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[MRG] install notebook in its own env (#651)
[MRG] install notebook in its own env
2 parents 7681a6c + e2c7de8 commit 9099def

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21 files changed

+119
-69
lines changed

21 files changed

+119
-69
lines changed

‎docs/source/changelog.rst‎

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@@ -13,6 +13,11 @@ New features
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:user:`davidanthoff`
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- Set JULIA_PROJECT globally, so that every julia instance starts with the
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julia environment activated in :pr:`612` by :user:`davidanthoff`.
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- Update Miniconda version to 4.6.14 and Conda version to 4.6.14 in :pr:`637` by
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:user:`jhamman`
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- Install notebook into `notebook` env instead of `root`.
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Activate conda environments and shell integration via ENTRYPOINT
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in :pr:`651` by :user:`minrk`
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API changes
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-----------

‎repo2docker/buildpacks/base.py‎

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@@ -155,9 +155,13 @@
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# Add start script
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{% if start_script is not none -%}
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RUN chmod +x "{{ start_script }}"
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ENTRYPOINT ["{{ start_script }}"]
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ENV R2D_ENTRYPOINT "{{ start_script }}"
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{% endif -%}
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# Add entrypoint
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COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint
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ENTRYPOINT ["/usr/local/bin/repo2docker-entrypoint"]
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# Specify the default command to run
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CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
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@@ -167,6 +171,11 @@
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{% endif %}
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"""
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ENTRYPOINT_FILE = os.path.join(
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os.path.dirname(os.path.abspath(__file__)),
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"repo2docker-entrypoint",
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)
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class BuildPack:
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"""
@@ -493,6 +502,8 @@ def _filter_tar(tar):
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src_path = os.path.join(os.path.dirname(__file__), *src_parts)
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tar.add(src_path, src, filter=_filter_tar)
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tar.add(ENTRYPOINT_FILE, "repo2docker-entrypoint", filter=_filter_tar)
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tar.add('.', 'src/', filter=_filter_tar)
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tar.close()

‎repo2docker/buildpacks/conda/__init__.py‎

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@@ -28,7 +28,7 @@ def get_build_env(self):
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"""
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env = super().get_build_env() + [
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('CONDA_DIR', '${APP_BASE}/conda'),
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('NB_PYTHON_PREFIX', '${CONDA_DIR}'),
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('NB_PYTHON_PREFIX', '${CONDA_DIR}/envs/notebook'),
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]
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if self.py2:
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env.append(('KERNEL_PYTHON_PREFIX', '${CONDA_DIR}/envs/kernel'))
@@ -42,9 +42,10 @@ def get_path(self):
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"""
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path = super().get_path()
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path.insert(0, '${CONDA_DIR}/bin')
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if self.py2:
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path.insert(0, '${KERNEL_PYTHON_PREFIX}/bin')
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path.insert(0, '${CONDA_DIR}/bin')
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path.insert(0, '${NB_PYTHON_PREFIX}/bin')
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return path
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def get_build_scripts(self):
@@ -97,6 +98,7 @@ def get_build_script_files(self):
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"""
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files = {
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'conda/install-miniconda.bash': '/tmp/install-miniconda.bash',
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'conda/activate-conda.sh': '/etc/profile.d/activate-conda.sh',
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}
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py_version = self.python_version
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self.log.info("Building conda environment for python=%s" % py_version)
@@ -174,16 +176,16 @@ def get_assemble_scripts(self):
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"""
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assembly_scripts = []
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environment_yml = self.binder_path('environment.yml')
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env_name = 'kernel' if self.py2 else 'root'
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env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}"
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if os.path.exists(environment_yml):
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assembly_scripts.append((
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'${NB_USER}',
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r"""
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conda env update -n {0} -f "{1}" && \
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conda env update -p {0} -f "{1}" && \
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conda clean -tipsy && \
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conda list -n {0} && \
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conda list -p {0} && \
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rm -rf /srv/conda/pkgs
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""".format(env_name, environment_yml)
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""".format(env_prefix, environment_yml)
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))
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return super().get_assemble_scripts() + assembly_scripts
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‎repo2docker/buildpacks/conda/activate-conda.sh‎

