Updating install scripts for Ubuntu 18.04 - WIP

requirements.txt

@@ -1,33 +1,14 @@
-astroplan
-astropy >= 3.0.0
-ccdproc
-codecov
-coveralls
-dateparser
+# These are packages that are NOT available via our
+# choice of conda repositories; there are less well
+# known repositories that do offer them, but that is
+# more of a security risk.
+
+# Python wrapper for ffmpeg.
 ffmpy
-gcloud
-google-cloud-storage
-matplotlib >= 2.0.0
-mocket
-numpy >= 1.12.1
-pycodestyle == 2.3.1
-pymongo >= 3.2.2
-pyserial >= 3.1.1
-pytest >= 3.4.0
-python_dateutil >= 2.5.3
-PyYAML >= 3.11
-pyzmq >= 15.3.0
-readline
-requests
-scikit_image >= 0.12.3
-scipy >= 0.17.1
 
-# Jupyter-notebook requires Tornado versions between 4 and 5. See:
-# https://stackoverflow.com/questions/49141525/install-jupyter-notebook-on-miniconda
-# https://github.com/ipython/ipython/issues/8249
-# https://github.com/jupyter/help/issues/324
+# Mock object support for Python testing.
+mocket
 
-tornado == 4.5.3
+# State machine library for Python.
 transitions >= 0.4.0
-tweepy
-wcsaxes
+

scripts/install/conda-packages-list.txt

@@ -1,3 +1,33 @@
-pandas
+astroplan
+astropy >= 3.0.0
+ccdproc
+codecov
+coveralls
 cython
+dateparser
+google-cloud-sdk
+google-cloud-storage
+matplotlib >= 2.0.0
+numpy >= 1.12.1
+pycodestyle == 2.3.1
+pymongo >= 3.2.2
+pyserial >= 3.1.1
+pytest >= 3.4.0
+pandas
+python
+python-dateutil >= 2.5.3
+PyYAML >= 3.11
+pyzmq >= 15.3.0
+readline
+requests
+scikit-image >= 0.12.3
+scipy >= 0.17.1
+
+# Jupyter-notebook requires Tornado versions between 4 and 5. See:
+# https://stackoverflow.com/questions/49141525/install-jupyter-notebook-on-miniconda
+# https://github.com/ipython/ipython/issues/8249
+# https://github.com/jupyter/help/issues/324
 
+tornado == 4.5.3
+tweepy
+wcsaxes

scripts/install/install-dependencies.sh

@@ -469,6 +469,24 @@ if [[ "${DO_CONDA}" -eq 1 ]] ; then
   install_conda_if_missing
 fi
 
+# Add the astropy channel, i.e. an additional repository in which to
+# look for packages. With conda 4.1.0 and later, by default the highest
+# priority repository that contains a package is used as the source for
+# that package, even if there is a newer version in a lower priority
+# package. And by default the most recently added repository is treated
+# as the highest priority repository. Here we use prepend to be clear
+# that we want astropy to be highest priority.
+if [[ -n "$(conda config --show channels | fgrep astropy)" ]] ; then
+  conda config --remove channels astropy
+fi
+conda config --prepend channels astropy
+
+# And put conda-forge at the back of the line.
+if [[ -n "$(conda config --show channels | fgrep conda-forge)" ]] ; then
+  conda config --remove channels conda-forge
+fi
+conda config --append channels conda-forge
+
 # Use the base Anaconda environment until we're ready to
 # work with the PANOPTES environment.
 conda activate base
@@ -491,7 +509,6 @@ if [[ "${DO_CONDA}" -eq 1 || "${DO_CREATE_CONDA_ENV}" -eq 1 || \
   echo
   echo "Updating base conda installation."
   conda update --quiet --yes -n base conda
-  conda update --quiet --all --yes
 fi
 
 if [[ "${DO_CREATE_CONDA_ENV}" -eq 1 ]] ; then
@@ -509,7 +526,8 @@ if [[ "${DO_CONDA}" -eq 1 || "${DO_CREATE_CONDA_ENV}" -eq 1 || \
   echo_bar
   echo
   echo "Updating packages in panoptes-env."
-  conda update --quiet --all --yes
+  conda update -n panoptes-env --quiet --yes conda
+  conda update -n panoptes-env --quiet --yes --all
 fi
 
 if [[ "${DO_INSTALL_CONDA_PACKAGES}" -eq 1 ]] ; then
@@ -523,6 +541,8 @@ echo_bar
 echo "PATH=$PATH"
 echo_bar
 
+exit
+
 if [[ "${DO_PIP_REQUIREMENTS}" -eq 1 ]] ; then
   echo_bar
   echo