Merge pull request #96 from molssi-seamm/dev

Enhancement to allow paths with directories.

Author: seamm

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2025.6.1 -- Enhancement to allow paths with directories.
+    * As in reading/writing structures, paths beginning with '/' are relative to the
+      root of the job, and relative paths are relative to the directory where the table
+      step is invoked.
+
 2023.11.10 -- Bugfix: title of edit dialog was wrong
 
 2023.10.30 -- Cleaned up output

devtools/conda-envs/test_env.yaml

@@ -31,6 +31,7 @@ dependencies:
     # Integration testing
     - custom-step
     - loop-step
+    - seamm-exec
     # Documentation
     - sphinx-copybutton
     - sphinxnotes-strike

table_step/table.py

@@ -3,8 +3,7 @@
 """Non-graphical part of the Table step in SEAMM"""
 
 import logging
-import os.path
-from pathlib import PurePath
+from pathlib import Path, PurePath
 
 import numpy as np
 import pandas
@@ -208,6 +207,9 @@ def run(self):
         )
         tablename = P["table name"]
 
+        # Pathnames are relative to current working directory
+        wd = Path(self.directory).parent
+
         # Print out header to the main output
         printer.important(self.description_text(P))
         printer.important("")
@@ -330,16 +332,21 @@ def run(self):
                 file_type = P["file type"]
                 table_handle = self.get_variable(tablename)
                 table = table_handle["table"]
+
                 if P["method"] == "Save as":
-                    filename = P["filename"]
+                    filename = P["filename"].strip()
+                    if filename.startswith("/"):
+                        filename = str(
+                            Path(self.flowchart.root_directory) / filename[1:]
+                        )
+                    else:
+                        filename = str(wd / filename)
                     table_handle["filename"] = filename
                 else:
                     if "filename" not in table_handle:
                         if file_type == "from extension":
                             file_type = ".csv"
-                        table_handle["filename"] = os.path.join(
-                            self.flowchart.root_directory, tablename + file_type
-                        )
+                        table_handle["filename"] = str(wd / tablename) + file_type
                     filename = table_handle["filename"]
 
                 index = table_handle["index column"]

table_step/table_parameters.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Control parameters for loops
-"""
+"""Control parameters for tables"""
 
 import logging
 import seamm

tests/test_flowcharts.py

@@ -4,7 +4,7 @@
 """Tests for `table_step` running full flowcharts."""
 from pathlib import Path
 import pytest
-from seamm import run_flowchart
+from seamm_exec import run
 
 test_dir = Path(__file__).resolve().parent
 
@@ -25,4 +25,4 @@ def test_flowchart(monkeypatch, tmp_path, flowchart):
         ],
     )
 
-    run_flowchart(wdir=str(tmp_path))
+    run(wdir=str(tmp_path))

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):