Replace print by logging where it makes sense

example/README.md

@@ -4,7 +4,7 @@ Example files showing typical conversions with voc4cat:
   - A draft of a photocatalysis vocabulary: This has still the original structure and contents; only spelling and link errors were fixed.
   - The hierarchy was created with voc4cat 0.30 by the `-r` / `--add-related` option from the extra column on the right in sheets Concepts & Collections. Note, this option was removed in 0.4.0 to foster using numeric IDs.
 - `Photocatalysis_LIKAT_template043_textids.xlsx`
-  - Same contents as the first file but the extra column in the sheets Concepts & Collections was removed. The concepts were sorted by IRI (this was done to assign IDs in a reproducible way to domonstrate round-tripping, see below).
+  - Same contents as the first file but the extra column in the sheets Concepts & Collections was removed. The concepts were sorted by IRI (this was done to assign IDs in a reproducible way to demonstrate round-tripping, see below).
 - `Photocatalysis_LIKAT_template043_final.xlsx`
   - This file was generate from the previous one by replacing the textual IDs with numeric ones using the `--make-ids` option added in version 0.4.0.
 - `Photocatalysis_LIKAT_template043_final.ttl`

pyproject.toml

@@ -248,7 +248,7 @@ max-complexity = 10
 classmethod-decorators = ["classmethod", "pydantic.validator"]
 
 [tool.codespell]
-skip = "pyproject.toml,./vocabularies,./example,./tests/data,./tmp"
+skip = "*.xlsx,pyproject.toml,./vocabularies,./example,./tests/data,./tmp"
 # Note: words have to be lowercased for the ignore-words-list
 ignore-words-list = "linke"
 quiet-level = 3

src/voc4cat/convert.py

@@ -541,6 +541,7 @@ def main(args=None):
     if args.logfile:
         # We import here to avoid a cyclic import when this is used via wrapper.main
         from voc4cat.wrapper import setup_logging
+
         setup_logging(logfile=args.logfile)
     elif run_via_entrypoint:
         setup_logging()

src/voc4cat/wrapper.py

@@ -113,7 +113,7 @@ def make_ids(fpath, outfile, search_prefix, start_id):
     If new_prefix is None the new IRI is a concatenation of VOC_BASE_IRI and ID.
     If new_prefix is given the new IRI is the CURI new_prefix:ID.
     """
-    print(f"\nReplacing {search_prefix}:... IRIs.")
+    logger.info("\nReplacing {search_prefix}:... IRIs.")
     # Load in data_only mode to get cell values not formulas.
     wb = openpyxl.load_workbook(fpath, data_only=True)
     is_supported_template(wb)
@@ -145,7 +145,8 @@ def make_ids(fpath, outfile, search_prefix, start_id):
                     iri_new = replaced_iris[iri]
                 else:
                     iri_new = voc_base_iri + f"{next(id_gen):07d}"
-                    print(f"[{sheet}] Replaced CURI {iri} by {iri_new}")
+                    msg = f"[{sheet}] Replaced CURI {iri} by {iri_new}"
+                    logger.debug(msg)
                     replaced_iris[iri] = iri_new
                 row[0].value = iri_new
 
@@ -168,15 +169,16 @@ def make_ids(fpath, outfile, search_prefix, start_id):
                     )
                     if count_new_iris:
                         new_iris = [replaced_iris.get(iri, iri) for iri in iris]
-                        print(
+                        msg = (
                             f"[{sheet}] Replaced {count_new_iris} CURIs "
                             f"in cell {row[col].coordinate}"
                         )
+                        logger.debug(msg)
                         row[col].value = ", ".join(new_iris)
                     # subsequent_empty_rows = 0
 
     wb.save(outfile)
-    print(f"Saved updated file as {outfile}")
+    logger.info("Saved updated file as %s", outfile)
     return 0
 
 
@@ -187,7 +189,7 @@ def hierarchy_from_indent(fpath, outfile, sep):
     If separator character(s) are given they will be replaced with
     Excel indent which is also the default if sep is None.
     """
-    print(f"\nReading concepts from file {fpath}")
+    logger.info("Reading concepts from file %s", fpath)
     # Load in data_only mode to get cell values not formulas.
     wb = openpyxl.load_workbook(fpath, data_only=True)
     is_supported_template(wb)
@@ -267,7 +269,7 @@ def hierarchy_from_indent(fpath, outfile, sep):
         row += 1
 
     wb.save(outfile)
-    print(f"Saved updated file as {outfile}")
+    logger.info("Saved updated file as %s", outfile)
     return 0
 
