kopia lustrzana https://github.com/jupyterhub/repo2docker
Split julia support into legacy and current
David Anthoff
rodzic
7f88531c9e
commit
c9770ee41e
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@ -30,7 +30,7 @@ from traitlets.config import Application
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from . import __version__
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from .buildpacks import (
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PythonBuildPack, DockerBuildPack, LegacyBinderDockerBuildPack,
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CondaBuildPack, JuliaBuildPack, RBuildPack, NixBuildPack
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CondaBuildPack, JuliaBuildPack, JuliaLegacyBuildPack, RBuildPack, NixBuildPack
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)
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from . import contentproviders
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from .utils import ByteSpecification, chdir
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@ -85,7 +85,8 @@ class Repo2Docker(Application):
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[
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LegacyBinderDockerBuildPack,
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DockerBuildPack,
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JuliaBuildPack,
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JuliaLegacyBuildPack,
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JuliaBuildPack,
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NixBuildPack,
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RBuildPack,
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CondaBuildPack,
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@ -2,6 +2,7 @@ from .base import BuildPack, BaseImage
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from .python import PythonBuildPack
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from .conda import CondaBuildPack
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from .julia import JuliaBuildPack
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from .julialegacy import JuliaLegacyBuildPack
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from .docker import DockerBuildPack
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from .legacy import LegacyBinderDockerBuildPack
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from .r import RBuildPack
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@ -0,0 +1,133 @@
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"""Generates a Dockerfile based on an input matrix for Julia"""
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import os
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from .python import PythonBuildPack
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class JuliaBuildPack(PythonBuildPack):
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"""
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Julia build pack which uses conda.
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"""
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minor_julias = {
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'1.0': '1.0.3',
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'1.1': '1.1.0',
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}
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major_julias = {
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'1': '1.1.0',
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}
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@property
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def julia_version(self):
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# TODO Read version out of the file
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return self.major_julias['1']
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def get_build_env(self):
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"""Get additional environment settings for Julia and Jupyter
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Returns:
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an ordered list of environment setting tuples
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The tuples contain a string of the environment variable name and
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a string of the environment setting:
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- `JULIA_PATH`: base path where all Julia Binaries and libraries
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will be installed
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- `JULIA_HOME`: path where all Julia Binaries will be installed
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- `JULIA_PKGDIR`: path where all Julia libraries will be installed
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- `JULIA_DEPOT_PATH`: path where Julia libraries are installed.
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Similar to JULIA_PKGDIR, used in 1.0.
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- `JULIA_VERSION`: default version of julia to be installed
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- `JUPYTER`: environment variable required by IJulia to point to
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the `jupyter` executable
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For example, a tuple may be `('JULIA_VERSION', '0.6.0')`.
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"""
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return super().get_build_env() + [
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('JULIA_PATH', '${APP_BASE}/julia'),
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('JULIA_HOME', '${JULIA_PATH}/bin'), # julia <= 0.6
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('JULIA_BINDIR', '${JULIA_HOME}'), # julia >= 0.7
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('JULIA_PKGDIR', '${JULIA_PATH}/pkg'),
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('JULIA_DEPOT_PATH', '${JULIA_PKGDIR}'), # julia >= 0.7
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('JULIA_VERSION', self.julia_version),
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('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter')
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]
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def get_path(self):
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"""Adds path to Julia binaries to user's PATH.
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Returns:
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an ordered list of path strings. The path to the Julia
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executable is added to the list.
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"""
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return super().get_path() + ['${JULIA_HOME}']
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def get_build_scripts(self):
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"""
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Return series of build-steps common to "ALL" Julia repositories
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All scripts found here should be independent of contents of a
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particular repository.
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This creates a directory with permissions for installing julia packages
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(from get_assemble_scripts).
