restage 0.5.0__tar.gz → 0.6.0__tar.gz

{restage-0.5.0 → restage-0.6.0}/.gitignore

@@ -3,3 +3,4 @@
 *.pyc
 *__pychache__/
 *.c
+*.instr

{restage-0.5.0/src/restage.egg-info → restage-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: restage
-Version: 0.5.0
+Version: 0.6.0
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 License: BSD-3-Clause
 Classifier: License :: OSI Approved :: BSD License
@@ -17,7 +17,7 @@ Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
 Requires-Dist: confuse
 Requires-Dist: psutil>=5.9.6
-Requires-Dist: mccode-antlr[hdf5]>=0.10.2
+Requires-Dist: mccode-antlr[hdf5]>=0.13.0
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: chopcal; extra == "test"

{restage-0.5.0 → restage-0.6.0}/pyproject.toml

@@ -9,7 +9,7 @@ dependencies = [
     'platformdirs>=3.11',
     'confuse',
     'psutil>=5.9.6',
-    'mccode-antlr[hdf5]>=0.10.2',
+    'mccode-antlr[hdf5]>=0.13.0',
 ]
 readme = "README.md"
 license = {text = "BSD-3-Clause"}

{restage-0.5.0 → restage-0.6.0}/src/restage/cache.py

@@ -107,24 +107,20 @@ def directory_under_module_data_path(sub: str, prefix=None, suffix=None, name=No
 
 def _compile_instr(entry: InstrEntry, instr: Instr, config: dict | None = None,
                    mpi: bool = False, acc: bool = False,
-                   target=None, generator=None):
-    from mccode_antlr import __version__
+                   target=None, flavor=None):
+    from mccode_antlr import __version__, Flavor
     from mccode_antlr.compiler.c import compile_instrument, CBinaryTarget
     if config is None:
         config = dict(default_main=True, enable_trace=False, portable=False, include_runtime=True,
                       embed_instrument_file=False, verbose=False)
     if target is None:
         target = CBinaryTarget(mpi=mpi or False, acc=acc or False, count=1, nexus=False)
-    if generator is None:
-        from mccode_antlr.translators.target import MCSTAS_GENERATOR
-        generator = MCSTAS_GENERATOR
+    if flavor is None:
+        flavor = Flavor.MCSTAS
 
     output = directory_under_module_data_path('bin')
-    # TODO consider adding `dump_source=True` _and_ putting the resulting file into
-    #      the cache in order to make debugging future problems a tiny bit easier.
-    # FIXME a future mccode-antlr will support setting 'source_file={file_path}'
-    #       to allow exactly this.
-    binary_path = compile_instrument(instr, target, output, generator=generator, config=config, dump_source=True)
+    source_file = output.joinpath(instr.name).with_suffix('.c')
+    binary_path = compile_instrument(instr, target, output, flavor=flavor, config=config, source_file=source_file)
     entry.mccode_version = __version__
     entry.binary_path = str(binary_path)
     return entry

{restage-0.5.0 → restage-0.6.0}/src/restage/mcpl.py

@@ -4,20 +4,26 @@ from pathlib import Path
 def mcpl_real_filename(filename: Path) -> Path:
     """MCPL_output from McCode instruments has the bad habit of changing the output file name silently.
     Find the _real_ output file name by looking for the expected variants"""
-    if filename.exists() and filename.is_file():
-        return filename
-    if filename.with_suffix('.mcpl').exists() and filename.with_suffix('.mcpl').is_file():
-        return filename.with_suffix('.mcpl')
-    if filename.with_suffix('.mcpl.gz').exists() and filename.with_suffix('.mcpl.gz').is_file():
-        return filename.with_suffix('.mcpl.gz')
+    base, ext = filename.parent / filename.stem, filename.suffix
+    if ext in ('.gz',):
+        ext = base.suffix + ext
+        base = base.parent / base.stem
+    extensions = {'.mcpl.gz', '.mcpl', ''}
+    if ext not in extensions:
+        ValueError(f'Unsupported file extension: {ext}')
+    for ext in extensions:
+        check = base.with_suffix(ext)
+        if check.exists() and check.is_file():
+            return check
+        print(f'{base} -> {check} not found')
     raise FileNotFoundError(f'Could not find MCPL file {filename}')
 
