Nexus: Package executables in with Nexus libraries

nexus/docs/installation.rst

@@ -11,10 +11,6 @@ to development or (currently) if any scripts/"binaries" are needed. Administrati
 Note that while many supercomputer systems have an outdated system Python, a recent Python version is usually provided via a
 loadable module: check the local documentation or discuss with your system administrators to find the simplest installation route.
 
-.. important::
-    Currently, Nexus installed via ``pip`` or ``uv`` does not include any scripts (``qmca``, ``nxs-test``, etc.) which are readily available in QMCPACK installations. 
-    Users may install them by following the manual installation method described in :ref:`manual_install`.
-
 .. contents::
 
 Installation using ``pip``
@@ -54,8 +50,11 @@ To subsequently use the environment:
     cd $HOME/somewhere # Wherever you created the environment
     source nexusenv/bin/activate
 
-Note that any versions of Nexus found via the ``PYTHONPATH`` environment variable will take precedence over a ``pip`` installed
-version.
+Note that any versions of Nexus found via the ``PYTHONPATH`` environment variable will take precedence over a ``pip`` installed version.
+
+.. important::
+    If you install Nexus into a virtual environment, the Nexus executables (e.g. ``qmca``, ``nxs-sim``, etc.) will only be accessible if you have activated that virtual environment.
+
 
 System-wide installation (not recommended in general)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -114,7 +113,6 @@ minimum set of dependencies. You can also install the full set of optional depen
 
     uv pip install "nexus[full]@git+https://github.com/QMCPACK/qmcpack.git@main#subdirectory=nexus"
 
-
 Note that when using ``uv`` as a package manager, your Python scripts can optionally use a modified `shebang
 <https://en.wikipedia.org/wiki/Shebang_(Unix)>`__ that tells it to use ``uv`` to run it. For example
 

nexus/bin/eshdf → nexus/nexus/bin/eshdf

@@ -15,11 +15,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/bin/nxs-redo → nexus/nexus/bin/nxs-redo

@@ -10,11 +10,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/bin/nxs-sim → nexus/nexus/bin/nxs-sim

@@ -10,11 +10,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/bin/nxs-test → nexus/nexus/bin/nxs-test

@@ -17,13 +17,75 @@ if host_dir is not None:
 #end if
 
 # save nexus directories
-library_dir   = parent_dir
-test_dir      = os.path.join(parent_dir,'nexus/tests')
-reference_dir = os.path.join(parent_dir,'nexus/tests/reference')
+library_dir   = os.path.dirname(parent_dir)
+test_dir      = os.path.join(parent_dir,'tests')
+reference_dir = os.path.join(parent_dir,'tests/reference')
 example_dir   = os.path.join(parent_dir,'examples')
 
 # ensure that nxs-test executable is resident in a nexus directory tree
-dirs_check = ['examples','bin','nexus','nexus/tests','nexus/tests/reference']
+dirs_check = [
+    "tests/",
+    "bin/",
+    "basisset.py",
+    "bundle.py",
+    "debug.py",
+    "developer.py",
+    "execute.py",
+    "fileio.py",
+    "gamess_analyzer.py",
+    "gamess_input.py",
+    "gamess.py",
+    "gaussian_process.py",
+    "generic.py",
+    "grid_functions.py",
+    "hdfreader.py",
+    "__init__.py",
+    "machines.py",
+    "memory.py",
+    "nexus_base.py",
+    "nexus_version.py",
+    "numerics.py",
+    "observables.py",
+    "periodic_table.py",
+    "physical_system.py",
+    "project_manager.py",
+    "pseudopotential.py",
+    "pwscf_analyzer.py",
+    "pwscf_data_reader.py",
+    "pwscf_input.py",
+    "pwscf_postprocessors.py",
+    "pwscf.py",
+    "pyscf_analyzer.py",
+    "pyscf_input.py",
+    "pyscf_sim.py",
+    "qmcpack_analyzer_base.py",
+    "qmcpack_analyzer.py",
+    "qmcpack_converters.py",
+    "qmcpack_input.py",
+    "qmcpack_method_analyzers.py",
+    "qmcpack_property_analyzers.py",
+    "qmcpack.py",
+    "qmcpack_quantity_analyzers.py",
+    "qmcpack_result_analyzers.py",
+    "quantum_package_analyzer.py",
+    "quantum_package_input.py",
+    "quantum_package.py",
+    "rmg_analyzer.py",
+    "rmg_input.py",
+    "rmg.py",
+    "scripts.py",
+    "simulation.py",
+    "structure.py",
+    "template_simulation.py",
+    "testing.py",
+    "unit_converter.py",
+    "utilities.py",
+    "vasp_analyzer.py",
+    "vasp_input.py",
+    "vasp.py",
+    "versions.py",
+    "xmlreader.py",
+]
 for d in dirs_check:
     pd = os.path.join(parent_dir,d)
     if not os.path.exists(pd):
@@ -1788,7 +1850,7 @@ def user_examples(label):
     # remove prexisting example files
     nenter(tpath,relative=True)
     # copy over nexus examples files just for this example
-    epath = os.path.join(example_dir,path)
+    epath = os.path.realpath(os.path.join(example_dir,path))
     command = 'rsync -av {0}/* ./'.format(epath)
     out,err,rc = execute(command)
     if rc>0:
@@ -2223,7 +2285,7 @@ if __name__=='__main__':
     testing_wrong_nexus_install = False
     try:
         import nexus
-        nexus_file = os.path.realpath(os.path.join(nexus.__file__,'../..'))
+        nexus_file = os.path.realpath(os.path.join(nexus.__file__,'../'))
         test_file  = os.path.realpath(os.path.join(__file__,'../..'))
         testing_wrong_nexus_install = nexus_file!=test_file
     except:

