feat: Set up proper type checking (#112)

.github/workflows/ci.yml

@@ -16,32 +16,31 @@ jobs:
           - '3.12'
 
     steps:
-      - name: Install Python via conda.
-        uses: s-weigand/setup-conda@v1
+      - name: Install Python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
+          python-version: "${{ matrix.python-version }}"
+
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           lfs: true
-      - name: Install mamba.
-        run: conda install -y mamba
+
       - name: Install test dependencies via pip
         run: pip install -r requirements/test_black.txt
+
+      - name: Lint
+        run: make lint
+
       - name: Run tests
-        run: pytest
-      - name: Create text report
-        run: coverage report
-      - name: Create XML report for codacy
-        run: coverage xml
+        run: |
+          make test
+          coverage report
+          coverage xml
+
       - name: Upload Python coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:
           flags: python
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - name: Check style with black
-        run: make black-check
-      - name: Check style with flake8
-        run: flake8 .

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 +2,25 @@
 """Conversion of ISA-Tab to dot.
 """
 
+from contextlib import ExitStack
 import json
-import sys
 import os
-import argparse
+import sys
+
+import attrs
+import typer
+from typing_extensions import Annotated
+
+from altamisa.isatab import AssayReader, InvestigationReader, StudyReader
+
+#: Typer application instance.
+app = typer.Typer()
 
-from altamisa.isatab import InvestigationReader, StudyReader, AssayReader
+
+@attrs.define
+class Arguments:
+    investigation_file: str
+    output_file: str
 
 
 def print_dot(
@@ -49,55 +62,78 @@ def print_dot(
         print("{}{} -> {};".format(indent, json.dumps(arc.tail), json.dumps(arc.head)), file=outf)
 
 
-def run(args):
+def run(args: Arguments):
     with open(args.investigation_file, "rt") as inputf:
         investigation = InvestigationReader.from_stream(inputf).read()
 
     path = os.path.dirname(args.investigation_file)
 
-    print("digraph investigation {", file=args.output_file)
-    print('  rankdir = "LR";', file=args.output_file)
-
-    for s, study_info in enumerate(investigation.studies):
-        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)
-        print("  subgraph clusterStudy{} {{".format(s), file=args.output_file)
-        print('    label = "Study: {}"'.format(study_info.info.path), file=args.output_file)
-        print_dot(study, args.output_file)
-        print("  }", file=args.output_file)
-
-        for a, assay_info in enumerate(study_info.assays):
-            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
-                ).read()
-            print("  /* assay {} */".format(assay_info.path), file=args.output_file)
-            print("  subgraph clusterAssayS{}A{} {{".format(s, a), file=args.output_file)
-            print('    label = "Assay: {}"'.format(assay_info.path), file=args.output_file)
-            print_dot(assay, args.output_file)
-            print("  }", file=args.output_file)
-
-    print("}", file=args.output_file)
-
-
-def main(argv=None):
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i", "--investigation-file", required=True, help="Path to investigation file"
-    )
-    parser.add_argument(
-        "-o",
-        "--output-file",
-        default="-",
-        type=argparse.FileType("wt"),
-        help='Path to output file, stdout ("-") by default',
+    with ExitStack() as stack:
+        if args.output_file == "-":
+            output_file = sys.stdout
+        else:
+            output_file = stack.enter_context(open(args.output_file, "wt"))
+
+        print("digraph investigation {", file=output_file)
+        print('  rankdir = "LR";', file=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=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=output_file)
+            print("  subgraph clusterStudy{} {{".format(s), file=output_file)
+            print('    label = "Study: {}"'.format(study_info.info.path), file=output_file)
+            print_dot(study, output_file)
+            print("  }", file=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=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
+                    ).read()
+                print("  /* assay {} */".format(assay_info.path), file=output_file)
+                print("  subgraph clusterAssayS{}A{} {{".format(s, a), file=output_file)
+                print('    label = "Assay: {}"'.format(assay_info.path), file=output_file)
+                print_dot(assay, output_file)
+                print("  }", file=output_file)
+
+        print("}", file=output_file)
+
+
+@app.command()
+def main(
+    investigation_file: Annotated[
+        str,
+        typer.Option(
+            "--investigation-file",
+            "-i",
+            help="Path to input investigation file",
+        ),
+    ],
+    output_file: Annotated[
+        str,
+        typer.Option(
+            "--output-file",
+            "-o",
+            help="Path to output file, stdout ('-') by default",
+        ),
+    ] = "-",
+):
+    """Main entry point."""
+    # Convert to `Arguments` object.
+    args = Arguments(
+        investigation_file=investigation_file,
+        output_file=output_file,
     )
-
-    args = parser.parse_args(argv)
-    return run(args)
+    # Actually run.
+    run(args)
 
 
-if __name__ == "__main__":
-    sys.exit(main())  # pragma: no cover
+if __name__ == "__main__":  # pragma: no cover
+    typer.run(main)