 
-# def mcpl_particle_count(filename):
-    # from mcpl import MCPLFile
-    # with MCPLFile(mcpl_real_filename(filename)) as f:
-    #     n = f.nparticles
-    # return n
+def mcpl_real_extension(filename: Path) -> str:
+    for ext in ('.mcpl.gz', '.mcpl'):
+        if str(filename).endswith(ext):
+            return ext
+    return ''
 
 
 def mcpl_particle_count(filename):
@@ -52,11 +58,7 @@ def mcpl_merge_files(files: list[Path], filepath: Path, keep_originals: bool = F
     from subprocess import run
     real_filenames = [mcpl_real_filename(f) for f in files]
     # if the real filenames have .mcpl or .mcpl.gz, the merged filename should too
-    ext = ''
-    if real_filenames[0].name.endswith('.mcpl.gz'):
-        ext = '.mcpl.gz'
-    elif real_filenames[0].name.endswith('.mcpl'):
-        ext = '.mcpl'
+    ext = mcpl_real_extension(real_filenames[0])
     filename = filepath.with_suffix(ext).as_posix()
 
     command = ['mcpltool', '--merge', filename] + [str(f) for f in real_filenames]
@@ -69,13 +71,8 @@ def mcpl_merge_files(files: list[Path], filepath: Path, keep_originals: bool = F
 
 
 def mcpl_rename_file(source: Path, dest: Path, strict: bool = False):
-    filepath = mcpl_real_filename(source)
-    filename = filepath.name  # this could be '{name}', '{name}.mcpl', or '{name}.mcpl.gz'
-    ext = ''
-    if filepath.name.endswith('.mcpl.gz'):
-        ext = '.mcpl.gz'
-    elif filepath.name.endswith('.mcpl'):
-        ext = '.mcpl'
+    filepath = mcpl_real_filename(source) # this could be '{name}', '{name}.mcpl', or '{name}.mcpl.gz'
+    ext = mcpl_real_extension(filepath)
 
     if not dest.name.endswith(ext):
         if strict:

{restage-0.5.0 → restage-0.6.0/src/restage.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: restage
-Version: 0.5.0
+Version: 0.6.0
 Author-email: Gregory Tucker <gregory.tucker@ess.eu>
 License: BSD-3-Clause
 Classifier: License :: OSI Approved :: BSD License
@@ -17,7 +17,7 @@ Requires-Dist: zenlog>=1.1
 Requires-Dist: platformdirs>=3.11
 Requires-Dist: confuse
 Requires-Dist: psutil>=5.9.6
-Requires-Dist: mccode-antlr[hdf5]>=0.10.2
+Requires-Dist: mccode-antlr[hdf5]>=0.13.0
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: chopcal; extra == "test"

{restage-0.5.0 → restage-0.6.0}/src/restage.egg-info/requires.txt

@@ -2,7 +2,7 @@ zenlog>=1.1
 platformdirs>=3.11
 confuse
 psutil>=5.9.6
-mccode-antlr[hdf5]>=0.10.2
+mccode-antlr[hdf5]>=0.13.0
 
 [test]
 pytest

restage-0.6.0/test/test_env_vars.py

@@ -0,0 +1,42 @@
+from unittest import TestCase
+from unittest.mock import patch
+from importlib import reload
+import restage.config
+
+
+class SettingsTests(TestCase):
+    import os
+    @patch.dict(os.environ, {"RESTAGE_CACHE": "/tmp/some/location"})
+    def test_restage_cache_config(self):
+        reload(restage.config)
+        from restage.config import config
+        self.assertTrue(config['cache'].exists())
+        self.assertEqual(config['cache'].as_str(), '/tmp/some/location')
+
+    @patch.dict(os.environ, {"RESTAGE_FIXED": "/tmp/some/location"})
+    def test_restage_single_fixed_config(self):
+        reload(restage.config)
+        from restage.config import config
+        self.assertTrue(config['fixed'].exists())
+        self.assertEqual(config['fixed'].as_str(), '/tmp/some/location')
+
+    @patch.dict(os.environ, {'RESTAGE_FIXED': '/tmp/a /tmp/b /tmp/c'})
+    def test_restage_multi_fixed_config(self):
+        reload(restage.config)
+        from restage.config import config
+        self.assertTrue(config['fixed'].exists())
+        more = config['fixed'].as_str_seq()
+        self.assertEqual(len(more), 3)
+        self.assertEqual(more[0],'/tmp/a')
+        self.assertEqual(more[1],'/tmp/b')
+        self.assertEqual(more[2],'/tmp/c')
+
+    def test_restage_standard_config(self):
+        from os import environ
+        reload(restage.config)
+        from restage.config import config
+        if 'cache' in config:
+            self.assertEqual(config['cache'].as_str(), environ['RESTAGE_CACHE'])
+        if 'fixed' in config:
+            self.assertEqual(config['fixed'].as_str(), environ['RESTAGE_FIXED'])
+

