Merge pull request #539 from yuvipanda/v3.7

Bump default python version to 3.7

docs/source/conf.py

@@ -80,9 +80,19 @@ author = 'Project Jupyter'
 # built documents.
 #
 # The short X.Y version.
-version = '0.1'
+import repo2docker
+version = repo2docker.__version__
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = version
+
+from repo2docker.buildpacks.conda import CondaBuildPack
+
+default_python = CondaBuildPack.major_pythons['3']
+
+rst_prolog = """
+.. |default_python| replace:: **Python {default_python}**
+.. |default_python_version| replace:: {default_python}
+""".format(default_python=default_python)
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/config_files.rst

@@ -28,10 +28,9 @@ Below is a list of supported configuration files (roughly in the order of build
 ``environment.yml`` - Install a Python environment
 ==================================================
 
-``environment.yml`` is the standard configuration file used by Anaconda, conda,
-and miniconda that lets you install packages in the data analytics stack (it
-primarily installs Python packages, though can be used to install a range of
-non-Python packages as well).
+``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.
 
 .. note::
 
@@ -41,10 +40,10 @@ non-Python packages as well).
    file.
 
 You can also specify which Python version to install in your built environment
-with ``environment.yml``. By default, ``repo2docker`` **installs
-Python 3.6** with your ``environment.yml`` unless you include the version of
-Python in the file.  ``conda`` supports Python versions 3.6, 3.5, 3.4, and 2.7.
-``repo2docker`` support is best with Python 3.6, 3.5, and 2.7.
+with ``environment.yml``. By default, ``repo2docker`` installs
+|default_python| with your ``environment.yml`` unless you include the version of
+Python in this file.  ``conda`` supports all versions of Python,
+though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7.
 
 .. warning::
    If you include a Python version in a ``runtime.txt`` file in addition to your
@@ -52,6 +51,8 @@ Python in the file.  ``conda`` supports Python versions 3.6, 3.5, 3.4, and 2.7.
 
 .. _requirements.txt:
 
+.. _requirements.txt:
+
 ``requirements.txt`` - Install a Python environment
 ===================================================
 
@@ -61,6 +62,8 @@ environment. Our
 on GitHub shows a typical requirements file.
 
 
+.. _setup.py:
+
 ``setup.py`` - Install Python packages
 ======================================
 
@@ -70,6 +73,8 @@ To install your repository like a Python package, you may include a
 
 .. _REQUIRE:
 
+.. _REQUIRE:
+
 ``REQUIRE`` - Install a Julia environment
 =========================================
 
@@ -78,6 +83,8 @@ Julia repository with ``REQUIRE`` and ``environment.yml``,
 visit `binder-examples/julia-python <https://github.com/binder-examples/julia-python>`_.
 
 
+.. _install.R:
+
 ``install.R`` - Install an R/RStudio environment
 ================================================
 
@@ -87,6 +94,8 @@ To set the date of the snapshot add a runtime.txt_.
 For an example ``install.R`` file, visit our `example install.R file <https://github.com/binder-examples/r/blob/master/install.R>`_.
 
 
+.. _apt.txt:
+
 ``apt.txt`` - Install packages with apt-get
 ===========================================
 
@@ -97,6 +106,8 @@ We use ``apt.txt``, for example, to install LaTeX in our
 `example apt.txt for LaTeX <https://github.com/binder-examples/latex/blob/master/apt.txt>`_.
 
 
+.. _DESCRIPTION:
+
 ``DESCRIPTION`` - Install an R package
 ======================================
 
@@ -108,6 +119,9 @@ You also need to have a ``runtime.txt`` file that is formatted as
 ``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot of MRAN that will be
 used for your R installation.
 
+
+.. _manifest.xml:
+
 ``manifest.xml`` - Install Stencila
 ===================================
 
@@ -156,21 +170,29 @@ If you only need to run things once during the build phase use :ref:`postBuild`.
 
 
 .. TODO: Discuss runtime limits, best practices, etc.
-   Also, point to an example.
 
