RPackage:move verification to separate method, only when testing
This commit is contained in:
Wouter Deconinck
parent
7314fce7e3
commit
99bfe06ae9
@ -7,12 +7,14 @@
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import llnl.util.filesystem as fs
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import llnl.util.lang as lang
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import llnl.util.tty as tty
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import spack.builder
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import spack.deptypes as dt
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from llnl.util.filesystem import mkdirp
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from llnl.util.lang import ClassProperty, classproperty
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from spack.dependency import Dependency
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from spack.directives import extends
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from spack.error import SpackError
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from spack.spec import Spec
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from .generic import GenericBuilder, Package
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@ -103,64 +105,108 @@ def append(field_value: Union[bytes, str]):
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# the last parsed package.
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if package:
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yield package
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def install(self, pkg, spec, prefix):
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"""Installs an R package."""
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mkdirp(pkg.module.r_lib_dir)
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try:
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# TODO: use a more sustainable dcf parser
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import pycran
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def verify_package(self):
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if not self.pkg.run_tests:
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return
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# Read DESCRIPTION file with dependency information
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# https://r-pkgs.org/description.html
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r_deps = []
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with open(fs.join_path(self.stage.source_path, 'DESCRIPTION')) as file:
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for desc in pycran.parse(file.read()):
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if "Imports" in desc:
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r_deps.extend([d.strip() for d in desc["Imports"].split(",") if d != ""])
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if "Depends" in desc:
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r_deps.extend([d.strip() for d in desc["Depends"].split(",") if d != ""])
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with open(fs.join_path(self.stage.source_path, "DESCRIPTION")) as file:
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for desc in RBuilder.parse_description(file.read()):
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for field in [f for f in ["Depends", "Imports", "LinkingTo"] if f in desc]:
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r_deps.extend([d.strip() for d in desc[field].split(",") if d != ""])
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tty.debug(f"DESCRIPTION: {r_deps}")
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# Convert to spack dependencies format for comparison
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deps = {}
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r_core = [
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"r-compiler",
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"r-graphics",
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"r-grdevices",
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"r-grid",
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"r-methods",
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"r-parallel",
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"r-splines",
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"r-stats",
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"r-stats4",
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"r-tcltk",
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"r-tools",
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"r-utils",
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]
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for r_dep in r_deps:
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p = re.search(r"^[\w_-]+", r_dep) # first word, incl. underscore or dash
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p = re.search(r"^[\w_.-]+", r_dep) # first word, incl. underscore, dot, or dash
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v = re.search("(?<=[(]).*(?=[)])", r_dep) # everything between parentheses
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# require valid package
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assert p, f"Unable to find package name in {r_dep}"
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r_spec = f"r-{p[0].strip().lower()}" if p[0].lower() != "r" else "r"
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r_spec = re.sub(r"\.", "-", r_spec) # dot to dash
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# filter R core packages
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if r_spec in r_core:
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r_spec = "r"
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# allow minimum or pinned versions
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if v:
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v = re.sub(r">=\s([\d.-]+)", r"@\1:", v[0]) # >=
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v = re.sub(r">\s([\d.-]+)", r"@\1.1:", v) # >
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v = re.sub(r"==\s([\d.-]+)", r"@\1", v) # ==
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deps[r_spec] = Dependency(pkg, Spec(r_spec + v), dt.BUILD | dt.RUN)
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else:
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deps[r_spec] = Dependency(pkg, Spec(r_spec), dt.BUILD | dt.RUN)
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v = ""
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# merge dependencies as they are added
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if r_spec in deps:
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deps[r_spec].merge(Dependency(self.pkg, Spec(r_spec + v), dt.BUILD | dt.RUN))
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else:
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deps[r_spec] = Dependency(self.pkg, Spec(r_spec + v), dt.BUILD | dt.RUN)
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tty.debug(f"Converted: {deps}")
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# Retrieve dependencies for current spack package and version
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spack_dependencies = []
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for when, dep in pkg.dependencies.items():
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if spec.satisfies(when):
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for when, dep in self.pkg.dependencies.items():
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if self.spec.satisfies(when):
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spack_dependencies.append(dep)
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tty.debug(f"Spack as read: {spack_dependencies}")
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merged_dependencies = {}
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for dep in spack_dependencies:
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for n, d in dep.items():
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if d in merged_dependencies:
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if n in merged_dependencies:
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merged_dependencies[n].merge(d)
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else:
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merged_dependencies[n] = d
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tty.debug(f"Spack merged: {merged_dependencies}")
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# For each R dependency, ensure Spack dependency is at least as strong
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missing_deps = []
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for dep in sorted(deps.keys()):
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if dep in merged_dependencies:
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if dep in list(merged_dependencies.keys()):
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# Spack dependency must satisfy R dependency
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if not merged_dependencies[dep].spec.satisfies(deps[dep].spec):
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tty.debug(f' depends_on("{deps[dep].spec}", when="@{pkg.version}:", type=("build", "run"))')
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missing_deps.append(
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f' depends_on("{deps[dep].spec}", type=("build", "run"), when="@{self.pkg.version}:")'
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)
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# Remove from dict
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del merged_dependencies[dep]
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else:
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tty.debug(f' depends_on("{deps[dep].spec}", when="@{pkg.version}:", type=("build", "run"))')
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missing_deps.append(
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f' depends_on("{deps[dep].spec}", type=("build", "run"), when="@{self.pkg.version}:")'
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)
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for dep in merged_dependencies:
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if re.match("^r-.*", dep):
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missing_deps.append(
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f' #depends_on("{merged_dependencies[dep].spec}") not needed anymore'
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)
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except ImportError:
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tty.debug("R package dependency verification requires pycran")
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pass
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# Raise exception
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if len(missing_deps) > 0:
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raise SpackError(
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"This package requires stricter dependencies than specified:\n\n"
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+ "\n".join(missing_deps)
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)
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spack.builder.run_before("install")(verify_package)
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def install(self, pkg, spec, prefix):
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"""Installs an R package."""
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mkdirp(pkg.module.r_lib_dir)
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config_args = self.configure_args()
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config_vars = self.configure_vars()
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