From 80e948d4935e5a2d1e424b06d71ecdb8bff84157 Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Thu, 2 Apr 2026 17:07:46 -0400
Subject: [PATCH 1/4] feat: auto-discover binaries from upstream release
 archive

Introduce binaries.txt as the single source of truth for the list of
dcmqi executables. CMakeLists.txt now reads it via file(STRINGS),
__init__.py discovers installed binaries dynamically at import time,
and tests parametrize from the file. The update-dcmqi workflow
extracts binary names from the Linux archive and updates binaries.txt
and pyproject.toml [project.scripts] automatically when a new release
is detected.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/update-dcmqi.yml | 37 ++++++++++++++++-
 CMakeLists.txt                     | 16 ++------
 binaries.txt                       |  6 +++
 src/dcmqi/__init__.py              | 66 +++++++++++++-----------------
 tests/test_executable.py           | 24 +++--------
 5 files changed, 79 insertions(+), 70 deletions(-)
 create mode 100644 binaries.txt

diff --git a/.github/workflows/update-dcmqi.yml b/.github/workflows/update-dcmqi.yml
index f53bd80..cac0795 100644
--- a/.github/workflows/update-dcmqi.yml
+++ b/.github/workflows/update-dcmqi.yml
@@ -50,15 +50,32 @@ jobs:
           echo "Assets: $assets"
 
           # Download assets and compute checksums
+          # Also extract binary names from one archive (Linux)
           declare -A checksums
+          binaries=""
           for asset in $assets; do
             echo "Downloading $asset..."
             url="https://github.com/QIICR/dcmqi/releases/download/$latest_tag/$asset"
-            sha256=$(curl -sL "$url" | sha256sum | awk '{print $1}')
+            tmpfile=$(mktemp)
+            curl -sL "$url" -o "$tmpfile"
+            sha256=$(sha256sum "$tmpfile" | awk '{print $1}')
             checksums["$asset"]="$sha256"
             echo "  SHA256: $sha256"
+
+            # Discover binaries from the Linux archive
+            if [[ "$asset" == *-linux.tar.gz ]] && [ -z "$binaries" ]; then
+              echo "Discovering binaries from $asset..."
+              binaries=$(tar -tzf "$tmpfile" | grep '^[^/]*/bin/[^/]*$' | grep -v '/$' | sed 's|.*/bin/||' | sort)
+              echo "  Discovered binaries: $(echo $binaries | tr '\n' ' ')"
+            fi
+            rm -f "$tmpfile"
           done
 
+          if [ -z "$binaries" ]; then
+            echo "ERROR: Could not discover binaries from Linux archive"
+            exit 1
+          fi
+
           # Determine macOS asset pattern
           has_mac_split=false
           for asset in $assets; do
@@ -140,6 +157,22 @@ jobs:
             echo 'set(dcmqi_archive_url "https://github.com/QIICR/dcmqi/releases/download/v${version}/${dcmqi_archive_filename}")'
           } > dcmqiUrls.cmake
 
+          # Update binaries.txt with discovered binary list
+          echo "$binaries" > binaries.txt
+
+          # Update pyproject.toml [project.scripts] to match binaries.txt
+          python3 - <<PYEOF
+import re
+
+binaries = open("binaries.txt").read().split()
+scripts_block = "[project.scripts]\n" + "".join(
+    f'{b} = "dcmqi:{b}"\n' for b in binaries
+)
+content = open("pyproject.toml").read()
+content = re.sub(r"\[project\.scripts\]\n[^\[]*", scripts_block + "\n", content)
+open("pyproject.toml", "w").write(content)
+PYEOF
+
           # Update README.md to reference the new dcmqi release version
           sed -i "s|dcmqi v${current_version}](https://github.com/QIICR/dcmqi/releases/tag/v${current_version})|dcmqi v${latest_version}](https://github.com/QIICR/dcmqi/releases/tag/v${latest_version})|" README.md
 
