Revert "Improve UC distribution and add new UCS + UC generator"

MANIFEST.in

@@ -1,13 +1,9 @@
 include README.rst
 include docs/*.txt
 
-recursive-include package/ClayCode/data/data *
-recursive-include package/ClayCode/data/user_data *
+recursive-include package/ClayCode/data *
 recursive-include package/ClayCode/builder/config *
+recursive-include package/ClayCode/builder/tests/ *
 recursive-include package/ClayCode/builder/data *
 recursive-include package/ClayCode/siminp/config *
-recursive-include package/ClayCode/siminp/scripts *
-recursive-include package/ClayCode/addmols/config *
-recursive-include package/tests/builder *
-recursive-include package/tests *
 

package/ClayCode/__init__.py

@@ -12,8 +12,6 @@
     AnyDir,
     AnyFile,
     FileNameMatchSelector,
-    NumOrListDictOf,
-    NumOrListOf,
     PathOrStr,
     PathType,
     StrNum,
@@ -110,9 +108,6 @@
     "ArgsFactory",
     "DirFactory",
     "FileFactory",
-    "PathListFactory",
-    "NumOrListOf",
-    "NumOrListDictOf",
 ]
 logging.setLoggerClass(ClayCodeLogger)
 # from Bio import BiopythonDeprecationWarning

package/ClayCode/__main__.py

@@ -17,97 +17,87 @@
 logger: ClayCodeLogger = logging.getLogger(__name__)
 
 
-def run_builder(args: BuildArgs):
-    from ClayCode.builder import Builder
+def run():
+    args = parser.parse_args(sys.argv[1:])
+    # logger.setLevel(args.DEBUG)
+    args_factory = ArgsFactory()
+    args = args_factory.init_subclass(args)
+    # file_handler = logging.FileHandler(filename=args.)
+    # logger.addHandler(file_handler)
+    if isinstance(args, SiminpArgs):
+        args.write_runs()
+    if isinstance(args, DataArgs):
+        uc_writer = UCWriter(args.ingro, args.uc_type, args.outpath)
+        uc_writer.write_new_uc(args.uc_name)
+    elif isinstance(args, BuildArgs):
+        from ClayCode.builder import Builder
 