nexus/bin/qdens → nexus/nexus/bin/qdens

@@ -11,11 +11,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/bin/qdens-radial → nexus/nexus/bin/qdens-radial

@@ -9,11 +9,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')
@@ -56,7 +56,6 @@ import nexus.memory as memory
 from nexus.observables import ChargeDensity, vlog
 from nexus.fileio import XsfFile
 
-
 # External imports
 try:
     import numpy as np

nexus/bin/qmc-fit → nexus/nexus/bin/qmc-fit

@@ -34,11 +34,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/bin/qmca → nexus/nexus/bin/qmca

@@ -13,11 +13,11 @@ def find_nexus_modules():
     import sys
     # Prepend the assumed path of a folder containing the closely coupled nexus module to module search path
     # It points to the top Nexus directory not necessarily the top QMCPACK directory.
-    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..'))
+    nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..'))
 
     # "import nexus" will succeed if nexus directory exists without __init__.py in it.
     # Explicitly check the existence of nexus/__init__.py at the closely coupled location
-    nexus_init = os.path.join(nexus_lib,'nexus','__init__.py')
+    nexus_init = os.path.join(nexus_lib,'nexus/__init__.py')
     if not os.path.exists(nexus_init):
         print('\nExpected file '+nexus_init+' does not exist!'
               '\nBroken Nexus installation! Please follow Nexus manual regarding installation.\n')

nexus/nexus/scripts.py

@@ -0,0 +1,44 @@
+import subprocess
+import sys
+from os import PathLike
+from pathlib import Path
+
+bin_dir = Path(__file__).parent/"bin"
+
+def run(script_name: PathLike):
+    script_path = bin_dir/script_name
+    result = subprocess.run([script_path] + sys.argv[1:])
+    sys.exit(result.returncode)
+#end def run
+
+def eshdf():
+    run("eshdf")
+#end def eshdf
+
+def nxs_redo():
+    run("nxs-redo")
+#end def nxs_redo
+
+def nxs_sim():
+    run("nxs-sim")
+#end def nxs_sim
+
+def nxs_test():
+    run("nxs-test")
+#end def nxs_test
+
+def qdens():
+    run("qdens")
+#end def qdens
+
+def qdens_radial():
+    run("qdens-radial")
+#end def qdens_radial
+
+def qmca():
+    run("qmca")
+#end def qmca
+
+def qmc_fit():
+    run("qmc-fit")
+#end def qmc_fit

nexus/nexus/testing.py

@@ -290,16 +290,14 @@ def nexus_path(append=None,location=None):
     assert(len(tokens)>=3)
     assert(tokens[-1].startswith('testing.py'))
     assert(tokens[-2]=='nexus')
-    assert(tokens[-3]=='nexus')
 
     path = os.path.dirname(testing_path)
-    path = os.path.dirname(path)
 
     assert(path.endswith('/nexus'))
 
