def csv_lines(self):
# a module with a dependency on a fortran and c file, plus a mo commented dep
data = [
AnalysedFile(fpath='my_mod.f90',
file_hash=123,
module_defs={'my_mod'},
symbol_defs={'my_mod'},
symbol_deps={'dep1_mod', 'dep2'},
mo_commented_file_deps={'mo_dep.c'}),
AnalysedFile(fpath='dep1_mod.f90',
file_hash=234,
module_defs={'dep1_mod'},
symbol_defs={'dep1_mod'}),
AnalysedFile(fpath='dep2.c', file_hash=345, symbol_defs={'dep2'}),
]
lines = [','.join(AnalysedFile.field_names())] # header row
for af in data:
str_dict = af.to_str_dict()
columns = [str_dict[field_name] for field_name in af.field_names()]
row = ','.join(columns)
lines.append(row)
return lines
def analysed_files():
a = AnalysedFile(fpath=Path('a.f90'),
file_deps={Path('b.f90')},
file_hash=None)
b = AnalysedFile(fpath=Path('b.f90'),
file_deps={Path('c.f90')},
file_hash=None)
c = AnalysedFile(fpath=Path('c.f90'), file_hash=None)
return a, b, c
def analysed_files(self):
return [
AnalysedFile(fpath=Path('foo.c'),
symbol_defs=['foo_1', 'foo_2'],
file_hash=None),
AnalysedFile(fpath=Path('bar.c'),
symbol_defs=['bar_1', 'bar_2'],
file_hash=None)
]
def test_analysis_results():
# using a physical analysis file, this tests:
# new source file
# changed source file
# previously analysed source file, unchanged
# source file no longer there
# source folder before change
previous_file_hashes = {
Path('change.f90'): 111,
Path('no_change.f90'): 222,
Path('remove.f90'): 333,
}
# source folder after change
latest_file_hashes = {
Path('change.f90'): 123,
Path('no_change.f90'): 222,
Path('new.f90'): 444,
}
previous_results = {
AnalysedFile(fpath=path, file_hash=file_hash)
for path, file_hash in previous_file_hashes.items()
}
with TemporaryDirectory() as tmpdir:
analyser = Analyse(root_symbol=None)
# simulate the effect of calling run, in which the superclass sets up the _config attribute (is this too ugly?)
analyser._config = mock.Mock(project_workspace=Path(tmpdir))
# create the initial analysis file
with analyser._new_analysis_file(unchanged=previous_results):
pass
# check it loads correctly with no changes detected
loaded_results = analyser._load_analysis_results(previous_file_hashes)
changed, unchanged = analyser._what_needs_reanalysing(
prev_results=loaded_results,
latest_file_hashes=previous_file_hashes)
assert not changed
assert unchanged == previous_results
# check we correctly identify new, changed, unchanged and removed files
loaded_results = analyser._load_analysis_results(latest_file_hashes)
changed, unchanged = analyser._what_needs_reanalysing(
prev_results=loaded_results, latest_file_hashes=latest_file_hashes)
assert unchanged == {
AnalysedFile(fpath=Path('no_change.f90'), file_hash=222)
}
assert changed == {
HashedFile(fpath=Path('change.f90'), file_hash=123),
HashedFile(fpath=Path('new.f90'), file_hash=444)
}
def src_tree():
return {
Path('foo.f90'): AnalysedFile(fpath=Path('foo.f90'), file_hash=None),
Path('root.f90'): AnalysedFile(
fpath=Path('root.f90'), file_deps={Path('a.f90'), Path('b.f90')}, file_hash=None),
Path('a.f90'): AnalysedFile(
fpath=Path('a.f90'), file_deps={Path('c.f90')}, file_hash=None),
Path('b.f90'): AnalysedFile(
fpath=Path('b.f90'), file_deps={Path('c.f90')}, file_hash=None),
Path('c.f90'): AnalysedFile(
fpath=Path('c.f90'), file_deps=set(), file_hash=None),
}
def run(self, hashed_file: HashedFile):
fpath, file_hash = hashed_file
log_or_dot(logger, f"analysing {fpath}")
analysed_file = AnalysedFile(fpath=fpath, file_hash=file_hash)
index = clang.cindex.Index.create()
translation_unit = index.parse(fpath, args=["-xc"])
# Create include region line mappings
self._locate_include_regions(translation_unit)
# Now walk the actual nodes and find all relevant external symbols
usr_symbols: List[str] = []
for node in translation_unit.cursor.walk_preorder():
if not node.spelling:
continue
# ignore sys include stuff
if self._check_for_include(node.location.line) == "sys_include":
continue
logger.debug('Considering node: %s', node.spelling)
if node.kind in {clang.cindex.CursorKind.FUNCTION_DECL, clang.cindex.CursorKind.VAR_DECL}:
self._process_symbol_declaration(analysed_file, node, usr_symbols)
elif node.kind in {clang.cindex.CursorKind.CALL_EXPR, clang.cindex.CursorKind.DECL_REF_EXPR}:
self._process_symbol_dependency(analysed_file, node, usr_symbols)
return analysed_file
def _load_analysis_results(
self, latest_file_hashes: Dict[Path,
int]) -> Dict[Path, AnalysedFile]:
"""
The analysis file includes the hash of each file when we last analysed it.
