feat: properly setup of type checking (#112)

MANIFEST.in

@@ -11,6 +11,7 @@ recursive-exclude * *.py[co]
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 
 include versioneer.py
-include vcfpy/_version.py
+include altamisa/_version.py
+include altamisa/py.typed
 
 include requirements.txt requirements/*.txt

Makefile

@@ -1,21 +1,59 @@
-.PHONY: default black flake8 test test-v test-vv
+.PHONY: default
+default: help
 
-default: black flake8
+.PHONY: help
+help:
+	@echo "make help         - show this help"
+	@echo "make lint         - run all linting"
+	@echo "make format       - run all formatting"
+	@echo "make lint-isort   - run isort linting"
+	@echo "make format-isort - run isort formatting"
+	@echo "make lint-black   - run black linting"
+	@echo "make format-black - run black formatting"
+	@echo "make lint-flake8  - run flake8 linting"
+	@echo "make lint-pyright - run pyright linting"
+	@echo "make test         - run all tests"
+	@echo "make test-v       - run all tests with verbose output"
+	@echo "make test-vv      - run all tests with very verbose output"
 
-black:
-	black -l 100 --exclude "versioneer.py|_version.py" .
+.PHONY: lint
+lint: lint-isort lint-black lint-flake8 lint-pyright
+
+.PHONY: format
+format: format-isort format-black
+
+.PHONY: lint-isort
+lint-isort:
+	isort --check-only --diff --force-sort-within-sections --profile=black .
+
+.PHONY: format-isort
+format-isort:
+	isort --force-sort-within-sections --profile=black .
 
-black-check:
+.PHONY: lint-black
+lint-black:
 	black -l 100 --exclude "versioneer.py|_version.py" --check .
 
-flake8:
+.PHONY: format-black
+format-black:
+	black -l 100 --exclude "versioneer.py|_version.py" .
+
+.PHONY: lint-flake8
+lint-flake8:
 	flake8 .
 
+.PHONY: lint-pyright
+lint-pyright:
+	pyright
+
+.PHONY: test
 test:
 	pytest
 
+.PHONY: test-v
 test-v:
 	pytest -v
 
+.PHONY: test-vv
 test-vv:
 	pytest -vv

altamisa/_version.py

@@ -12,12 +12,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]:

altamisa/apps/isatab2dot.py

@@ -2,12 +2,12 @@
 """Conversion of ISA-Tab to dot.
 """
 
+import argparse
 import json
-import sys
 import os
-import argparse
+import sys
 
-from altamisa.isatab import InvestigationReader, StudyReader, AssayReader
+from altamisa.isatab import AssayReader, InvestigationReader, StudyReader
 
 
 def print_dot(
@@ -59,6 +59,9 @@ def run(args):
     print('  rankdir = "LR";', file=args.output_file)
 
     for s, study_info in enumerate(investigation.studies):
+        if not study_info.info.path:
+            print("  /* no file for study {} */".format(s + 1), file=args.output_file)
+            continue
         with open(os.path.join(path, study_info.info.path), "rt") as inputf:
             study = StudyReader.from_stream("S{}".format(s + 1), inputf).read()
         print("  /* study {} */".format(study_info.info.path), file=args.output_file)
@@ -68,6 +71,9 @@ def run(args):
         print("  }", file=args.output_file)
 
         for a, assay_info in enumerate(study_info.assays):
+            if not assay_info.path:
+                print("  /* no file for assay {} */".format(a + 1), file=args.output_file)
+                continue
             with open(os.path.join(path, assay_info.path), "rt") as inputf:
                 assay = AssayReader.from_stream(
                     "S{}".format(s + 1), "A{}".format(a + 1), inputf

altamisa/apps/isatab2isatab.py

@@ -7,6 +7,7 @@
 import sys
 import warnings
 
+from altamisa.exceptions import IsaException
 from altamisa.isatab import (
     AssayReader,
     AssayValidator,
@@ -18,7 +19,6 @@
     StudyValidator,
     StudyWriter,
 )
-from altamisa.exceptions import IsaException
 
 
 def run(args):
@@ -30,7 +30,11 @@ def run(args):
     if not args.no_warnings:
         for record in records:
             warnings.showwarning(
-                record.message, record.category, record.filename, record.lineno, record.line
+                record.message,
+                record.category,
+                record.filename,
+                lineno=record.lineno,
+                line=record.line,
             )
 
 

altamisa/apps/isatab_validate.py

@@ -2,11 +2,13 @@
 """Read from ISA-Tab and print validation warnings, if any.
 """
 
-import argparse
 import os
-import sys
 import warnings
 
+import attrs
+import typer
+from typing_extensions import Annotated
+
 from altamisa.isatab import (
     AssayReader,
     AssayValidator,
@@ -16,8 +18,40 @@
     StudyValidator,
 )
 
+#: Typer application instance.
+app = typer.Typer()
+
+
+@attrs.define
+class Arguments:
+    input_investigation_file: str
+    show_duplicate_warnings: bool
+
 
