Fixed bugs with .gz file handling.

Added more control over configurations to write and how many per file.

read_structure_step/write_structure.py

@@ -21,7 +21,6 @@
 from seamm_util import ureg, Q_  # noqa: F401
 import seamm_util.printing as printing
 from seamm_util.printing import FormattedText as __
-from .utils import guess_extension
 
 logger = logging.getLogger(__name__)
 job = printing.getPrinter()
@@ -119,19 +118,20 @@ def run(self):
 
         # What type of file?
         filename = P["file"].strip()
+        path = PurePath(filename)
         file_type = P["file type"]
 
         if file_type != "from extension":
             extension = file_type.split()[0]
         else:
-            path = PurePath(filename)
             extension = path.suffix
             if extension == ".gz":
-                extension = path.stem.suffix
+                extension = path.with_suffix("").suffix
 
         if extension == "":
-            extension = guess_extension(filename, use_file_name=False)
-            P["file type"] = extension
+            raise RuntimeError(
+                "Can't write the file without knowing the type (extension)"
+            )
 
         # Print what we are doing
         printer.important(__(self.description_text(P), indent=4 * " "))
@@ -141,37 +141,78 @@ def run(self):
         system, configuration = self.get_system_configuration(P)
 
         structures = P["structures"]
+        configs = P["configurations"]
+        errors = not P["ignore missing"]
+        configurations = []
         if structures == "current configuration":
-            configurations = [configuration]
-        elif structures == "all configurations of current system":
-            for configuration in system.configurations():
-                configurations.append(configuration)
-        elif structures == "all systems":
-            configurations = []
-            for system in system_db.systems():
-                for configuration in system.configurations():
+            configurations.append(configuration)
+        elif structures == "current system":
+            if configs == "all":
+                for configuration in system.configurations:
                     configurations.append(configuration)
-
-        write(
-            filename,
-            configurations,
-            extension=extension,
-            remove_hydrogens=P["remove hydrogens"],
-            printer=printer.important,
-            references=self.references,
-            bibliography=self._bibliography,
-        )
+                else:
+                    cid = system.get_configuration_id(configs, errors=errors)
+                    if cid is not None:
+                        configurations.append(system.get_configuration(cid))
+        elif structures == "all systems":
+            if configs == "all":
+                for system in system_db.systems:
+                    for configuration in system.configurations:
+                        configurations.append(configuration)
+            else:
+                for system in system_db.systems:
+                    cid = system.get_configuration_id(configs, errors=errors)
+                    if cid is not None:
+                        configurations.append(system.get_configuration(cid))
+
+        n_per_file = P["number per file"]
+        n_configurations = len(configurations)
+        if n_per_file == "all" or n_configurations <= n_per_file:
+            write(
+                filename,
+                configurations,
+                extension=extension,
+                remove_hydrogens=P["remove hydrogens"],
+                printer=printer.important,
+                references=self.references,
+                bibliography=self._bibliography,
+            )
+        else:
+            n_per_file = int(n_per_file)
+            if path.suffix == ".gz":
+                base = path.with_suffix("")
+                suffix = base.suffix + ".gz"
+                stem = str(base.with_suffix(""))
+            else:
+                suffix = path.suffix
+                stem = str(path.with_suffix(""))
+            last = 1  # Note that counting from 1 for users.
+
+            while last <= n_configurations:
+                first = last
+                last += n_per_file
+                tmp_name = stem + f"_{first}" + suffix
+                write(
+                    tmp_name,
+                    configurations[first - 1 : last - 1],
+                    extension=extension,
+                    remove_hydrogens=P["remove hydrogens"],
+                    printer=printer.important,
+                    references=self.references,
+                    bibliography=self._bibliography,
+                )
 
         # Finish the output
-        printer.important(
-            __(
-                f"\n    Wrote the structure with {configuration.n_atoms} "
-                "atoms."
-                f"\n           System name = {system.name}"
-                f"\n    Configuration name = {configuration.name}",
-                indent=4 * " ",
+        if n_configurations == 1:
+            printer.important(
+                __(
+                    f"\n    Wrote the structure with {configuration.n_atoms} "
+                    "atoms."
+                    f"\n           System name = {system.name}"
+                    f"\n    Configuration name = {configuration.name}",
+                    indent=4 * " ",
+                )
             )
-        )
         printer.important("")
 
         return next_node