 
@@ -278,7 +280,7 @@ def hierarchy_to_indent(fpath, outfile, sep):
     If separator character(s) are given they will be used.
     If sep is None, Excel indent will be used.
     """
-    print(f"\nReading concepts from file {fpath}")
+    logger.info("Reading concepts from file %s", fpath)
     wb = openpyxl.load_workbook(fpath)
     is_supported_template(wb)
     ws = wb["Concepts"]
@@ -363,7 +365,7 @@ def hierarchy_to_indent(fpath, outfile, sep):
             iri_written.append((iri, lang))
 
     wb.save(outfile)
-    print(f"Saved updated file as {outfile}")
+    logger.info("Saved updated file as %s", outfile)
     return 0
 
 
@@ -378,7 +380,7 @@ def run_pylode(file_path, output_path):
         return 1
 
     for turtle_file in turtle_files:
-        print(f"\nBuilding pyLODE documentation for {turtle_file}")
+        logger.info("Building pyLODE documentation for %s", turtle_file)
         filename = Path(turtle_file)  # .resolve())
         outdir = output_path / filename.with_suffix("").name
         outdir.mkdir(exist_ok=True)
@@ -400,7 +402,7 @@ def run_pylode(file_path, output_path):
         )
         with open(outfile, "w") as html_file:
             html_file.write(content)
-        print(f"Done!\n=> {outfile.resolve().as_uri()}")
+        logger.info("Done!\n=> %s", outfile.resolve().as_uri())
     return 0
 
 
@@ -419,7 +421,7 @@ def run_ontospy(file_path, output_path):
     for turtle_file in turtle_files:
         title = config.VOCAB_TITLE
 
-        print(f"\nBuilding ontospy documentation for {turtle_file}")
+        logger.info("Building ontospy documentation for %s", turtle_file)
         specific_output_path = (Path(output_path) / Path(turtle_file).stem).resolve()
 
         g = ontospy.Ontospy(Path(turtle_file).resolve().as_uri())
@@ -439,12 +441,12 @@ def find_files_to_document(file_path):
     if Path(file_path).is_dir():
         turtle_files = glob.glob(f"{file_path}/*.ttl")
         if not turtle_files:
-            print(f"No turtle file(s) found to document in {file_path}")
+            logger.warning("No turtle file(s) found to document in %s", file_path)
             turtle_files = []
     elif Path(file_path).exists():
         turtle_files = [file_path]
     else:
-        print(f"File/dir not found (for docs): {file_path}")
+        logger.warning("File/dir not found (for docs): %s", file_path)
         turtle_files = []
     return turtle_files
 
@@ -458,7 +460,7 @@ def build_docs(file_path, output_path, doc_builder):
     elif doc_builder == "pylode":
         errcode = run_pylode(file_path, output_path)
     else:
-        print(f"Unsupported document builder '{doc_builder}'.")
+        logger.error("Unsupported document builder '%s'.", doc_builder)
         errcode = 1
     return errcode
 
@@ -471,7 +473,7 @@ def check(fpath, outfile):
     - The "Concept IRI" must be unique; this is the case when no language
       is used more than once per concept.
     """
-    print(f"\nRunning check of Concepts sheet for file {fpath}")
+    logger.info("Running check of Concepts sheet for file %s", fpath)
     wb = openpyxl.load_workbook(fpath)
     is_supported_template(wb)
     ws = wb["Concepts"]
@@ -489,10 +491,11 @@ def check(fpath, outfile):
             new_concept_iri = f'"{concept_iri}"@{lang.lower()}'
             if new_concept_iri in seen_concept_iris:
                 failed_check = True
-                print(
+                msg = (
                     f'ERROR: Same Concept IRI "{concept_iri}" used more than once for '
                     f'language "{lang}"'
                 )
+                logger.error(msg)
                 # colorize problematic cells
                 row[0].fill = color
                 row[2].fill = color
@@ -513,14 +516,15 @@ def check(fpath, outfile):
 
     if failed_check:
         wb.save(outfile)
-        print(f"Saved file with highlighted errors as {outfile}")
+        logger.info("Saved file with highlighted errors as %s", outfile)
         return 1
 
