Merge pull request #1350 from minrk/rm-julia-06

Remove support for deprecated Julia REQUIRE, Julia < 1.3

docs/source/architecture.md

@@ -87,7 +87,7 @@ the `build` method of the `BuildPack` base class.
 
 The **assemble** stage builds the specific environment that is requested by the repository.
 This usually means installing required libraries specified in a format native to the language
-(`requirements.txt`, `environment.yml`, `REQUIRE`, `install.R`, etc).
+(`requirements.txt`, `environment.yml`, `Project.toml`, `install.R`, etc).
 
 Most of this work is done in `get_assemble_scripts` method. It can return arbitrary bash script
 lines that can be run as different users, and has access to the repository contents (unlike

docs/source/config_files.rst

@@ -102,14 +102,8 @@ of the Julia packages that are installed.
 ``REQUIRE`` - Install a Julia environment (legacy)
 ==================================================
 
-A ``REQUIRE`` file can specify both the version of Julia to be used and
-which Julia packages should be used. The use of ``REQUIRE`` is only
-recommended for pre 1.0 Julia versions. The recommended way of installing
-a Julia environment that uses Julia 1.0 or newer is to use a ``Project.toml``
-file. If both a ``REQUIRE`` and a ``Project.toml`` file are detected,
-the ``REQUIRE`` file is ignored. To see an example of a Julia repository
-with ``REQUIRE`` and ``environment.yml``, visit
-`binder-examples/julia-python <https://github.com/binder-examples/julia-python>`_.
+``REQUIRE`` files no longer work, and are no longer supported.
+The recommended way of installing a Julia environment is to use a ``Project.toml`` file.
 
 
 .. _install.R:

