Merge pull request #475 from betatim/bump-notebook

[WIP] Update notebook to latest release

.gitignore

@@ -25,8 +25,5 @@ include/
 generated/
 test_file_text.txt
 
-# Untracked artifacts from the conda script
-repo2docker/buildpacks/conda/environment.py-3.5.yml
-repo2docker/buildpacks/conda/environment.py-3.6.yml
 
 \.vscode/

repo2docker/buildpacks/conda/environment.frozen.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.py-3.6.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2018-11-12 20:48:01 UTC
+# Frozen on 2018-12-11 21:19:13 UTC
 name: r2d
 channels:
   - conda-forge
@@ -9,20 +9,20 @@ dependencies:
   - attrs=18.2.0=py_0
   - backcall=0.1.0=py_0
   - bleach=3.0.2=py_0
-  - ca-certificates=2018.10.15=ha4d7672_0
+  - ca-certificates=2018.11.29=ha4d7672_0
-  - certifi=2018.10.15=py36_1000
+  - certifi=2018.11.29=py36_1000
   - decorator=4.3.0=py_0
   - defusedxml=0.5.0=py_1
   - entrypoints=0.2.3=py36_1002
   - gmp=6.1.2=hfc679d8_0
   - ipykernel=5.1.0=py36h24bf2e0_1001
-  - ipython=7.1.1=py36h24bf2e0_1000
+  - ipython=7.2.0=py36h24bf2e0_1000
   - ipython_genutils=0.2.0=py_1
   - ipywidgets=7.2.1=py36_1
   - jedi=0.13.1=py36_1000
   - jinja2=2.10=py_1
   - jsonschema=3.0.0a3=py36_1000
-  - jupyter_client=5.2.3=py_1
+  - jupyter_client=5.2.4=py_0
   - jupyter_core=4.4.0=py_0
   - jupyterlab=0.34.9=py36_0
   - jupyterlab_launcher=0.13.1=py_2
@@ -34,8 +34,8 @@ dependencies:
   - mistune=0.8.4=py36h470a237_0
   - nbconvert=5.4.0=1
   - nbformat=4.4.0=py_1
-  - ncurses=6.1=hfc679d8_1
+  - ncurses=6.1=hfc679d8_2
-  - notebook=5.6.0=py36_1
+  - notebook=5.7.2=py36_1000
   - openssl=1.0.2p=h470a237_1
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
@@ -43,43 +43,43 @@ dependencies:
   - pexpect=4.6.0=py36_1000
   - pickleshare=0.7.5=py36_1000
   - pip=18.1=py36_1000
-  - prometheus_client=0.4.2=py_0
+  - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.7=py_0
   - ptyprocess=0.6.0=py36_1000
-  - pygments=2.2.0=py_1
+  - pygments=2.3.0=py_0
-  - pyrsistent=0.14.5=py36h470a237_1
+  - pyrsistent=0.14.7=py36h470a237_0
-  - python=3.6.6=h5001a0f_3
+  - python=3.6.7=h5001a0f_1
   - python-dateutil=2.7.5=py_0
   - pyzmq=17.1.2=py36hae99301_1
   - readline=7.0=haf1bffa_1
   - send2trash=1.5.0=py_0
-  - setuptools=40.5.0=py36_0
+  - setuptools=40.6.2=py36_0
-  - six=1.11.0=py36_1001
+  - six=1.12.0=py36_1000
-  - sqlite=3.25.3=hb1c47c0_0
+  - sqlite=3.26.0=hb1c47c0_0
   - terminado=0.8.1=py36_1001
   - testpath=0.4.2=py36_1000
-  - tk=8.6.8=ha92aebf_0
+  - tk=8.6.9=ha92aebf_0
-  - tornado=4.5.3=py36_0
+  - tornado=5.1.1=py36h470a237_0
   - traitlets=4.3.2=py36_1000
