Prevent duplicate effort on vcs revision recording of NEMO and XIOS-2…

… code repository clones (#69)

* Prevent vcs revision recording of duplicate repos

A check was added to 'salishsea_cmd/prepare.py' to prevent vcs revision
recording of the NEMO and XIOS-2 code repositories. That duplication could
happen because the code always records the vcs revision of the NEMO and XIOS-2
code repositories, but the user could cause duplicated effort by including those
repositories in their YAML file list of other repos to record. Corresponding
tests were updated to reflect these changes.

re: issue #11

* Update test_prepare.py to use tmp_path & os.fspath

This commit replaces instances of `tmpdir` with `tmp_path` from pytest and uses
`pathlib` to handle file paths. Additionally, all path conversions now use
`os.fspath()` for consistent, cross-platform compatibility. These changes
improve code readability and ensure the test suite is using more modern file
handling practices.

salishsea_cmd/prepare.py

@@ -157,6 +157,7 @@ def _record_vcs_revisions(run_desc, run_dir):
             run_desc, ("vcs revisions", vcs_tool), run_dir=run_dir
         )
         for repo in repos:
-            nemo_cmd.prepare.write_repo_rev_file(
-                Path(repo), run_dir, vcs_funcs[vcs_tool]
-            )
+            if not Path(repo) in (nemo_code_config.parent.parent, xios_code_repo):
+                nemo_cmd.prepare.write_repo_rev_file(
+                    Path(repo), run_dir, vcs_funcs[vcs_tool]
+                )

tests/test_prepare.py

@@ -18,13 +18,13 @@
 
 """SalishSeaCmd prepare sub-command plug-in unit tests
 """
+import os
 from pathlib import Path
 from unittest.mock import call, Mock, patch
 
 import cliff.app
 import nemo_cmd.prepare
 import pytest
-
 import salishsea_cmd.prepare
 
 
@@ -125,27 +125,29 @@ def test_no_paths_forcing_key(self):
     )
     @patch("nemo_cmd.prepare.write_repo_rev_file")
     def test_write_repo_rev_file_default_calls(
-        self, m_write, config_name_key, nemo_code_config_key, tmpdir
+        self, m_write, config_name_key, nemo_code_config_key, tmp_path
     ):
-        nemo_code_repo = tmpdir.ensure_dir("NEMO-3.6-code")
-        nemo_config = nemo_code_repo.ensure_dir("NEMOGCM", "CONFIG")
-        xios_code_repo = tmpdir.ensure_dir("XIOS")
+        nemo_code_repo = tmp_path / Path("NEMO-3.6-code")
+        nemo_config = nemo_code_repo / Path("NEMOGCM", "CONFIG")
+        nemo_config.mkdir(parents=True)
+        xios_code_repo = tmp_path / Path("XIOS")
+        xios_code_repo.mkdir()
         run_desc = {
             config_name_key: "SalishSea",
             "paths": {
-                nemo_code_config_key: str(nemo_config),
-                "XIOS": str(xios_code_repo),
+                nemo_code_config_key: os.fspath(nemo_config),
+                "XIOS": os.fspath(xios_code_repo),
             },
         }
         salishsea_cmd.prepare._record_vcs_revisions(run_desc, Path("run_dir"))
         assert m_write.call_args_list == [
             call(
-                Path(str(nemo_code_repo)),
+                nemo_code_repo,
                 Path("run_dir"),
                 nemo_cmd.prepare.get_git_revision,
             ),
             call(
-                Path(str(xios_code_repo)),
+                xios_code_repo,
                 Path("run_dir"),
                 nemo_cmd.prepare.get_git_revision,
             ),
@@ -157,24 +159,31 @@ def test_write_repo_rev_file_default_calls(
     )
     @patch("nemo_cmd.prepare.write_repo_rev_file")
     def test_write_repo_rev_file_vcs_revisions_hg_call(
-        self, m_write, config_name_key, nemo_code_config_key, tmpdir
+        self, m_write, config_name_key, nemo_code_config_key, tmp_path
     ):
-        nemo_config = tmpdir.ensure_dir("NEMO-3.6-code", "NEMOGCM", "CONFIG")
-        xios_code_repo = tmpdir.ensure_dir("XIOS")
-        nemo_forcing = tmpdir.ensure_dir("NEMO-forcing")
-        ss_run_sets = tmpdir.ensure_dir("SS-run-sets")
+        nemo_code_repo = tmp_path / Path("NEMO-3.6-code")
+        nemo_config = nemo_code_repo / Path("NEMOGCM", "CONFIG")
+        nemo_config.mkdir(parents=True)
+        xios_code_repo = tmp_path / Path("XIOS")
+        xios_code_repo.mkdir()
+        nemo_forcing = tmp_path / Path("NEMO-forcing")
+        nemo_forcing.mkdir()
+        ss_run_sets = tmp_path / Path("SS-run-sets")
+        ss_run_sets.mkdir()
         run_desc = {
             config_name_key: "SalishSea",
             "paths": {
-                nemo_code_config_key: str(nemo_config),
-                "XIOS": str(xios_code_repo),
-                "forcing": str(nemo_forcing),
+                nemo_code_config_key: os.fspath(nemo_config),
+                "XIOS": os.fspath(xios_code_repo),
+                "forcing": os.fspath(nemo_forcing),
             },
-            "vcs revisions": {"hg": [str(ss_run_sets)]},
+            "vcs revisions": {"hg": [os.fspath(ss_run_sets)]},
         }
         salishsea_cmd.prepare._record_vcs_revisions(run_desc, Path("run_dir"))
         assert m_write.call_args_list[-1] == call(
-            Path(str(ss_run_sets)), Path("run_dir"), nemo_cmd.prepare.get_hg_revision
+            Path(os.fspath(ss_run_sets)),
+            Path("run_dir"),
+            nemo_cmd.prepare.get_hg_revision,
         )
 
