wip

Makefile

@@ -11,12 +11,13 @@ help:
 	@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"
 
 .PHONY: lint
-lint: lint-isort lint-black lint-flake8
+lint: lint-isort lint-black lint-flake8 lint-pyright
 
 .PHONY: format
 format: format-isort format-black
@@ -41,6 +42,10 @@ format-black:
 lint-flake8:
 	flake8 .
 
+.PHONY: lint-pyright
+lint-pyright:
+	pyright .
+
 .PHONY: test
 test:
 	pytest

altamisa/apps/isatab_validate.py

@@ -7,6 +7,10 @@
 import sys
 import warnings
 
+import attrs
+import typer
+from typing_extensions import Annotated
+
 from altamisa.isatab import (
     AssayReader,
     AssayValidator,
@@ -16,8 +20,40 @@
     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 +65,20 @@ 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 +105,5 @@ 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)

pyproject.toml

@@ -0,0 +1,23 @@
+[tool.pyright]
+include = [
+    "altamisa",
+    "tests",
+]
+exclude = [
+    "**/node_modules",
+    "**/__pycache__",
+    "src/experimental",
+    "src/typestubs"
+]
+defineConstant = { DEBUG = true }
+stubPath = "stubs"
+
+reportMissingImports = true
+reportMissingTypeStubs = false
+
+pythonVersion = "3.8"
+pythonPlatform = "Linux"
+
+executionEnvironments = [
+  { root = "src" }
+]

requirements/base.txt

@@ -1,3 +1,4 @@
 # Base requirements
 
 attrs
+typer[all]

setup.py

@@ -52,9 +52,9 @@ def parse_requirements(path):
     ],
     entry_points={
         "console_scripts": (
-            "isatab2dot = altamisa.apps.isatab2dot:main",
-            "isatab2isatab = altamisa.apps.isatab2isatab:main",
-            "isatab_validate = altamisa.apps.isatab_validate:main",
+            "isatab2dot = altamisa.apps.isatab2dot:app",
+            "isatab2isatab = altamisa.apps.isatab2isatab:app",
+            "isatab_validate = altamisa.apps.isatab_validate:app",
         )
     },
     description="Implementation of ISA-tools data model and ISA-TAB",