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
-  - wheel=0.32.2=py36_0
+  - wheel=0.32.3=py36_0
   - widgetsnbextension=3.2.1=py36_1
   - xz=5.2.4=h470a237_1
   - zeromq=4.2.5=hfc679d8_6
   - zlib=1.2.11=h470a237_3
   - pip:
-    - alembic==1.0.2
+    - alembic==1.0.5
     - async-generator==1.10
     - chardet==3.0.4
-    - idna==2.7
+    - idna==2.8
     - jupyterhub==0.9.4
     - mako==1.0.7
     - nteract-on-jupyter==1.9.6
     - pamela==0.3.0
     - python-editor==1.0.3
     - python-oauth2==1.1.0
-    - requests==2.20.1
+    - requests==2.21.0
     - sqlalchemy==1.2.14
     - urllib3==1.24.1
 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 2018-11-12 20:35:26 UTC
+# Frozen on 2018-12-11 21:15:11 UTC
 name: r2d
 channels:
   - conda-forge
@@ -9,47 +9,45 @@ dependencies:
   - backports=1.0=py_2
   - backports.shutil_get_terminal_size=1.0.0=py_3
   - backports_abc=0.5=py_1
-  - ca-certificates=2018.10.15=ha4d7672_0
+  - ca-certificates=2018.11.29=ha4d7672_0
-  - certifi=2018.10.15=py27_1000
+  - certifi=2018.11.29=py27_1000
   - decorator=4.3.0=py_0
   - enum34=1.1.6=py27_1001
+  - futures=3.2.0=py27_1000
   - ipykernel=4.8.2=py27_0
   - ipython=5.8.0=py27_0
   - ipython_genutils=0.2.0=py_1
-  - jupyter_client=5.2.3=py_1
+  - jupyter_client=5.2.4=py_0
   - jupyter_core=4.4.0=py_0
   - libffi=3.2.1=hfc679d8_5
   - libgcc-ng=7.2.0=hdf63c60_3
   - libsodium=1.0.16=h470a237_1
   - libstdcxx-ng=7.2.0=hdf63c60_3
-  - ncurses=6.1=hfc679d8_1
+  - ncurses=6.1=hfc679d8_2
   - openssl=1.0.2p=h470a237_1
-  - pathlib2=2.3.2=py27_1000
+  - pathlib2=2.3.3=py27_1000
   - pexpect=4.6.0=py27_1000
   - pickleshare=0.7.5=py27_1000
   - pip=18.1=py27_1000
   - prompt_toolkit=1.0.15=py_1
   - ptyprocess=0.6.0=py27_1000
-  - pygments=2.2.0=py_1
+  - pygments=2.3.0=py_0
-  - python=2.7.15=h33da82c_4
+  - python=2.7.15=h33da82c_6
   - python-dateutil=2.7.5=py_0
   - pyzmq=17.1.2=py27hae99301_1
   - readline=7.0=haf1bffa_1
   - scandir=1.9.0=py27h470a237_0
-  - setuptools=40.5.0=py27_0
+  - setuptools=40.6.2=py27_0
   - simplegeneric=0.8.1=py_1
   - singledispatch=3.4.0.3=py27_1000
-  - six=1.11.0=py27_1001
+  - six=1.12.0=py27_1000
-  - sqlite=3.25.3=hb1c47c0_0
+  - sqlite=3.26.0=hb1c47c0_0
-  - ssl_match_hostname=3.5.0.1=py27_1001
+  - tk=8.6.9=ha92aebf_0
-  - tk=8.6.8=ha92aebf_0
+  - tornado=5.1.1=py27h470a237_0
-  - tornado=4.5.3=py27_0
   - traitlets=4.3.2=py27_1000
   - wcwidth=0.1.7=py_1
-  - wheel=0.32.2=py27_0
+  - wheel=0.32.3=py27_0
   - zeromq=4.2.5=hfc679d8_6
   - zlib=1.2.11=h470a237_3
-  - pip:
-    - backports.ssl-match-hostname==3.5.0.1
 prefix: /opt/conda/envs/r2d
 