 .. _runtime.txt:
 
 ``runtime.txt`` - Specifying runtimes
 =====================================
 
-This allows you to control the runtime of Python or R.
+Sometimes you want to specify the version of the runtime
+(e.g. the version of Python or R),
+but the environment specification format don't let you specify this information
+(e.g. requirements.txt or install.R).
+For these cases, we have a special file, ``runtime.txt``.
+
+.. note::
+
+   ``runtime.txt`` is only supported when used with environment specifications
+   that do not already support specifying the runtime
+   (e.g. when using ``environment.yml`` for conda or ``REQUIRE`` for Julia,
+   ``runtime.txt`` will be ignored).
 
 To use python-2.7: add ``python-2.7`` in runtime.txt file.
-The repository will run in a virtualenv with
+The repository will run in an env with
 Python 2 installed. To see a full example repository, visit our
 `Python2 example <https://github.com/binder-examples/python2_runtime/blob/master/runtime.txt>`_.
-**Python versions in** ``runtime.txt`` **are ignored when** ``environment.yml`` **is
-present in the same folder**.
 
 repo2docker uses R libraries pinned to a specific snapshot on
 `MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.

docs/source/faq.rst

@@ -9,7 +9,8 @@ and have found an answer, send a PR to add it here!
 How should I specify another version of Python?
 -----------------------------------------------
 
-One can specify a Python version in the ``environment.yml`` file of a repository.
+One can specify a Python version in the ``environment.yml`` file of a repository
+or ``runtime.txt`` file if using ``requirements.txt`` instead of ``environment.yml``.
 
 What versions of Python (or R or Julia...) are supported?
 ---------------------------------------------------------
@@ -21,8 +22,8 @@ Repo2docker officially supports the following versions of Python
 (specified in your :ref:`environment.yml <environment.yml>` or
 :ref:`runtime.txt <runtime.txt>` file):
 
-- 3.7 (added in 0.7)
-- 3.6 (default)
+- 3.7 (added in 0.7, default in 0.8)
+- 3.6 (default in 0.7 and earlier)
 - 3.5
 - 2.7
 

docs/source/howto/languages.rst

@@ -16,30 +16,41 @@ you use one of the following configuration files:
 * ``requirements.txt``
 * ``environment.yml``
 
-Note that by default, the environment will have **Python 3** installed.
+.. note::
+
+  By default, the environment will have |default_python|.
+
+.. versionchanged:: 0.8
+
+  Upgraded default Python from 3.6 to 3.7.
+
 
 Specifying a version of Python
 ------------------------------
 
 To specify a specific version of Python, you have two options:
 
-* Use ``runtime.txt``. Include a line that specifies the Python version in
-  this file. This line takes the following form::
-
-    python=X.X
-
-  For example,::
-
-    python=2.7
-* Use ``environment.yml``. The Anaconda distribution also lets you define
-  the Python environment within ``environment.yml``. To do so, add ``python=X.X``
-  to your dependencies section, like so::
+* Use :ref:`environment.yml <environment.yml>`. Conda environments let you define
+  the Python version in ``environment.yml``.
+  To do so, add ``python=X.X`` to your dependencies section, like so::
 
     name: python 2.7
     dependencies:
       - python=2.7
       - numpy
 
+* Use :ref:`runtime.txt <runtime.txt>` with :ref:`requirements.txt <requirements.txt>`.
+  If you are using ``requirements.txt`` instead of ``environment.yml``,
+  you can specify the Python runtime version in a separate file called ``runtime.txt``.
+  This file contains a single line of the following form::
+
+    python-X.X
+
+  For example::
+
+    python-3.6
+
+
 The R Language
 ==============
 

repo2docker/buildpacks/conda/__init__.py

@@ -77,7 +77,7 @@ class CondaBuildPack(BaseImage):
 
     major_pythons = {
         '2': '2.7',
-        '3': '3.6',
+        '3': '3.7',
     }
 
     def get_build_script_files(self):

