Merge pull request #24 from molssi-seamm/dev

Improved naming of loop subdirectories

.github/workflows/CI.yaml

@@ -7,11 +7,6 @@ on:
   pull_request:
     branches:
       - "main"
-  schedule:
-    # Run on master by default Sunday morning at 3:30:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "30 3 * * 0"
 
 jobs:
   ci:

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2024.7.28 -- Improved naming of loop subdirectories
+   * The subdirectories now start at 1, not 0, to make counting more normal
+   * When looping over systems, now have the option to name the directories
+     after the system or configuration name, not the iteration number.
+
 2023.11.9 -- Bugfix: "For" loops could crash
    * For loops could crash writing to write final_structure.mmcif before the directory
      had been made.

loop_step/loop.py

@@ -38,6 +38,7 @@ def __init__(self, flowchart=None, extension=None):
         self._loop_value = None
         self._loop_length = None
         self._file_handler = None
+        self._custom_directory_name = None
 
         super().__init__(
             flowchart=flowchart, title="Loop", extension=extension, logger=logger
@@ -66,7 +67,11 @@ def git_revision(self):
 
     @property
     def working_path(self):
-        return Path(self.directory) / f"iter_{self._loop_value:{self.iter_format}}"
+        if self._custom_directory_name is not None:
+            tmp = Path(self.directory) / self._custom_directory_name
+        else:
+            tmp = Path(self.directory) / f"iter_{self._loop_value+1:{self.iter_format}}"
+        return tmp
 
     def describe(self):
         """Write out information about what this node will do"""
@@ -145,6 +150,9 @@ def run(self):
             context=seamm.flowchart_variables._data
         )
 
+        # Reset variables to initial state.
+        self._custom_directory_name = None
+
         # Print out header to the main output
         printer.important(__(self.description_text(P), indent=self.indent))
 
@@ -551,6 +559,7 @@ def run(self):
                     if self._loop_value >= self._loop_length:
                         self._loop_value = None
                         self._loop_length = None
+                        self._custom_directory_name = None
 
                         # Revert the loop index variables to the next outer loop
                         # if there is one, or remove them.
@@ -573,6 +582,15 @@ def run(self):
                     system_db.system = configuration.system
                     system.configuration = configuration
 
+                    if P["directory name"] == "system name":
+                        self._custom_directory_name = self.safe_filename(system.name)
+                    elif P["directory name"] == "configuration name":
+                        self._custom_directory_name = self.safe_filename(
+                            configuration.name
+                        )
+                    else:
+                        self._custom_directory_name = None
+
                     # Set up the index variables
                     tmp = self.get_variable("_loop_indices")
                     self.set_variable(
@@ -605,9 +623,8 @@ def run(self):
                 # Add the iteration to the ids so the directory structure is
                 # reasonable
                 self.flowchart.reset_visited()
-                self.set_subids(
-                    (*self._id, f"iter_{self._loop_value:{self.iter_format}}")
-                )
+                tmp = self.working_path.name
+                self.set_subids((*self._id, tmp))
 
             # Run through the steps in the loop body
             try:
@@ -617,9 +634,8 @@ def run(self):
                 traceback.print_exc(file=sys.stderr)
                 traceback.print_exc(file=sys.stdout)
             except Exception as e:
-                printer.job(
-                    f"Caught exception in loop iteration {self._loop_value}: {str(e)}"
-                )
+                tmp = self.working_path.name
+                printer.job(f"Caught exception in loop iteration {tmp}: {str(e)}")
                 with open(iter_dir / "stderr.out", "a") as fd:
                     traceback.print_exc(file=fd)
                 if "continue" in P["errors"]:
@@ -783,3 +799,15 @@ def loop_node(self):
         # There is no body of the loop!
         self.logger.debug("There is no loop body")
         return None
+
+    def safe_filename(self, filename):
+        clean = re.sub(r"[/\\?%*:|\"<>\x7F\x00-\x1F]", "-", filename)
+
+        # Check for duplicates...
+        path = Path(self.directory) / clean
+        count = 1
+        while path.exists():
+            count += 1
+            path = Path(self.directory) / f"{clean}_{count}"
+
+        return path.name

loop_step/loop_parameters.py

@@ -165,6 +165,19 @@ class LoopParameters(seamm.Parameters):
             "description": "",
             "help_text": "The filter for the configuration name",
         },
+        "directory name": {
+            "default": "loop iteration",
+            "kind": "string",
+            "default_units": "",
+            "enumeration": (
+                "loop iteration",
+                "system name",
+                "configuration name",
+            ),
+            "format_string": "s",
+            "description": "Directory names:",
+            "help_text": "The directory name for the loop iteration.",
+        },
         "errors": {
             "default": "continue to next iteration",
             "kind": "string",

loop_step/tk_loop.py

@@ -225,6 +225,8 @@ def reset_dialog(self, widget=None):
                     row=row, column=2, columnspan=2, sticky=tk.EW
                 )
             frame.columnconfigure(3, weight=1)
+            row += 1
+            self["directory name"].grid(row=row, column=0, columnspan=3, sticky=tk.W)
         else:
             raise RuntimeError("Don't recognize the loop_type {}".format(loop_type))
         row += 1

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):