Merge branch 'bird-house:master' into master

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.18.3
+current_version = 1.18.5
 commit = True
 tag = False
 tag_name = {new_version}

CHANGES.md

@@ -16,6 +16,90 @@
 
 [//]: # (list changes here, using '-' for each new entry, remove this when items are added)
 
+[1.18.5](https://github.com/bird-house/birdhouse-deploy/tree/1.18.5) (2022-01-27)
+------------------------------------------------------------------------------------------------------------------
+
+## Changes:
+- Jupyter: update Jupyter env for latest XClim, RavenPy and all packages
+
+  Deploy new Jupyter env from PR https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/95 on PAVICS.
+
+  Detailed changes can be found at https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/pull/95.
+
+  Relevant changes:
+  ```diff
+  <   - xclim=0.31.0=pyhd8ed1ab_0
+  >   - xclim=0.32.1=pyhd8ed1ab_0
+
+  <   - ravenpy=0.7.5=pyhff6ddc9_0
+  >   - ravenpy=0.7.8=pyh8a188c0_0
+
+  <   - python=3.7.12=hb7a2778_100_cpython
+  >   - python=3.8.12=hb7a2778_2_cpython
+
+  # removed
+  <   - vcs=8.2.1=pyh9f0ad1d_0
+
+  <   - numpy=1.21.4=py37h31617e3_0
+  >   - numpy=1.21.5=py38h87f13fb_0
+
+  <   - xarray=0.20.1=pyhd8ed1ab_0
+  >   - xarray=0.20.2=pyhd8ed1ab_0
+
+  <   - rioxarray=0.8.0=pyhd8ed1ab_0
+  >   - rioxarray=0.9.1=pyhd8ed1ab_0
+
+  <   - cf_xarray=0.6.1=pyh6c4a22f_0
+  >   - cf_xarray=0.6.3=pyhd8ed1ab_0
+
+  <   - gdal=3.3.2=py37hd5a0ba4_2
+  >   - gdal=3.3.3=py38hcf2042a_0
+
+  <   - rasterio=1.2.6=py37hc20819c_2
+  >   - rasterio=1.2.10=py38hfd64e68_0
+
+  <   - climpred=2.1.6=pyhd8ed1ab_1
+  >   - climpred=2.2.0=pyhd8ed1ab_0
+
+  <   - clisops=0.7.0=pyh6c4a22f_0
+  >   - clisops=0.8.0=pyh6c4a22f_0
+
+  <   - xesmf=0.6.0=pyhd8ed1ab_0
+  >   - xesmf=0.6.2=pyhd8ed1ab_0
+
+  <   - birdy=v0.8.0=pyh6c4a22f_1
+  >   - birdy=0.8.1=pyh6c4a22f_1
+
+  <   - cartopy=0.20.0=py37hbe109c4_0
+  >   - cartopy=0.20.1=py38hf9a4893_1
+
+  <   - dask=2021.11.2=pyhd8ed1ab_0
+  >   - dask=2022.1.0=pyhd8ed1ab_0
+
+  <   - numba=0.53.1=py37hb11d6e1_1
+  >   - numba=0.55.0=py38h4bf6c61_0
+
+  <   - pandas=1.3.4=py37he8f5f7f_1
+  >   - pandas=1.3.5=py38h43a58ef_0
+  ```
+
+
+[1.18.4](https://github.com/bird-house/birdhouse-deploy/tree/1.18.4) (2022-01-25)
+------------------------------------------------------------------------------------------------------------------
+
+## Changes:
+- vagrant: support RockyLinux
+
+  RockyLinux 8 is the successor to Centos 7.
+
+  Centos 8 has become like a "RHEL 8 beta" than the equivalent of RHEL 8.
+
+  RockyLinux 8 is the new equivalent of RHEL 8, following the original spirit
+  of the Centos project.
+
+  More info at https://rockylinux.org/about.
+
+
 [1.18.3](https://github.com/bird-house/birdhouse-deploy/tree/1.18.3) (2021-12-17)
 ------------------------------------------------------------------------------------------------------------------
 

README.rst

@@ -14,13 +14,13 @@ for a full-fledged production platform.
     * - releases
       - | |latest-version| |commits-since|
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/bird-house/birdhouse-deploy/1.18.3.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/bird-house/birdhouse-deploy/1.18.5.svg
     :alt: Commits since latest release
-    :target: https://github.com/bird-house/birdhouse-deploy/compare/1.18.3...master
+    :target: https://github.com/bird-house/birdhouse-deploy/compare/1.18.5...master
 