@@ -149,7 +182,7 @@ jobs:
 
           branch="dcmqi-v${latest_version}"
           git checkout -b "$branch"
-          git add dcmqiUrls.cmake README.md
+          git add dcmqiUrls.cmake binaries.txt pyproject.toml README.md
           git commit -m "feat: update dcmqi from version v$current_version to v$latest_version"
           git push origin "$branch"
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 40ceecd..533a6e2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,16 +32,8 @@ set(_permissions PERMISSIONS
   WORLD_READ WORLD_EXECUTE
   )
 
-set(itkimage2segimage_executable_name "itkimage2segimage${CMAKE_EXECUTABLE_SUFFIX}")
-set(segimage2itkimage_executable_name "segimage2itkimage${CMAKE_EXECUTABLE_SUFFIX}")
-set(tid1500writer_executable_name "tid1500writer${CMAKE_EXECUTABLE_SUFFIX}")
-set(tid1500reader_executable_name "tid1500reader${CMAKE_EXECUTABLE_SUFFIX}")
-set(itkimage2paramap_executable_name "itkimage2paramap${CMAKE_EXECUTABLE_SUFFIX}")
-set(paramap2itkimage_executable_name "paramap2itkimage${CMAKE_EXECUTABLE_SUFFIX}")
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/binaries.txt" _dcmqi_binaries)
 
-install(PROGRAMS ${extract_dir}/bin/${itkimage2segimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
-install(PROGRAMS ${extract_dir}/bin/${segimage2itkimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
-install(PROGRAMS ${extract_dir}/bin/${tid1500writer_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
-install(PROGRAMS ${extract_dir}/bin/${tid1500reader_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
-install(PROGRAMS ${extract_dir}/bin/${itkimage2paramap_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
-install(PROGRAMS ${extract_dir}/bin/${paramap2itkimage_executable_name} DESTINATION "dcmqi/bin" ${_permissions})
+foreach(_binary IN LISTS _dcmqi_binaries)
+  install(PROGRAMS "${extract_dir}/bin/${_binary}${CMAKE_EXECUTABLE_SUFFIX}" DESTINATION "dcmqi/bin" ${_permissions})
+endforeach()
diff --git a/binaries.txt b/binaries.txt
new file mode 100644
index 0000000..4b9727e
--- /dev/null
+++ b/binaries.txt
@@ -0,0 +1,6 @@
+itkimage2segimage
+segimage2itkimage
+tid1500writer
+tid1500reader
+itkimage2paramap
+paramap2itkimage
diff --git a/src/dcmqi/__init__.py b/src/dcmqi/__init__.py
index 0e1564d..747729e 100644
--- a/src/dcmqi/__init__.py
+++ b/src/dcmqi/__init__.py
@@ -14,19 +14,6 @@
 
 from ._version import version as __version__
 
-__all__ = [
-    "__version__",
-    "itkimage2paramap",
-    "itkimage2segimage",
-    "paramap2itkimage",
-    "segimage2itkimage",
-    "tid1500reader",
-    "tid1500writer",
-]
-
-
-DCMQI_BIN_DIR: Path = Path(__file__).parent
-
 
 def _lookup(name: str) -> Path:
     executable_path = f"dcmqi/bin/{name}"
@@ -43,31 +30,34 @@ def _program(name: str, args: list[str]) -> int:
     return subprocess.call([_lookup(name), *args], close_fds=False)
 
 
-def itkimage2segimage() -> NoReturn:
-    """Run the itkimage2segimage executable with arguments passed to a Python script."""
-    raise SystemExit(_program("itkimage2segimage", sys.argv[1:]))
-
-
-def segimage2itkimage() -> NoReturn:
-    """Run the segimage2itkimage executable with arguments passed to a Python script."""
-    raise SystemExit(_program("segimage2itkimage", sys.argv[1:]))
-
+def _make_wrapper(name: str):
+    def _wrapper() -> NoReturn:
+        raise SystemExit(_program(name, sys.argv[1:]))
 