We discard previous results from files which are no longer present.
"""
prev_results: Dict[Path, AnalysedFile] = dict()
try:
with open(self._config.project_workspace / "__analysis.csv",
"rt") as csv_file:
dict_reader = csv.DictReader(csv_file)
for row in dict_reader:
analysed_file = AnalysedFile.from_str_dict(row)
# file no longer there?
if analysed_file.fpath not in latest_file_hashes:
logger.info(
f"file no longer present: {analysed_file.fpath}")
continue
# ok, we have previously analysed this file
prev_results[analysed_file.fpath] = analysed_file
logger.info(
f"loaded {len(prev_results)} previous analysis results")
except FileNotFoundError:
logger.info("no previous analysis results")
pass
return prev_results
def test_vanilla(self):
# ensure the command is formed correctly
config = SimpleNamespace(project_workspace=Path('foo'),
source_root=Path('foo/src'),
multiprocessing=False,
reuse_artefacts=False)
c_compiler = CompileC(compiler='gcc',
common_flags=['-c'],
path_flags=[
AddFlags(
match='foo/src/*',
flags=['-I', 'foo/include', '-Dhello'])
])
analysed_files = {
Path('foo/src/foo.c'):
AnalysedFile(fpath=Path('foo/src/foo.c'), file_hash=None)
}
with mock.patch('fab.steps.compile_c.run_command') as mock_run:
with mock.patch('fab.steps.compile_c.send_metric'):
c_compiler.run(
artefact_store={BUILD_TREES: {
None: analysed_files
}},
config=config)
mock_run.assert_called_with([
'gcc', '-c', '-I', 'foo/include', '-Dhello',
'foo/src/foo.c', '-o', 'foo/src/foo.o'
])
def module_expected(module_fpath):
return AnalysedFile(
fpath=module_fpath,
file_hash=None,
module_defs={'foo_mod'},
symbol_defs={'external_sub', 'external_func', 'foo_mod'},
module_deps={'bar_mod'},
symbol_deps={'monty_func', 'bar_mod'},
file_deps=set(),
mo_commented_file_deps={'some_file.c'},
)
def test_nothing_changed(self, analyser, csv_lines, latest_file_hashes):
# a simple example of a fortran module depending on a fortran and a c file
file_data = "\n".join(csv_lines)
with mock.patch('fab.steps.analyse.open',
mock_open(read_data=file_data)):
results = analyser._load_analysis_results(
latest_file_hashes=latest_file_hashes)
expected = {
Path('my_mod.f90'):
AnalysedFile(fpath=Path('my_mod.f90'),
file_hash=123,
module_defs={
'my_mod',
},
symbol_defs={
'my_mod',
},
symbol_deps={'dep1_mod', 'dep2'},
mo_commented_file_deps={
'mo_dep.c',
}),
Path('dep1_mod.f90'):
AnalysedFile(fpath=Path('dep1_mod.f90'),
file_hash=234,
module_defs={
'dep1_mod',
},
symbol_defs={
'dep1_mod',
}),
Path('dep2.c'):
AnalysedFile(fpath=Path('dep2.c'),
file_hash=345,
symbol_defs={
'dep2',
}),
}
assert results == expected
def test_missing_file(self, analyser, csv_lines, latest_file_hashes):
# a previously analysed file is no longer present
# remove a file
del latest_file_hashes[Path('dep2.c')]
file_data = "\n".join(csv_lines)
with mock.patch('fab.steps.analyse.open',
mock_open(read_data=file_data)):
results = analyser._load_analysis_results(
latest_file_hashes=latest_file_hashes)
expected = {
Path('my_mod.f90'):
AnalysedFile(fpath=Path('my_mod.f90'),
file_hash=123,
module_defs={
'my_mod',
},
symbol_defs={
'my_mod',
},
symbol_deps={'dep1_mod', 'dep2'},
mo_commented_file_deps={
'mo_dep.c',
}),
Path('dep1_mod.f90'):
AnalysedFile(fpath=Path('dep1_mod.f90'),
