Merge branch 'master' into change-julia-env-handling

README.md

@@ -9,6 +9,8 @@ the configuration files found in the repository.
 See the [repo2docker documentation](http://repo2docker.readthedocs.io)
 for more information on using repo2docker.
 
+For support questions please search or post to https://discourse.jupyter.org/c/binder.
+
 See the [contributing guide](CONTRIBUTING.md) for information on contributing to
 repo2docker.
 

docs/issue_template.md

@@ -0,0 +1,13 @@
+<!--
+Welcome!
+
+Help us stay on top of things (and get faster replies) by submitting them to
+the right place:
+
+* for support questions please use https://discourse.jupyter.org/c/binder
+* repo2docker development related issues https://github.com/jupyter/repo2docker/issues/new
+* if the https://mybinder.org site is down or has inaccessible pages: https://github.com/jupyterhub/mybinder.org-deploy/issues/new
+
+If you aren't sure where to go use https://discourse.jupyter.org/c/binder.
+
+-->

docs/source/changelog.rst

@@ -17,6 +17,8 @@ API changes
 
 Bug fixes
 ---------
+- Install IJulia kernel into ${NB_PYTHON_PREFIX}/share/jupyter in :pr:`622` by
+  :user:`davidanthoff`.
 
 
 Version 0.8.0

docs/source/config_files.rst

@@ -32,6 +32,10 @@ Below is a list of supported configuration files (roughly in the order of build
 ``environment.yml`` is the standard configuration file used by `conda <https://conda.io>`_
 that lets you install any kind of package,
 including Python, R, and C/C++ packages.
+``repo2docker`` does not use ``environment.yml`` to create and activate a new conda environment.
+Rather, it updates a base conda environment with the packages listed in ``environment.yml``.
+This means that the environment will always have the same default name, not the name
+specified in ``environment.yml``.
 
 .. note::
 

docs/source/faq.rst

@@ -53,6 +53,8 @@ Only R 3.4.4 is currently supported, which is installed via ``apt`` from the
 `ubuntu bionic repository <https://packages.ubuntu.com/bionic/r-base>`_.
 
 
+
+
 Why is my repository is failing to build with ``ResolvePackageNotFound`` ?
 --------------------------------------------------------------------------
 
@@ -147,3 +149,17 @@ notebooks (among others).
     the container, use the ``--volumes`` option instead. Similarly,
     for a fully customized user Dockerfile, this option is not
     guaranteed to work.
+    
+    
+Why is my R shiny app not launching?
+----------------------------------------------------------------------------------
+
+If you are trying to run an R shiny app using the ``/shiny/folder_containing_shiny``
+url option, but the launch returns "The application exited during initialization.",
+there might be something wrong with the specification of the app. One way of debugging
+the app in the container is by running the ``rstudio`` url, open either the ui or 
+server file for the app, and run the app in the container rstudio. This way you can 
+see the rstudio logs as it tries to initialise the shiny app. If you a missing a 
+package or other dependency for the container, this will be obvious at this stage.
+
+

docs/source/howto/languages.rst

@@ -73,10 +73,10 @@ Julia
 
 To build an environment with Julia, include a configuration file called
 ``Project.toml``. The format of this file is documented at
-`the Julia Pkg.jl documentation <https://julialang.github.io/Pkg.jl/stable/>`_.
+`the Julia Pkg.jl documentation <https://julialang.github.io/Pkg.jl/v1/>`_.
 To specify a specific version of Julia to install, put a Julia version in the
-``Compat`` section of the ``Project.toml`` file, as described
+``[compat]`` section of the ``Project.toml`` file, as described
-here: https://julialang.github.io/Pkg.jl/stable/compatibility.
+here: https://julialang.github.io/Pkg.jl/v1/compatibility/.
 