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@@ -0,0 +1,11 @@
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# enable conda and activate the notebook environment
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CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/conda.sh"
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test -f $CONDA_PROFILE && . $CONDA_PROFILE
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if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
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# if the kernel is a separate env, stack them
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# so both are on PATH
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conda activate ${KERNEL_PYTHON_PREFIX}
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conda activate --stack ${NB_PYTHON_PREFIX}
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else
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conda activate ${NB_PYTHON_PREFIX}
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fi

‎repo2docker/buildpacks/conda/environment.frozen.yml‎

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# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
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# Frozen on 2019-04-24 18:01:25 UTC
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# Frozen on 2019-04-26 14:12:19 UTC
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name: r2d
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channels:
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- conda-forge
@@ -16,7 +16,7 @@ dependencies:
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- defusedxml=0.5.0=py_1
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- entrypoints=0.3=py37_1000
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- ipykernel=5.1.0=py37h24bf2e0_1002
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- ipython=7.4.0=py37h24bf2e0_0
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- ipython=7.5.0=py37h24bf2e0_0
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- ipython_genutils=0.2.0=py_1
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- ipywidgets=7.4.2=py_0
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- jedi=0.13.3=py37_0
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- jupyterlab=0.35.4=py37_0
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- jupyterlab_server=0.2.0=py_0
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- libffi=3.2.1=he1b5a44_1006
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- libgcc-ng=8.2.0=hdf63c60_1
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- libsodium=1.0.16=h14c3975_1001
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- markupsafe=1.1.1=py37h14c3975_0
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- mistune=0.8.4=py37h14c3975_1000
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- nbconvert=5.4.1=py_2
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- prompt_toolkit=2.0.9=py_0
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- ptyprocess=0.6.0=py_1001
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- pygments=2.3.1=py_0
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- pyrsistent=0.14.11=py37h14c3975_0
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- pyrsistent=0.15.1=py37h516909a_0
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- python=3.7.3=h5b0a415_0
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- python-dateutil=2.8.0=py_0
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- pyzmq=18.0.1=py37hc4ba49a_1
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- xz=5.2.4=h14c3975_1001
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- zeromq=4.3.1=hf484d3e_1000
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- zlib=1.2.11=h14c3975_1004
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- libgcc-ng=8.2.0=hdf63c60_1
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- pip:
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- alembic==1.0.9
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- async-generator==1.10

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

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# AUTO GENERATED FROM environment.py-2.7.yml, DO NOT MANUALLY MODIFY
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# Frozen on 2019-04-24 17:58:08 UTC
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# Frozen on 2019-04-26 14:09:19 UTC
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name: r2d
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channels:
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- conda-forge
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- jupyter_client=5.2.4=py_3
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- jupyter_core=4.4.0=py_0
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- libffi=3.2.1=he1b5a44_1006
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- libgcc-ng=8.2.0=hdf63c60_1
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- libsodium=1.0.16=h14c3975_1001
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- ncurses=6.1=hf484d3e_1002
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- openssl=1.1.1b=h14c3975_1
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- pathlib2=2.3.3=py27_1000
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- wheel=0.33.1=py27_0
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- zeromq=4.3.1=hf484d3e_1000
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- zlib=1.2.11=h14c3975_1004
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- libgcc-ng=8.2.0=hdf63c60_1
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- libstdcxx-ng=8.2.0=hdf63c60_1
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prefix: /opt/conda/envs/r2d
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‎repo2docker/buildpacks/conda/environment.py-3.6.frozen.yml‎