     @pytest.mark.parametrize(
@@ -183,22 +192,64 @@ def test_write_repo_rev_file_vcs_revisions_hg_call(
     )
     @patch("nemo_cmd.prepare.write_repo_rev_file")
     def test_write_repo_rev_file_vcs_revisions_git_call(
-        self, m_write, config_name_key, nemo_code_config_key, tmpdir
+        self, m_write, config_name_key, nemo_code_config_key, tmp_path
     ):
-        nemo_config = tmpdir.ensure_dir("NEMO-3.6-code", "NEMOGCM", "CONFIG")
-        xios_code_repo = tmpdir.ensure_dir("XIOS")
-        nemo_forcing = tmpdir.ensure_dir("NEMO-forcing")
-        ss_run_sets = tmpdir.ensure_dir("SS-run-sets")
+        nemo_code_repo = tmp_path / Path("NEMO-3.6-code")
+        nemo_config = nemo_code_repo / Path("NEMOGCM", "CONFIG")
+        nemo_config.mkdir(parents=True)
+        xios_code_repo = tmp_path / Path("XIOS")
+        xios_code_repo.mkdir()
+        nemo_forcing = tmp_path / Path("NEMO-forcing")
+        nemo_forcing.mkdir()
+        ss_run_sets = tmp_path / Path("SS-run-sets")
+        ss_run_sets.mkdir()
         run_desc = {
             config_name_key: "SalishSea",
             "paths": {
-                nemo_code_config_key: str(nemo_config),
-                "XIOS": str(xios_code_repo),
-                "forcing": str(nemo_forcing),
+                nemo_code_config_key: os.fspath(nemo_config),
+                "XIOS": os.fspath(xios_code_repo),
+                "forcing": os.fspath(nemo_forcing),
+            },
+            "vcs revisions": {"git": [os.fspath(ss_run_sets)]},
+        }
+        salishsea_cmd.prepare._record_vcs_revisions(run_desc, Path("run_dir"))
+        assert m_write.call_args_list[-1] == call(
+            Path(os.fspath(ss_run_sets)),
+            Path("run_dir"),
+            nemo_cmd.prepare.get_git_revision,
+        )
+
+    @pytest.mark.parametrize(
+        "config_name_key, nemo_code_config_key",
+        [("config name", "NEMO code config"), ("config_name", "NEMO-code-config")],
+    )
+    @patch("nemo_cmd.prepare.write_repo_rev_file")
+    def test_write_repo_rev_file_vcs_revisions_git_call_no_dups(
+        self, m_write, config_name_key, nemo_code_config_key, tmp_path
+    ):
+        nemo_code_repo = tmp_path / Path("NEMO-3.6-code")
+        nemo_config = nemo_code_repo / Path("NEMOGCM", "CONFIG")
+        nemo_config.mkdir(parents=True)
+        xios_code_repo = tmp_path / Path("XIOS")
+        xios_code_repo.mkdir()
+        nemo_forcing = tmp_path / Path("NEMO-forcing")
+        nemo_forcing.mkdir()
+        ss_run_sets = tmp_path / Path("SS-run-sets")
+        ss_run_sets.mkdir()
+        run_desc = {
+            config_name_key: "SalishSea",
+            "paths": {
+                nemo_code_config_key: os.fspath(nemo_config),
+                "XIOS": os.fspath(xios_code_repo),
+                "forcing": os.fspath(nemo_forcing),
+            },
+            "vcs revisions": {
+                "git": [os.fspath(ss_run_sets), os.fspath(nemo_code_repo)]
             },
-            "vcs revisions": {"git": [str(ss_run_sets)]},
         }
         salishsea_cmd.prepare._record_vcs_revisions(run_desc, Path("run_dir"))
         assert m_write.call_args_list[-1] == call(
-            Path(str(ss_run_sets)), Path("run_dir"), nemo_cmd.prepare.get_git_revision
+            Path(os.fspath(ss_run_sets)),
+            Path("run_dir"),
+            nemo_cmd.prepare.get_git_revision,
         )