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

@@ -1,4 +1,3 @@
 dependencies:
 - python=2.7.*
 - ipykernel==4.8.2
-- tornado==4.5.3

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

@@ -1,5 +1,6 @@
-# AUTO GENERATED FROM environment.py-3.5.yml, DO NOT MANUALLY MODIFY
+# py3.5 conda packages are no longer being updated as of 12/2018
-# Frozen on 2018-11-12 20:43:21 UTC
+# this file is hand-maintained now
+# and should only receive security fixes, no new features
 name: r2d
 channels:
   - conda-forge
@@ -35,7 +36,6 @@ dependencies:
   - nbconvert=5.4.0=1
   - nbformat=4.4.0=py_1
   - ncurses=6.1=hfc679d8_1
-  - notebook=5.6.0=py35_1
   - openssl=1.0.2p=h470a237_1
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
@@ -58,8 +58,8 @@ dependencies:
   - sqlite=3.25.3=hb1c47c0_0
   - terminado=0.8.1=py35_1
   - testpath=0.3.1=py35_1
-  - tk=8.6.8=ha92aebf_0
+  - tk=8.6.9=ha92aebf_0
-  - tornado=4.5.3=py35_0
+  - tornado=5.1.1=py35h470a237_0
   - traitlets=4.3.2=py35_0
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
@@ -69,12 +69,13 @@ dependencies:
   - zeromq=4.2.5=hfc679d8_6
   - zlib=1.2.11=h470a237_3
   - pip:
-    - alembic==1.0.2
+    - alembic==1.0.3
     - async-generator==1.10
     - chardet==3.0.4
     - idna==2.7
     - jupyterhub==0.9.4
     - mako==1.0.7
+    - notebook==5.7.2
     - nteract-on-jupyter==1.9.6
     - pamela==0.3.0
     - python-editor==1.0.3
@@ -83,4 +84,3 @@ dependencies:
     - sqlalchemy==1.2.14
     - urllib3==1.24.1
 prefix: /opt/conda/envs/r2d
-

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

@@ -0,0 +1,2 @@
+# py3.5 is not being auto-generated from this file anymore
+# update environment.py-3.5.frozen.yml directly

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 2018-11-12 20:48:01 UTC
+# Frozen on 2018-12-11 21:19:13 UTC
 name: r2d
 channels:
   - conda-forge
@@ -9,20 +9,20 @@ dependencies:
   - attrs=18.2.0=py_0
   - backcall=0.1.0=py_0
   - bleach=3.0.2=py_0
-  - ca-certificates=2018.10.15=ha4d7672_0
+  - ca-certificates=2018.11.29=ha4d7672_0
-  - certifi=2018.10.15=py36_1000
+  - certifi=2018.11.29=py36_1000
   - decorator=4.3.0=py_0
   - defusedxml=0.5.0=py_1
   - entrypoints=0.2.3=py36_1002
   - gmp=6.1.2=hfc679d8_0
   - ipykernel=5.1.0=py36h24bf2e0_1001
-  - ipython=7.1.1=py36h24bf2e0_1000
+  - ipython=7.2.0=py36h24bf2e0_1000
   - ipython_genutils=0.2.0=py_1
   - ipywidgets=7.2.1=py36_1
   - jedi=0.13.1=py36_1000
   - jinja2=2.10=py_1
   - jsonschema=3.0.0a3=py36_1000
-  - jupyter_client=5.2.3=py_1
+  - jupyter_client=5.2.4=py_0
   - jupyter_core=4.4.0=py_0
   - jupyterlab=0.34.9=py36_0
   - jupyterlab_launcher=0.13.1=py_2
@@ -34,8 +34,8 @@ dependencies:
   - mistune=0.8.4=py36h470a237_0
   - nbconvert=5.4.0=1
   - nbformat=4.4.0=py_1
-  - ncurses=6.1=hfc679d8_1
+  - ncurses=6.1=hfc679d8_2
-  - notebook=5.6.0=py36_1
+  - notebook=5.7.2=py36_1000
   - openssl=1.0.2p=h470a237_1
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
@@ -43,43 +43,43 @@ dependencies:
   - pexpect=4.6.0=py36_1000
   - pickleshare=0.7.5=py36_1000
   - pip=18.1=py36_1000
-  - prometheus_client=0.4.2=py_0
+  - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.7=py_0
   - ptyprocess=0.6.0=py36_1000
-  - pygments=2.2.0=py_1
+  - pygments=2.3.0=py_0
-  - pyrsistent=0.14.5=py36h470a237_1
+  - pyrsistent=0.14.7=py36h470a237_0
-  - python=3.6.6=h5001a0f_3
+  - python=3.6.7=h5001a0f_1
   - python-dateutil=2.7.5=py_0
   - pyzmq=17.1.2=py36hae99301_1
   - readline=7.0=haf1bffa_1
   - send2trash=1.5.0=py_0
-  - setuptools=40.5.0=py36_0
+  - setuptools=40.6.2=py36_0
-  - six=1.11.0=py36_1001
+  - six=1.12.0=py36_1000
-  - sqlite=3.25.3=hb1c47c0_0
+  - sqlite=3.26.0=hb1c47c0_0
   - terminado=0.8.1=py36_1001
   - testpath=0.4.2=py36_1000
-  - tk=8.6.8=ha92aebf_0
+  - tk=8.6.9=ha92aebf_0
-  - tornado=4.5.3=py36_0
+  - tornado=5.1.1=py36h470a237_0
   - traitlets=4.3.2=py36_1000
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
-  - wheel=0.32.2=py36_0
+  - wheel=0.32.3=py36_0
   - widgetsnbextension=3.2.1=py36_1
   - xz=5.2.4=h470a237_1
   - zeromq=4.2.5=hfc679d8_6
   - zlib=1.2.11=h470a237_3
   - pip:
-    - alembic==1.0.2
+    - alembic==1.0.5
     - async-generator==1.10
     - chardet==3.0.4
-    - idna==2.7
+    - idna==2.8
     - jupyterhub==0.9.4
     - mako==1.0.7
     - nteract-on-jupyter==1.9.6
     - pamela==0.3.0
     - python-editor==1.0.3
     - python-oauth2==1.1.0
-    - requests==2.20.1
+    - requests==2.21.0
     - sqlalchemy==1.2.14
     - urllib3==1.24.1
 prefix: /opt/conda/envs/r2d

