DEP version 5.0.0 package updates (civisanalytics#66)

Author: elsander

.circleci/config.yml

@@ -34,5 +34,5 @@ jobs:
           name: List packages installed from conda-forge
           command: docker run ds-python /bin/bash -c "conda list|grep conda-forge"
       - run:
-          name: Check that the expected number of packages come from conda-forge
-          command: docker run ds-python /bin/bash -c "conda list|grep -c conda-forge|python -c \"import sys; actual_count = int(sys.stdin.readlines()[0]); expected_count = 11; assert actual_count == expected_count, 'There should be %d conda-forge packages, but there are actually %d.' % (expected_count, actual_count)\""
+          name: Check for conda-pip conflicts
+          command: docker run ds-python /bin/bash -c "conda list|python -c \"import sys; from collections import Counter; duplicates = {k for k, v in Counter([l.split()[0] for l in sys.stdin.readlines() if not l.startswith('#')]).items() if v>1}; assert not duplicates, f'These packages are installed by both pip and conda:\n{duplicates}'\""

CHANGELOG.md

@@ -9,6 +9,59 @@ Version number changes (major.minor.micro) in this package denote the following:
 
 ## Unreleased
 
+## [5.0.0] - 2019-03-12
+### Changed
+- python 3.6.4 -> 3.7.1
+- conda 4.3.30 -> 4.6.8
+
+### New Packages
+- explicitly installs click=6.7
+
+### Package Updates
+- awscli 1.15.4 -> 1.16.121
+- beautifulsoup4 4.5.3 -> 4.7.1
+- botocore 1.10.4 -> 1.12.111
+- boto 2.46.1 -> 2.49.0
+- boto3 1.7.4 -> 1.9.111
+- bqplot 0.10.2 -> 0.11.5
+- cloudpickle 0.5.2 -> 0.8.0
+- cython 0.27.3 -> 0.29.6
+- dask 0.17.2 -> 1.1.4
+- ipython 6.1.0 -> 7.3.0
+- ipywidgets 7.1.0 -> 7.4.2
+- jinja2 2.9.6 -> 2.10
+- jsonschema 2.5.1 -> 3.0.1
+- libtiff 4.0.6 -> 4.0.10
+- libxml2 2.9.2 -> 2.9.8
+- matplotlib 2.2.2 -> 3.0.3
+- notebook 5.4.1 -> 5.7.5
+- numexpr 2.6.2 -> 2.6.9
+- numpy 1.13.3 -> 1.16.2
+- openblas 0.2.20 -> 0.3.5
+- pandas 0.22.0 -> 0.24.1
+- patsy 0.4.1 -> 0.5.1
+- psycopg2 2.6.2 -> 2.7.7
+- pyarrow 0.8.0 -> 0.12.1
+- pytest 3.1.3 -> 4.3.0
+- pyyaml 3.12 -> 3.13
+- requests 2.18.4 -> 2.21.0
+- s3fs 0.1.2 -> 0.2.0
+- seaborn 0.8 -> 0.9.0
+- scipy 1.0.1 -> 1.2.0
+- scikit-learn 0.19.1 -> 0.19.2
+- statsmodels 0.8.0 -> 0.9.0
+- urllib3 1.22 -> 1.24.1
+- xgboost 0.6a2 -> 0.81
+- civis 1.9.0 -> 1.9.4
+- civisml-extensions 0.1.8 -> 0.1.10
+- dropbox 7.1.1 -> 9.3.0
+- glmnet 2.0.0 -> 2.1.1
+- muffnn 2.1.0 -> 2.2.0
+- pubnub 4.0.13 -> 4.1.2
+- requests-toolbelt 0.8.0 -> 0.9.1
+- tensorflow 1.7.0 -> 1.13.1
+
+
 ### Maintenance
 - Update CircleCI config to v2 (#62).
 

Dockerfile

@@ -11,8 +11,9 @@ ENV LANG=en_US.UTF-8 \
     CONDARC=/opt/conda/.condarc \
     BASH_ENV=/etc/profile \
     PATH=/opt/conda/bin:$PATH \
-    CIVIS_CONDA_VERSION=4.3.30 \
-    CIVIS_PYTHON_VERSION=3.6.4
+    CIVIS_MINICONDA_VERSION=4.5.12 \
+    CIVIS_CONDA_VERSION=4.6.8 \
+    CIVIS_PYTHON_VERSION=3.7.1
 
