Merge remote-tracking branch 'origin/master' into update-thredds-5.4

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.6.0
+current_version = 2.6.2
 commit = True
 tag = False
 tag_name = {new_version}
@@ -30,11 +30,11 @@ search = {current_version}
 replace = {new_version}
 
 [bumpversion:file:RELEASE.txt]
-search = {current_version} 2024-11-19T13:53:14Z
+search = {current_version} 2024-12-03T20:46:32Z
 replace = {new_version} {utcnow:%Y-%m-%dT%H:%M:%SZ}
 
 [bumpversion:part:releaseTime]
-values = 2024-11-19T13:53:14Z
+values = 2024-12-03T20:46:32Z
 
 [bumpversion:file(version):birdhouse/components/canarie-api/docker_configuration.py.template]
 search = 'version': '{current_version}'

CHANGES.md

@@ -22,6 +22,53 @@
   Unidata has dropped support for TDS versions < 5.x. This updates Thredds to version 5.5.
 
 
+[2.6.2](https://github.com/bird-house/birdhouse-deploy/tree/2.6.2) (2024-12-03)
+------------------------------------------------------------------------------------------------------------------
+
+## Changes
+
+- Fix help string description for `bin/birdhouse configs` command
+
+  Update description of the `configs` subcommand to better describe it.
+  The description when calling `bin/birdhouse -h` now matches the description when calling `bin/birdhouse configs -h`
+
+- Jupyterhub: Update recommended paths for public share folders
+
+  The recommended public share folders in the `env.local.example` file create a conflict with the default
+  `PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR` path when both are enabled and mounted on a Jupyterlab container.
+  This change updates the recommended paths for the public share folders to avoid this conflict and adds a
+  warning helping users to avoid this conflict.
+
+  Note: the conflict arises when `PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR` is mounted to a container as read-only
+  volume and then Jupyterhub tries to mount the public share folder within that volume. Since the parent volume
+  is read-only, the second volume mount fails.
+
+
+## Fixes
+
+- Correct docker image for `stac-populator` optional component
+
+  This sets the docker image for the `stac-populator` component to a version that actually contains the code
+  that is executed when `stac-populator` is called. The previous image no longer contained the relevant code.
+
+[2.6.1](https://github.com/bird-house/birdhouse-deploy/tree/2.6.1) (2024-11-22)
+------------------------------------------------------------------------------------------------------------------
+
+## Fixes
+
+- Fix regressions introduced by PR #359 "Flexible locations for data served by thredds"
+
+  In [PR #359](https://github.com/bird-house/birdhouse-deploy/pull/359/):
+
+  `secure-thredds/config/magpie/permissions.cfg` started to use variable but was never renamed to `.template`
+  so those variable never get template expanded
+  (commit [317d96c3](https://github.com/bird-house/birdhouse-deploy/commit/317d96c39db7a6d79d1568a7094441ccdedc55ae)).
+
+  `bootstrap-testdata` default value was removed but did not source `read-configs.include.sh` so the variable
+   stayed blank (commit [4ab0fc74](https://github.com/bird-house/birdhouse-deploy/commit/4ab0fc74cb8fa601d75ecfc2a94749b23f60109c)).
+   The default value was there initially so the script can be used in standalone situation (not inside a checkout).
+
+
 [2.6.0](https://github.com/bird-house/birdhouse-deploy/tree/2.6.0) (2024-11-19)
 ------------------------------------------------------------------------------------------------------------------
 

Makefile

@@ -1,7 +1,7 @@
 # Generic variables
 override SHELL       := bash
 override APP_NAME    := birdhouse-deploy
-override APP_VERSION := 2.6.0
+override APP_VERSION := 2.6.2
 
 # utility to remove comments after value of an option variable
 override clean_opt = $(shell echo "$(1)" | $(_SED) -r -e "s/[ '$'\t'']+$$//g")