-    extra_il_space = {True: 1.5, False: 1}
-    clay_builder = Builder(args)
-    clay_builder.get_solvated_il()
-    # clay_builder.write_sheet_crds(backup=clay_builder.args.backup)
-    # clay_builder.solvate_il = lambda: clay_builder.construct_solvent(
-    #     solvate=args.il_solv,
-    #     ion_charge=args.match_charge["tot"],
-    #     solvate_add_func=clay_builder.solvate_clay_sheets,
-    #     ion_add_func=clay_builder.add_il_ions,
-    #     solvent_remove_func=clay_builder.remove_il_solv,
-    #     solvent_rename_func=clay_builder.rename_il_solv,
-    #     backup=clay_builder.args.backup,
-    # )
-    logger.finfo(f"Wrote interlayer sheet to {clay_builder.il_solv.name!r}")
-    completed = False
-    while completed is False:
+        extra_il_space = {True: 1.5, False: 1}
+        clay_builder = Builder(args)
         clay_builder.write_sheet_crds(backup=clay_builder.args.backup)
+        clay_builder.construct_solvent(
+            solvate=args.il_solv,
+            ion_charge=args.match_charge["tot"],
+            solvate_add_func=clay_builder.solvate_clay_sheets,
+            ion_add_func=clay_builder.add_il_ions,
+            solvent_remove_func=clay_builder.remove_il_solv,
+            solvent_rename_func=clay_builder.rename_il_solv,
+            backup=clay_builder.args.backup,
+        )
+        logger.finfo(
+            f"Wrote interlayer sheet to {clay_builder.il_solv.name!r}"
+        )
         clay_builder.stack_sheets(
             extra=extra_il_space[args.il_solv], backup=clay_builder.args.backup
         )
         clay_builder.extend_box(backup=clay_builder.args.backup)
-        if clay_builder.extended_box:
-            clay_builder.construct_solvent(
-                solvate=args.bulk_solv,
-                ion_charge=args.bulk_ion_conc,
-                solvate_add_func=clay_builder.solvate_box,
-                ion_add_func=clay_builder.add_bulk_ions,
-                solvent_remove_func=clay_builder.remove_SOL,
-                backup=clay_builder.args.backup,
-            )
-        completed = clay_builder.run_em(backup=clay_builder.args.backup)
-        if completed is None:
-            if clay_builder.extended_box and (
-                args.bulk_solv or args.bulk_ion_conc != 0.0
-            ):
-                completed = select_input_option(
-                    instance_or_manual_setup=True,
-                    query="Repeat bulk setup? [y]es/[n]o\n",
-                    options=["y", "n"],
-                    result=None,
-                    result_map={"y": False, "n": None},
+        completed = False
+        while completed is False:
+            if clay_builder.extended_box:
+                clay_builder.construct_solvent(
+                    solvate=args.bulk_solv,
+                    ion_charge=args.bulk_ion_conc,
+                    solvate_add_func=clay_builder.solvate_box,
+                    ion_add_func=clay_builder.add_bulk_ions,
+                    solvent_remove_func=clay_builder.remove_SOL,
+                    backup=clay_builder.args.backup,
                 )
-                # if repeat == "y":
-                #     completed = False
-                #     logger.finfo(get_subheader("Repeating solvation"))
-            if completed is False:
-                logger.finfo("Repeating bulk setup.\n", initial_linebreak=True)
+            completed = clay_builder.run_em(backup=clay_builder.args.backup)
+            if completed is None:
+                if clay_builder.extended_box and (
+                    args.bulk_solv or args.bulk_ion_conc != 0.0
+                ):
+                    completed = select_input_option(
+                        instance_or_manual_setup=True,
+                        query="Repeat bulk setup? [y]es/[n]o\n",
+                        options=["y", "n"],
+                        result=None,
+                        result_map={"y": False, "n": None},
+                    )
+                    # if repeat == "y":
+                    #     completed = False
+                    #     logger.finfo(get_subheader("Repeating solvation"))
+                if completed is False:
+                    logger.finfo(
+                        "Repeating bulk setup.\n", initial_linebreak=True
+                    )
+                else:
+                    logger.finfo(
+                        "Finishing setup without energy minimisation.\n",
+                        initial_linebreak=True,
+                    )
             else:
                 logger.finfo(
-                    "Finishing setup without energy minimisation.\n",
+                    completed,
                     initial_linebreak=True,
+                    fix_sentence_endings=False,
+                    expand_tabs=False,
+                    replace_whitespace=False,
                 )
-        else:
-            logger.finfo(
-                completed,
-                initial_linebreak=True,
-                fix_sentence_endings=False,
-                expand_tabs=False,
-                replace_whitespace=False,
-            )
-            logger.debug("\nFinished setup!")
-    clay_builder.conclude()
-    if isinstance(args, SiminpArgs):
-        print("siminp")
-    return 0
-
-
-def run():
-    """Run ClayCode."""
-    args = parser.parse_args(sys.argv[1:])
-    args_factory = ArgsFactory()
-    args = args_factory.init_subclass(args)
-    if isinstance(args, SiminpArgs):
-        args.write_runs()
-    if isinstance(args, DataArgs):
-        uc_writer = UCWriter(
-            args.ingro,
-            args.uc_type,
-            args.outpath,
-            default_solv=args.default_solv,
-            substitutions=args.substitutions,
-        )
-        uc_writer.write_new_uc(args.uc_name)
-        uc_writer.add_single_substitutions()
-        uc_writer.add_double_substitutions()
-        uc_writer.add_triple_substitutions()
-    elif isinstance(args, BuildArgs):
-        run_builder(args)
+                logger.debug("\nFinished setup!")
+        clay_builder.conclude()
+        if isinstance(args, SiminpArgs):
+            print("siminp")
     return 0