fixing conflict

.travis.yml

@@ -16,7 +16,11 @@ install:
 script:
   # cd into tests so CWD being repo2docker does not hide
   # possible issues with MANIFEST.in
-  - cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE}
+  - if [ ${REPO_TYPE} == "r" ];
+    then cd tests && travis_wait pytest --cov repo2docker -v ${REPO_TYPE};
+    else cd tests && travis_retry pytest --cov repo2docker -v ${REPO_TYPE};
+    fi
+
 after_success:
   - pip install codecov
   - codecov

docs/source/faq.md

@@ -9,6 +9,19 @@ If you have a question & have found an answer, send a PR to add it here!
 Currently the best way to do this is by using a conda ``environment.yml``
 file and setting the language to whichever version of Python you like.
 
+## Can I add executable files to the user's PATH?
+
+Yes! Using a ``postBuild`` file, you can place any files that should be called
+from the command line in the folder ``~/.local/``. This folder will be
+available in a user's PATH, and can be run from the command line (or as
+a subsequent build step.)
+
+## How do I set environment variables?
+
+Use the `-e` or `--env` flag for each variable that you want to define.
+
+For example `jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...`
+
 ## Can I use repo2docker to bootstrap my own Dockerfile?
 
 No, you can't.
@@ -24,9 +37,3 @@ or similar traditional docker command.
 
 Check out the [binder-examples](http://github.com/binder-examples/) github
 organization for example Dockerfiles you can copy & modify for your own use!
-
-## How do I set environment variables?
-
-Use the `-e` or `--env` flag for each variable that you want to define.
-
-For example `jupyter-repo2docker -e VAR1=val1 -e VAR2=val2 ...` 

docs/source/index.rst

@@ -5,6 +5,11 @@ jupyter-repo2docker
 images from source code repositories. See the list below for various
 ways in which you can use ``repo2docker``.
 
+Please report `Bugs <https://github.com/jupyter/repo2docker/issues>`_,
+`ask questions <https://gitter.im/jupyterhub/binder>`_ or
+`contribute to the project <https://github.com/jupyter/repo2docker/blob/master/CONTRIBUTING.md>`_.
+
+
 Site Contents
 -------------
 .. toctree::
@@ -17,4 +22,3 @@ Site Contents
    design
    architecture
    dev_newbuildpack
-

repo2docker/app.py

@@ -29,7 +29,7 @@ from traitlets.config import Application
 from . import __version__
 from .buildpacks import (
     PythonBuildPack, DockerBuildPack, LegacyBinderDockerBuildPack,
-    CondaBuildPack, JuliaBuildPack, Python2BuildPack, BaseImage,
+    CondaBuildPack, JuliaBuildPack, BaseImage,
     RBuildPack
 )
 from .utils import (
@@ -66,9 +66,8 @@ class Repo2Docker(Application):
             LegacyBinderDockerBuildPack,
             DockerBuildPack,
             JuliaBuildPack,
-            CondaBuildPack,
-            Python2BuildPack,
             RBuildPack,
+            CondaBuildPack,
             PythonBuildPack,
         ],
         config=True,

repo2docker/buildpacks/__init__.py

@@ -1,5 +1,5 @@
 from .base import BuildPack, BaseImage
-from .python import Python2BuildPack, PythonBuildPack
+from .python import PythonBuildPack
 from .conda import CondaBuildPack
 from .julia import JuliaBuildPack
 from .docker import DockerBuildPack

repo2docker/buildpacks/base.py

@@ -9,7 +9,10 @@ import docker
 import sys
 
 TEMPLATE = r"""
-FROM buildpack-deps:artful
+FROM buildpack-deps:bionic
+
+# avoid prompts from apt
+ENV DEBIAN_FRONTEND=noninteractive
 
 # Set up locales properly
 RUN apt-get update && \
@@ -198,7 +201,10 @@ class BuildPack:
         Just sets the PATH environment variable. Separated out since
         it is very commonly set by various buildpacks.
         """
-        return []
+        # Allow local user installs into ~/.local, which is where the
+        # XDG desktop standard suggests these should be
+        # See https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html
+        return ['$HOME/.local/bin']
 
     def get_labels(self):
         """

repo2docker/buildpacks/conda/__init__.py

@@ -25,17 +25,26 @@ class CondaBuildPack(BaseImage):
         the `NB_PYTHON_PREFIX` to the location of the jupyter binary.
 
         """
-        return super().get_env() + [
+        env = super().get_env() + [
             ('CONDA_DIR', '${APP_BASE}/conda'),
             ('NB_PYTHON_PREFIX', '${CONDA_DIR}'),
         ]
+        if self.py2:
+            env.append(('KERNEL_PYTHON_PREFIX', '${CONDA_DIR}/envs/kernel'))
+        else:
+            env.append(('KERNEL_PYTHON_PREFIX', '${NB_PYTHON_PREFIX}'))
+        return env
 
     def get_path(self):
         """Return paths (including conda environment path) to be added to
         the PATH environment variable.
 