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# AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
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# Frozen on 2019-04-24 17:59:15 UTC
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# Frozen on 2019-04-26 14:10:28 UTC
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name: r2d
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- conda-forge
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- defusedxml=0.5.0=py_1
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- entrypoints=0.3=py36_1000
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- ipykernel=5.1.0=py36h24bf2e0_1002
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- ipython=7.4.0=py36h24bf2e0_0
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- ipython=7.5.0=py36h24bf2e0_0
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- ipython_genutils=0.2.0=py_1
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- ipywidgets=7.4.2=py_0
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- jedi=0.13.3=py36_0
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- jupyterlab=0.35.4=py36_0
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- jupyterlab_server=0.2.0=py_0
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- libffi=3.2.1=he1b5a44_1006
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- libgcc-ng=8.2.0=hdf63c60_1
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- libsodium=1.0.16=h14c3975_1001
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- markupsafe=1.1.1=py36h14c3975_0
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- mistune=0.8.4=py36h14c3975_1000
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- nbconvert=5.4.1=py_2
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- prompt_toolkit=2.0.9=py_0
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- ptyprocess=0.6.0=py_1001
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- pygments=2.3.1=py_0
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- pyrsistent=0.14.11=py36h14c3975_0
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- pyrsistent=0.15.1=py36h516909a_0
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- python=3.6.7=h381d211_1004
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- python-dateutil=2.8.0=py_0
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- pyzmq=18.0.1=py36hc4ba49a_1
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- xz=5.2.4=h14c3975_1001
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- zeromq=4.3.1=hf484d3e_1000
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- zlib=1.2.11=h14c3975_1004
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- libgcc-ng=8.2.0=hdf63c60_1
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- pip:
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- alembic==1.0.9
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- async-generator==1.10

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

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# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
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# Generated on 2019-04-24 17:59:15 UTC
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# Generated on 2019-04-26 14:10:28 UTC
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dependencies:
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- python=3.6.*
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- ipywidgets==7.4.2

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

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# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
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# Frozen on 2019-04-24 18:01:25 UTC
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# Frozen on 2019-04-26 14:12:19 UTC
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name: r2d
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channels:
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- conda-forge
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- defusedxml=0.5.0=py_1
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- entrypoints=0.3=py37_1000
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- ipykernel=5.1.0=py37h24bf2e0_1002
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- ipython=7.4.0=py37h24bf2e0_0
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- ipython=7.5.0=py37h24bf2e0_0
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- ipython_genutils=0.2.0=py_1
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- ipywidgets=7.4.2=py_0
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- jedi=0.13.3=py37_0
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- jupyterlab=0.35.4=py37_0
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- jupyterlab_server=0.2.0=py_0
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- libffi=3.2.1=he1b5a44_1006
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- libgcc-ng=8.2.0=hdf63c60_1
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- libsodium=1.0.16=h14c3975_1001
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- markupsafe=1.1.1=py37h14c3975_0
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- mistune=0.8.4=py37h14c3975_1000
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- nbconvert=5.4.1=py_2
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- prompt_toolkit=2.0.9=py_0
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- ptyprocess=0.6.0=py_1001
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- pygments=2.3.1=py_0
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- pyrsistent=0.14.11=py37h14c3975_0
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- pyrsistent=0.15.1=py37h516909a_0
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- python=3.7.3=h5b0a415_0
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- python-dateutil=2.8.0=py_0
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- pyzmq=18.0.1=py37hc4ba49a_1
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- xz=5.2.4=h14c3975_1001
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- zeromq=4.3.1=hf484d3e_1000
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- zlib=1.2.11=h14c3975_1004
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- libgcc-ng=8.2.0=hdf63c60_1
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- libstdcxx-ng=8.2.0=hdf63c60_1
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- pip:
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- alembic==1.0.9
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- async-generator==1.10

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

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# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
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# Generated on 2019-04-24 18:01:25 UTC
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# Generated on 2019-04-26 14:12:19 UTC
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dependencies:
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- python=3.7.*
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- ipywidgets==7.4.2

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