README.rst

@@ -18,13 +18,13 @@ for a full-fledged production platform.
     * - citation
       - | |citation|
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/bird-house/birdhouse-deploy/2.6.0.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/bird-house/birdhouse-deploy/2.6.2.svg
     :alt: Commits since latest release
-    :target: https://github.com/bird-house/birdhouse-deploy/compare/2.6.0...master
+    :target: https://github.com/bird-house/birdhouse-deploy/compare/2.6.2...master
 
-.. |latest-version| image:: https://img.shields.io/badge/tag-2.6.0-blue.svg?style=flat
+.. |latest-version| image:: https://img.shields.io/badge/tag-2.6.2-blue.svg?style=flat
     :alt: Latest Tag
-    :target: https://github.com/bird-house/birdhouse-deploy/tree/2.6.0
+    :target: https://github.com/bird-house/birdhouse-deploy/tree/2.6.2
 
 .. |readthedocs| image:: https://readthedocs.org/projects/birdhouse-deploy/badge/?version=latest
     :alt: ReadTheDocs Build Status (latest version)

RELEASE.txt

@@ -1 +1 @@
-2.6.0 2024-11-19T13:53:14Z
+2.6.2 2024-12-03T20:46:32Z

bin/birdhouse

@@ -15,7 +15,7 @@ Manage the Birdhouse software stack.
 Commands:
   info      Print build information
   compose   Run a \"docker compose\" command for the Birdhouse project
-  configs   Print a command that can be used to load configuration settings as environment variables
+  configs   Load or execute commands in the Birdhouse configuration environment
 
 Options:
   -h, --help                   Print this message and exit

birdhouse/components/canarie-api/docker_configuration.py.template

@@ -108,8 +108,8 @@ SERVICES = {
             # NOTE:
             #   Below version and release time auto-managed by 'make VERSION=x.y.z bump'.
             #   Do NOT modify it manually. See 'Tagging policy' in 'birdhouse/README.rst'.
-            'version': '2.6.0',
-            'releaseTime': '2024-11-19T13:53:14Z',
+            'version': '2.6.2',
+            'releaseTime': '2024-12-03T20:46:32Z',
             'institution': '${BIRDHOUSE_INSTITUTION}',
             'researchSubject': '${BIRDHOUSE_SUBJECT}',
             'supportEmail': '${BIRDHOUSE_SUPPORT_EMAIL}',
@@ -141,8 +141,8 @@ PLATFORMS = {
             # NOTE:
             #   Below version and release time auto-managed by 'make VERSION=x.y.z bump'.
             #   Do NOT modify it manually. See 'Tagging policy' in 'birdhouse/README.rst'.
-            'version': '2.6.0',
-            'releaseTime': '2024-11-19T13:53:14Z',
+            'version': '2.6.2',
+            'releaseTime': '2024-12-03T20:46:32Z',
             'institution': '${BIRDHOUSE_INSTITUTION}',
             'researchSubject': '${BIRDHOUSE_SUBJECT}',
             'supportEmail': '${BIRDHOUSE_SUPPORT_EMAIL}',

birdhouse/env.local.example

@@ -388,8 +388,8 @@ export GEOSERVER_ADMIN_PASSWORD="${__DEFAULT__GEOSERVER_ADMIN_PASSWORD}"
 ## /data/jupyterhub_user_data/public-share/
 #public_read_on_disk = join(jupyterhub_data_dir, 'public-share')
 #
-## /notebook_dir/public/
-#public_read_in_container = join(notebook_dir, 'public')
+## /notebook_dir/public-share/
+#public_read_in_container = join(notebook_dir, 'public-share')
 #
 #c.DockerSpawner.volumes[public_read_on_disk] = {
 #    'bind': public_read_in_container,
@@ -401,14 +401,17 @@ export GEOSERVER_ADMIN_PASSWORD="${__DEFAULT__GEOSERVER_ADMIN_PASSWORD}"
 ## /data/jupyterhub_user_data/public-share/{username}-public
 #public_share_on_disk = join(public_read_on_disk, '{username}-public')
 #
-## /notebook_dir/mypublic
-#public_share_in_container = join(notebook_dir, 'mypublic')
+## /notebook_dir/mypublic-share
+#public_share_in_container = join(notebook_dir, 'mypublic-share')
 #
 #c.DockerSpawner.volumes[public_share_on_disk] = {
 #    'bind': public_share_in_container,
 #    'mode': 'rw',
 #}
 #
+## If enabling the public-share paths above, make sure that the paths in the container don't conflict
+## with the PUBLIC_WORKSPACE_WPS_OUTPUTS_SUBDIR path.
+#
 ### create dir with proper permissions
 #
 #def custom_create_dir_hook(spawner):