 Languages not covered here
 ==========================

repo2docker/buildpacks/julia/julia_project.py

@@ -2,7 +2,7 @@
 import os
 import toml
 from ..python import PythonBuildPack
-from .julia_semver import find_semver_match
+from .semver import find_semver_match
 
 class JuliaProjectTomlBuildPack(PythonBuildPack):
     """
@@ -61,7 +61,8 @@ class JuliaProjectTomlBuildPack(PythonBuildPack):
             ('JULIA_PATH', '${APP_BASE}/julia'),
             ('JULIA_DEPOT_PATH', '${JULIA_PATH}/pkg'),
             ('JULIA_VERSION', self.julia_version),
-            ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter')
+            ('JUPYTER', '${NB_PYTHON_PREFIX}/bin/jupyter'),
+            ('JUPYTER_DATA_DIR', '${NB_PYTHON_PREFIX}/share/jupyter'),
         ]
 
     def get_env(self):
@@ -122,7 +123,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack):
             (
                 "${NB_USER}",
                 r"""
-                JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", env=Dict(\"JUPYTER_DATA_DIR\"=>\"${NB_PYTHON_PREFIX}/share/jupyter\"));" && \
+                JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && \
                 julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); pkg"precompile"'
                 """
             )

repo2docker/buildpacks/julia/julia_semver.py

@@ -1,119 +0,0 @@
-# This file implements the julia-specific logic for handling SemVer (Semantic
-# Versioning) strings in .toml files.
-#
-# It uses the python "semver" package to do most version string comparisons, but
-# the places where julia's SemVer handling differs from the semver package have
-# been implemented directly.
-#
-# Here, we use tuples to represent a Version, and functors as "matchers". The matcher
-# functors take a version string and return true if it passes its constraints.
-
-import re
-import semver
-
-# Main algorithm:
-# Create an AbstractMatcher instance from the constraint string, and check it
-# against each version in the versions_list, returning the first success.
-def find_semver_match(constraint, versions_list):
-    matcher = create_semver_matcher(constraint)
-    for vstr in reversed(versions_list):
-        if matcher.match(str_to_version(vstr)):
-            return vstr
-    return None
-
-def str_to_version(vstr):
-    return tuple([int(n) for n in vstr.split('.')])
-
-# --- Matcher interface -------------------------------------------
-
-class AbstractMatcher:
-    def match(self, v):
-        pass
-
-class SemverMatcher(AbstractMatcher):
-    """ Match a version tuple to a given constraint_str using the `semver` package. """
-    def __init__(self, constraint_str):
-        self.constraint_str = constraint_str
-    def match(self, v):
-        while len(v) < 3:
-            v = v+(0,)
-        v_str = '.'.join(map(str, v))
-        return semver.match(v_str, self.constraint_str)
-    def __repr__(self):
-        return self.constraint_str
-
-# --- Custom matcher for julia-specific SemVer handling: ---------
-
-from enum import Enum
-class Exclusivity(Enum):
-    EXCLUSIVE = 1
-    INCLUSIVE = 2
-
-class VersionRange(AbstractMatcher):