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

@@ -0,0 +1,11 @@
+# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
+# Generated on 2018-12-11 21:19:13 UTC
+dependencies:
+- python=3.6.*
+- ipywidgets==7.2.1
+- jupyterlab==0.34.9
+- nbconvert==5.4.0
+- notebook==5.7.2
+- pip:
+  - nteract_on_jupyter==1.9.6
+  - jupyterhub==0.9.4

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 2018-11-12 20:38:27 UTC
+# Frozen on 2018-12-11 21:16:37 UTC
 name: r2d
 channels:
   - conda-forge
@@ -10,19 +10,19 @@ dependencies:
   - backcall=0.1.0=py_0
   - bleach=3.0.2=py_0
   - bzip2=1.0.6=h470a237_2
-  - ca-certificates=2018.10.15=ha4d7672_0
+  - ca-certificates=2018.11.29=ha4d7672_0
-  - certifi=2018.10.15=py37_1000
+  - certifi=2018.11.29=py37_1000
   - decorator=4.3.0=py_0
   - defusedxml=0.5.0=py_1
   - entrypoints=0.2.3=py37_1002
   - gmp=6.1.2=hfc679d8_0
   - ipykernel=5.1.0=py37h24bf2e0_1001
-  - ipython=7.1.1=py37h24bf2e0_1000
+  - ipython=7.2.0=py37h24bf2e0_1000
   - ipython_genutils=0.2.0=py_1
   - jedi=0.13.1=py37_1000
   - jinja2=2.10=py_1
   - jsonschema=3.0.0a3=py37_1000
-  - jupyter_client=5.2.3=py_1
+  - jupyter_client=5.2.4=py_0
   - jupyter_core=4.4.0=py_0
   - jupyterlab_launcher=0.13.1=py_2
   - libffi=3.2.1=hfc679d8_5
@@ -33,8 +33,8 @@ dependencies:
   - mistune=0.8.4=py37h470a237_0
   - nbconvert=5.4.0=1
   - nbformat=4.4.0=py_1
-  - ncurses=6.1=hfc679d8_1
+  - ncurses=6.1=hfc679d8_2
-  - notebook=5.6.0=py37_1
+  - notebook=5.7.2=py37_1000
   - openssl=1.0.2p=h470a237_1
   - pandoc=1.19.2=0
   - pandocfilters=1.4.2=py_1
@@ -42,45 +42,46 @@ dependencies:
   - pexpect=4.6.0=py37_1000
   - pickleshare=0.7.5=py37_1000
   - pip=18.1=py37_1000
-  - prometheus_client=0.4.2=py_0
+  - prometheus_client=0.5.0=py_0
   - prompt_toolkit=2.0.7=py_0
   - ptyprocess=0.6.0=py37_1000
-  - pygments=2.2.0=py_1
+  - pygments=2.3.0=py_0
-  - pyrsistent=0.14.5=py37h470a237_1
+  - pyrsistent=0.14.7=py37h470a237_0
-  - python=3.7.0=h5001a0f_6
+  - python=3.7.1=h5001a0f_0
   - python-dateutil=2.7.5=py_0
   - pyzmq=17.1.2=py37hae99301_1
   - readline=7.0=haf1bffa_1
   - send2trash=1.5.0=py_0
-  - setuptools=40.5.0=py37_0
+  - setuptools=40.6.2=py37_0
-  - six=1.11.0=py37_1001
+  - six=1.12.0=py37_1000
-  - sqlite=3.25.3=hb1c47c0_0
+  - sqlite=3.26.0=hb1c47c0_0
   - terminado=0.8.1=py37_1001
   - testpath=0.4.2=py37_1000
-  - tk=8.6.8=ha92aebf_0
+  - tk=8.6.9=ha92aebf_0
+  - tornado=5.1.1=py37h470a237_0
   - traitlets=4.3.2=py37_1000
   - wcwidth=0.1.7=py_1
   - webencodings=0.5.1=py_1
-  - wheel=0.32.2=py37_0
+  - wheel=0.32.3=py37_0
   - widgetsnbextension=3.4.2=py37_1000
   - xz=5.2.4=h470a237_1
   - zeromq=4.2.5=hfc679d8_6
   - zlib=1.2.11=h470a237_3
   - ipywidgets=7.2.1=py37_0
   - jupyterlab=0.34.9=py37_0
-  - tornado=4.5.3=py37_0
   - pip:
-    - alembic==1.0.2
+    - alembic==1.0.5
     - async-generator==1.10
     - chardet==3.0.4
-    - idna==2.7
+    - idna==2.8
     - jupyterhub==0.9.4
     - mako==1.0.7
     - nteract-on-jupyter==1.9.6
     - pamela==0.3.0
     - python-editor==1.0.3
     - python-oauth2==1.1.0
-    - requests==2.20.1
+    - requests==2.21.0
     - sqlalchemy==1.2.14
     - urllib3==1.24.1
 prefix: /opt/conda/envs/r2d
+