repo2docker/buildpacks/conda/environment.frozen.yml

@@ -1,5 +1,5 @@
-# AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2019-01-30 18:42:13 UTC
+# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
+# Frozen on 2019-02-11 20:26:36 UTC
 name: r2d
 channels:
   - conda-forge
@@ -9,65 +9,66 @@ dependencies:
   - attrs=18.2.0=py_0
   - backcall=0.1.0=py_0
   - bleach=3.1.0=py_0
+  - bzip2=1.0.6=h14c3975_1002
   - ca-certificates=2018.11.29=ha4d7672_0
-  - certifi=2018.11.29=py36_1000
+  - certifi=2018.11.29=py37_1000
   - decorator=4.3.2=py_0
   - defusedxml=0.5.0=py_1
-  - entrypoints=0.3=py36_1000
+  - entrypoints=0.3=py37_1000
   - gmp=6.1.2=hf484d3e_1000
-  - ipykernel=5.1.0=py36h24bf2e0_1002
-  - ipython=7.2.0=py36h24bf2e0_1000
+  - ipykernel=5.1.0=py37h24bf2e0_1002
+  - ipython=7.2.0=py37h24bf2e0_1000
   - ipython_genutils=0.2.0=py_1
-  - ipywidgets=7.2.1=py36_1
-  - jedi=0.13.2=py36_1000
+  - jedi=0.13.2=py37_1000
   - jinja2=2.10=py_1
-  - jsonschema=3.0.0a3=py36_1000
+  - jsonschema=3.0.0a3=py37_1000
   - jupyter_client=5.2.4=py_1
   - jupyter_core=4.4.0=py_0
-  - jupyterlab=0.34.9=py36_0
   - jupyterlab_launcher=0.13.1=py_2
   - libffi=3.2.1=hf484d3e_1005
   - libgcc-ng=7.3.0=hdf63c60_0
   - libsodium=1.0.16=h14c3975_1001
   - libstdcxx-ng=7.3.0=hdf63c60_0
-  - markupsafe=1.1.0=py36h14c3975_1000
-  - mistune=0.8.4=py36h14c3975_1000
+  - markupsafe=1.1.0=py37h14c3975_1000
+  - mistune=0.8.4=py37h14c3975_1000
   - nbconvert=5.4.0=1
   - nbformat=4.4.0=py_1
   - ncurses=6.1=hf484d3e_1002
-  - notebook=5.7.4=py36_1000
+  - notebook=5.7.4=py37_1000
   - openssl=1.0.2p=h14c3975_1002
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
-  - parso=0.3.2=py_0
-  - pexpect=4.6.0=py36_1000
-  - pickleshare=0.7.5=py36_1000
-  - pip=19.0.1=py36_0
+  - parso=0.3.3=py_0
+  - pexpect=4.6.0=py37_1000
+  - pickleshare=0.7.5=py37_1000
+  - pip=19.0.2=py37_0
   - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.8=py_0
-  - ptyprocess=0.6.0=py36_1000
+  - ptyprocess=0.6.0=py37_1000
   - pygments=2.3.1=py_0
-  - pyrsistent=0.14.9=py36h14c3975_1000
-  - python=3.6.7=hd21baee_1001
-  - python-dateutil=2.7.5=py_0
-  - pyzmq=17.1.2=py36h6afc9c9_1001
+  - pyrsistent=0.14.10=py37h14c3975_0
+  - python=3.7.1=hd21baee_1000
+  - python-dateutil=2.8.0=py_0
+  - pyzmq=17.1.2=py37h6afc9c9_1001
   - readline=7.0=hf8c457e_1001
   - send2trash=1.5.0=py_0
-  - setuptools=40.7.1=py36_0
-  - six=1.12.0=py36_1000
+  - setuptools=40.8.0=py37_0
+  - six=1.12.0=py37_1000
   - sqlite=3.26.0=h67949de_1000
-  - terminado=0.8.1=py36_1001
-  - testpath=0.4.2=py36_1000
+  - terminado=0.8.1=py37_1001
+  - testpath=0.4.2=py37_1000
   - tk=8.6.9=h84994c4_1000
-  - tornado=5.1.1=py36h14c3975_1000
-  - traitlets=4.3.2=py36_1000
+  - tornado=5.1.1=py37h14c3975_1000
+  - traitlets=4.3.2=py37_1000
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
-  - wheel=0.32.3=py36_0
-  - widgetsnbextension=3.2.1=py36_1
+  - wheel=0.32.3=py37_0
+  - widgetsnbextension=3.4.2=py37_1000
   - xz=5.2.4=h14c3975_1001
   - zeromq=4.2.5=hf484d3e_1006
   - zlib=1.2.11=h14c3975_1004
+  - ipywidgets=7.2.1=py37_0
+  - jupyterlab=0.34.9=py37_0
   - pip:
     - alembic==1.0.7
     - async-generator==1.10
@@ -77,7 +78,7 @@ dependencies:
     - mako==1.0.7
     - nteract-on-jupyter==2.0.0
     - pamela==1.0.0
-    - python-editor==1.0.3
+    - python-editor==1.0.4
     - python-oauth2==1.1.0
     - requests==2.21.0
     - sqlalchemy==1.2.17