birdhouse/optional-components/secure-thredds/config/magpie/.gitignore

@@ -0,0 +1 @@
+permissions.cfg

birdhouse/optional-components/stac-populator/default.env

@@ -1,3 +1,7 @@
+export STAC_POPULATOR_DOCKER=ghcr.io/crim-ca/stac-populator
+export STAC_POPULATOR_VERSION=0.0.0
+export STAC_POPULATOR_IMAGE='${STAC_POPULATOR_DOCKER}:${STAC_POPULATOR_VERSION}'
+
 export STAC_ASSET_GENERATOR_TIMEOUT=200
 
 # add any new variables not already in 'VARS' or 'OPTIONAL_VARS' that must be replaced in templates here
@@ -13,3 +17,8 @@ VARS="$VARS $EXTRA_VARS"
 COMPONENT_DEPENDENCIES="
   ./components/stac
 "
+
+export DELAYED_EVAL="
+  $DELAYED_EVAL
+  STAC_POPULATOR_IMAGE
+"

birdhouse/optional-components/stac-populator/docker-compose-extra.yml

@@ -11,7 +11,7 @@ services:
   # populates STAC catalog with sample collection items
   stac-populator:
     container_name: stac-populator
-    image: ghcr.io/crim-ca/stac-populator:master
+    image: ${STAC_POPULATOR_IMAGE}
     environment:
       - STAC_ASSET_GENERATOR_TIMEOUT=${STAC_ASSET_GENERATOR_TIMEOUT}
       - STAC_HOST=http://stac:8000/stac  # STAC API internally accessed to avoid Twitcher authentication

birdhouse/scripts/bootstrap-testdata

@@ -10,8 +10,22 @@
 # Need write-access to DATASET_ROOT (/data/datasets/).
 
 
+THIS_FILE="$(readlink -f "$0" || realpath "$0")"
+THIS_DIR="$(dirname "${THIS_FILE}")"
+COMPOSE_DIR="${COMPOSE_DIR:-$(dirname "${THIS_DIR}")}"
+
+if [ -f "${COMPOSE_DIR}/read-configs.include.sh" ]; then
+    . "${COMPOSE_DIR}/read-configs.include.sh"
+
+    # Get THREDDS_SERVICE_DATA_LOCATION_ON_HOST, BIRDHOUSE_DATA_PERSIST_ROOT
+    read_configs
+fi
+
+
 if [ -z "${DATASET_ROOT}" ]; then
-    DATASET_ROOT="${BIRDHOUSE_DATA_PERSIST_ROOT}/${THREDDS_SERVICE_DATA_LOCATION_ON_HOST}"
+    # Default for when unable to source read-configs.include.sh (ie when
+    # used standalone outside of the checkout).
+    DATASET_ROOT="${DATASET_ROOT:-${THREDDS_SERVICE_DATA_LOCATION_ON_HOST:-${BIRDHOUSE_DATA_PERSIST_ROOT:-/data}/datasets}}"
 fi
 
 FROM_SERVER=${FROM_SERVER:-"https://pavics.ouranos.ca/twitcher/ows/proxy/thredds/fileServer/birdhouse"}
@@ -39,6 +53,8 @@ for afile in ${FILE_LIST}; do
         if [ ! -d "${PARENT_DIRS}" ]; then
             mkdir -p "${PARENT_DIRS}"
         fi
+        set -e  # Fail on error.
         curl "${FROM_SERVER}/${afile}" --output "${afile}"
+        set +e
     fi
 done

docs/source/conf.py

@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.6.0'
+version = '2.6.2'
 # The full version, including alpha/beta/rc tags.
-release = '2.6.0'
+release = '2.6.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.