         """
-        return super().get_path() + ['${CONDA_DIR}/bin']
+        path = super().get_path()
+        if self.py2:
+            path.insert(0, '${KERNEL_PYTHON_PREFIX}/bin')
+        path.insert(0, '${CONDA_DIR}/bin')
+        return path
 
     def get_build_scripts(self):
         """
@@ -127,6 +136,12 @@ class CondaBuildPack(BaseImage):
             py_version = None
             with open(environment_yml) as f:
                 env = YAML().load(f)
+                # check if the env file is empty, if so instantiate an empty dictionary.
+                if env is None:
+                    env = {}
+                # check if the env file has a dictionary not a list or other data structure.
+                if not isinstance(env, dict):
+                    raise TypeError("environment.yml should contain a dictionary. Got %r" % type(env))
                 for dep in env.get('dependencies', []):
                     if not isinstance(dep, str):
                         continue

repo2docker/buildpacks/conda/environment.frozen.yml

@@ -1,23 +1,24 @@
 # AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2018-04-02 07:27:43 UTC
+# Frozen on 2018-05-08 20:22:20 UTC
 name: r2d
 channels:
   - conda-forge
   - defaults
   - conda-forge/label/broken
 dependencies:
+  - backcall=0.1.0=py_0
   - bleach=2.1.3=py_0
-  - ca-certificates=2018.1.18=0
+  - ca-certificates=2018.4.16=0
-  - certifi=2018.1.18=py36_0
+  - certifi=2018.4.16=py36_0
-  - decorator=4.2.1=py36_0
+  - decorator=4.3.0=py_0
   - entrypoints=0.2.3=py36_1
   - gmp=6.1.2=0
   - html5lib=1.0.1=py_0
   - ipykernel=4.8.2=py36_0
-  - ipython=6.2.1=py36_1
+  - ipython=6.3.1=py36_0
   - ipython_genutils=0.2.0=py36_0
   - ipywidgets=7.1.1=py36_0
-  - jedi=0.11.1=py36_0
+  - jedi=0.12.0=py36_0
   - jinja2=2.10=py36_0
   - jsonschema=2.6.0=py36_1
   - jupyter_client=5.2.3=py36_0
@@ -26,27 +27,27 @@ dependencies:
   - jupyterlab_launcher=0.10.5=py36_0
   - libsodium=1.0.16=0
   - markupsafe=1.0=py36_0
-  - mistune=0.8.3=py_0
+  - mistune=0.8.3=py36_1
   - nbconvert=5.3.1=py_1
   - nbformat=4.4.0=py36_0
   - ncurses=5.9=10
   - notebook=5.4.1=py36_0
-  - openssl=1.0.2n=0
+  - openssl=1.0.2o=0
-  - pandoc=2.1.3=0
+  - pandoc=2.2=0
-  - pandocfilters=1.4.1=py36_0
+  - pandocfilters=1.4.2=py36_0
-  - parso=0.1.1=py_0
+  - parso=0.2.0=py_0
-  - pexpect=4.4.0=py36_0
+  - pexpect=4.5.0=py36_0
   - pickleshare=0.7.4=py36_0
   - pip=9.0.3=py36_0
   - prompt_toolkit=1.0.15=py36_0
   - ptyprocess=0.5.2=py36_0
   - pygments=2.2.0=py36_0
-  - python=3.6.5=0
+  - python=3.6.5=1
   - python-dateutil=2.7.2=py_0
   - pyzmq=17.0.0=py36_4
   - readline=7.0=0
   - send2trash=1.5.0=py_0
-  - setuptools=39.0.1=py36_0
+  - setuptools=39.1.0=py36_0
   - simplegeneric=0.8.1=py36_0
   - six=1.11.0=py36_1
   - sqlite=3.20.1=2
@@ -57,12 +58,12 @@ dependencies:
   - traitlets=4.3.2=py36_0
   - wcwidth=0.1.7=py36_0
   - webencodings=0.5=py36_0
-  - wheel=0.30.0=py36_2
+  - wheel=0.31.0=py36_0
-  - widgetsnbextension=3.2.0=py36_0
+  - widgetsnbextension=3.2.1=py36_0
   - xz=5.2.3=0
   - zeromq=4.2.5=1
   - zlib=1.2.11=0
   - pip:
-    - nteract-on-jupyter==1.6.0
+    - nteract-on-jupyter==1.7.0
 prefix: /opt/conda/envs/r2d
 

