Remove pip from scripts and use only conda (#3993)

* Remove pip from scripts and use only conda

* Remove dev dependency on black_nbconvert

* Use requirements.txt in tests

* Add parameterized to dev requirements

* Add some py37 leftovers

* Update conda packages during travis tests

* Remove Keras dependency

* Use conda to uninstall arviz for travis test

* Install black_nbconvert in testenv

* Use conda environmnent file for testenv

Co-authored-by: Thomas Wiecki <[email protected]>

Author: aseyboldt

.travis.yml

@@ -48,7 +48,7 @@ jobs:
     stage: test
     install:
       - . ./scripts/create_testenv.sh
-      - pip uninstall arviz -y
+      - conda uninstall arviz -y
       # replace ArviZ with the lastest master
       - pip install git+git://github.com/arviz-devs/arviz.git
       - pip install codecov

environment-dev.yml

@@ -0,0 +1,40 @@
+name: testenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.6
+  - arviz>=0.9
+  - theano>=1.0.4
+  - numpy>=1.13
+  - scipy>=0.18
+  - pandas >=0.18
+  - patsy>=0.5
+  - fastprogress>=0.2
+  - h5py>=2.7
+  - typing-extensions>=3.7
+  - bokeh>=0.12
+  - coverage>=5.1
+  - python-graphviz
+  - ipython>=7.16
+  - nbsphinx>=0.4
+  - nose>=1.3
+  - nose-parameterized>=0.6
+  - numpydoc>=0.9
+  - pycodestyle>=2.3
+  - pyflakes>=1.5
+  - pylint>=1.7
+  - pytest-cov>=2.5
+  - pytest>=3.0
+  - recommonmark>=0.4
+  - seaborn>=0.8
+  - sphinx-autobuild>=0.7
+  - sphinx>=1.5
+  - watermark
+  - parameterized
+  - black
+  - ipywidgets
+  - dataclasses  # python_version < 3.7
+  - contextvars  # python_version < 3.7
+  - pip:
+    - black_nbconvert

requirements-dev.txt

@@ -1,9 +1,7 @@
-black_nbconvert
 bokeh>=0.12.13
-coverage<5.0
+coverage>=5.1
 graphviz>=0.8.3
 ipython
-Keras>=2.0.8
 nbsphinx>=0.4.2
 nose>=1.3.7
 nose-parameterized==0.6.0
@@ -18,4 +16,5 @@ seaborn>=0.8.1
 sphinx-autobuild==0.7.1
 sphinx>=1.5.5
 watermark
-dill
+parameterized
+dill

scripts/create_testenv.sh

@@ -20,27 +20,19 @@ command -v conda >/dev/null 2>&1 || {
 }
 
 ENVNAME="${ENVNAME:-testenv}"         # if no ENVNAME is specified, use testenv
-PYTHON_VERSION=${PYTHON_VERSION:-3.6} # if no python specified, use 3.6
 
 if [ -z ${GLOBAL} ]; then
   if conda env list | grep -q ${ENVNAME}; then
     echo "Environment ${ENVNAME} already exists, keeping up to date"
   else
-    conda create -n ${ENVNAME} --yes pip python=${PYTHON_VERSION}
+    conda config --add channels conda-forge
+    conda config --set channel_priority strict
+    conda env create -f environment-dev.yml
   fi
   source activate ${ENVNAME}
 fi
-pip install --upgrade pip
 
-conda install --yes mkl-service
-conda install --yes -c conda-forge python-graphviz
-
-# Travis env is unable to import cached mpl sometimes https://github.com/pymc-devs/pymc3/issues/3423
-pip install --no-cache-dir --force-reinstall -e .
-pip install --no-cache-dir --force-reinstall -r requirements-dev.txt
-
-# Install untested, non-required code (linter fails without them)
-pip install ipython ipywidgets
+conda update --yes --all
 
 #  Install editable using the setup.py
 if [ -z ${NO_SETUP} ]; then

scripts/install_miniconda.sh

@@ -46,5 +46,3 @@ fi
 export PATH="$INSTALL_FOLDER/bin:$PATH"
 echo "Adding $INSTALL_FOLDER to PATH.  Consider adding it in your .rc file as well."
 conda update -q -y conda
-# Uninstalling miniconda's numpy to avoid conflicting versions when creating the test env
-pip uninstall -y numpy