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 2019-01-30 18:36:55 UTC
+# Frozen on 2019-02-11 20:20:33 UTC
 name: r2d
 channels:
   - conda-forge
@@ -28,16 +28,16 @@ dependencies:
   - pathlib2=2.3.3=py27_1000
   - pexpect=4.6.0=py27_1000
   - pickleshare=0.7.5=py27_1000
-  - pip=19.0.1=py27_0
+  - pip=19.0.2=py27_0
   - prompt_toolkit=1.0.15=py_1
   - ptyprocess=0.6.0=py27_1000
   - pygments=2.3.1=py_0
   - python=2.7.15=h938d71a_1006
-  - python-dateutil=2.7.5=py_0
+  - python-dateutil=2.8.0=py_0
   - pyzmq=17.1.2=py27h6afc9c9_1001
   - readline=7.0=hf8c457e_1001
   - scandir=1.9.0=py27h14c3975_1000
-  - setuptools=40.7.1=py27_0
+  - setuptools=40.8.0=py27_0
   - simplegeneric=0.8.1=py_1
   - singledispatch=3.4.0.3=py27_1000
   - six=1.12.0=py27_1000

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

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2019-01-30 18:42:13 UTC
+# Frozen on 2019-02-11 20:22:50 UTC
 name: r2d
 channels:
   - conda-forge
@@ -39,21 +39,21 @@ dependencies:
   - openssl=1.0.2p=h14c3975_1002
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
-  - parso=0.3.2=py_0
+  - parso=0.3.3=py_0
   - pexpect=4.6.0=py36_1000
   - pickleshare=0.7.5=py36_1000
-  - pip=19.0.1=py36_0
+  - pip=19.0.2=py36_0
   - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.8=py_0
   - ptyprocess=0.6.0=py36_1000
   - pygments=2.3.1=py_0
-  - pyrsistent=0.14.9=py36h14c3975_1000
+  - pyrsistent=0.14.10=py36h14c3975_0
   - python=3.6.7=hd21baee_1001
-  - python-dateutil=2.7.5=py_0
+  - python-dateutil=2.8.0=py_0
   - pyzmq=17.1.2=py36h6afc9c9_1001
   - readline=7.0=hf8c457e_1001
   - send2trash=1.5.0=py_0
-  - setuptools=40.7.1=py36_0
+  - setuptools=40.8.0=py36_0
   - six=1.12.0=py36_1000
   - sqlite=3.26.0=h67949de_1000
   - terminado=0.8.1=py36_1001
@@ -77,7 +77,7 @@ dependencies:
     - mako==1.0.7
     - nteract-on-jupyter==2.0.0
     - pamela==1.0.0
-    - python-editor==1.0.3
+    - python-editor==1.0.4
     - python-oauth2==1.1.0
     - requests==2.21.0
     - sqlalchemy==1.2.17