-    """ Match a version tuple between lower and upper bounds. """
-    def __init__(self, lower, upper, upper_exclusivity):
-        self.lower = lower
-        self.upper = upper
-        self.upper_exclusivity = upper_exclusivity
-    def match(self, v):
-        if self.upper_exclusivity == Exclusivity.EXCLUSIVE:
-            return self.lower <= v < self.upper
-        else:
-            return self.lower <= v <= self.upper
-    def __repr__(self):
-        return ("["+".".join(map(str, self.lower)) +"-"+ ".".join(map(str, self.upper)) +
-                    (")" if self.upper_exclusivity == Exclusivity.EXCLUSIVE else "]"))
-
-# Helpers
-def major(v): return v[0]
-def minor(v): return v[1] if len(v) >= 2 else 0
-def patch(v): return v[2] if len(v) >= 3 else 0
-
-# --- main constraint parser function ------------------------------------
-
-def create_semver_matcher(constraint_str):
-    """
-    Returns a derived-class instance of AbstractMatcher that matches version
-    tuples against the provided constraint_str.
-    """
-    constraint_str = constraint_str.strip()
-    first_digit = re.search(r"\d", constraint_str)
-    if not first_digit:
-        # Invalid version string (no numbers in it)
-        return ""
-    constraint = str_to_version(constraint_str[first_digit.start():])
-
-    comparison_symbol = constraint_str[0:first_digit.start()].strip()
-
-    # Default to "^" search if no matching mode specified (up to next major version)
-    if (first_digit.start() == 0) or (comparison_symbol == "^"):
-        if major(constraint) == 0:
-            # Also, julia treats pre-1.0 releases specially, as if the first
-            # non-zero number is actually a major number:
-            # https://docs.julialang.org/en/latest/stdlib/Pkg/#Caret-specifiers-1
-            # So we need to handle it separately by bumping the first non-zero number.
-            for i,n in enumerate(constraint):
-                if n != 0 or i == len(constraint)-1: # (using the last existing number handles situations like "^0.0" or "^0")
-                    upper = constraint[0:i] + (n+1,)
-                    break
-            return VersionRange(constraint, upper, Exclusivity.EXCLUSIVE)
-        else:
-            return VersionRange(constraint, (major(constraint)+1,), Exclusivity.EXCLUSIVE)
-
-    # '~' matching (only allowed to bump the last present number by one)
-    if (comparison_symbol == "~"):
-        return VersionRange(constraint, constraint[:-1] +(constraint[-1]+1,), Exclusivity.INCLUSIVE)
-
-    # Use semver package's comparisons for everything else:
-
-    # semver requires three version numbers
-    if len(constraint) < 3:
-        while len(constraint) < 3:
-            constraint = constraint+(0,)
-        constraint_str = constraint_str[0:first_digit.start()] + ".".join(map(str, constraint))
-
-    # Convert special comparison strings to format accepted by `semver` library.
-    constraint_str = constraint_str.replace("≥", ">=").replace("≤", "<=")
-    constraint_str = re.sub(r"(^|\b)=\b", "==", constraint_str)
-
-    return SemverMatcher(constraint_str)

