test: reorganize pytest testing (mult. OSes & Python versions)

The logic of pytest tests was edited; now it is based on iterating
lists of tuples.  Eventually, the edits allow to test the script
on multiple operating systems ("runner images" in GitHub's parlance)
vs either Python 3.10, or Python 3.12.

Signed-off-by: Norwid Behrnd <[email protected]>

.github/workflows/pytest.yml

@@ -3,7 +3,7 @@ name: CI_pytest_datawarrior_saturate_murcko_scaffolds
 # name    : pytest.yml
 # purpose : regularly run pytest on the saturator script
 # date    : [2024-03-21 Thu]
-# edit    : [2024-03-27 Wed]
+# edit    : [2024-11-11 Mon]
 
 on:
   push:
@@ -17,27 +17,31 @@ on:
     - cron: "0 0 1 * *"  # once each 1st of a month, at 00:00 UTC (cf. https://crontab.guru/)
 
 jobs:
-  linux-static:
-    runs-on: ubuntu-latest
-    timeout-minutes: 2
+  test:
+    strategy:
+      matrix:
+        # for a factorial test, an explicit selection of GitHUb runner images
+        # https://github.com/actions/runner-images?tab=readme-ov-file#available-images
+        # state of commit 23478d3 as visited on 2024-11-11 Mon
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04, windows-2019, windows-2022, macos-14]
+        python-version: ["3.10", "3.12"]
+    runs-on: ${{ matrix.os }}
+
+    timeout-minutes: 3  # Timeout for each job individually
 
     steps:
-      - name: Check number of cores
-        run: |
-          lscpu
-          lscpu | grep "CPU(s):                       " | awk '{print $2}' > num_cores
-          echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
-
       - uses: actions/checkout@v4
         # by [2024-10-23 Wed], this version possibly will be considered "old", cf.
         # https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.x'
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies with PyPI
         run: pip install pytest
 
-      - name: run the check by pytest
+      - name: Run the check with pytest
         run: python -m pytest
+
+

saturate_murcko_scaffolds.py

@@ -4,7 +4,7 @@
 # name:   saturate_murcko_scaffolds.py
 # author: [email protected]
 # date:   [2019-06-07 Fri]
-# edit:   <2023-05-23 Wed>
+# edit:   [2024-11-11 Mon]
 #
 """Read Smiles of Murcko scaffolds and return these as 'saturated'.
 
@@ -36,7 +36,7 @@
     http://www.openmolecules.org, https://github.com/thsa/datawarrior
 [3] https://en.wikipedia.org/wiki/Benomyl
 
-License: Norwid Behrnd, 2019--2023, GPLv3.
+License: Norwid Behrnd, 2019--2024, GPLv3.
 """
 import argparse
 import io
@@ -62,24 +62,17 @@ def get_args():
     )
 
     parser.add_argument(
-        "text",
-        type=str,
-        help="process a single SMILES from the CLI, or access an input file")
+        "inputs",
+        nargs="+",
+        help="provide one or multiple SMILES from the CLI, or an input text file listing SMILES")
 
-    parser.add_argument(
-        "-o",
-        "--outfile",
-        help="output file name, else results are reported back to the CLI",
-        metavar="",
-        default="",
-    )
 
     args = parser.parse_args()
 
-    if os.path.isfile(args.text):
-        args.text = open(file=args.text, mode="rt", encoding="utf-8")
-    else:
-        args.text = io.StringIO(args.text + "\n")
+#    if os.path.isfile(args.text):
+#        args.text = open(file=args.text, mode="rt", encoding="utf-8")
+#    else:
+#        args.text = io.StringIO(args.text + "\n")
 
     return args
 
@@ -221,25 +214,43 @@ def write_record(input_file, listing):
         sys.exit()
 
 
+def process_smiles(smiles):
+    """sequentially pass a SMILES string to reduction"""
+    only_single_bonds = saturator(smiles)
+    on_carbon = saturate_carbon(only_single_bonds)
+    on_nitrogen = saturate_nitrogen(on_carbon)
+    on_oxygen = saturate_oxygen(on_nitrogen)
+    on_phosphorus = saturate_phosphorus(on_oxygen)
+    on_sulfur = saturate_sulfur(on_phosphorus)
+    result = on_sulfur
+
+    print(f"{result}")
+
+
+def process_input_files(input_files):
+    """sequentially process input files with lists of SMILES strings"""
+    for file in input_files:
+        try:
+            with open (file, mode="r", encoding="utf-8") as source:
+                for line in source:
+                    smiles = str(line).strip()
+                    process_smiles(smiles)
+        except:
+            print(f"file {file} is not accessible")
+
+
 def main():
     """Join the functions."""
     args = get_args()
 
-    output = (
-        open(args.outfile, mode="wt", encoding="utf-8") if args.outfile else sys.stdout
-    )
-    for line in args.text:
-        raw_data = str(line).strip()
-
-        only_single_bonds = saturate_bonds(raw_data)
-        on_carbon = saturate_carbon(only_single_bonds)
-        on_nitrogen = saturate_nitrogen(on_carbon)
-        on_oxygen = saturate_oxygen(on_nitrogen)
-        on_phosphorus = saturate_phosphorus(on_oxygen)
-        on_sulfur = saturate_sulfur(on_phosphorus)
-
-        result = on_sulfur
-        output.write(result + "\n")
+    smiles_strings = [arg for arg in args.inputs if not os.path.isfile(arg)]
+    if smiles_strings:
+        for smiles in smiles_strings:
+            process_smiles(smiles)
+
+    input_files = [arg for arg in args.inputs if os.path.isfile(arg)]
+    if input_files:
+        process_input_files(input_files)
 
 
 if __name__ == "__main__":