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

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2019-01-30 18:42:13 UTC
+# Generated on 2019-02-11 20:22:50 UTC
 dependencies:
 - python=3.6.*
 - ipywidgets==7.2.1

repo2docker/buildpacks/conda/environment.py-3.7.frozen.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2019-01-30 18:38:58 UTC
+# Frozen on 2019-02-11 20:26:36 UTC
 name: r2d
 channels:
   - conda-forge
@@ -38,21 +38,21 @@ dependencies:
   - openssl=1.0.2p=h14c3975_1002
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
-  - parso=0.3.2=py_0
+  - parso=0.3.3=py_0
   - pexpect=4.6.0=py37_1000
   - pickleshare=0.7.5=py37_1000
-  - pip=19.0.1=py37_0
+  - pip=19.0.2=py37_0
   - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.8=py_0
   - ptyprocess=0.6.0=py37_1000
   - pygments=2.3.1=py_0
-  - pyrsistent=0.14.9=py37h14c3975_1000
+  - pyrsistent=0.14.10=py37h14c3975_0
   - python=3.7.1=hd21baee_1000
-  - python-dateutil=2.7.5=py_0
+  - python-dateutil=2.8.0=py_0
   - pyzmq=17.1.2=py37h6afc9c9_1001
   - readline=7.0=hf8c457e_1001
   - send2trash=1.5.0=py_0
-  - setuptools=40.7.1=py37_0
+  - setuptools=40.8.0=py37_0
   - six=1.12.0=py37_1000
   - sqlite=3.26.0=h67949de_1000
   - terminado=0.8.1=py37_1001
@@ -78,7 +78,7 @@ dependencies:
     - mako==1.0.7
     - nteract-on-jupyter==2.0.0
     - pamela==1.0.0
-    - python-editor==1.0.3
+    - python-editor==1.0.4
     - python-oauth2==1.1.0
     - requests==2.21.0
     - sqlalchemy==1.2.17

repo2docker/buildpacks/conda/environment.py-3.7.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2019-01-30 18:38:58 UTC
+# Generated on 2019-02-11 20:26:36 UTC
 dependencies:
 - python=3.7.*
 - ipywidgets==7.2.1

repo2docker/buildpacks/conda/environment.yml

@@ -1,5 +1,5 @@
 dependencies:
-  - python=3.6.*
+  - python=3.7.*
   - ipywidgets==7.2.1
   - jupyterlab==0.34.9
   - nbconvert==5.4.0

repo2docker/buildpacks/conda/freeze.py

@@ -107,7 +107,7 @@ def set_python(py_env_file, py):
 
 if __name__ == '__main__':
     # allow specifying which Pythons to update on argv
-    pys = sys.argv[1:] or ('2.7', '3.7', '3.5', '3.6')
+    pys = sys.argv[1:] or ('2.7', '3.5', '3.6', '3.7')
     for py in pys:
         env_file = ENV_FILE_T.format(py=py)
         set_python(env_file, py)

tests/conda/requirements/verify

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import sys
 
-assert sys.version_info[:2] == (3, 6), sys.version
+assert sys.version_info[:2] == (3, 7), sys.version
 
 import numpy
 try:

tests/conda/simple-py2/verify

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import sys
 
-assert sys.version_info[:2] == (3, 6), sys.version
+assert sys.version_info[:2] == (3, 7), sys.version
 
 # verify that we have Python 2 and Python 3 kernelspecs
 from jupyter_client.kernelspec import KernelSpecManager

tests/conda/simple/verify

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import sys
 
-assert sys.version_info[:2] == (3, 6), sys.version
+assert sys.version_info[:2] == (3, 7), sys.version
 
 import numpy

tests/external/reproductions.repos.yaml

@@ -22,7 +22,7 @@
 # Test that tags work + ref is added to tag if not present
 - name: Binder Examples - Requirements
   url: https://github.com/binder-examples/requirements
-  ref: test
+  ref: python-3.7
   verify: python -c 'import matplotlib'
 # Test that custom channels and downgrades don't
 # get blocked by pinning

tests/venv/default/verify

@@ -2,7 +2,7 @@
 # Verify that the default just provides a py3 environment with jupyter
 import sys
 
-assert sys.version_info[:2] == (3, 6), sys.version
+assert sys.version_info[:2] == (3, 7), sys.version
 import jupyter
 
 with open('/tmp/appendix') as f:

tests/venv/numpy/verify

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import sys
 
-assert sys.version_info[:2] == (3, 6)
+assert sys.version_info[:2] == (3, 7)
 
 import numpy