Add new settings *Mesh* > *(Copy|Link)AsFiles

nasa-ddalle · nasa-ddalle · commit ac3202db4df7 · 2025-09-19T12:45:40.000-07:00
diff --git a/cape/cfdx/cntl.py b/cape/cfdx/cntl.py
@@ -4497,17 +4497,51 @@ def abspath(self, fname: str) -> str:
             return os.path.join(self.RootDir, fname_sys)
 
     # Copy files
-    @run_rootdir
     def copy_files(self, i: int):
+        r"""Copy files from *Mesh* section
+
+        This applies to both *CopyFiles* and *CopyAsFiles* in the
+        *Mesh* section. The former will copy a given file into the run
+        folder for case *i* using the base name of the original (source)
+        file. Using
+
+        .. code-block:: javascript
+
+            "Mesh": {
+                "CopyAsFiles": {
+                    "inputs/mesh-config02.ugrid": "mesh.ugrid"
+                }
+            }
+
+        will copy the file ``inputs/mesh-config02.ugrid`` into the run
+        folder but name it ``mesh.ugrid`` there.
+
+        :Call:
+            >>> cntl.copy_files(i)
+        :Inputs:
+            *cntl*: :class:`cape.cfdx.cntl.Cntl`
+                Overall CAPE control instance
+            *i*: :class:`int`
+                Case index
+        :Versions:
+            * 2025-09-19 ``@ddalle``: v1.0
+        """
+        # Ensure case index is set
+        self.opts.setx_i(i)
+        # Create case folder
+        self.make_case_folder(i)
+        # Two categories
+        self._copy_as_files(i)
+        self._copy_files(i)
+
+    # Copy files w/o renaming
+    @run_rootdir
+    def _copy_files(self, i: int):
         # Get list of files to copy
         files = self.opts.get_CopyFiles()
         # Check for any
         if files is None or len(files) == 0:
             return
-        # Ensure case index is set
-        self.opts.setx_i(i)
-        # Create case folder
-        self.make_case_folder(i)
         # Name of case folder
         frun = self.x.GetFullFolderNames(i)
         # Loop through files
@@ -4525,18 +4559,76 @@ def copy_files(self, i: int):
             # Copy file
             shutil.copy(fabs, fdest)
 
-    # Link files
+    # Copy files with renaming
     @run_rootdir
-    def link_files(self, i: int):
-        # Get list of files to copy
-        files = self.opts.get_LinkFiles()
+    def _copy_as_files(self, i: int):
+        # Get dict of files to copy
+        filedict = self.opts.get_CopyAsFiles()
         # Check for any
-        if files is None or len(files) == 0:
+        if filedict is None or len(filedict) == 0:
             return
+        # Name of case folder
+        frun = self.x.GetFullFolderNames(i)
+        # Loop through files
+        for src, trg in filedict.items():
+            # Absolutize source
+            fabs = self.abspath(src)
+            # Destination file
+            fdest = os.path.join(self.RootDir, frun, trg)
+            # Check for overwrite
+            if os.path.isfile(fdest):
+                print(f"  Replacing file '{src}' -> '{fdest}'")
+                os.remove(fdest)
+            # Copy file
+            shutil.copy(fabs, fdest)
+
+    # Link files
+    def link_files(self, i: int):
+        r"""Link files from *Mesh* section
+
+        This applies to both *LinkFiles* and *LinkAsFiles* in the
+        *Mesh* section. The former will copy a given file into the run
+        folder for case *i* using the base name of the original (source)
+        file. Using
+
+        .. code-block:: javascript
+
+            "Mesh": {
+                "LinkAsFiles": {
+                    "inputs/mesh-config02.ugrid": "mesh.ugrid"
+                }
+            }
+
+        will create a link (using the absolute path) from
+        ``inputs/mesh-config02.ugrid`` to ``mesh.ugrid`` in the case run
+        folder.
+
+        :Call:
+            >>> cntl.link_files(i)
+        :Inputs:
+            *cntl*: :class:`cape.cfdx.cntl.Cntl`
+                Overall CAPE control instance
+            *i*: :class:`int`
+                Case index
+        :Versions:
+            * 2025-09-19 ``@ddalle``: v1.0
+        """
         # Ensure case index is set
         self.opts.setx_i(i)
         # Create case folder
         self.make_case_folder(i)
+        # Two parts
+        self._link_as_files(i)
+        self._link_files(i)
+
+    # Link files w/o renaming
+    @run_rootdir
+    def _link_files(self, i: int):
+        # Get list of files to copy
+        files = self.opts.get_LinkFiles()
+        # Check for any
+        if files is None or len(files) == 0:
+            return
         # Name of case folder
         frun = self.x.GetFullFolderNames(i)
         # Loop through files
@@ -4553,6 +4645,30 @@ def link_files(self, i: int):
             # Copy file
             os.symlink(fabs, fdest)
 
+    # Link files with renaming
+    @run_rootdir
+    def _link_as_files(self, i: int):
+        # Get dict of files to copy
+        filedict = self.opts.get_LinkAsFiles()
+        # Check for any
+        if filedict is None or len(filedict) == 0:
+            return
+        # Name of case folder
+        frun = self.x.GetFullFolderNames(i)
+        # Loop through files
+        for src, trg in filedict.items():
+            # Absolutize source
+            fabs = self.abspath(src)
+            # Destination file
+            fdest = os.path.join(self.RootDir, frun, trg)
+            # Check for overwrite
+            if os.path.isfile(fdest):
+                raise FileExistsError(
+                    f"  Cannot copy '{os.path.basename(src)}' -> "
+                    f"'{src}'; file exists")
+            # Copy file
+            os.symlink(fabs, fdest)
+
    # --- Archiving ---
     # Function to archive results and remove files
     def ArchiveCases(self, **kw):
diff --git a/cape/cfdx/options/meshopts.py b/cape/cfdx/options/meshopts.py
@@ -27,7 +27,9 @@ class MeshOpts(OptionsDict):
 
     # List of options
     _optlist = {
+        "CopyAsFiles",
         "CopyFiles",
+        "LinkAsFiles",
         "LinkFiles",
         "MeshFile",
         "TriFile",
@@ -39,22 +41,32 @@ class MeshOpts(OptionsDict):
         "CopyFiles": 1,
         "LinkFiles": 1,
     }
-    
+
     # Defaults
     _rc = {
         "LinkMesh": False,
     }
 
     # Types
     _opttypes = {
+        "CopyAsFiles": dict,
+        "CopyFiles": str,
+        "LinkAsFiles": dict,
+        "LinkFiles": str,
         "MeshFile": str,
         "TriFile": str,
         "LinkMesh": BOOL_TYPES,
     }
 
     # Descriptions
     _rst_descriptions = {
+        "CopyAsFiles": (
+            "file(s) to copy and rename; source file is left-hand side and "
+            "target file name is right-hand side"),
         "CopyFiles": "file(s) to copy to run folder w/o changing file name",
+        "LinkAsFiles": (
+            "file(s) to link and rename; source file is left-hand side and "
+            "target file name is right-hand side"),
         "LinkFiles": "file(s) to link into run folder w/o changing file name",
         "LinkMesh": "option to link mesh file(s) instead of copying",
         "MeshFile": "original mesh file name(s)",