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

@@ -1,12 +1,11 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2018-11-12 20:38:27 UTC
+# Generated on 2018-12-11 21:16:37 UTC
 dependencies:
 - python=3.7.*
 - ipywidgets==7.2.1
 - jupyterlab==0.34.9
 - nbconvert==5.4.0
-- tornado==4.5.3
+- notebook==5.7.2
-- notebook==5.6.0
 - pip:
   - nteract_on_jupyter==1.9.6
   - jupyterhub==0.9.4

repo2docker/buildpacks/conda/environment.yml

@@ -3,8 +3,7 @@ dependencies:
   - ipywidgets==7.2.1
   - jupyterlab==0.34.9
   - nbconvert==5.4.0
-  - tornado==4.5.3
+  - notebook==5.7.2
-  - notebook==5.6.0
   - pip:
     - nteract_on_jupyter==1.9.6
     - jupyterhub==0.9.4

repo2docker/buildpacks/conda/freeze.py

@@ -45,9 +45,16 @@ def freeze(env_file, frozen_file):
 
     Result will be stored in frozen_file
     """
+    frozen_dest = HERE / frozen_file
+    if frozen_dest.exists():
+        with frozen_dest.open('r') as f:
+            line = f.readline()
+            if 'GENERATED' not in line:
+                print(f"{frozen_file} not autogenerated, not refreezing")
+                return
     print(f"Freezing {env_file} -> {frozen_file}")
 
-    with open(HERE / frozen_file, 'w') as f:
+    with frozen_dest.open('w') as f:
         f.write(f"# AUTO GENERATED FROM {env_file}, DO NOT MANUALLY MODIFY\n")
         f.write(f"# Frozen on {datetime.utcnow():%Y-%m-%d %H:%M:%S UTC}\n")
 
@@ -78,8 +85,8 @@ def set_python(py_env_file, py):
     if os.path.exists(py_env_file):
         # only clobber auto-generated files
         with open(py_env_file) as f:
-            text = f.read()
+            text = f.readline()
-            if text and 'GENERATED' not in text:
+            if 'GENERATED' not in text:
                 return
 
     print(f"Regenerating {py_env_file} from {ENV_FILE}")