-def tid1500writer() -> NoReturn:
-    """Run the tid1500writer executable with arguments passed to a Python script."""
-    raise SystemExit(_program("tid1500writer", sys.argv[1:]))
+    _wrapper.__name__ = name
+    _wrapper.__qualname__ = name
+    _wrapper.__doc__ = f"Run the {name} executable with arguments passed to a Python script."
+    return _wrapper
 
 
-def tid1500reader() -> NoReturn:
-    """Run the tid1500reader executable with arguments passed to a Python script."""
-    raise SystemExit(_program("tid1500reader", sys.argv[1:]))
-
-
-def itkimage2paramap() -> NoReturn:
-    """Run the itkimage2paramap executable with arguments passed to a Python script."""
-    raise SystemExit(_program("itkimage2paramap", sys.argv[1:]))
-
-
-def paramap2itkimage() -> NoReturn:
-    """Run the paramap2itkimage executable with arguments passed to a Python script."""
-    raise SystemExit(_program("paramap2itkimage", sys.argv[1:]))
+def _discover_binaries() -> list[str]:
+    """Return names of all executables installed in dcmqi/bin/."""
+    files = distribution("dcmqi").files
+    if files is None:
+        return []
+    binaries = []
+    for _file in files:
+        parts = Path(str(_file)).parts
+        if len(parts) == 3 and parts[0] == "dcmqi" and parts[1] == "bin":
+            # Strip platform suffix (.exe on Windows)
+            name = Path(parts[2]).stem
+            binaries.append(name)
+    return sorted(binaries)
+
+
+# Dynamically create wrapper functions for each installed binary
+_binaries = _discover_binaries()
+for _name in _binaries:
+    globals()[_name] = _make_wrapper(_name)
+
+__all__ = ["__version__", *_binaries]
diff --git a/tests/test_executable.py b/tests/test_executable.py
index 24ecf21..4a8157a 100644
--- a/tests/test_executable.py
+++ b/tests/test_executable.py
@@ -11,28 +11,16 @@
 
 from . import push_argv
 
-all_tools = pytest.mark.parametrize(
-    "tool",
-    [
-        "itkimage2segimage",
-        "segimage2itkimage",
-        "tid1500writer",
-        "tid1500reader",
-        "itkimage2paramap",
-        "paramap2itkimage",
-    ],
+_BINARIES_FILE = Path(__file__).parent.parent / "binaries.txt"
+_EXPECTED_TOOLS = sorted(
+    line.strip() for line in _BINARIES_FILE.read_text().splitlines() if line.strip()
 )
 
+all_tools = pytest.mark.parametrize("tool", _EXPECTED_TOOLS)
+
 all_tools_version = pytest.mark.parametrize(
     ("tool", "expected_version"),
-    [
-        ("itkimage2segimage", "1.0"),
-        ("segimage2itkimage", "1.0"),
-        ("tid1500writer", "1.0"),
-        ("tid1500reader", "1.0"),
-        ("itkimage2paramap", "1.0"),
-        ("paramap2itkimage", "1.0"),
-    ],
+    [(t, "1.0") for t in _EXPECTED_TOOLS],
 )
 
 

From 9776eb0878e3f2e0b502f95657e58e528b9f3ea7 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Apr 2026 21:08:25 +0000
Subject: [PATCH 2/4] style: pre-commit fixes

---
 src/dcmqi/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/dcmqi/__init__.py b/src/dcmqi/__init__.py
index 747729e..718a9dd 100644
--- a/src/dcmqi/__init__.py
+++ b/src/dcmqi/__init__.py
@@ -36,7 +36,9 @@ def _wrapper() -> NoReturn:
 
     _wrapper.__name__ = name
     _wrapper.__qualname__ = name
-    _wrapper.__doc__ = f"Run the {name} executable with arguments passed to a Python script."
+    _wrapper.__doc__ = (
+        f"Run the {name} executable with arguments passed to a Python script."
+    )
     return _wrapper
 
