Fix missing CLI executables in quippy-ase wheel (#703)

Bundle quip, gap_fit, and md executables in the wheel by:

- Add [project.scripts] entry points to pyproject.toml for CLI commands
- Create install_executables.py to copy executables during meson install
- Update meson.build to run install script via meson.add_install_script()
- Improve cli.py error handling with helpful messages when executables missing
- Add CIBW_TEST_COMMAND to verify executables are bundled and functional

The executables are copied to the quippy package directory during install,
and delocate/auditwheel will bundle the required shared libraries.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: jameskermode

.github/workflows/build-wheels.yml

@@ -138,6 +138,16 @@ jobs:
           # Architecture setting
           CIBW_ARCHS: ${{ steps.arch.outputs.arch }}
 
+          # Test that the wheel works correctly
+          CIBW_TEST_COMMAND: >
+            python -c "import quippy; print(quippy.__version__)" &&
+            python -c "import os, quippy; assert os.path.exists(os.path.join(quippy.__path__[0], 'quip')), 'quip executable missing'" &&
+            python -c "import os, quippy; assert os.path.exists(os.path.join(quippy.__path__[0], 'gap_fit')), 'gap_fit executable missing'" &&
+            python -c "import os, quippy; assert os.path.exists(os.path.join(quippy.__path__[0], 'md')), 'md executable missing'" &&
+            quip --help &&
+            gap_fit --help &&
+            md --help
+
       - name: Debug - list environment
         if: failure()
         run: |

quippy/install_executables.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+"""Install QUIP executables into the quippy package directory."""
+import os
+import sys
+import shutil
+import stat
+
+def main():
+    # Arguments: source_dir, dest_dir
+    if len(sys.argv) < 3:
+        print("Usage: install_executables.py <source_dir> <dest_dir>")
+        sys.exit(1)
+
+    source_dir = sys.argv[1]
+    dest_dir = sys.argv[2]
+
+    # Handle DESTDIR for meson install (used for staged installs / wheel building)
+    destdir = os.environ.get('DESTDIR', '')
+    if destdir:
+        # dest_dir is absolute, so we need to handle the join carefully
+        if dest_dir.startswith('/'):
+            dest_dir = destdir + dest_dir
+        else:
+            dest_dir = os.path.join(destdir, dest_dir)
+
+    executables = ['quip', 'gap_fit', 'md']
+
+    os.makedirs(dest_dir, exist_ok=True)
+
+    for exe in executables:
+        src = os.path.join(source_dir, exe)
+        dst = os.path.join(dest_dir, exe)
+        if os.path.exists(src):
+            shutil.copy2(src, dst)
+            # Ensure executable permissions
+            os.chmod(dst, os.stat(dst).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
+            print(f"Installed {exe} to {dst}")
+        else:
+            print(f"Warning: {exe} not found at {src}", file=sys.stderr)
+
+if __name__ == '__main__':
+    main()

quippy/meson.build

@@ -330,4 +330,15 @@ install_subdir(
   strip_directory: false,
 )
 
+# Install CLI executables (quip, gap_fit, md) into the quippy package
+# Use install script to handle files from external build directory
+install_exe_script = find_program('install_executables.py', required: true)
+programs_builddir = quip_builddir / 'Programs'
+
+meson.add_install_script(
+  install_exe_script,
+  programs_builddir,
+  py.get_install_dir() / 'quippy',
+)
+
 message('f90wrap wrapper generation and extension build configured')

quippy/pyproject.toml

@@ -23,6 +23,12 @@ dependencies = [
 [project.optional-dependencies]
 dev = ["pytest"]
 
+[project.scripts]
+quip = "quippy.cli:quip"
+gap_fit = "quippy.cli:gap_fit"
+md = "quippy.cli:md"
+quip-config = "quippy.cli:quip_config"
+
 [tool.meson-python.args]
 setup = ["-Dbuildtype=release"]
 compile = []

quippy/quippy/cli.py

@@ -4,25 +4,27 @@
 import quippy
 import argparse
 
-def gap_fit():
+def _run_command(name):
+    """Run a bundled QUIP executable."""
     path = quippy.__path__[0]
-    command = os.path.join(path, 'gap_fit')
-    sp.call([command] + sys.argv[1:])
+    command = os.path.join(path, name)
+    if not os.path.exists(command):
+        print(f"Error: '{name}' executable not found at {command}", file=sys.stderr)
+        print("This may indicate an incomplete installation.", file=sys.stderr)
+        sys.exit(1)
+    return sp.call([command] + sys.argv[1:])
+
+def gap_fit():
+    sys.exit(_run_command('gap_fit'))
 
 def quip():
-    path = quippy.__path__[0]
-    command = os.path.join(path, 'quip')
-    sp.call([command] + sys.argv[1:])
+    sys.exit(_run_command('quip'))
 
 def md():
-    path = quippy.__path__[0]
-    command = os.path.join(path, 'md')
-    sp.call([command] + sys.argv[1:])
+    sys.exit(_run_command('md'))
 
 def vasp_driver():
-    path = quippy.__path__[0]
-    command = os.path.join(path, 'vasp_driver')
-    sp.call([command] + sys.argv[1:])
+    sys.exit(_run_command('vasp_driver'))
 
 def quip_config():
     parser = argparse.ArgumentParser(description='Configuration tool for QUIP')