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"""
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return super().get_build_scripts() + [
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(
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"root",
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r"""
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mkdir -p ${JULIA_PATH} && \
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curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1
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"""
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),
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(
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"root",
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r"""
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mkdir -p ${JULIA_PKGDIR} && \
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chown ${NB_USER}:${NB_USER} ${JULIA_PKGDIR}
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"""
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),
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(
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"${NB_USER}",
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# HACK: Can't seem to tell IJulia to install in sys-prefix
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# FIXME: Find way to get it to install under /srv and not $HOME?
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r"""
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julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && \
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mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*}
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"""
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)
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]
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def get_assemble_scripts(self):
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"""
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Return series of build-steps specific to "this" Julia repository
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Instantiate and then precompile all packages in the repos julia
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environment.
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The parent, CondaBuildPack, will add the build steps for
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any needed Python packages found in environment.yml.
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"""
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return super().get_assemble_scripts() + [
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(
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"${NB_USER}",
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r"""
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julia --project=. -e 'using Pkg; Pkg.instantiate(); pkg"precompile"'
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"""
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)
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]
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def detect(self):
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"""
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Check if current repo should be built with the Julia Build pack
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super().detect() is not called in this function - it would return
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false unless an `environment.yml` is present and we do not want to
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require the presence of a `environment.yml` to use Julia.
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Instead we just check if the path to `Project.toml` or
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`JuliaProject.toml` exists.
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"""
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return os.path.exists(self.binder_path('Project.toml')) or os.path.exists(self.binder_path('JuliaProject.toml'))
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@ -1,229 +0,0 @@
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"""Generates a Dockerfile based on an input matrix for Julia"""
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import os
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from ..python import PythonBuildPack
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class JuliaBuildPack(PythonBuildPack):
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"""
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Julia build pack which uses conda.
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"""
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minor_julias = {
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'0.6': '0.6.4',
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'0.7': '0.7.0',
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'1.0': '1.0.3',
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'1.1': '1.1.0',
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}
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major_julias = {
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'1': '1.1.0',
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}
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@property
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def julia_env_exists(self):
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return os.path.exists(self.binder_path('Project.toml')) or os.path.exists(self.binder_path('JuliaProject.toml'))
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@property
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def julia_version(self):
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if self.julia_env_exists:
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# TODO Read version out of the file
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return self.major_julias['1']
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else:
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require = self.binder_path('REQUIRE')
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try:
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with open(require) as f:
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julia_version_line = f.readline().strip() # First line is optionally a julia version
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except FileNotFoundError:
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julia_version_line = ''
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if not julia_version_line.startswith('julia '):
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# not a Julia version line.
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# use the default Julia.
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self._julia_version = self.minor_julias['0.6']
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return self._julia_version
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julia_version_info = julia_version_line.split(' ', 1)[1].split('.')
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julia_version = ''
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if len(julia_version_info) == 1:
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julia_version = self.major_julias[julia_version_info[0]]
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elif len(julia_version_info) == 2:
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# get major.minor
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julia_version = self.minor_julias['.'.join(julia_version_info)]
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else:
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# use supplied julia version
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julia_version = '.'.join(julia_version_info)
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self._julia_version = julia_version
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return self._julia_version
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def get_build_env(self):
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"""Get additional environment settings for Julia and Jupyter
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Returns:
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an ordered list of environment setting tuples
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The tuples contain a string of the environment variable name and
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a string of the environment setting:
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- `JULIA_PATH`: base path where all Julia Binaries and libraries
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will be installed
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- `JULIA_HOME`: path where all Julia Binaries will be installed
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- `JULIA_PKGDIR`: path where all Julia libraries will be installed
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- `JULIA_DEPOT_PATH`: path where Julia libraries are installed.
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Similar to JULIA_PKGDIR, used in 1.x.
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- `JULIA_VERSION`: default version of julia to be installed
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- `JUPYTER`: environment variable required by IJulia to point to
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the `jupyter` executable
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For example, a tuple may be `('JULIA_VERSION', '0.6.0')`.