docs/source/faq.rst

@@ -55,9 +55,10 @@ We **strongly** recommend specifying a Python version (in environment.yml, runti
 Julia
 ~~~~~
 
-All Julia versions since Julia 0.7.0 are supported via a :ref:`Project.toml <Project.toml>`
+All Julia versions since Julia 1.3 are supported via a :ref:`Project.toml <Project.toml>`
 file, and this is the recommended way to install Julia environments.
-Julia versions 0.6.x and earlier are supported via a :ref:`REQUIRE <REQUIRE>` file.
+
+Julia < 1.3 and the older Julia REQUIRE file is no longer supported because required infrastructure has been removed.
 
 R
 ~

docs/source/specification.rst

@@ -5,14 +5,14 @@ The Reproducible Execution Environment Specification
 ====================================================
 
 repo2docker scans a repository for particular :ref:`config-files`, such
-as ``requirements.txt`` or ``REQUIRE``. The collection of files, their contents,
+as ``requirements.txt`` or ``Project.toml``. The collection of files, their contents,
 and the resulting actions that repo2docker takes is known
 as the **Reproducible Execution Environment Specification** (or REES).
 
 The goal of the REES is to automate and encourage existing community best practices
 for reproducible computational environments. This includes installing pacakges using
 community-standard specification files and their corresponding tools,
-such as ``requirements.txt`` (with ``pip``), ``REQUIRE`` (with Julia), or
+such as ``requirements.txt`` (with ``pip``), ``Project.toml`` (with Julia), or
 ``apt.txt`` (with ``apt``). While repo2docker automates the
 creation of the environment, a human should be able to look at a REES-compliant
 repository and reproduce the environment using common, clear steps without

repo2docker/buildpacks/julia/julia_require.py

@@ -1,205 +1,29 @@
-"""Generates a Dockerfile based on an input matrix with REQUIRE for legacy Julia"""
+"""
+DEPRECATED - Dependencies of REQUIRE have been removed
+"""
 
 import os
-from functools import lru_cache
 
-from ...semver import parse_version as V
 from ..python import PythonBuildPack
 
 
 class JuliaRequireBuildPack(PythonBuildPack):
     """
     Julia build pack which uses conda and REQUIRE.
-    """
-
-    minor_julias = {"0.6": "0.6.4", "0.7": "0.7.0", "1.0": "1.0.4", "1.1": "1.1.1"}
-    major_julias = {"1": "1.1.1"}
-
-    @property
-    def python_version(self):
-        # IJulia doesn't build on julia 0.6
-        # due to old incompatibilities with Jupyter-core >= 4.5,
-        # so use the similarly-old Python 3.5 base environment
-        if V(self.julia_version) < V("0.7"):
-            return "3.5"
-        else:
-            return super().python_version
-
-    @property
-    def julia_version(self):
-        require = self.binder_path("REQUIRE")
-        try:
-            with open(require) as f:
-                julia_version_line = (
-                    f.readline().strip()
-                )  # First line is optionally a julia version
-        except FileNotFoundError:
-            julia_version_line = ""
-
-        if not julia_version_line.startswith("julia "):
-            # not a Julia version line.
-            # use the default Julia.
-            self._julia_version = self.minor_julias["0.6"]
-            return self._julia_version
-
-        julia_version_info = julia_version_line.split(" ", 1)[1].split(".")
-        julia_version = ""
-        if len(julia_version_info) == 1:
-            julia_version = self.major_julias[julia_version_info[0]]
-        elif len(julia_version_info) == 2:
-            # get major.minor
-            julia_version = self.minor_julias[".".join(julia_version_info)]
-        else:
-            # use supplied julia version
-            julia_version = ".".join(julia_version_info)
-        self._julia_version = julia_version
-        return self._julia_version
-
-    @lru_cache()
-    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
-            - `JULIA_ARCH`: machine architecture used in Julia download URLs
-            - `JULIA_ARCH_SHORT`: machine architecture used in Julia download URLs
-            - `JUPYTER`: environment variable required by IJulia to point to
-                the `jupyter` executable
-
-            For example, a tuple may be `('JULIA_VERSION', '0.6.0')`.
-
-        """
-        if self.platform == "linux/arm64":
-            julia_arch = julia_arch_short = "aarch64"
-        else:
-            julia_arch = "x86_64"
-            julia_arch_short = "x64"
-
-        if V(self.julia_version) < V("0.7"):
-            # IJulia with Julia 0.6 isn't compatible with more recent jupyter-core
-            # point it to the one in the kernel env
-            # I _think_ this is only relevant during installation
-            jupyter = "${KERNEL_PYTHON_PREFIX}/bin/jupyter"
-        else:
-            jupyter = "${NB_PYTHON_PREFIX}/bin/jupyter"
-        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", "${JULIA_PKGDIR}"),  # julia >= 0.7
-            ("JULIA_VERSION", self.julia_version),
-            ("JULIA_ARCH", julia_arch),
-            ("JULIA_ARCH_SHORT", julia_arch_short),
-            ("JUPYTER", jupyter),
-        ]
-
-    @lru_cache()
-    def get_path(self):
-        """Adds path to Julia binaries to user's PATH.
-
-        Returns:
-            an ordered list of path strings. The path to the Julia
-            executable is added to the list.
-
-        """
-        return super().get_path() + ["${JULIA_HOME}"]
-
-    @lru_cache()
-    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 ${JULIA_PATH} && \
-                curl -sSL "https://julialang-s3.julialang.org/bin/linux/${JULIA_ARCH_SHORT}/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.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%[.-]*}
-                """,
-            ),
-        ]
-
-    @lru_cache()
-    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
-            )
-        ]
+    Now just an informative error message.
+    """
 
-    @lru_cache()
-    def get_build_script_files(self):
-        files = {
-            "julia/install-repo-dependencies.jl": "/tmp/install-repo-dependencies.jl"
-        }
-        files.update(super().get_build_script_files())
-        return files
+    def build(self, *args, **kwargs):
+        raise ValueError(
+            "Julia REQUIRE no longer supported due to removed infrastructure. Use Project.toml."
+        )
 
     def detect(self):
         """
-        Check if current repo should be built with the Julia Legacy 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 and that there is
-        no julia 1.0 style environment
+        Check if current repo exects tp be built with the Julia Legacy Build pack
 
+        This no longer works, but try to raise an informative error.
         """
         return os.path.exists(self.binder_path("REQUIRE")) and not (
             os.path.exists(self.binder_path("Project.toml"))

tests/julia/project-1.0.2-binder-dir/.binder/Project.toml → tests/julia/project-binder-dir/.binder/Project.toml

@@ -2,4 +2,4 @@
 IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d"
 
 [compat]
-julia = "=1.0.2"
+julia = "=1.3"

tests/julia/project-1.0.2-binder-dir/verify → tests/julia/project-binder-dir/verify

@@ -1,7 +1,7 @@
 #!/usr/bin/env julia
 
-if VERSION != v"1.0.2"
-    println("Julia version should be 1.0.2")
+if VERSION != v"1.3"
+    println("Julia version should be 1.3, got $VERSION")
     exit(1)
 end