repo2docker/buildpacks/conda/environment.py-2.7.frozen.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.py-2.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2018-04-02 07:21:15 UTC
+# Frozen on 2018-05-08 20:15:09 UTC
 name: r2d
 channels:
   - conda-forge
@@ -9,31 +9,31 @@ dependencies:
   - backports=1.0=py27_1
   - backports.shutil_get_terminal_size=1.0.0=py_3
   - backports_abc=0.5=py27_0
-  - ca-certificates=2018.1.18=0
+  - ca-certificates=2018.4.16=0
-  - certifi=2018.1.18=py27_0
+  - certifi=2018.4.16=py27_0
-  - decorator=4.2.1=py27_0
+  - decorator=4.3.0=py_0
   - enum34=1.1.6=py27_1
   - ipykernel=4.8.2=py27_0
-  - ipython=5.5.0=py27_0
+  - ipython=5.6.0=py27_0
   - ipython_genutils=0.2.0=py27_0
   - jupyter_client=5.2.3=py27_0
   - jupyter_core=4.4.0=py_0
   - libsodium=1.0.16=0
   - ncurses=5.9=10
-  - openssl=1.0.2n=0
+  - openssl=1.0.2o=0
-  - pathlib2=2.3.0=py27_0
+  - pathlib2=2.3.2=py27_0
-  - pexpect=4.4.0=py27_0
+  - pexpect=4.5.0=py27_0
   - pickleshare=0.7.4=py27_0
   - pip=9.0.3=py27_0
   - prompt_toolkit=1.0.15=py27_0
   - ptyprocess=0.5.2=py27_0
   - pygments=2.2.0=py27_0
-  - python=2.7.14=5
+  - python=2.7.15=0
   - python-dateutil=2.7.2=py_0
   - pyzmq=17.0.0=py27_4
   - readline=7.0=0
   - scandir=1.7=py27_0
-  - setuptools=39.0.1=py27_0
+  - setuptools=39.1.0=py27_0
   - simplegeneric=0.8.1=py27_0
   - singledispatch=3.4.0.3=py27_0
   - six=1.11.0=py27_1
@@ -43,7 +43,7 @@ dependencies:
   - tornado=4.5.3=py27_0
   - traitlets=4.3.2=py27_0
   - wcwidth=0.1.7=py27_0
-  - wheel=0.30.0=py27_2
+  - wheel=0.31.0=py27_0
   - zeromq=4.2.5=1
   - zlib=1.2.11=0
   - pip:

repo2docker/buildpacks/conda/environment.py-3.5.frozen.yml

@@ -1,23 +1,24 @@
 # AUTO GENERATED FROM environment.py-3.5.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2018-04-02 07:23:18 UTC
+# Frozen on 2018-05-08 20:18:13 UTC
 name: r2d
 channels:
   - conda-forge
   - defaults
   - conda-forge/label/broken
 dependencies:
+  - backcall=0.1.0=py_0
   - bleach=2.1.3=py_0
-  - ca-certificates=2018.1.18=0
+  - ca-certificates=2018.4.16=0
-  - certifi=2018.1.18=py35_0
+  - certifi=2018.4.16=py35_0
-  - decorator=4.2.1=py35_0
+  - decorator=4.3.0=py_0
   - entrypoints=0.2.3=py35_1
   - gmp=6.1.2=0
   - html5lib=1.0.1=py_0
   - ipykernel=4.8.2=py35_0
-  - ipython=6.2.1=py35_1
+  - ipython=6.3.1=py35_0
   - ipython_genutils=0.2.0=py35_0
   - ipywidgets=7.1.1=py35_0
-  - jedi=0.11.1=py35_0
+  - jedi=0.12.0=py35_0
   - jinja2=2.10=py35_0
   - jsonschema=2.6.0=py35_1
   - jupyter_client=5.2.3=py35_0
@@ -26,27 +27,27 @@ dependencies:
   - jupyterlab_launcher=0.10.5=py35_0
   - libsodium=1.0.16=0
   - markupsafe=1.0=py35_0
-  - mistune=0.8.3=py_0
+  - mistune=0.8.3=py35_1
   - nbconvert=5.3.1=py_1
   - nbformat=4.4.0=py35_0
   - ncurses=5.9=10
   - notebook=5.4.1=py35_0
-  - openssl=1.0.2n=0
+  - openssl=1.0.2o=0
-  - pandoc=2.1.3=0
+  - pandoc=2.2=0
-  - pandocfilters=1.4.1=py35_0
+  - pandocfilters=1.4.2=py35_0
-  - parso=0.1.1=py_0
+  - parso=0.2.0=py_0
-  - pexpect=4.4.0=py35_0
+  - pexpect=4.5.0=py35_0
   - pickleshare=0.7.4=py35_0
   - pip=9.0.3=py35_0
   - prompt_toolkit=1.0.15=py35_0
   - ptyprocess=0.5.2=py35_0
   - pygments=2.2.0=py35_0
-  - python=3.5.5=0
+  - python=3.5.5=1
   - python-dateutil=2.7.2=py_0
   - pyzmq=17.0.0=py35_4
   - readline=7.0=0
   - send2trash=1.5.0=py_0
-  - setuptools=39.0.1=py35_0
+  - setuptools=39.1.0=py35_0
   - simplegeneric=0.8.1=py35_0
   - six=1.11.0=py35_1
   - sqlite=3.20.1=2
@@ -57,12 +58,12 @@ dependencies:
   - traitlets=4.3.2=py35_0
   - wcwidth=0.1.7=py35_0
   - webencodings=0.5=py35_0
-  - wheel=0.30.0=py35_2
+  - wheel=0.31.0=py35_0
-  - widgetsnbextension=3.2.0=py35_0
+  - widgetsnbextension=3.2.1=py35_0
   - xz=5.2.3=0
   - zeromq=4.2.5=1
   - zlib=1.2.11=0
   - pip:
-    - nteract-on-jupyter==1.6.0
+    - nteract-on-jupyter==1.7.0
 prefix: /opt/conda/envs/r2d
 