{restage-0.5.0 → restage-0.6.0}/test/test_single.py

@@ -149,18 +149,10 @@ class SplitRunTestCase(unittest.TestCase):
     def _define_instr(self):
         from math import pi, asin, sqrt
         from mccode_antlr.reader import MCSTAS_REGISTRY
-        from mccode_antlr.reader import GitHubRegistry
         from mccode_antlr.loader.loader import parse_mccode_instr
 
         def parse(contents):
-            # registries = [LocalRegistry(name='test_files', root=Path(__file__).parent.as_posix()), MCSTAS_REGISTRY]
-            mcpl_input_once_registry = GitHubRegistry(
-                name='mcpl_input_once',
-                url='https://github.com/g5t/mccode-mcpl-input-once',
-                version='main',
-                filename='pooch-registry.txt'
-            )
-            registries = [MCSTAS_REGISTRY, mcpl_input_once_registry]
+            registries = [MCSTAS_REGISTRY]
             return parse_mccode_instr(contents, registries, '<test string>')
 
         d_spacing = 3.355  # (002) for Highly-ordered Pyrolytic Graphite
@@ -241,8 +233,13 @@ class SplitRunTestCase(unittest.TestCase):
             output.mkdir(parents=True)
 
         # run the scan
-        splitrun(self.instr, scan, precision={}, split_at='split_at', grid=False, ncount=10_000, dir=output,
-                 mcpl_input_component='MCPL_input_once')
+        splitrun(self.instr, scan, precision={}, split_at='split_at', grid=False,
+                 ncount=10_000,
+                 dir=output,
+                 mcpl_output_parameters={'weight_mode': '1'},
+                 mcpl_input_component='MCPL_input_once',
+                 mcpl_input_parameters={'preload': '1'}
+                 )
 
         # check the scan directory for output
         for x in self.dir.glob('**/*.dat'):
@@ -261,6 +258,13 @@ class SplitRunTestCase(unittest.TestCase):
         default installed location, /usr/local/lib64/libmcpl.so; so this test must
         be invoked with that location specified, e.g.,
             $ LD_LIBRARY_PATH=/usr/local/lib64 pytest test/test_single.py -k test_parallel_scan
+
+        Another potential issue to address, the `MCPL_*.comp` components may use a
+        special `@MCPLFLAGS@` directive to read flags from a configuration file instead
+        of using the provided `mcpl-config --show buildflags` command.
+        You might need to use `mccode-antlr config save -v` to create/locate the
+        mccode-antlr `config.yml` file then edit/add the entry for `flags.mcpl` with
+        the output of the tool above.
         """
         from restage.splitrun import splitrun
         from restage.range import parse_scan_parameters
@@ -270,7 +274,10 @@ class SplitRunTestCase(unittest.TestCase):
             output.mkdir(parents=True)
         splitrun(self.instr, scan, precision={}, split_at='split_at', grid=False, ncount=100_000, dir=output,
                  parallel=True, process_count=4,
-                 mcpl_input_component='MCPL_input_once', mcpl_input_parameters={'preload': '1'})
+                 mcpl_output_parameters={'weight_mode': '1'},
+                 mcpl_input_component='MCPL_input_once',
+                 mcpl_input_parameters={'preload': '1'}
+                 )
 
         # check the scan directory for output
         for x in self.dir.glob('**/*.dat'):

restage-0.5.0/test/test_env_vars.py

@@ -1,43 +0,0 @@
-import os
-from unittest import TestCase, mock
-from pathlib import Path
-
-
-def restage_loaded():
-    import sys
-    return 'restage' in sys.modules or 'restage.config' in sys.modules
-
-
-def first(test):
-    import unittest
-    @unittest.skipIf(restage_loaded(), reason="Environment variable patching must be done before restage is loaded")
-    def first_test(*args, **kwargs):
-        return test(*args, **kwargs)
-    return first_test
-
-
-class SettingsTests(TestCase):
-    @first
-    @mock.patch.dict(os.environ, {"RESTAGE_CACHE": "/tmp/some/location"})
-    def test_restage_cache_config(self):
-        from restage.config import config
-        self.assertTrue(config['cache'].exists())
-        self.assertEqual(config['cache'].as_path(), Path('/tmp/some/location'))
-
-    @first
-    @mock.patch.dict(os.environ, {"RESTAGE_FIXED": "/tmp/some/location"})
-    def test_restage_single_fixed_config(self):
-        from restage.config import config
-        self.assertTrue(config['fixed'].exists())
-        self.assertEqual(config['fixed'].as_path(), Path('/tmp/some/location'))
-
-    @first
-    @mock.patch.dict(os.environ, {'RESTAGE_FIXED': '/tmp/a /tmp/b /tmp/c'})
-    def test_restage_multi_fixed_config(self):
-        from restage.config import config
-        self.assertTrue(config['fixed'].exists())
-        more = config['fixed'].as_str_seq()
-        self.assertEqual(len(more), 3)
-        self.assertEqual(Path(more[0]), Path('/tmp/a'))
-        self.assertEqual(Path(more[1]), Path('/tmp/b'))
-        self.assertEqual(Path(more[2]), Path('/tmp/c'))