Merge pull request #28 from paulsaxe/main

Cleaned up the output and added space group symmetry to output.

.github/workflows/BranchCI.yaml

@@ -35,7 +35,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff read_structure_step tests
+        black --extend-exclude '_version.py' --check --diff read_structure_step tests
         flake8 read_structure_step tests
     - name: Run tests
       shell: bash -l {0}

.github/workflows/CI.yaml

@@ -43,7 +43,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff read_structure_step tests
+        black --extend-exclude '_version.py' --check --diff read_structure_step tests
         flake8 read_structure_step tests
 
   test:

.github/workflows/Release.yaml

@@ -36,7 +36,7 @@ jobs:
     - name: Run linters
       shell: bash -l {0}
       run: |
-        black --check --diff read_structure_step tests
+        black --extend-exclude '_version.py' --check --diff read_structure_step tests
         flake8 read_structure_step tests
 
   test:

Makefile

@@ -50,11 +50,11 @@ clean-test: ## remove test and coverage artifacts
 	find . -name '.pytype' -exec rm -fr {} +
 
 lint: ## check style with black and flake8
-	black --check --diff $(MODULE) tests
+	black --extend-exclude '_version.py' --check --diff $(MODULE) tests
 	flake8 $(MODULE) tests
 
-format: ## reformat with with yapf and isort
-	black $(MODULE) tests
+format: ## reformat with with black
+	black --extend-exclude '_version.py' $(MODULE) tests
 
 typing: ## check typing
 	pytype $(MODULE)

read_structure_step/read_structure.py

@@ -13,6 +13,7 @@
 
 import logging
 from pathlib import PurePath, Path
+import textwrap
 
 from .formats.registries import get_format_metadata
 import read_structure_step
@@ -110,7 +111,8 @@ def description_text(self, P=None):
         else:
             text += seamm.standard_parameters.structure_handling_description(P)
 
-        return text
+        text = textwrap.fill(text, initial_indent=4 * " ", subsequent_indent=4 * " ")
+        return self.header + "\n" + text
 
     def run(self):
         """Run a Read Structure step."""
@@ -141,7 +143,7 @@ def run(self):
             P["file type"] = extension
 
         # Print what we are doing
-        printer.important(__(self.description_text(P), indent=4 * " "))
+        printer.important(self.description_text(P))
 
         # Read the file into the system
         system_db = self.get_variable("_system_db")
@@ -168,15 +170,31 @@ def run(self):
         )
 
         # Finish the output
-        printer.important(
-            __(
-                f"\n    Created a molecular structure with {configuration.n_atoms} "
-                "atoms."
-                f"\n           System name = {system.name}"
-                f"\n    Configuration name = {configuration.name}",
-                indent=4 * " ",
+        if configuration.periodicity == 3:
+            space_group = configuration.symmetry.group
+            if space_group == "":
+                symmetry_info = ""
+            else:
+                symmetry_info = f" The space group is {space_group}."
+            printer.important(
+                __(
+                    f"\n    Created a periodic structure with {configuration.n_atoms} "
+                    f"atoms.{symmetry_info}"
+                    f"\n           System name = {system.name}"
+                    f"\n    Configuration name = {configuration.name}",
+                    indent=4 * " ",
+                )
+            )
+        else:
+            printer.important(
+                __(
+                    f"\n    Created a molecular 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