repo2docker/buildpacks/conda/environment.py-3.6.frozen.yml

@@ -1,23 +1,24 @@
 # AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2018-04-02 07:27:43 UTC
+# Frozen on 2018-05-08 20:22:20 UTC
 name: r2d
 channels:
   - conda-forge
   - defaults
   - conda-forge/label/broken
 dependencies:
+  - backcall=0.1.0=py_0
   - bleach=2.1.3=py_0
-  - ca-certificates=2018.1.18=0
+  - ca-certificates=2018.4.16=0
-  - certifi=2018.1.18=py36_0
+  - certifi=2018.4.16=py36_0
-  - decorator=4.2.1=py36_0
+  - decorator=4.3.0=py_0
   - entrypoints=0.2.3=py36_1
   - gmp=6.1.2=0
   - html5lib=1.0.1=py_0
   - ipykernel=4.8.2=py36_0
-  - ipython=6.2.1=py36_1
+  - ipython=6.3.1=py36_0
   - ipython_genutils=0.2.0=py36_0
   - ipywidgets=7.1.1=py36_0
-  - jedi=0.11.1=py36_0
+  - jedi=0.12.0=py36_0
   - jinja2=2.10=py36_0
   - jsonschema=2.6.0=py36_1
   - jupyter_client=5.2.3=py36_0
@@ -26,27 +27,27 @@ dependencies:
   - jupyterlab_launcher=0.10.5=py36_0
   - libsodium=1.0.16=0
   - markupsafe=1.0=py36_0
-  - mistune=0.8.3=py_0
+  - mistune=0.8.3=py36_1
   - nbconvert=5.3.1=py_1
   - nbformat=4.4.0=py36_0
   - ncurses=5.9=10
   - notebook=5.4.1=py36_0
-  - openssl=1.0.2n=0
+  - openssl=1.0.2o=0
-  - pandoc=2.1.3=0
+  - pandoc=2.2=0
-  - pandocfilters=1.4.1=py36_0
+  - pandocfilters=1.4.2=py36_0
-  - parso=0.1.1=py_0
+  - parso=0.2.0=py_0
-  - pexpect=4.4.0=py36_0
+  - pexpect=4.5.0=py36_0
   - pickleshare=0.7.4=py36_0
   - pip=9.0.3=py36_0
   - prompt_toolkit=1.0.15=py36_0
   - ptyprocess=0.5.2=py36_0
   - pygments=2.2.0=py36_0
-  - python=3.6.5=0
+  - python=3.6.5=1
   - python-dateutil=2.7.2=py_0
   - pyzmq=17.0.0=py36_4
   - readline=7.0=0
   - send2trash=1.5.0=py_0
-  - setuptools=39.0.1=py36_0
+  - setuptools=39.1.0=py36_0
   - simplegeneric=0.8.1=py36_0
   - six=1.11.0=py36_1
   - sqlite=3.20.1=2
@@ -57,12 +58,12 @@ dependencies:
   - traitlets=4.3.2=py36_0
   - wcwidth=0.1.7=py36_0
   - webencodings=0.5=py36_0
-  - wheel=0.30.0=py36_2
+  - wheel=0.31.0=py36_0
-  - widgetsnbextension=3.2.0=py36_0
+  - widgetsnbextension=3.2.1=py36_0
   - xz=5.2.3=0
   - zeromq=4.2.5=1
   - zlib=1.2.11=0
   - pip:
-    - nteract-on-jupyter==1.6.0
+    - nteract-on-jupyter==1.7.0
 prefix: /opt/conda/envs/r2d
 

repo2docker/buildpacks/conda/environment.yml

@@ -5,4 +5,4 @@ dependencies:
   - tornado==4.5.3
   - notebook==5.4.1
   - pip:
-    - nteract_on_jupyter==1.6.0
+    - nteract_on_jupyter==1.7.0

repo2docker/buildpacks/conda/install-miniconda.bash

@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-CONDA_VERSION=4.3.30
+CONDA_VERSION=4.5.1
 URL="https://repo.continuum.io/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/miniconda-installer.sh
 
@@ -12,7 +12,7 @@ chmod +x ${INSTALLER_PATH}
 
 # Only MD5 checksums are available for miniconda
 # Can be obtained from https://repo.continuum.io/miniconda/
-MD5SUM="0b80a152332a4ce5250f3c09589c7a81"
+MD5SUM="0c28787e3126238df24c5d4858bd0744"
 
 if ! echo "${MD5SUM}  ${INSTALLER_PATH}" | md5sum  --quiet -c -; then
     echo "md5sum mismatch for ${INSTALLER_PATH}, exiting!"

repo2docker/buildpacks/legacy/__init__.py

@@ -23,7 +23,7 @@ class LegacyBinderDockerBuildPack(DockerBuildPack):
     RUN conda install -yq conda>=4.3 && \
         conda install -yq conda==4.4.11 && \
         conda env update -n python3 -f /tmp/python3.frozen.yml && \
-        conda remove -yq -n python3 nb_conda_kernels && \
+        conda remove -yq -n python3 nb_conda_kernels _nb_ext_conf && \
         conda env update -n root -f /tmp/root.frozen.yml && \
         /home/main/anaconda2/envs/python3/bin/ipython kernel install --sys-prefix && \
         /home/main/anaconda2/bin/ipython kernel install --prefix=/home/main/anaconda2/envs/python3 && \

repo2docker/buildpacks/python/__init__.py

@@ -1,139 +1,70 @@
 """Generates Dockerfiles based on an input matrix based on Python."""
 import os
 
-from ..base import BaseImage
+from ..conda import CondaBuildPack
 
 
-class PythonBuildPack(BaseImage):
+class PythonBuildPack(CondaBuildPack):
-    """Setup Python 3 for use with a repository."""
+    """Setup Python for use with a repository."""
-    def get_packages(self):
-        """Return a list of the Python 3 core language packages to be installed
-           via apt-get for this BuildPack.
 