file_hash=234,
module_defs={
'dep1_mod',
},
symbol_defs={
'dep1_mod',
}),
}
assert results == expected
def test_vanilla(self):
analyser = Analyse(root_symbol=None)
# we analysed the source folder and found these symbols
symbols = {
"root": Path("root.f90"),
"root_dep": Path("root_dep.f90"),
"util": Path("util.f90"),
"util_dep": Path("util_dep.f90"),
}
# we extracted the build tree
build_tree = {
Path('root.f90'): AnalysedFile(fpath=Path(), file_hash=None),
Path('root_dep.f90'): AnalysedFile(fpath=Path(), file_hash=None),
}
# we want to force this symbol into the build [because it's not used via modules]
analyser.unreferenced_deps = ['util']
# the stuff to add to the build tree will be found in here
all_analysed_files = {
# root.f90 and root_util.f90 would also be in here but the test doesn't need them
Path('util.f90'):
AnalysedFile(fpath=Path('util.f90'),
file_deps={Path('util_dep.f90')},
file_hash=None),
Path('util_dep.f90'):
AnalysedFile(fpath=Path('util_dep.f90'), file_hash=None),
}
analyser._add_unreferenced_deps(symbols=symbols,
all_analysed_files=all_analysed_files,
build_tree=build_tree)
assert Path('util.f90') in build_tree
assert Path('util_dep.f90') in build_tree
def test_simple_result(tmp_path):
fpath = Path(Path(__file__).parent / "test_c_analyser.c")
result = CAnalyser().run(HashedFile(fpath, None))
expected = AnalysedFile(
fpath=fpath,
file_hash=None,
symbol_deps={'usr_var', 'usr_func'},
symbol_defs={
'func_decl', 'func_def', 'var_def', 'var_extern_def', 'main'
},
file_deps=set(),
mo_commented_file_deps=set(),
)
assert result == expected
def _new_analysis_file(self, unchanged: Iterable[AnalysedFile]):
"""
Create the analysis file from scratch, containing any content from its previous version which is still valid.
The returned context is a csv.DictWriter.
"""
with TimerLogger("starting analysis progress file"):
analysis_progress_file = open(
self._config.project_workspace / "__analysis.csv", "wt")
analysis_dict_writer = csv.DictWriter(
analysis_progress_file, fieldnames=AnalysedFile.field_names())
analysis_dict_writer.writeheader()
# re-write the progress so far
unchanged_rows = (af.to_str_dict() for af in unchanged)
analysis_dict_writer.writerows(unchanged_rows)
analysis_progress_file.flush()
yield analysis_dict_writer
analysis_progress_file.close()
def run(self, hashed_file: HashedFile):
fpath, file_hash = hashed_file
log_or_dot(logger, f"analysing {fpath}")
# parse the file
try:
tree = self._parse_file(fpath=fpath)
except Exception as err:
return err
if tree.content[0] is None:
logger.debug(f" empty tree found when parsing {fpath}")
return EmptySourceFile(fpath)
analysed_file = AnalysedFile(fpath=fpath, file_hash=file_hash)
# see what's in the tree
try:
for obj in iter_content(tree):
obj_type = type(obj)
# todo: ?replace these with function lookup dict[type, func]? - Or the new match statement, Python 3.10
if obj_type == Use_Stmt:
self._process_use_statement(analysed_file, obj) # raises
elif obj_type == Program_Stmt:
analysed_file.add_symbol_def(str(obj.get_name()))
elif obj_type == Module_Stmt:
analysed_file.add_module_def(str(obj.get_name()))
elif obj_type in (Subroutine_Stmt, Function_Stmt):
self._process_subroutine_or_function(analysed_file, fpath, obj)
