From 70e8ad9cf112b35ddca11d2c713ee799ecf5b04e Mon Sep 17 00:00:00 2001 From: Alputer Date: Thu, 24 Oct 2024 11:29:58 +0200 Subject: [PATCH] chore(master): update reana-commons to 0.95.0a5 (#706) --- requirements.txt | 29 ++++++++++++++++++----------- setup.py | 2 +- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/requirements.txt b/requirements.txt index 1fb21c50..5a912080 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,6 +9,7 @@ alembic==1.10.4 # via flask-alembic, invenio-db, reana-db amqp==5.2.0 # via kombu appdirs==1.4.4 # via fs, snakemake argcomplete==3.4.0 # via cwltool +argparse-dataclass==2.0.0 # via snakemake-interface-common, snakemake-interface-executor-plugins arrow==1.3.0 # via isoduration asttokens==2.4.1 # via stack-data attrs==23.2.0 # via jsonschema @@ -33,7 +34,8 @@ click-plugins==1.1.1 # via celery click-repl==0.3.0 # via celery coloredlogs==15.0.1 # via cwltool commonmark==0.9.1 # via rich -configargparse==1.7 # via snakemake +conda-inject==1.3.2 # via snakemake +configargparse==1.7 # via snakemake, snakemake-interface-common connection-pool==0.0.3 # via snakemake cryptography==43.0.0 # via invenio-accounts, pyjwt, sqlalchemy-utils cwltool==3.1.20210628163208 # via reana-commons @@ -42,7 +44,7 @@ decorator==5.1.1 # via ipython, jsonpath-rw deprecated==1.2.14 # via limits dnspython==2.6.1 # via email-validator docutils==0.21.2 # via snakemake -dpath==2.2.0 # via yte +dpath==2.2.0 # via snakemake, yte email-validator==2.2.0 # via flask-security-invenio, wtforms-components executing==2.0.1 # via stack-data fastjsonschema==2.20.0 # via nbformat @@ -71,6 +73,7 @@ flask-wtf==1.2.1 # via flask-security-invenio, invenio-oauth2server fqdn==1.5.1 # via jsonschema fs==2.4.16 # via reana-commons future==1.0.0 # via invenio-oauth2server +gherkin-official==29.0.0 # via reana-commons gitdb==4.0.11 # via gitpython github3-py==4.0.1 # via invenio-oauthclient gitpython==3.1.43 # via reana-server (setup.py), snakemake @@ -79,6 +82,7 @@ google-auth==2.32.0 # via kubernetes greenlet==3.0.3 # via sqlalchemy humanfriendly==10.0 # via coloredlogs, snakemake idna==3.7 # via email-validator, jsonschema, requests +immutables==0.21 # via snakemake importlib-metadata==4.13.0 # via invenio-base, invenio-oauth2server, reana-server (setup.py) importlib-resources==6.4.0 # via invenio-base, limits, swagger-spec-validator infinity==1.5 # via intervals @@ -136,6 +140,7 @@ oauthlib==2.1.0 # via flask-oauthlib, invenio-oauthclient, requests-oa ordered-set==4.1.0 # via flask-limiter packaging==24.1 # via limits, snakemake packtivity==0.16.2 # via reana-server (setup.py), yadage +parse==1.20.2 # via reana-commons parso==0.8.4 # via jedi passlib==1.7.4 # via flask-security-invenio pexpect==4.9.0 # via ipython @@ -147,7 +152,7 @@ prov==1.5.1 # via cwltool psutil==6.0.0 # via cwltool, snakemake, yadage psycopg2-binary==2.9.9 # via invenio-db, reana-db ptyprocess==0.7.0 # via pexpect -pulp==2.7.0 # via reana-commons, snakemake +pulp==2.7.0 # via snakemake pure-eval==0.2.3 # via stack-data pyasn1==0.6.0 # via pyasn1-modules, rsa pyasn1-modules==0.4.0 # via google-auth @@ -161,14 +166,14 @@ pyrsistent==0.20.0 # via jsonschema python-dateutil==2.9.0.post0 # via arrow, bravado, bravado-core, celery, github3-py, kubernetes, prov pytz==2024.1 # via bravado-core, flask-babel pywebpack==2.0.0 # via flask-webpackext, invenio-assets -pyyaml==6.0.1 # via bravado, bravado-core, kubernetes, packtivity, reana-commons, snakemake, swagger-spec-validator, yadage, yadage-schemas, yte +pyyaml==6.0.1 # via