-           Note: The packages specified here are for the core Python3 language.
+    @property
-           Third party libraries are specified in other configuration files.
+    def python_version(self):
+        if hasattr(self, '_python_version'):
+            return self._python_version
 
-        """
+        try:
-        return super().get_packages().union({
+            with open(self.binder_path('runtime.txt')) as f:
-            'python3',
+                runtime = f.read().strip()
-            'python3-venv',
+        except FileNotFoundError:
-            'python3-dev',
+            runtime = ''
-        })
 
-    def get_env(self):
+        if not runtime.startswith('python-'):
-        """
+            # not a Python runtime (e.g. R, which subclasses this)
-        Return environment variables to be set.
+            # use the default Python
+            self._python_version = self.major_pythons['3']
+            return self._python_version
 
-        We set `VENV_PATH` to the virtual environment location and
+        py_version_info = runtime.split('-', 1)[1].split('.')
-        the `NB_PYTHON_PREFIX` to the location of the jupyter binary.
+        py_version = ''
-
+        if len(py_version_info) == 1:
-        """
+            py_version = self.major_pythons[py_version_info[0]]
-        return super().get_env() + [
+        else:
-            ("VENV_PATH", "${APP_BASE}/venv"),
+            # get major.minor
-            # Prefix to use for installing kernels and finding jupyter binary
+            py_version = '.'.join(py_version_info[:2])
-            ("NB_PYTHON_PREFIX", "${VENV_PATH}"),
+        self._python_version = py_version
-        ]
+        return self._python_version
-
-    def get_path(self):
-        """Return paths (including virtual environment path) to be added to
-        the PATH environment variable.
-
-        """
-        return super().get_path() + [
-            "${VENV_PATH}/bin"
-        ]
-
-    def get_build_script_files(self):
-        """
-        Dict of files to be copied to the container image for use in building.
-
-        This is copied before the `build_scripts` & `assemble_scripts` are
-        run, so can be executed from either of them.
-
-        It's a dictionary where the key is the source file path in the host
-        system, and the value is the destination file path inside the
-        container image.
-
-        This currently adds a frozen set of Python 3 requirements to the dict
-        of files.
-
-        """
-        files = {
-            'python/requirements.frozen.txt': '/tmp/requirements.frozen.txt',
-        }
-        files.update(super().get_build_script_files())
-        return files
-
-    def get_build_scripts(self):
-        """
-        Return series of build-steps common to all Python 3 repositories.
-
-        All scripts here should be independent of contents of the repository.
-
-        This sets up:
-
-        - a directory for the virtual environment and its ownership by the
-          notebook user
-        - a Python 3 interpreter for the virtual environement
-        - a Python 3 jupyter kernel including a base set of requirements
-        - support for Jupyter widgets
-        - support for JupyterLab
-        - support for nteract
-
-        """
-        return super().get_build_scripts() + [
-            (
-                "root",
-                r"""
-                mkdir -p ${VENV_PATH} && \
-                chown -R ${NB_USER}:${NB_USER} ${VENV_PATH}
-                """
-            ),
-            (
-                "${NB_USER}",
-                r"""
-                python3 -m venv ${VENV_PATH}
-                """
-            ),
-            (
-                "${NB_USER}",
-                r"""
-                pip install --no-cache-dir -r /tmp/requirements.frozen.txt && \
-                jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
-                jupyter serverextension enable --py jupyterlab --sys-prefix && \
-                jupyter serverextension enable nteract_on_jupyter --sys-prefix
-                """
-            )
-        ]
 
     def get_assemble_scripts(self):
         """Return series of build-steps specific to this repository.
         """
         # If we have a runtime.txt & that's set to python-2.7,
-        # we will *not* install requirements.txt but will find &
+        # requirements.txt will be installed in the *kernel* env
-        # install a requirements3.txt file if it exists.
+        # and requirements3.txt (if it exists)
-        # This way, when using python2 venv, requirements.txt will
+        # will be installed in the python 3 notebook server env.
-        # be installed in the python2 venv, and requirements3.txt
-        # will be installed in python3 venv. This is less of a
-        # surprise than requiring python2 to be requirements2.txt tho.
         assemble_scripts = super().get_assemble_scripts()
         setup_py = 'setup.py'
-        try:
+        # KERNEL_PYTHON_PREFIX is the env with the kernel,
-            with open(self.binder_path('runtime.txt')) as f:
+        # whether it's distinct from the notebook or the same.
-                runtime = f.read().strip()
+        pip = '${KERNEL_PYTHON_PREFIX}/bin/pip'
-        except FileNotFoundError:
+        if self.py2:
-            runtime = 'python-3.5'
+            # using python 2 kernel,
-        if runtime == 'python-2.7':
+            # requirements3.txt allows installation in the notebook server env
-            pip = "pip2"
+            nb_requirements_file = self.binder_path('requirements3.txt')
-            requirements_file = self.binder_path('requirements3.txt')
+            if os.path.exists(nb_requirements_file):
-        else:
+                assemble_scripts.append((
-            pip = "pip3"
+                    '${NB_USER}',
-            requirements_file = self.binder_path('requirements.txt')
+                    '${NB_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "{}"'.format(nb_requirements_file)
+                ))
+
+        # install requirements.txt in the kernel env
+        requirements_file = self.binder_path('requirements.txt')
         if os.path.exists(requirements_file):
             assemble_scripts.append((
                 '${NB_USER}',
-                'pip3 install --no-cache-dir -r "{}"'.format(requirements_file)
+                '{} install --no-cache-dir -r "{}"'.format(pip, requirements_file)
             ))
+
+        # setup.py exists *and* binder dir is not used
         if not os.path.exists('binder') and os.path.exists(setup_py):
             assemble_scripts.append((
                 '${NB_USER}',
@@ -142,7 +73,7 @@ class PythonBuildPack(BaseImage):
         return assemble_scripts
 