# todo: we've not needed this so far, for jules or um...(?)
elif obj_type == "variable binding not yet supported":
return self._process_variable_binding(fpath)
elif obj_type == Comment:
self._process_comment(analysed_file, obj)
except Exception as err:
return err
logger.debug(f" analysed {analysed_file.fpath}")
return analysed_file
def um_atmos_safe_config(revision):
um_revision = revision.replace('vn', 'um')
config = BuildConfig(
project_label=f'um atmos safe {revision}',
# multiprocessing=False,
reuse_artefacts=True,
)
# Locate the gcom library. UM 12.1 intended to be used with gcom 7.6
gcom_build = os.getenv('GCOM_BUILD') or \
os.path.expanduser(config.project_workspace / "../gcom-object-archive-vn7.6/build_output")
logger.info(f"expecting gcom at {gcom_build}")
config.steps = [
# todo: these repo defs could make a good set of reusable variables
# UM 12.1, 16th November 2021
GrabFcm(src='fcm:um.xm_tr/src', dst='um', revision=revision),
# JULES 6.2, for UM 12.1
GrabFcm(src='fcm:jules.xm_tr/src', dst='jules', revision=um_revision),
# SOCRATES 21.11, for UM 12.1
GrabFcm(src='fcm:socrates.xm_tr/src',
dst='socrates',
revision=um_revision),
# SHUMLIB, for UM 12.1
GrabFcm(src='fcm:shumlib.xm_tr/', dst='shumlib', revision=um_revision),
# CASIM, for UM 12.1
GrabFcm(src='fcm:casim.xm_tr/src', dst='casim', revision=um_revision),
MyCustomCodeFixes(name="my custom code fixes"),
FindSourceFiles(path_filters=file_filtering),
RootIncFiles(),
CPragmaInjector(),
c_preprocessor(
source=CollectionGetter('pragmad_c'),
path_flags=[
# todo: this is a bit "codey" - can we safely give longer strings and split later?
AddFlags(match="$source/um/*",
flags=[
'-I$source/um/include/other',
'-I$source/shumlib/common/src',
'-I$source/shumlib/shum_thread_utils/src'
]),
AddFlags(match="$source/shumlib/*",
flags=[
'-I$source/shumlib/common/src',
'-I$source/shumlib/shum_thread_utils/src'
]),
# todo: just 3 folders use this
AddFlags("$source/um/*",
['-DC95_2A', '-I$source/shumlib/shum_byteswap/src']),
],
),
# todo: explain fnmatch
fortran_preprocessor(
common_flags=['-P'],
path_flags=[
AddFlags("$source/jules/*", ['-DUM_JULES']),
AddFlags("$source/um/*", ['-I$relative/include']),
# coupling defines
AddFlags("$source/um/control/timer/*", ['-DC97_3A']),
AddFlags("$source/um/io_services/client/stash/*",
['-DC96_1C']),
],
),
Analyse(
root_symbol='um_main',
# fparser2 fails to parse this file, but it does compile.
special_measure_analysis_results={
AnalysedFile(fpath=Path(config.project_workspace /
BUILD_OUTPUT / "casim/lookup.f90"),
file_hash=None,
symbol_defs={'lookup'},
symbol_deps={
'mphys_die', 'variable_precision',
'mphys_switches', 'mphys_parameters',
'special', 'passive_fields',
'casim_moments_mod', 'yomhook', 'parkind1'
},
file_deps={},
mo_commented_file_deps={}),
}),
CompileC(compiler='gcc', common_flags=['-c', '-std=c99']),
CompileFortran(
# compiler='mpifort',
compiler='gfortran',
common_flags=[
'-fdefault-integer-8',
'-fdefault-real-8',
'-fdefault-double-8',
'-c',
'-J',
'$output', # .mod file output and include folder
# '-O2'
],
path_flags=[
# mpl include - todo: just add this for everything?
AddFlags("$output/um/*", ['-I' + gcom_build]),
AddFlags("$output/jules/*", ['-I' + gcom_build]),
# required for newer compilers
# # todo: allow multiple filters per instance?
# *[AddFlags(*i) for i in ALLOW_MISMATCH_FLAGS]
]),
# this step just makes linker error messages more manageable
ArchiveObjects(),
LinkExe(
linker='mpifort',
flags=[
'-lc', '-lgfortran', '-L', '~/.conda/envs/sci-fab/lib', '-L',
gcom_build, '-l', 'gcom'
],
)
]
return config