 RUN DEBIAN_FRONTEND=noninteractive apt-get update -y --no-install-recommends && \
   apt-get install -y --no-install-recommends software-properties-common && \
@@ -52,7 +53,7 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get update -y --no-install-recommends &&
 #
 # The ordering of these steps seems to matter. You seem to have to
 # install a specific python version by hand and then pin it.
-# 1) install conda
+# 1) install conda using CIVIS_MINICONDA_VERSION (may not be most up to date conda version)
 # 2) pin conda to the version given by CIVIS_CONDA_VERSION
 # 3) install the python version CIVIS_PYTHON_VERSION
 # 4) pin the python version
@@ -61,10 +62,11 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get update -y --no-install-recommends &&
 #   Red Hat and Debian use different names for this file. git2R wants the latter.
 #   See conda-recipes GH 423
 RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
-    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${CIVIS_CONDA_VERSION}-Linux-x86_64.sh && \
-    /bin/bash /Miniconda3-${CIVIS_CONDA_VERSION}-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniconda3-${CIVIS_CONDA_VERSION}-Linux-x86_64.sh && \
-    /opt/conda/bin/conda install --yes conda==${CIVIS_CONDA_VERSION} && \
+    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${CIVIS_MINICONDA_VERSION}-Linux-x86_64.sh && \
+    /bin/bash /Miniconda3-${CIVIS_MINICONDA_VERSION}-Linux-x86_64.sh -b -p /opt/conda && \
+    rm Miniconda3-${CIVIS_MINICONDA_VERSION}-Linux-x86_64.sh && \
+    /opt/conda/bin/conda install --yes conda==${CIVIS_MINICONDA_VERSION} && \
+    conda install conda=${CIVIS_CONDA_VERSION} && \
     echo "conda ==${CIVIS_CONDA_VERSION}" > /opt/conda/conda-meta/pinned && \
     conda install --yes python==${CIVIS_PYTHON_VERSION} && \
     echo "python ==${CIVIS_PYTHON_VERSION}" >> /opt/conda/conda-meta/pinned && \

environment.yml

@@ -3,58 +3,59 @@ channels:
 - defaults
 - conda-forge
 dependencies:
-- awscli=1.15.4
-- beautifulsoup4=4.5.3
-- botocore=1.10.4
-- boto=2.46.1
-- boto3=1.7.4
-- bqplot=0.10.2
-- cython=0.27.3
-- dask=0.17.2
+- awscli=1.16.121
+- beautifulsoup4=4.7.1
+- botocore=1.12.111
+- boto=2.49.0
+- boto3=1.9.111
+- bqplot=0.11.5
+- click=6.7
+- cloudpickle=0.8.0
+- cython=0.29.6
+- dask=1.1.4
 - feather-format=0.4.0
-- ipython=6.1.0
-- ipywidgets=7.1.0
-- jinja2=2.9.6
-- jsonschema=2.5.1
+- ipython=7.3.0
+- ipywidgets=7.4.2
+- jinja2=2.10
+- jsonschema=3.0.1
 - jupyter=1.0.0
 - libffi=3.2.1
 - libgfortran=3.0.0
-- libtiff=4.0.6
-- libxml2=2.9.2
-- matplotlib=2.2.2
+- libtiff=4.0.10
+- libxml2=2.9.8
+- matplotlib=3.0.3
 - nomkl=1.0
-- notebook=5.4.1
+- notebook=5.7.5
 - nose=1.3.7
-- numexpr=2.6.2
-- numpy=1.13.3
-- openblas=0.2.20
-- pandas=0.22.0
-- patsy=0.4.1
-- psycopg2=2.6.2
-- pyarrow=0.8.0
+- numexpr=2.6.9
+- numpy=1.16.2
+- openblas=0.3.5
+- pandas=0.24.1
+- patsy=0.5.1
+- psycopg2=2.7.7
+- pyarrow=0.12.1
 - pycrypto=2.6.1
-- pytest=3.1.3
-- python=3.6.4
-- pyyaml=3.12
-- requests=2.18.4
-- s3fs=0.1.2
-- seaborn=0.8
-- scipy=1.0.1
-- scikit-learn=0.19.1
-- statsmodels=0.8.0
-- urllib3=1.22
-- xgboost=0.6a2
+- pytest=4.3.0
+- python=3.7.1
+- pyyaml=3.13
+- requests=2.21.0
+- s3fs=0.2.0
+- seaborn=0.9.0
+- scipy=1.2.0
+- scikit-learn=0.19.2
+- statsmodels=0.9.0
+- urllib3=1.24.1
+- xgboost=0.81
 - pip:
-  - civis==1.9.0
-  - civisml-extensions==0.1.8
-  - cloudpickle==0.5.2
-  - dropbox==7.1.1
+  - civis==1.9.4
+  - civisml-extensions==0.1.10
+  - dropbox==9.3.0
   - ftputil==3.4
-  - glmnet==2.0.0
+  - glmnet==2.1.1
   - joblib==0.11.0
-  - muffnn==2.1.0
-  - pubnub==4.0.13
+  - muffnn==2.2.0
+  - pubnub==4.1.2
   - pysftp==0.2.9
   - python-simple-hipchat==0.4.0
-  - requests-toolbelt==0.8.0
-  - tensorflow==1.7.0
+  - requests-toolbelt==0.9.1
+  - tensorflow==1.13.1