     def detect(self):
-        """Check if current repo should be built with the Python 3 Build pack.
+        """Check if current repo should be built with the Python buildpack.
         """
         requirements_txt = self.binder_path('requirements.txt')
         runtime_txt = self.binder_path('runtime.txt')
@@ -151,136 +82,10 @@ class PythonBuildPack(BaseImage):
         if os.path.exists(runtime_txt):
             with open(runtime_txt) as f:
                 runtime = f.read().strip()
-            if runtime.startswith("python-3"):
+            if runtime.startswith("python-"):
                 return True
             else:
                 return False
         if not os.path.exists('binder') and os.path.exists(setup_py):
             return True
         return os.path.exists(requirements_txt)
-
-
-class Python2BuildPack(PythonBuildPack):
-    """Setup Python 2 for use with a repository."""
-    def get_packages(self):
-        """Return a list of the Python 2 core language packages to be installed
-           via apt-get for this BuildPack.
-
-           Note: The packages specified here are for the core Python2 language.
-           Third party libraries are specified in other configuration files.
-
-        """
-        return super().get_packages().union({
-            'python',
-            'python-dev',
-            'virtualenv'
-        })
-
-    def get_env(self):
-        """
-        Return environment variables to be set.
-
-        We set `VENV_PATH` to the virtual environment location containing
-        Python 2.
-
-        """
-        return super().get_env() + [
-            ('VENV2_PATH', '${APP_BASE}/venv2')
-        ]
-
-    def get_path(self):
-        """Return paths (including virtual environment path) to be added to
-        the PATH environment variable.
-
-        """
-        return super().get_path() + [
-            "${VENV2_PATH}/bin"
-        ]
-
-    def get_build_script_files(self):
-        """
-        Dict of files to be copied to the container image for use in building.
-
-        This is copied before the `build_scripts` & `assemble_scripts` are
-        run, so can be executed from either of them.
-
-        It's a dictionary where the key is the source file path in the host
-        system, and the value is the destination file path inside the
-        container image.
-
-        This currently adds a frozen set of Python 2 requirements to the dict
-        of files.
-
-        """
-        files = {
-            'python/requirements2.frozen.txt': '/tmp/requirements2.frozen.txt',
-        }
-        files.update(super().get_build_script_files())
-        return files
-
-    def get_build_scripts(self):
-        """
-        Return series of build-steps common to all Python 2 repositories.
-
-        All scripts here should be independent of contents of the repository.
-
-        This sets up:
-
-        - a directory for the virtual environment and its ownership by the
-          notebook user
-        - a Python 2 interpreter for the virtual environement
-        - a Python 2 jupyter kernel
-
-        """
-        return super().get_build_scripts() + [
-            (
-                "root",
-                r"""
-                mkdir -p ${VENV2_PATH} && \
-                chown -R ${NB_USER}:${NB_USER} ${VENV2_PATH}
-                """
-            ),
-            (
-                "${NB_USER}",
-                r"""
-                virtualenv -p python2 ${VENV2_PATH}
-                """
-            ),
-            (
-                "${NB_USER}",
-                r"""
-                pip2 install --no-cache-dir -r /tmp/requirements2.frozen.txt && \
-                python2 -m ipykernel install --prefix=${NB_PYTHON_PREFIX}
-                """
-            )
-        ]
-
-    def get_assemble_scripts(self):
-        """Return series of build-steps specific to this repository.
-        """
-        requirements_txt = self.binder_path('requirements.txt')
-        assemble_scripts = super().get_assemble_scripts()
-        if os.path.exists(requirements_txt):
-            assemble_scripts.insert(0, (
-                '${NB_USER}',
-                'pip2 install --no-cache-dir -r "{}"'.format(requirements_txt)
-            ))
-        return assemble_scripts
-
-    def detect(self):
-        """Check if current repo should be built with the Python 2 Build pack.
-        """
-        runtime_txt = self.binder_path('runtime.txt')
-
-        if os.path.exists(runtime_txt):
-            with open(runtime_txt) as f:
-                runtime = f.read().strip()
-            if runtime == 'python-2.7':
-                return True
-            elif runtime.startswith('python-2'):
-                raise ValueError(
-                    "Only python-2.7 or python-3.x is supported in "
-                    "runtime.txt, not '{}'".format(runtime_txt))
-            else:
-                return False
-        return False

