f"{mock_netcdf_root}/include/Intel",
+        "CFLAGS": "-O2 -fp-model precise",
+        "LDFLAGS": f"-L{mock_netcdf_root}/lib/Intel -O0",
+        "LD": "-lnetcdf -lnetcdff",
+        "FC": "ifort",
+    }
+
     # This is required so that we can use the NETCDF_ROOT environment variable
     # when running `make`, and `serial_cable` and `parallel_cable` scripts:
     os.environ["NETCDF_ROOT"] = mock_netcdf_root
@@ -188,17 +197,8 @@ def test_run_build():
     mock_subprocess = MockSubprocessWrapper()
     repo = get_mock_repo(subprocess_handler=mock_subprocess)
     repo.run_build(mock_modules)
-    assert all(
-        kv in mock_subprocess.env.items()
-        for kv in {
-            "NCDIR": f"{mock_netcdf_root}/lib/Intel",
-            "NCMOD": f"{mock_netcdf_root}/include/Intel",
-            "CFLAGS": "-O2 -fp-model precise",
-            "LDFLAGS": f"-L{mock_netcdf_root}/lib/Intel -O0",
-            "LD": "-lnetcdf -lnetcdff",
-            "FC": "ifort",
-        }.items()
-    )
+    for kv in environment_vars.items():
+        assert (kv in mock_subprocess.env.items())
 
     # Success case: test non-verbose standard output
     repo = get_mock_repo()