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"""
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return super().get_build_env() + [
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('JULIA_PATH', '${APP_BASE}/julia'),
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('JULIA_HOME', '${JULIA_PATH}/bin'), # julia <= 0.6
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('JULIA_BINDIR', '${JULIA_HOME}'), # julia >= 0.7
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('JULIA_PKGDIR', '${JULIA_PATH}/pkg'),
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('JULIA_DEPOT_PATH', '${JULIA_PKGDIR}'), # julia >= 0.7
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('JULIA_VERSION', self.julia_version),
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('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter')
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]
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def get_path(self):
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"""Adds path to Julia binaries to user's PATH.
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Returns:
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an ordered list of path strings. The path to the Julia
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executable is added to the list.
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"""
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return super().get_path() + ['${JULIA_HOME}']
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def get_build_scripts(self):
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"""
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Return series of build-steps common to "ALL" Julia repositories
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All scripts found here should be independent of contents of a
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particular repository.
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This creates a directory with permissions for installing julia packages
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(from get_assemble_scripts).
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"""
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if self.julia_env_exists:
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return super().get_build_scripts() + [
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(
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"root",
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r"""
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mkdir -p ${JULIA_PATH} && \
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curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1
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"""
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),
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(
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"root",
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r"""
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mkdir -p ${JULIA_PKGDIR} && \
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chown ${NB_USER}:${NB_USER} ${JULIA_PKGDIR}
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"""
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)
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]
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else:
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return super().get_build_scripts() + [
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(
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"root",
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r"""
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mkdir -p ${JULIA_PATH} && \
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curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1
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"""
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),
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(
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"root",
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r"""
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mkdir -p ${JULIA_PKGDIR} && \
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chown ${NB_USER}:${NB_USER} ${JULIA_PKGDIR}
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"""
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),
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(
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"${NB_USER}",
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# HACK: Can't seem to tell IJulia to install in sys-prefix
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# FIXME: Find way to get it to install under /srv and not $HOME?
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r"""
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julia -e 'if (VERSION > v"0.7-") using Pkg; else Pkg.init(); end; Pkg.add("IJulia"); using IJulia;' && \
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mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*}
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"""
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)
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]
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def get_assemble_scripts(self):
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"""
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Return series of build-steps specific to "this" Julia repository
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Precompile all Julia libraries found in the repository's REQUIRE
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file. The parent, CondaBuildPack, will add the build steps for
|
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any needed Python packages found in environment.yml.
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"""
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if self.julia_env_exists:
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return super().get_assemble_scripts() + [
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(
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"${NB_USER}",
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# HACK: Can't seem to tell IJulia to install in sys-prefix
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# FIXME: Find way to get it to install under /srv and not $HOME?
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r"""
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julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");"
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"""
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),
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(
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"${NB_USER}",
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# HACK: Can't seem to tell IJulia to install in sys-prefix
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# FIXME: Find way to get it to install under /srv and not $HOME?
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r"""
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mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*}
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"""
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),
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(
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"${NB_USER}",
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# Install and pre-compile all libraries if they've opted into it.
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# In v0.6, Pkg.resolve() installs all the packages, but in v0.7+, we
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# have to manually Pkg.add() each of them (since the REQUIRES file
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# format is deprecated).
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# The precompliation is done via `using {libraryname}`.
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r"""
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julia --project=. -e 'using Pkg; Pkg.instantiate(); pkg"precompile"'
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"""
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# TODO: For some reason, `rm`ing the file fails with permission denied.
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# && rm /tmp/install-repo-dependencies.jl
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)
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]
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else:
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require = self.binder_path('REQUIRE')
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return super().get_assemble_scripts() + [(
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"${NB_USER}",
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# Install and pre-compile all libraries if they've opted into it.
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# In v0.6, Pkg.resolve() installs all the packages, but in v0.7+, we
|
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# have to manually Pkg.add() each of them (since the REQUIRES file
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# format is deprecated).
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# The precompliation is done via `using {libraryname}`.
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r"""
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julia /tmp/install-repo-dependencies.jl "%(require)s"
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""" % {"require": require}
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# TODO: For some reason, `rm`ing the file fails with permission denied.