repo2docker/buildpacks/python/freeze.bash

@@ -1,39 +0,0 @@
-#!/bin/bash
-set -euo pipefail
-# Freeze requirements.txt into requirements.frozen.txt, pinning all dependent library versions to
-# versions that are resolved at time of freezing.
-# Does the same for requirements2.txt to requirements2.frozen.txt...
-
-# cd to the directory where the freeze script is located
-if [[ ! -z "$(which realpath 2>/dev/null)" ]]; then
-    realpath=realpath
-else
-    realpath="readlink -f"
-fi
-
-cd $(dirname "$($realpath "$0")")
-
-
-function freeze-requirements {
-    # Freeze a requirements file $2 into a frozen requirements file $3
-    # Requires that a completely empty venv of appropriate version exist in $1
-    PYTHON_VERSION="$1"
-    REQUIREMENTS_FILE="$2"
-    FROZEN_FILE="$3"
-    if [[ $(echo ${PYTHON_VERSION} | cut -d. -f 1) == "2" ]]; then
-        VENV=virtualenv
-    else
-        VENV=venv
-    fi
-
-    echo "# AUTO GENERATED FROM ${REQUIREMENTS_FILE}, DO NOT MANUALLY MODIFY" > ${FROZEN_FILE}
-    echo "# Frozen on $(date -u)" >> ${FROZEN_FILE}
-    docker run --rm -v $PWD:/python -it python:${PYTHON_VERSION} \
-        sh -c "
-            python -m $VENV /venv
-            /venv/bin/pip install -r /python/${REQUIREMENTS_FILE} &&
-            /venv/bin/pip freeze | sort --ignore-case >> /python/${FROZEN_FILE}"
-}
-
-freeze-requirements 3.5 requirements.txt requirements.frozen.txt
-freeze-requirements 2.7 requirements2.txt requirements2.frozen.txt

repo2docker/buildpacks/python/requirements.frozen.txt

@@ -1,42 +0,0 @@
-# AUTO GENERATED FROM requirements.txt, DO NOT MANUALLY MODIFY
-# Frozen on Mon Apr  2 07:17:48 UTC 2018
-bleach==2.1.3
-decorator==4.2.1
-entrypoints==0.2.3
-html5lib==1.0.1
-ipykernel==4.8.2
-ipython-genutils==0.2.0
-ipython==6.2.1
-ipywidgets==7.1.1
-jedi==0.11.1
-Jinja2==2.10
-jsonschema==2.6.0
-jupyter-client==5.2.3
-jupyter-core==4.4.0
-jupyterlab-launcher==0.10.5
-jupyterlab==0.31.5
-MarkupSafe==1.0
-mistune==0.8.3
-nbconvert==5.3.1
-nbformat==4.4.0
-notebook==5.4.1
-nteract-on-jupyter==1.6.0
-pandocfilters==1.4.2
-parso==0.1.1
-pexpect==4.4.0
-pickleshare==0.7.4
-prompt-toolkit==1.0.15
-ptyprocess==0.5.2
-Pygments==2.2.0
-python-dateutil==2.7.2
-pyzmq==17.0.0
-Send2Trash==1.5.0
-simplegeneric==0.8.1
-six==1.11.0
-terminado==0.8.1
-testpath==0.3.1
-tornado==4.5.3
-traitlets==4.3.2
-wcwidth==0.1.7
-webencodings==0.5.1
-widgetsnbextension==3.1.4

repo2docker/buildpacks/python/requirements.txt

@@ -1,5 +0,0 @@
-notebook==5.4.1
-tornado==4.5.3
-ipywidgets==7.1.1
-jupyterlab==0.31.5
-nteract_on_jupyter==1.6.0

repo2docker/buildpacks/python/requirements2.frozen.txt

@@ -1,27 +0,0 @@
-# AUTO GENERATED FROM requirements2.txt, DO NOT MANUALLY MODIFY
-# Frozen on Mon Apr  2 07:19:00 UTC 2018
-backports-abc==0.5
-backports.shutil-get-terminal-size==1.0.0
-certifi==2018.1.18
-decorator==4.2.1
-enum34==1.1.6
-ipykernel==4.8.2
-ipython-genutils==0.2.0
-ipython==5.5.0
-jupyter-client==5.2.3
-jupyter-core==4.4.0
-pathlib2==2.3.0
-pexpect==4.4.0
-pickleshare==0.7.4
-prompt-toolkit==1.0.15
-ptyprocess==0.5.2
-Pygments==2.2.0
-python-dateutil==2.7.2
-pyzmq==17.0.0
-scandir==1.7
-simplegeneric==0.8.1
-singledispatch==3.4.0.3
-six==1.11.0
-tornado==4.5.3
-traitlets==4.3.2
-wcwidth==0.1.7

repo2docker/buildpacks/python/requirements2.txt

@@ -1,2 +0,0 @@
-ipykernel==4.8.2
-tornado==4.5.3

repo2docker/buildpacks/r.py

@@ -4,6 +4,7 @@ import datetime
 
 from .python import PythonBuildPack
 
+
 class RBuildPack(PythonBuildPack):
     """
     Setup R for use with a repository
@@ -128,6 +129,10 @@ class RBuildPack(PythonBuildPack):
         # This is MD5, because that is what RStudio download page provides!
         rstudio_checksum = '24cd11f0405d8372b4168fc9956e0386'
 