repo2docker/buildpacks/julia/semver.py

@@ -0,0 +1,165 @@
+"""
+Julia specific handling of SemVer strings
+
+It uses the python "semver" package to do most version string comparisons, but
+the places where julia's SemVer handling differs from the semver package have
+been implemented directly.
+
+We use tuples to represent a Version, and functors as "matchers". The
+matcher functors take a version string and return True if it passes its
+constraints.
+"""
+
+
+import re
+
+import semver
+
+
+def find_semver_match(constraint, versions_list):
+    matcher = create_semver_matcher(constraint)
+    for vstr in reversed(versions_list):
+        if matcher.match(str_to_version(vstr)):
+            return vstr
+    return None
+
+
+def str_to_version(vstr):
+    return tuple([int(n) for n in vstr.split(".")])
+
+
+# Helpers
+def major(v):
+    return v[0]
+
+
+def minor(v):
+    return v[1] if len(v) >= 2 else 0
+
+
+def patch(v):
+    return v[2] if len(v) >= 3 else 0
+
+
+def create_semver_matcher(constraint_str):
+    """Create a matcher that can be used to match version tuples
+
+    Version tuples are matched against the provided regex `constraint_str`.
+    """
+    constraint_str = constraint_str.strip()
+    first_digit = re.search(r"\d", constraint_str)
+    if not first_digit:
+        # Invalid version string (no numbers in it)
+        return ""
+    constraint = str_to_version(constraint_str[first_digit.start() :])
+
+    comparison_symbol = constraint_str[0 : first_digit.start()].strip()
+
+    # Default to "^" search if no matching mode specified (up to next major version)
+    if (first_digit.start() == 0) or (comparison_symbol == "^"):
+        if major(constraint) == 0:
+            # Also, julia treats pre-1.0 releases specially, as if the first
+            # non-zero number is actually a major number:
+            # https://docs.julialang.org/en/latest/stdlib/Pkg/#Caret-specifiers-1
+            # So we need to handle it separately by bumping the first non-zero
+            # enumber.
+            for i, n in enumerate(constraint):
+                if (
+                    n != 0 or i == len(constraint) - 1
+                ):  # (using the last existing number handles situations like "^0.0" or "^0")
+                    upper = constraint[0:i] + (n + 1,)
+                    break
+            return VersionRange(constraint, upper, True)
+        else:
+            return VersionRange(
+                constraint, (major(constraint) + 1,), True
+            )
+
+    # '~' matching (only allowed to bump the last present number by one)
+    if comparison_symbol == "~":
+        return VersionRange(
+            constraint,
+            constraint[:-1] + (constraint[-1] + 1,),
+            exclusive=False
+        )
+
+    # Use semver package's comparisons for everything else:
+
+    # semver requires three version numbers
+    if len(constraint) < 3:
+        while len(constraint) < 3:
+            constraint = constraint + (0,)
+        constraint_str = constraint_str[0 : first_digit.start()] + ".".join(
+            map(str, constraint)
+        )
+
+    # Convert special comparison strings to format accepted by `semver` library.
+    constraint_str = constraint_str.replace("≥", ">=").replace("≤", "<=")
+    constraint_str = re.sub(r"(^|\b)=\b", "==", constraint_str)
+
+    return SemverMatcher(constraint_str)
+
+
+class SemverMatcher:
+    """Provides a utility for using `semver` package to do version matching.
+
+    The `SemverMatcher` takes a `constraint_str` to represent a regex to
+    determine if a version tuple matches the constraint.
+
+    The matching is handled via the `semver` package.
+    """
+
+    def __init__(self, constraint_str):
+        self.constraint_str = constraint_str
+
+    def match(self, v):
+        """Check if `v` matches the constraint"""
+        while len(v) < 3:
+            v = v + (0,)
+        v_str = ".".join(map(str, v))
+        return semver.match(v_str, self.constraint_str)
+
+    def __eq__(self, rhs):
+        return self.constraint_str == rhs.constraint_str
+
+    def __repr__(self):
+        return self.constraint_str
+
+
+class VersionRange:
+    """Represents a range of release versions.
+
+    A `VersionRange` contains versions from a `lower` to `upper` bound
+    which may be inclusive (default: `exclusive=False`) or exclusive (`exclusive=True`).
+
+    A release version (represented by a tuple) can be checked to see if it
+    falls within a `VersionRange`
+    """
+
+    def __init__(self, lower, upper, exclusive=False):
+        self.lower = lower
+        self.upper = upper
+        self.exclusive = exclusive
+
+    def match(self, v):
+        """Check if `v` falls into the version range"""
+        if self.exclusive:
+            return self.lower <= v < self.upper
+        else:
+            return self.lower <= v <= self.upper
+
+    def __eq__(self, rhs):
+        return (
+            self.lower == rhs.lower
+            and self.upper == rhs.upper
+            and self.exclusive == rhs.exclusive
+        )
+
+    def __repr__(self):
+        return (
+            "["
+            + ".".join(map(str, self.lower))
+            + "-"
+            + ".".join(map(str, self.upper))
+            + (")" if self.exclusive else "]")
+        )

tests/julia/julia_version-1.0.2/verify

@@ -14,4 +14,12 @@ catch
     exit(1)
 end
 
+# Verify that kernels are not installed in home directory (issue #620)
+try
+    using IJulia
+    @assert IJulia.kerneldir() == "/srv/conda/share/jupyter/kernels"
+catch
+    exit(1)
+end
+
 exit(0)

tests/julia/julia_version-default/verify

@@ -14,4 +14,12 @@ catch
     exit(1)
 end
 
+# Verify that kernels are not installed in home directory (issue #620)
+try
+    using IJulia
+    @assert IJulia.kerneldir() == "/srv/conda/share/jupyter/kernels"
+catch
+    exit(1)
+end
+
 exit(0)