     if location is not None:
         if location=='unit':
-            append = 'nexus/tests'
+            append = 'tests'
         elif location=='bin':
             append = 'bin'
         else:

nexus/nexus/tests/CMakeLists.txt

@@ -5,13 +5,13 @@ include("${PROJECT_SOURCE_DIR}/CMake/python.cmake")
 check_python_reqs(numpy "nexus base" ADD_TEST)
 
 if(ADD_TEST)
-  file(TIMESTAMP ${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test NEXUS_TESTLIST_TIMESTAMP)
+  file(TIMESTAMP ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test NEXUS_TESTLIST_TIMESTAMP)
   if(NOT "${NEXUS_TESTLIST_TIMESTAMP}" STREQUAL "${CACHE_NEXUS_TESTLIST_TIMESTAMP}")
     message("Generating Nexus test list for the first time or after a nxs-test time stamp change")
-    execute_process(COMMAND ${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test --ctestlist
+    execute_process(COMMAND ${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test --ctestlist
                     RESULT_VARIABLE NEXUS_TESTLIST_RESULT OUTPUT_VARIABLE NEXUS_TESTLIST)
     if(NOT NEXUS_TESTLIST_RESULT EQUAL 0)
-      message(FATAL_ERROR "Command line '${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test --ctestlist' failed!")
+      message(FATAL_ERROR "Command line '${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test --ctestlist' failed!")
     endif()
 
     set(CACHE_NEXUS_TESTLIST
@@ -31,7 +31,7 @@ if(ADD_TEST)
   endif()
   foreach(TESTNAME ${NEXUS_TESTLIST})
     #message("Adding test ntest_nexus_${TESTNAME}")
-    set(NTEST "${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test")
+    set(NTEST "${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test")
     IF(ENABLE_PYCOV)
       add_test(NAME ntest_nexus_${TESTNAME} COMMAND ${PYTHON_COVERAGE_EXECUTABLE} run -p ${NTEST} -R ${TESTNAME}\$ --ctest
                                                     --pythonpath=${PROJECT_SOURCE_DIR}/nexus:$ENV{PYTHONPATH})

nexus/nexus/tests/test_pseudopotential.py

@@ -234,7 +234,7 @@ def test_pseudopotential_classes():
     f = open(files['C.BFD.xml'],'r')
     pp_relpath = f.read().strip()
     pp_path = os.path.split(files['C.BFD.xml'])[0]
-    filepath = os.path.join(pp_path,pp_relpath)
+    filepath = os.path.realpath(os.path.join(pp_path,pp_relpath))
     f.close()
 
     qpp = QmcpackPP(filepath)

nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf

@@ -1 +1 @@
-../../../examples/qmcpack/pseudopotentials/C.BFD.upf
+../../examples/qmcpack/pseudopotentials/C.BFD.upf

nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml

@@ -1 +1 @@
-../../../examples/qmcpack/pseudopotentials/C.BFD.xml
+../../examples/qmcpack/pseudopotentials/C.BFD.xml

nexus/pyproject.toml

@@ -17,16 +17,15 @@ dependencies = [
     "numpy (>=2.3.0, !=2.4.0)  ; python_version >= '3.14.0'", # 
 ]
 
-# TODO Restructure to support including the scripts with the package distribution
-# [project.scripts]
-# eshdf = "nexus.scripts:eshdf"
-# nxs-redo = "nexus.scripts:nxs_redo"
-# nxs-sim = "nexus.scripts:nxs_sim"
-# nxs-test = "nexus.scripts:nxs_test"
-# qdens = "nexus.scripts:qdens"
-# qdens-radial = "nexus.scripts:qdens_radial"
-# qmca = "nexus.scripts:qmca"
-# qmc-fit = "nexus.scripts:qmc_fit"
+[project.scripts]
+eshdf = "nexus.scripts:eshdf"
+nxs-redo = "nexus.scripts:nxs_redo"
+nxs-sim = "nexus.scripts:nxs_sim"
+nxs-test = "nexus.scripts:nxs_test"
+qdens = "nexus.scripts:qdens"
+qdens-radial = "nexus.scripts:qdens_radial"
+qmca = "nexus.scripts:qmca"
+qmc-fit = "nexus.scripts:qmc_fit"
 
 [build-system]
 requires = ["hatchling"]