+        # Via https://www.rstudio.com/products/shiny/download-server/
+        shiny_url = 'https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb'
+        shiny_checksum = '78371a8361ba0e7fec44edd2b8e425ac'
+
         # Version of MRAN to pull devtools from.
         devtools_version = '2018-02-01'
 
@@ -155,6 +160,20 @@ class RBuildPack(PythonBuildPack):
                     rstudio_checksum=rstudio_checksum
                 )
             ),
+            (
+                "root",
+                # Install Shiny Server!
+                r"""
+                curl --silent --location --fail {url} > {deb} && \
+                echo '{checksum} {deb}' | md5sum -c - && \
+                dpkg -i {deb} && \
+                rm {deb}
+                """.format(
+                    url=shiny_url,
+                    checksum=shiny_checksum,
+                    deb='/tmp/shiny.deb'
+                )
+            ),
             (
                 "root",
                 # Set paths so that RStudio shares libraries with base R
@@ -169,7 +188,7 @@ class RBuildPack(PythonBuildPack):
                 "${NB_USER}",
                 # Install nbrsessionproxy
                 r"""
-                pip install --no-cache-dir nbrsessionproxy==0.6.1 && \
+                pip install --no-cache-dir nbrsessionproxy==0.7.0 && \
                 jupyter serverextension enable nbrsessionproxy --sys-prefix && \
                 jupyter nbextension install --py nbrsessionproxy --sys-prefix && \
                 jupyter nbextension enable --py nbrsessionproxy --sys-prefix
@@ -186,7 +205,16 @@ class RBuildPack(PythonBuildPack):
                     devtools_version=devtools_version,
                     irkernel_version=irkernel_version
                 )
-            )
+            ),
+            (
+                "${NB_USER}",
+                # Install shiny library
+                r"""
+                R --quiet -e "install.packages('shiny', repos='https://mran.microsoft.com/snapshot/{}', method='libcurl')"
+                """.format(
+                    self.checkpoint_date.isoformat()
+                )
+            ),
         ]
 
     def get_assemble_scripts(self):
@@ -208,6 +236,16 @@ class RBuildPack(PythonBuildPack):
                 echo "options(repos = c(CRAN='{mran_url}'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
                 """.format(mran_url=mran_url)
             ),
+            (
+                # Not all of these locations are configurable; log_dir is
+                "root",
+                r"""
+                install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
+                install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
+                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
+                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
+                """
+            ),
         ]
 
         installR_path = self.binder_path('install.R')

setup.cfg

@@ -1,2 +1,5 @@
 [wheel]
-universal=1
+universal=1
+
+[metadata]
+license_file = LICENSE

tests/conda/simple-py2/verify

@@ -13,7 +13,7 @@ assert sorted(specs) == ['python2', 'python3'], specs.keys()
 import json
 from subprocess import check_output
 envs = json.loads(check_output(['conda', 'env', 'list', '--json']).decode('utf8'))
-assert envs == {'envs': ['/srv/conda/envs/kernel']}, envs
+assert envs == {'envs': ['/srv/conda', '/srv/conda/envs/kernel']}, envs
 
 pkgs = json.loads(check_output(['conda', 'list', '-n', 'kernel', '--json']).decode('utf8'))
 pkg_names = [pkg['name'] for pkg in pkgs]

tests/test_env_yml.py

@@ -0,0 +1,26 @@
+"""
+Test if the environment.yml is empty or it constains other data structure than a dictionary
+"""
+import os
+import sys
+import pytest
+from repo2docker import buildpacks
+
+
+def test_empty_env_yml(tmpdir):
+    tmpdir.chdir()
+    p = tmpdir.join("environment.yml")
+    p.write("")
+    bp = buildpacks.CondaBuildPack()
+    py_ver = bp.python_version
+    # If the environment.yml is empty python_version will get an empty string
+    assert py_ver == ''
+
+def test_no_dict_env_yml(tmpdir):
+    tmpdir.chdir()
+    q = tmpdir.join("environment.yml")
+    q.write("numpy\n "
+            "matplotlib\n")
+    bq = buildpacks.CondaBuildPack()
+    with pytest.raises(TypeError):
+        py_ver = bq.python_version

tests/venv/py3/README.rst

@@ -1,20 +0,0 @@
-System - Specifying runtime environments
-----------------------------------------
-
-You can specify runtime environments (such as Python 2 or 3) with a
-``runtime.txt`` file. To do so, include a line of the following form in
-your ``runtime.txt`` file:
-
-```
-python-N
-```
-
-Where ``N`` is either ``2`` or ``3``. If ``N==2``, Python 2.7 will be used.
-If ``N==3``, Python 3.6 will be used.
-
-This is an example that selects Python 3. Currently you can not use
-this to select a specific version of Python 3 (e.g. 3.4 vs 3.6). If you
-need this level of control we recommend you use a `environment.yml`.
-
-Note that you can also install Python environments using the Anaconda
-distribution by using an ``environment.yml`` file.

tests/venv/py35/runtime.txt

@@ -0,0 +1 @@
+python-3.5

tests/venv/py35/verify

@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+import sys
+
+print(sys.version_info)
+assert sys.version_info[:2] == (3, 5), sys.version

tests/venv/usr-bin/verify

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+# Verify that ~/.local/bin is on the PATH
+import os
+
+assert os.path.expanduser('~/.local/bin') in os.getenv("PATH"), os.getenv("PATH")