tests/unit/test_semver.py

@@ -0,0 +1,210 @@
+from repo2docker.buildpacks.julia import semver
+
+
+def test_str_to_version():
+    assert semver.str_to_version("1.5.2") == (1, 5, 2)
+    assert semver.str_to_version("1") == (1,)
+
+
+def test_major_minor_patch():
+    V = (1, 2, 3)
+    assert (semver.major(V), semver.minor(V), semver.patch(V)) == (1, 2, 3)
+    assert semver.major((1,)) == 1
+    assert semver.minor((1,)) == 0
+    assert semver.patch((1,)) == 0
+
+
+def test_simple_matches():
+    assert repr(semver.create_semver_matcher("1.2.5")) == "[1.2.5-2)"
+    assert repr(semver.create_semver_matcher("1.2.5")) == "[1.2.5-2)"
+    assert repr(semver.create_semver_matcher("^1.2.3")) == "[1.2.3-2)"
+    assert repr(semver.create_semver_matcher("^1.2")) == "[1.2-2)"
+    assert repr(semver.create_semver_matcher("^1")) == "[1-2)"
+    assert repr(semver.create_semver_matcher("^0.2.3")) == "[0.2.3-0.3)"
+    assert repr(semver.create_semver_matcher("^0.0.3")) == "[0.0.3-0.0.4)"
+    assert repr(semver.create_semver_matcher("^0.0")) == "[0.0-0.1)"
+    assert repr(semver.create_semver_matcher("^0")) == "[0-1)"
+    # This one seems wrong: `~1.2.3 = [1.2.3, 1.2.4)` but ~ is special in Julia
+    # from https://docs.julialang.org/en/latest/stdlib/Pkg/#Tilde-specifiers-1
+    assert repr(semver.create_semver_matcher("~1.2.3")) == "[1.2.3-1.2.4]"
+    assert repr(semver.create_semver_matcher("~1.3.5")) == "[1.3.5-1.3.6]"
+    assert repr(semver.create_semver_matcher("~1.2")) == "[1.2-1.3]"
+    assert repr(semver.create_semver_matcher("~1")) == "[1-2]"
+
+
+def test_range_matches():
+    assert semver.create_semver_matcher(
+        "1.2.3"
+    ) == semver.create_semver_matcher("^1.2.3")
+    assert semver.create_semver_matcher(
+        "1.2.3"
+    ) == semver.create_semver_matcher("^1.2.3")
+    assert semver.create_semver_matcher("1.2") == semver.create_semver_matcher(
+        "^1.2"
+    )
+    assert semver.create_semver_matcher("1") == semver.create_semver_matcher(
+        "^1"
+    )
+    assert semver.create_semver_matcher(
+        "0.0.3"
+    ) == semver.create_semver_matcher("^0.0.3")
+    assert semver.create_semver_matcher("0") == semver.create_semver_matcher(
+        "^0"
+    )
+
+
+def test_match_particular_version():
+    assert semver.create_semver_matcher("1.2.3").match(
+        semver.str_to_version("1.5.2")
+    )
+    assert semver.create_semver_matcher("1.2.3").match(
+        semver.str_to_version("1.2.3")
+    )
+    assert (
+        semver.create_semver_matcher("1.2.3").match(
+            semver.str_to_version("2.0.0")
+        )
+        == False
+    )
+    assert (
+        semver.create_semver_matcher("1.2.3").match(
+            semver.str_to_version("1.2.2")
+        )
+        == False
+    )
+    assert semver.create_semver_matcher("~1.2.3").match(
+        semver.str_to_version("1.2.4")
+    )
+    assert semver.create_semver_matcher("~1.2.3").match(
+        semver.str_to_version("1.2.3")
+    )
+    assert (
+        semver.create_semver_matcher("~1.2.3").match(
+            semver.str_to_version("1.3")
+        )
+        == False
+    )
+    assert semver.create_semver_matcher("1.2").match(
+        semver.str_to_version("1.2.0")
+    )
+    assert semver.create_semver_matcher("1.2").match(
+        semver.str_to_version("1.9.9")
+    )
+    assert (
+        semver.create_semver_matcher("1.2").match(