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# && rm /tmp/install-repo-dependencies.jl
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)]
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def get_build_script_files(self):
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files = {
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'julia/install-repo-dependencies.jl': '/tmp/install-repo-dependencies.jl',
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}
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files.update(super().get_build_script_files())
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return files
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def detect(self):
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"""
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Check if current repo should be built with the Julia Build pack
|
||||
|
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super().detect() is not called in this function - it would return
|
||||
false unless an `environment.yml` is present and we do not want to
|
||||
require the presence of a `environment.yml` to use Julia.
|
||||
|
||||
Instead we just check if the path to `REQUIRE`, `Project.toml` or
|
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`JuliaProject.toml` exists
|
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|
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"""
|
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return os.path.exists(self.binder_path('REQUIRE')) or self.julia_env_exists
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||||
|
|
@ -0,0 +1,170 @@
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"""Generates a Dockerfile based on an input matrix for Julia"""
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import os
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from ..python import PythonBuildPack
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class JuliaLegacyBuildPack(PythonBuildPack):
|
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"""
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Julia build pack which uses conda.
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"""
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minor_julias = {
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'0.6': '0.6.4',
|
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'0.7': '0.7.0',
|
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'1.0': '1.0.3',
|
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'1.1': '1.1.0',
|
||||
}
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major_julias = {
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'1': '1.1.0',
|
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}
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@property
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def julia_version(self):
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require = self.binder_path('REQUIRE')
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try:
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with open(require) as f:
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julia_version_line = f.readline().strip() # First line is optionally a julia version
|
||||
except FileNotFoundError:
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julia_version_line = ''
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||||
|
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if not julia_version_line.startswith('julia '):
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# not a Julia version line.
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||||
# use the default Julia.
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self._julia_version = self.minor_julias['0.6']
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return self._julia_version
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julia_version_info = julia_version_line.split(' ', 1)[1].split('.')
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julia_version = ''
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if len(julia_version_info) == 1:
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julia_version = self.major_julias[julia_version_info[0]]
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elif len(julia_version_info) == 2:
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# get major.minor
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||||
julia_version = self.minor_julias['.'.join(julia_version_info)]
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||||
else:
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# use supplied julia version
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||||
julia_version = '.'.join(julia_version_info)
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self._julia_version = julia_version
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return self._julia_version
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||||
|
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def get_build_env(self):
|
||||
"""Get additional environment settings for Julia and Jupyter
|
||||
|
||||
Returns:
|
||||
an ordered list of environment setting tuples
|
||||
|
||||
The tuples contain a string of the environment variable name and
|
||||
a string of the environment setting:
|
||||
- `JULIA_PATH`: base path where all Julia Binaries and libraries
|
||||
will be installed
|
||||
- `JULIA_HOME`: path where all Julia Binaries will be installed
|
||||
- `JULIA_PKGDIR`: path where all Julia libraries will be installed
|
||||
- `JULIA_DEPOT_PATH`: path where Julia libraries are installed.
|
||||
Similar to JULIA_PKGDIR, used in 1.x.
|
||||
- `JULIA_VERSION`: default version of julia to be installed
|
||||
- `JUPYTER`: environment variable required by IJulia to point to
|
||||
the `jupyter` executable
|
||||
|
||||
For example, a tuple may be `('JULIA_VERSION', '0.6.0')`.
|
||||
|
||||
"""
|
||||
return super().get_build_env() + [
|
||||
('JULIA_PATH', '${APP_BASE}/julia'),
|
||||
('JULIA_HOME', '${JULIA_PATH}/bin'), # julia <= 0.6
|
||||
('JULIA_BINDIR', '${JULIA_HOME}'), # julia >= 0.7
|
||||
('JULIA_PKGDIR', '${JULIA_PATH}/pkg'),
|
||||
('JULIA_DEPOT_PATH', '${JULIA_PKGDIR}'), # julia >= 0.7
|
||||
('JULIA_VERSION', self.julia_version),
|
||||
('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter')
|
||||
]
|
||||
|
||||
def get_path(self):
|
||||
"""Adds path to Julia binaries to user's PATH.
