release: 0.9.1

CHANGES.rst

@@ -1,23 +1,32 @@
 Changes
 =======
 
-Version 0.9.1 (UNRELEASED)
+Version 0.9.1 (2023-09-27)
 --------------------------
 
-- Fixes ``quota-set-default-limits`` command to propagate default quota limits to all users without custom quota limit values..
-- Changes ``launch`` endpoint also include the warnings of the validation of the workflow specification.
-- Changes OpenAPI specification with respect to return the maximum inactivity time before automatic closure of interactive sessions in ``info`` endpoint.
+- Adds new ``prune_workspace`` endpoint to allow users to delete all the files of a workflow, specifying whether to also delete the inputs and/or the outputs.
+- Adds new ``interactive-session-cleanup`` command that can be used by REANA administrators to close interactive sessions that are inactive for more than the specified number of days.
+- Adds logic to support SSO with third-party Keycloak authentication services.
 - Adds the timestamp of when the workflow was stopped (``run_stopped_at``) to the workflow list and the workflow status endpoints.
 - Adds the content of the ``REANA_GITLAB_HOST`` environment variable to the list of GitLab instances from which it is possible to launch a workflow.
-- Adds new ``prune_workspace`` endpoint to allow users to delete all the files of a workflow, specifying whether to also delete the inputs and/or the outputs.
-- Adds ``interactive-session-cleanup`` command that can be used by REANA administrators to close interactive sessions that are inactive for more than the specified number of days.
+- Adds progress meter to the logs of the periodic quota updater.
+- Changes CPU and disk quota calculations to improve the performance of periodic quota updater.
 - Changes the system status report to simplify and clarify the disk usage summary.
 - Changes ``check-workflows`` command to also check the presence of workspaces on the shared volume.
+- Changes ``check-workflows`` command to not show in-sync runs by default. If needed, they can be shown using the new ``--show-all`` option.
+- Changes ``launch`` endpoint to also include the warnings of the validation of the workflow specification.
+- Changes OpenAPI specification of the ``info`` endpoint to return the maximum inactivity time before automatic closure of interactive sessions.
+- Changes ``apispec`` dependency version in order to be compatible with ``PyYAML`` v6.
+- Changes ``reana-admin`` command options to require the passing of ``--admin-access-token`` argument more globally.
+- Fixes the workflow priority calculation to avoid workflows stuck in the ``queued`` status when the number of allowed concurrent workflow is set to zero.
 - Fixes GitLab integration to automatically redirect the user to the correct URL when the access request is accepted.
+- Fixes ``quota-set-default-limits`` command to propagate default quota limits to all users without custom quota limit values.
 - Fixes authentication flow to correctly deny access to past revoked tokens in case the same user has also other new active tokens.
-- Fixes the email templates to show the correct ``kubectl`` commands when REANA is deployed inside a non-default namespace or with a custom component name prefix.
+- Fixes email templates to show the correct ``kubectl`` commands when REANA is deployed inside a non-default namespace or with a custom component name prefix.
+- Fixes email sender for system emails to ``notifications.email_config.sender`` Helm value.
+- Fixes email receiver for token request emails to use ``notifications.email_config.receiver`` Helm value.
 - Fixes ``start-scheduler`` command to gracefully stop when being terminated.
-- Adds logic to support SSO with third-party Keycloak authentication services to ``config.py``.
+- Fixes container image names to be Podman-compatible.
 
 Version 0.9.0 (2023-01-19)
 --------------------------

docs/openapi.json

@@ -2,7 +2,7 @@
   "info": {
     "description": "Submit workflows to be run on REANA Cloud",
     "title": "REANA Server",
-    "version": "0.9.1a4"
+    "version": "0.9.1"
   },
   "paths": {
     "/account/settings/linkedaccounts/": {},

reana_server/version.py

@@ -14,4 +14,4 @@
 
 from __future__ import absolute_import, print_function
 
-__version__ = "0.9.1a4"
+__version__ = "0.9.1"