+            semver.str_to_version("2.0.0")
+        )
+        == False
+    )
+    assert (
+        semver.create_semver_matcher("1.2").match(
+            semver.str_to_version("1.1.9")
+        )
+        == False
+    )
+    assert semver.create_semver_matcher("0.2.3").match(
+        semver.str_to_version("0.2.3")
+    )
+    assert (
+        semver.create_semver_matcher("0.2.3").match(
+            semver.str_to_version("0.3.0")
+        )
+        == False
+    )
+    assert (
+        semver.create_semver_matcher("0.2.3").match(
+            semver.str_to_version("0.2.2")
+        )
+        == False
+    )
+    assert semver.create_semver_matcher("0").match(
+        semver.str_to_version("0.0.0")
+    )
+    assert semver.create_semver_matcher("0").match(
+        semver.str_to_version("0.99.0")
+    )
+    assert (
+        semver.create_semver_matcher("0").match(semver.str_to_version("1.0.0"))
+        == False
+    )
+    assert semver.create_semver_matcher("0.0").match(
+        semver.str_to_version("0.0.0")
+    )
+    assert semver.create_semver_matcher("0.0").match(
+        semver.str_to_version("0.0.99")
+    )
+    assert (
+        semver.create_semver_matcher("0.0").match(
+            semver.str_to_version("0.1.0")
+        )
+        == False
+    )
+
+
+def test_less_than_prefix():
+    assert repr(semver.create_semver_matcher("<1.2.3")) == "<1.2.3"
+    assert repr(semver.create_semver_matcher("<1")) == "<1.0.0"
+    assert repr(semver.create_semver_matcher("<0.2.3")) == "<0.2.3"
+
+    assert semver.create_semver_matcher("<2.0.3").match(
+        semver.str_to_version("2.0.2")
+    )
+    assert semver.create_semver_matcher("<2").match(
+        semver.str_to_version("0.0.1")
+    )
+    assert semver.create_semver_matcher("<2.0.3").match(
+        semver.str_to_version("0.2.3")
+    )
+    assert (
+        semver.create_semver_matcher("<0.2.4").match(
+            semver.str_to_version("0.2.4")
+        )
+        == False
+    )
+
+
+def test_equal_prefix():
+    assert repr(semver.create_semver_matcher("=1.2.3")) == "==1.2.3"
+    assert repr(semver.create_semver_matcher("=1.2")) == "==1.2.0"
+    assert repr(semver.create_semver_matcher("  =1")) == "==1.0.0"
+    assert semver.create_semver_matcher("=1.2.3").match(
+        semver.str_to_version("1.2.3")
+    )
+    assert (
+        semver.create_semver_matcher("=1.2.3").match(
+            semver.str_to_version("1.2.4")
+        )
+        == False
+    )
+    assert (
+        semver.create_semver_matcher("=1.2.3").match(
+            semver.str_to_version("1.2.2")
+        )
+        == False
+    )
+
+
+def test_fancy_unicode():
+    assert semver.create_semver_matcher(
+        "≥1.3.0"
+    ) == semver.create_semver_matcher(">=1.3.0")
+
+
+def test_largerthan_equal():
+    assert repr(semver.create_semver_matcher(">=   1.2.3")) == ">=   1.2.3"
+    assert repr(semver.create_semver_matcher("  >=  1")) == ">=  1.0.0"
+    assert semver.create_semver_matcher(">=1").match(
+        semver.str_to_version("1.0.0")
+    )
+    assert semver.create_semver_matcher(">=0").match(
+        semver.str_to_version("0.0.1")
+    )
+    assert semver.create_semver_matcher(">=1.2.3").match(
+        semver.str_to_version("1.2.3")
+    )
+    assert (
+        semver.create_semver_matcher(">=1.2.3").match(
+            semver.str_to_version("1.2.2")
+        )
+        == False
+    )