|
||||
|
||||
Returns:
|
||||
an ordered list of path strings. The path to the Julia
|
||||
executable is added to the list.
|
||||
|
||||
"""
|
||||
return super().get_path() + ['${JULIA_HOME}']
|
||||
|
||||
def get_build_scripts(self):
|
||||
"""
|
||||
Return series of build-steps common to "ALL" Julia repositories
|
||||
|
||||
All scripts found here should be independent of contents of a
|
||||
particular repository.
|
||||
|
||||
This creates a directory with permissions for installing julia packages
|
||||
(from get_assemble_scripts).
|
||||
|
||||
"""
|
||||
return super().get_build_scripts() + [
|
||||
(
|
||||
"root",
|
||||
r"""
|
||||
mkdir -p ${JULIA_PATH} && \
|
||||
curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1
|
||||
"""
|
||||
),
|
||||
(
|
||||
"root",
|
||||
r"""
|
||||
mkdir -p ${JULIA_PKGDIR} && \
|
||||
chown ${NB_USER}:${NB_USER} ${JULIA_PKGDIR}
|
||||
"""
|
||||
),
|
||||
(
|
||||
"${NB_USER}",
|
||||
# HACK: Can't seem to tell IJulia to install in sys-prefix
|
||||
# FIXME: Find way to get it to install under /srv and not $HOME?
|
||||
r"""
|
||||
julia -e 'if (VERSION > v"0.7-") using Pkg; else Pkg.init(); end; Pkg.add("IJulia"); using IJulia;' && \
|
||||
mv ${HOME}/.local/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*} ${NB_PYTHON_PREFIX}/share/jupyter/kernels/julia-${JULIA_VERSION%[.-]*}
|
||||
"""
|
||||
)
|
||||
]
|
||||
|
||||
def get_assemble_scripts(self):
|
||||
"""
|
||||
Return series of build-steps specific to "this" Julia repository
|
||||
|
||||
Precompile all Julia libraries found in the repository's REQUIRE
|
||||
file. The parent, CondaBuildPack, will add the build steps for
|
||||
any needed Python packages found in environment.yml.
|
||||
|
||||
"""
|
||||
require = self.binder_path('REQUIRE')
|
||||
return super().get_assemble_scripts() + [(
|
||||
"${NB_USER}",
|
||||
# Install and pre-compile all libraries if they've opted into it.
|
||||
# In v0.6, Pkg.resolve() installs all the packages, but in v0.7+, we
|
||||
# have to manually Pkg.add() each of them (since the REQUIRES file
|
||||
# format is deprecated).
|
||||
# The precompliation is done via `using {libraryname}`.
|
||||
r"""
|
||||
julia /tmp/install-repo-dependencies.jl "%(require)s"
|
||||
""" % {"require": require}
|
||||
# TODO: For some reason, `rm`ing the file fails with permission denied.
|
||||
# && rm /tmp/install-repo-dependencies.jl
|
||||
)]
|
||||
|
||||
def get_build_script_files(self):
|
||||
files = {
|
||||
'julialegacy/install-repo-dependencies.jl': '/tmp/install-repo-dependencies.jl',
|
||||
}
|
||||
files.update(super().get_build_script_files())
|
||||
return files
|
||||
|
||||
def detect(self):
|
||||
"""
|
||||
Check if current repo should be built with the Julia Build pack
|
||||
|
||||
super().detect() is not called in this function - it would return
|
||||
false unless an `environment.yml` is present and we do not want to
|
||||
require the presence of a `environment.yml` to use Julia.
|
||||
|
||||
Instead we just check if the path to `REQUIRE` exists
|
||||
|
||||
"""
|
||||
# TODO(nhdaly): Add support for Project.toml here as well.
|
||||
return os.path.exists(self.binder_path('REQUIRE')) and not(os.path.exists(self.binder_path('Project.toml')) or os.path.exists(self.binder_path('JuliaProject.toml')))
|
||||
Ładowanie…
Reference in New Issue