-def run(args):
+@app.command()
+def main(
+    input_investigation_file: Annotated[
+        str,
+        typer.Option(
+            "--input-investigation-file",
+            "-i",
+            help="Path to input investigation file",
+        ),
+    ],
+    show_duplicate_warnings: Annotated[
+        bool,
+        typer.Option(
+            "--show-duplicate-warnings/--no-show-duplicate_warnings",
+            help="Show duplicated warnings, i.e. with same message and same category (False by default)",
+        ),
+    ] = False,
+):
+    """Main entry point."""
+    # Convert to `Arguments` object.
+    args = Arguments(
+        input_investigation_file=input_investigation_file,
+        show_duplicate_warnings=show_duplicate_warnings,
+    )
     # Show all warnings of same type and content
     if args.show_duplicate_warnings:
         warnings.simplefilter("always")
@@ -29,20 +63,20 @@ def run(args):
     # Print warnings
     for record in records:
         warnings.showwarning(
-            record.message, record.category, record.filename, record.lineno, record.line
+            record.message, record.category, record.filename, lineno=record.lineno, line=record.line
         )
 
 
-def run_warnings_caught(args):
+def run_warnings_caught(args: Arguments):
     # Read investigation
-    investigation = InvestigationReader.from_stream(args.input_investigation_file).read()
-    args.input_investigation_file.close()
+    with open(args.input_investigation_file, "rt") as inputf:
+        investigation = InvestigationReader.from_stream(inputf).read()
 
     # Validate investigation
     InvestigationValidator(investigation).validate()
 
     # Read studies and assays
-    path_in = os.path.normpath(os.path.dirname(args.input_investigation_file.name))
+    path_in = os.path.normpath(os.path.dirname(args.input_investigation_file))
     studies = {}
     assays = {}
     for s, study_info in enumerate(investigation.studies):
@@ -69,29 +103,5 @@ def run_warnings_caught(args):
                 ).validate()
 
 
-def main(argv=None):
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i",
-        "--input-investigation-file",
-        required=True,
-        type=argparse.FileType("rt"),
-        help="Path to input investigation file",
-    )
-    parser.add_argument(
-        "--show-duplicate-warnings",
-        dest="show_duplicate_warnings",
-        action="store_true",
-        help=(
-            "Show duplicated warnings, i.e. with same message and same category (False by default)"
-        ),
-    )
-    parser.set_defaults(no_warnings=False)
-
-    args = parser.parse_args(argv)
-    return run(args)
-
-
 if __name__ == "__main__":  # pragma: no cover
-    sys.exit(main())
+    typer.run(main)

altamisa/constants/investigation_headers.py

@@ -7,8 +7,8 @@
 
 
 __author__ = (
-    "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>, "
-    "Mathias Kuhring <mathias.kuhring@bihealth.de>"
+    "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>, "
+    "Mathias Kuhring <mathias.kuhring@bih-charite.de>"
 )
 
 

altamisa/constants/table_headers.py

@@ -7,8 +7,8 @@
 
 
 __author__ = (
-    "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>, "
-    "Mathias Kuhring <mathias.kuhring@bihealth.de>"
+    "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>, "
+    "Mathias Kuhring <mathias.kuhring@bih-charite.de>"
 )
 
 

altamisa/constants/table_restrictions.py

@@ -3,14 +3,13 @@
 
 
 __author__ = (
-    "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>, "
-    "Mathias Kuhring <mathias.kuhring@bihealth.de>"
+    "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>, "
+    "Mathias Kuhring <mathias.kuhring@bih-charite.de>"
 )
 
 
 from . import table_headers
 
-
 # Assay measurement types (only the once needed for special validations)
 PROTEIN_EXPRESSION_PROFILING = "protein expression profiling"  #:
 PROTEIN_IDENTIFICATION = "protein identification"  #:

altamisa/constants/table_tokens.py

@@ -3,8 +3,8 @@
 
 
 __author__ = (
-    "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>, "
-    "Mathias Kuhring <mathias.kuhring@bihealth.de>"
+    "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>, "
+    "Mathias Kuhring <mathias.kuhring@bih-charite.de>"
 )
 
 

altamisa/exceptions.py

@@ -3,7 +3,7 @@
 Exceptions and Warnings used in the AltamISA library.
 """
 
-__author__ = "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>"
+__author__ = "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"
 
 
 class IsaException(Exception):

altamisa/isatab/__init__.py

@@ -14,5 +14,5 @@
 from .parse_investigation import InvestigationReader  # noqa: F401
 from .validate_assay_study import AssayValidator, StudyValidator  # noqa: F401
 from .validate_investigation import InvestigationValidator  # noqa: F401
-from .write_assay_study import AssayWriter, StudyWriter, RefTableBuilder  # noqa: F401
+from .write_assay_study import AssayWriter, RefTableBuilder, StudyWriter  # noqa: F401
 from .write_investigation import InvestigationWriter  # noqa: F401