requirements.txt

@@ -8,7 +8,7 @@ adage==0.10.1             # via reana-commons, reana-server (setup.py), yadage
 alembic==1.12.0           # via flask-alembic, reana-db
 amqp==5.1.1               # via kombu
 appdirs==1.4.4            # via fs, snakemake
-argcomplete==3.1.1        # via cwltool
+argcomplete==3.1.2        # via cwltool
 asttokens==2.4.0          # via stack-data
 async-timeout==4.0.3      # via redis
 attrs==23.1.0             # via jsonschema
@@ -36,7 +36,7 @@ click-repl==0.3.0         # via celery
 coloredlogs==15.0.1       # via cwltool
 configargparse==1.7       # via snakemake
 connection-pool==0.0.3    # via snakemake
-cryptography==41.0.3      # via invenio-accounts, pyopenssl, requests, sqlalchemy-utils
+cryptography==41.0.4      # via invenio-accounts, pyopenssl, requests, sqlalchemy-utils
 cwltool==3.1.20210628163208  # via reana-commons
 datrie==0.8.2             # via snakemake
 decorator==5.1.1          # via ipython, jsonpath-rw, networkx
@@ -45,7 +45,7 @@ docutils==0.20.1          # via snakemake
 email-validator==2.0.0.post2  # via invenio-accounts, wtforms-components
 executing==1.2.0          # via stack-data
 fastjsonschema==2.18.0    # via nbformat
-filelock==3.12.3          # via cachecontrol, snakemake
+filelock==3.12.4          # via cachecontrol, snakemake
 flask==2.1.3              # via flask-alembic, flask-babelex, flask-breadcrumbs, flask-caching, flask-celeryext, flask-collect-invenio, flask-cors, flask-kvsession-invenio, flask-limiter, flask-login, flask-mail, flask-menu, flask-oauthlib, flask-principal, flask-security, flask-shell-ipython, flask-sqlalchemy, flask-webpackext, flask-wtf, invenio-base, invenio-config, invenio-mail, reana-server (setup.py)
 flask-alembic==2.0.1      # via invenio-db
 flask-babelex==0.9.4      # via flask-security, invenio-i18n
@@ -70,13 +70,13 @@ flask-wtf==1.1.1          # via flask-security, invenio-accounts, invenio-oauth2
 fs==2.4.16                # via reana-commons
 future==0.18.3            # via invenio-oauth2server
 gitdb==4.0.10             # via gitpython
-gitpython==3.1.34         # via reana-server (setup.py), snakemake
+gitpython==3.1.37         # via reana-server (setup.py), snakemake
 glob2==0.7                # via packtivity, yadage
-google-auth==2.22.0       # via kubernetes
+google-auth==2.23.0       # via kubernetes
 humanfriendly==10.0       # via coloredlogs
 idna==2.10                # via email-validator, jsonschema, requests
 importlib-metadata==4.13.0  # via alembic, flask, invenio-base, invenio-celery, invenio-oauth2server
-importlib-resources==6.0.1  # via alembic, invenio-base, schema-salad
+importlib-resources==6.1.0  # via alembic, invenio-base, schema-salad
 infinity==1.5             # via intervals
 intervals==0.9.2          # via wtforms-components
 invenio-accounts==1.4.13  # via invenio-oauth2server, invenio-oauthclient, invenio-userprofiles, reana-server (setup.py)
@@ -100,7 +100,7 @@ isodate==0.6.1            # via rdflib
 itsdangerous==2.0.1       # via flask, flask-kvsession-invenio, flask-security, flask-wtf, invenio-base, invenio-rest
 jedi==0.19.0              # via ipython
 jinja2==3.1.2             # via flask, flask-babelex, invenio-accounts
-jq==1.5.0                 # via packtivity, yadage
+jq==1.6.0                 # via packtivity, yadage
 jsmin==3.0.1              # via invenio-theme
 jsonpath-rw==1.4.0        # via packtivity, yadage
 jsonpointer==2.4          # via jsonschema, packtivity, yadage
@@ -120,7 +120,7 @@ maxminddb-geolite2==2018.703  # via invenio-accounts
 mistune==2.0.5            # via schema-salad
 mock==3.0.5               # via packtivity, reana-commons
 monotonic==1.6            # via bravado
-msgpack==1.0.5            # via bravado-core, cachecontrol, invenio-celery
+msgpack==1.0.6            # via bravado-core, cachecontrol, invenio-celery
 msgpack-python==0.5.6     # via bravado
 mypy-extensions==1.0.0    # via cwltool, schema-salad
 nbformat==5.9.2           # via snakemake
@@ -157,9 +157,9 @@ pywebpack==1.2.0          # via flask-webpackext
 pyyaml==6.0.1             # via bravado, bravado-core, kubernetes, packtivity, reana-commons, snakemake, swagger-spec-validator, yadage, yadage-schemas
 ratelimiter==1.2.0.post0  # via snakemake
 rdflib==5.0.0             # via cwltool, prov, schema-salad
-reana-commons[cwl,kubernetes,snakemake,yadage]==0.9.3a6  # via reana-db, reana-server (setup.py)