-.. |latest-version| image:: https://img.shields.io/badge/tag-1.18.3-blue.svg?style=flat
+.. |latest-version| image:: https://img.shields.io/badge/tag-1.18.5-blue.svg?style=flat
     :alt: Latest Tag
-    :target: https://github.com/bird-house/birdhouse-deploy/tree/1.18.3
+    :target: https://github.com/bird-house/birdhouse-deploy/tree/1.18.5
 
 .. |readthedocs| image:: https://readthedocs.org/projects/birdhouse-deploy/badge/?version=latest
     :alt: ReadTheDocs Build Status (latest version)

Vagrantfile

@@ -12,7 +12,13 @@ Vagrant.configure("2") do |config|
 
   # bug https://github.com/hashicorp/vagrant/issues/3341 still happening as of
   # 2019-07-03 with VirtualBox 6.0.8
-  config.vbguest.auto_update = false
+  if Vagrant.has_plugin?("vagrant-vbguest") then
+    # vagrant plugin list
+    # vagrant vbguest --status
+    # vagrant vbguest --do install  # manual re-install if OS update wiped it
+    # Sometime manual re-install do not work, best to take a VM snapshot before OS update for rollback.
+    config.vbguest.auto_update = false
+  end
 
   # https://blog.centos.org/2018/01/updated-centos-vagrant-images-available-v1801-01/
   # Fix /vagrant shared folders (together with vagrant-vbguest) for Centos 7.

birdhouse/default.env

@@ -2,7 +2,7 @@
 # All env in this default.env must not depend on any env in env.local.
 
 # Jupyter single-user server images, can be overriden in env.local to have a space separated list of multiple images
-export DOCKER_NOTEBOOK_IMAGES="pavics/workflow-tests:211123-update211216"
+export DOCKER_NOTEBOOK_IMAGES="pavics/workflow-tests:220121"
 
 # Name of the image displayed on the JupyterHub image selection page
 # Can be overriden in env.local to have a space separated list of multiple images, the name order must correspond

birdhouse/vagrant-utils/configure-pagekite

@@ -4,7 +4,7 @@ ACCOUNT_CONF="/etc/pagekite.d/10_account.rc"
 
 if [ -n "$KITENAME" -a -n "$KITESECRET" -a -n "$KITESUBDOMAIN" ]; then
 
-    if ! grep centos /etc/os-release; then
+    if ! grep centos /etc/os-release && ! grep rocky /etc/os-release; then
         DEBIAN_FRONTEND=noninteractive apt-get install --yes pagekite
     else
         yum install --assumeyes epel-release
@@ -26,7 +26,7 @@ EOF
 else
 
     DISABLE_PAGEKITE=""
-    if ! grep centos /etc/os-release; then
+    if ! grep centos /etc/os-release && ! grep rocky /etc/os-release; then
         if dpkg -l pagekite; then
             DISABLE_PAGEKITE=true
         fi

birdhouse/vagrant-utils/install-docker.sh

@@ -3,7 +3,7 @@
 set -e # Exit if any subcommand fails
 set -x # Print commands for troubleshooting
 
-if ! grep centos /etc/os-release; then
+if ! grep centos /etc/os-release && ! grep rocky /etc/os-release; then
 
     # Install Docker CE on Ubuntu per
     # https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/
@@ -93,7 +93,7 @@ fi
 echo 'export PATH="$PATH:/usr/local/bin"' | sudo tee /etc/profile.d/usr_local_path.sh
 
 # install docker-compose, from https://gist.github.com/wdullaer/f1af16bd7e970389bad3
-LATEST_COMPOSE_VERSION="`git ls-remote https://github.com/docker/compose | grep refs/tags | grep -v refs/tags/v | grep -oP "[0-9]+\.[0-9][0-9]+\.[0-9]+$"|tail -1`"
+LATEST_COMPOSE_VERSION="`git ls-remote https://github.com/docker/compose | grep refs/tags | grep -oP "v[0-9]+\.[0-9]\.[0-9]+$"|tail -1`"
 # LATEST_COMPOSE_VERSION=$(curl --silent https://api.github.com/repos/docker/compose/releases/latest | jq .name -r)  # need jq :(
 sudo curl -L "https://github.com/docker/compose/releases/download/$LATEST_COMPOSE_VERSION/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
 sudo chmod +x /usr/local/bin/docker-compose

vagrant_variables.yml.example

@@ -74,3 +74,4 @@ domain: ouranos.ca
 # disksize: '100GB'
 # box: 'ubuntu/bionic64'  # no manual steps required
 # box: 'centos/7'  # will require manual 'vagrant-utils/disk-resize' inside box
+# box: 'rockylinux/8'  # will require manual 'vagrant-utils/disk-resize' inside box