 

From 2dae5d62f4d2ca2c7437d63dcbaee15543cd9093 Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Thu, 2 Apr 2026 17:14:14 -0400
Subject: [PATCH 3/4] style: fix pre-commit issues

- Fix YAML-invalid heredoc in update-dcmqi.yml by collapsing Python
  script to a single-line python3 -c invocation
- Add noqa: PLE0604 for dynamic __all__ in __init__.py
- Add return type annotation to _make_wrapper
- Apply ruff-format fix

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/update-dcmqi.yml | 12 +-----------
 src/dcmqi/__init__.py              |  6 +++---
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/update-dcmqi.yml b/.github/workflows/update-dcmqi.yml
index cac0795..cc20520 100644
--- a/.github/workflows/update-dcmqi.yml
+++ b/.github/workflows/update-dcmqi.yml
@@ -161,17 +161,7 @@ jobs:
           echo "$binaries" > binaries.txt
 
           # Update pyproject.toml [project.scripts] to match binaries.txt
-          python3 - <<PYEOF
-import re
-
-binaries = open("binaries.txt").read().split()
-scripts_block = "[project.scripts]\n" + "".join(
-    f'{b} = "dcmqi:{b}"\n' for b in binaries
-)
-content = open("pyproject.toml").read()
-content = re.sub(r"\[project\.scripts\]\n[^\[]*", scripts_block + "\n", content)
-open("pyproject.toml", "w").write(content)
-PYEOF
+          python3 -c 'import re; b=open("binaries.txt").read().split(); blk="[project.scripts]\n"+"".join(f"{x} = \"dcmqi:{x}\"\n" for x in b)+"\n"; c=open("pyproject.toml").read(); open("pyproject.toml","w").write(re.sub(r"\[project\.scripts\]\n[^\[]*\n",blk,c))'
 
           # Update README.md to reference the new dcmqi release version
           sed -i "s|dcmqi v${current_version}](https://github.com/QIICR/dcmqi/releases/tag/v${current_version})|dcmqi v${latest_version}](https://github.com/QIICR/dcmqi/releases/tag/v${latest_version})|" README.md
diff --git a/src/dcmqi/__init__.py b/src/dcmqi/__init__.py
index 718a9dd..9f90a82 100644
--- a/src/dcmqi/__init__.py
+++ b/src/dcmqi/__init__.py
@@ -10,7 +10,7 @@
 import sys
 from importlib.metadata import distribution
 from pathlib import Path
-from typing import NoReturn
+from typing import Callable, NoReturn
 
 from ._version import version as __version__
 
@@ -30,7 +30,7 @@ def _program(name: str, args: list[str]) -> int:
     return subprocess.call([_lookup(name), *args], close_fds=False)
 
 
-def _make_wrapper(name: str):
+def _make_wrapper(name: str) -> Callable[[], NoReturn]:
     def _wrapper() -> NoReturn:
         raise SystemExit(_program(name, sys.argv[1:]))
 
@@ -62,4 +62,4 @@ def _discover_binaries() -> list[str]:
 for _name in _binaries:
     globals()[_name] = _make_wrapper(_name)
 
-__all__ = ["__version__", *_binaries]
+__all__ = ["__version__", *_binaries]  # noqa: PLE0604

From 88f0b0043f635f49059bbd8d3449fc4ec6be5272 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 2 Apr 2026 21:14:42 +0000
Subject: [PATCH 4/4] style: pre-commit fixes

---
 src/dcmqi/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/dcmqi/__init__.py b/src/dcmqi/__init__.py
index 9f90a82..5135cf3 100644
--- a/src/dcmqi/__init__.py
+++ b/src/dcmqi/__init__.py
@@ -8,9 +8,10 @@
 
 import subprocess
 import sys
+from collections.abc import Callable
 from importlib.metadata import distribution
 from pathlib import Path
-from typing import Callable, NoReturn
+from typing import NoReturn
 
 from ._version import version as __version__