-reana-db==0.9.2a1         # via reana-server (setup.py)
-redis==5.0.0              # via invenio-accounts, invenio-celery
+reana-commons[cwl,kubernetes,snakemake,yadage]==0.9.3  # via reana-db, reana-server (setup.py)
+reana-db==0.9.2           # via reana-server (setup.py)
+redis==5.0.1              # via invenio-accounts, invenio-celery
 requests[security]==2.25.0  # via bravado, bravado-core, cachecontrol, cwltool, kubernetes, packtivity, reana-server (setup.py), requests-oauthlib, schema-salad, snakemake, yadage, yadage-schemas
 requests-oauthlib==1.1.0  # via flask-oauthlib, invenio-oauth2server, invenio-oauthclient, kubernetes
 rfc3987==1.3.8            # via jsonschema
@@ -170,9 +170,9 @@ schema-salad==8.4.20230808163024  # via cwltool
 shellescape==3.8.1        # via cwltool
 simplejson==3.19.1        # via bravado, bravado-core
 simplekv==0.14.1          # via flask-kvsession-invenio, invenio-accounts
-six==1.16.0               # via asttokens, bravado, bravado-core, flask-breadcrumbs, flask-kvsession-invenio, flask-limiter, flask-menu, flask-talisman, fs, google-auth, isodate, jsonpath-rw, jsonschema, kubernetes, limits, mock, prov, python-dateutil, rdflib, reana-server (setup.py), sqlalchemy-continuum, wtforms-components
-smart-open==6.3.0         # via snakemake
-smmap==5.0.0              # via gitdb
+six==1.16.0               # via asttokens, bravado, bravado-core, flask-breadcrumbs, flask-kvsession-invenio, flask-limiter, flask-menu, flask-talisman, fs, isodate, jsonpath-rw, jsonschema, kubernetes, limits, mock, prov, python-dateutil, rdflib, reana-server (setup.py), sqlalchemy-continuum, wtforms-components
+smart-open==6.4.0         # via snakemake
+smmap==5.0.1              # via gitdb
 snakemake==6.8.0          # via reana-commons
 speaklater==1.3           # via flask-babelex
 sqlalchemy==1.3.24        # via alembic, flask-alembic, flask-sqlalchemy, invenio-db, reana-db, sqlalchemy-continuum, sqlalchemy-utils, wtforms-alchemy
@@ -185,8 +185,8 @@ swagger-spec-validator==3.0.3  # via bravado-core
 tablib==3.5.0             # via reana-server (setup.py)
 tabulate==0.8.10          # via reana-commons, snakemake
 toposort==1.10            # via snakemake
-traitlets==5.9.0          # via ipython, jupyter-core, matplotlib-inline, nbformat
-typing-extensions==4.7.1  # via alembic, bravado, cwltool, filelock, ipython, kombu, swagger-spec-validator
+traitlets==5.10.1         # via ipython, jupyter-core, matplotlib-inline, nbformat
+typing-extensions==4.8.0  # via alembic, bravado, cwltool, ipython, kombu, swagger-spec-validator
 tzdata==2023.3            # via backports-zoneinfo, celery
 ua-parser==0.18.0         # via invenio-accounts
 uritools==4.0.2           # via invenio-app, invenio-oauthclient
@@ -200,15 +200,15 @@ wcmatch==8.4.1            # via reana-commons
 wcwidth==0.2.6            # via prompt-toolkit
 webargs==5.5.3            # via invenio-rest
 webcolors==1.13           # via jsonschema
-websocket-client==1.6.2   # via kubernetes
+websocket-client==1.6.3   # via kubernetes
 werkzeug==2.0.3           # via flask, flask-kvsession-invenio, invenio-base, reana-commons, reana-server (setup.py)
 wrapt==1.15.0             # via snakemake
 wtforms==2.3.3            # via flask-wtf, invenio-oauth2server, reana-server (setup.py), wtforms-alchemy, wtforms-components
 wtforms-alchemy==0.18.0   # via invenio-oauth2server
 wtforms-components==0.10.5  # via wtforms-alchemy
 yadage==0.20.1            # via reana-commons, reana-server (setup.py)
 yadage-schemas==0.10.6    # via packtivity, reana-commons, reana-server (setup.py), yadage
-zipp==3.16.2              # via importlib-metadata, importlib-resources
+zipp==3.17.0              # via importlib-metadata, importlib-resources
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools

setup.py

@@ -19,7 +19,7 @@
 history = open("CHANGES.rst").read()
 
 tests_require = [
-    "pytest-reana>=0.9.1a1,<0.10.0",
+    "pytest-reana>=0.9.1,<0.10.0",
 ]
 
 extras_require = {
@@ -59,8 +59,8 @@
     "flask-celeryext<0.5.0",
     "gitpython>=3.1",
     "marshmallow>2.13.0,<=2.20.1",
-    "reana-commons[kubernetes,yadage,snakemake,cwl]>=0.9.3a6,<0.10.0",
-    "reana-db>=0.9.2a1,<0.10.0",
+    "reana-commons[kubernetes,yadage,snakemake,cwl]>=0.9.3,<0.10.0",
+    "reana-db>=0.9.2,<0.10.0",
     "requests==2.25.0",
     "tablib>=0.12.1",
     "uWSGI>=2.0.17",