bravado, bravado-core, conda-inject, kubernetes, packtivity, reana-commons, snakemake, swagger-spec-validator, yadage, yadage-schemas, yte rdflib==5.0.0 # via cwltool, prov, schema-salad -reana-commons[cwl,kubernetes,snakemake,yadage]==0.95.0a3 # via reana-db, reana-server (setup.py) +reana-commons[cwl,kubernetes,snakemake,yadage]==0.95.0a5 # via reana-db, reana-server (setup.py) reana-db==0.95.0a4 # via reana-server (setup.py) redis==5.0.7 # via invenio-celery requests[security]==2.32.3 # via bravado, bravado-core, cachecontrol, cwltool, github3-py, 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 -reretry==0.11.8 # via snakemake +reretry==0.11.8 # via snakemake, snakemake-interface-storage-plugins rfc3339-validator==0.1.4 # via jsonschema rfc3987==1.3.8 # via jsonschema rich==12.6.0 # via flask-limiter @@ -182,18 +187,20 @@ simplekv==0.14.1 # via flask-kvsession-invenio, invenio-accounts six==1.16.0 # via asttokens, bravado, bravado-core, flask-kvsession-invenio, flask-talisman, fs, isodate, jsonpath-rw, kubernetes, mock, prov, python-dateutil, rdflib, reana-server (setup.py), rfc3339-validator, wtforms-components smart-open==7.0.4 # via snakemake smmap==5.0.1 # via gitdb -snakemake==7.32.4 # via reana-commons +snakemake==8.24.1 # via reana-commons +snakemake-interface-common==1.17.4 # via reana-commons, snakemake, snakemake-interface-executor-plugins, snakemake-interface-report-plugins, snakemake-interface-storage-plugins +snakemake-interface-executor-plugins==9.3.2 # via reana-commons, snakemake +snakemake-interface-report-plugins==1.1.0 # via reana-commons, snakemake +snakemake-interface-storage-plugins==3.3.0 # via reana-commons, snakemake speaklater==1.3 # via flask-security-invenio sqlalchemy[asyncio]==1.4.52 # via alembic, flask-alembic, flask-sqlalchemy, invenio-db, reana-db, sqlalchemy-continuum, sqlalchemy-utils, wtforms-alchemy sqlalchemy-continuum==1.4.1 # via invenio-db sqlalchemy-utils[encrypted]==0.38.3 # via invenio-db, reana-db, sqlalchemy-continuum, sqlalchemy-utils, wtforms-alchemy stack-data==0.6.3 # via ipython -stopit==1.1.2 # via snakemake swagger-spec-validator==3.0.4 # via bravado-core tablib==3.6.1 # via reana-server (setup.py) tabulate==0.9.0 # via snakemake -throttler==1.2.2 # via snakemake -toposort==1.10 # via snakemake +throttler==1.2.2 # via snakemake, snakemake-interface-executor-plugins, snakemake-interface-storage-plugins traitlets==5.14.3 # via ipython, jupyter-core, matplotlib-inline, nbformat types-python-dateutil==2.9.0.20240316 # via arrow typing-extensions==4.12.2 # via alembic, bravado, cwltool, flask-limiter, limits, swagger-spec-validator @@ -215,7 +222,7 @@ webargs==5.5.3 # via invenio-rest webcolors==24.6.0 # via jsonschema websocket-client==1.8.0 # via kubernetes werkzeug==2.2.3 # via flask, flask-kvsession-invenio, flask-login, invenio-base, reana-commons -wrapt==1.16.0 # via deprecated, smart-open, snakemake +wrapt==1.16.0 # via deprecated, smart-open, snakemake, snakemake-interface-storage-plugins wtforms==2.3.3 # via flask-admin, 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 diff --git a/setup.py b/setup.py index 3c402400..bcf810ee 100644 --- a/setup.py +++ b/setup.py @@ -48,7 +48,7 @@ "Flask>=2.1.1,<2.3.0", # same upper pin as invenio-base "gitpython>=3.1", "marshmallow>2.13.0,<3.0.0", - "reana-commons[kubernetes,yadage,snakemake,cwl] @ git+https://github.com/reanahub/reana-commons.git@0.95.0a4", + "reana-commons[kubernetes,yadage,snakemake,cwl]>=0.95.0a5,<0.96.0", "reana-db>=0.95.0a4,<0.96.0", "requests>=2.25.0", "tablib>=0.12.1",