-    print("All checks passed successfully.")
+    logger.info("All checks passed successfully.")
 
     if fpath != outfile:  # Save to new directory (important for --forward option)
         wb.save(outfile)
-        print(f"Saved checked file as {outfile}")
+        msg = f"Saved checked file as {outfile}"
+        logger.info(msg)
 
     return 0
 

tests/test_wrapper.py

@@ -1,3 +1,4 @@
+import logging
 import os
 import shutil
 from pathlib import Path
@@ -442,30 +443,31 @@ def test_build_docs_ontospy(datadir, tmp_path, test_file):
     "doc_builder",
     ["pylode", "ontospy"],
 )
-def test_build_docs(tmp_path, capsys, doc_builder):
+def test_build_docs(tmp_path, caplog, doc_builder):
     """Check handling of missing dir/file on documentation build."""
-    exit_code = build_docs(tmp_path, tmp_path, doc_builder)
-    captured = capsys.readouterr()
+    with caplog.at_level(logging.INFO):
+        exit_code = build_docs(tmp_path, tmp_path, doc_builder)
     assert exit_code == 1
-    assert f"No turtle file(s) found to document in {tmp_path}" in captured.out
-    exit_code = build_docs(tmp_path / CS_CYCLES_TURTLE, tmp_path, doc_builder)
-    captured = capsys.readouterr()
+    assert f"No turtle file(s) found to document in {tmp_path}" in caplog.text
+
+    with caplog.at_level(logging.INFO):
+        exit_code = build_docs(tmp_path / CS_CYCLES_TURTLE, tmp_path, doc_builder)
     assert exit_code == 1
-    assert f"File/dir not found (for docs): {tmp_path/CS_CYCLES_TURTLE}" in captured.out
+    assert f"File/dir not found (for docs): {tmp_path/CS_CYCLES_TURTLE}" in caplog.text
 
-    exit_code = build_docs(tmp_path / CS_CYCLES_TURTLE, tmp_path, "ontospy")
-    captured = capsys.readouterr()
+    with caplog.at_level(logging.INFO):
+        exit_code = build_docs(tmp_path / CS_CYCLES_TURTLE, tmp_path, "ontospy")
     assert exit_code == 1
-    assert f"File/dir not found (for docs): {tmp_path/CS_CYCLES_TURTLE}" in captured.out
+    assert f"File/dir not found (for docs): {tmp_path/CS_CYCLES_TURTLE}" in caplog.text
 
 
-def test_build_docs_unknown_builder(tmp_path, capsys):
+def test_build_docs_unknown_builder(tmp_path, caplog):
     """Check handling of unknown documentation builder."""
     unknown_doc_builder = "123doc"
-    exit_code = build_docs(tmp_path, tmp_path, unknown_doc_builder)
-    captured = capsys.readouterr()
+    with caplog.at_level(logging.INFO):
+        exit_code = build_docs(tmp_path, tmp_path, unknown_doc_builder)
     assert exit_code == 1
-    assert f"Unsupported document builder '{unknown_doc_builder}'." in captured.out
+    assert f"Unsupported document builder '{unknown_doc_builder}'." in caplog.text
 
 
 @pytest.mark.parametrize(
@@ -481,14 +483,14 @@ def test_build_docs_unknown_builder(tmp_path, capsys):
     ],
     ids=["no error", "with error"],
 )
-def test_check(datadir, tmp_path, capsys, test_file, err, msg):  # noqa: PLR0913
+def test_check(datadir, tmp_path, caplog, test_file, err, msg):  # noqa: PLR0913
     dst = tmp_path / test_file
     shutil.copy(datadir / test_file, dst)
-    exit_code = main_cli(["--check", "--no-warn", str(dst)])
-    captured = capsys.readouterr()
-    # TODO check that erroneous cells get colored.
+    with caplog.at_level(logging.INFO):
+        exit_code = main_cli(["--check", "--no-warn", str(dst)])
     assert exit_code == err
-    assert msg in captured.out
+    assert msg in caplog.text
+    # TODO check that erroneous cells get colored.
 
 
 def test_unsupported_filetype(datadir, capsys):