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environment-minimal.yaml
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environment-minimal.yaml
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# SPDX-FileCopyrightText: 2023 The WESkit Contributors
#
# SPDX-License-Identifier: MIT
# This (almost) minimal environment specification should contain only the minimal set of packages.
# Use it to update the environment.yaml that contains all packages:
#
# ```bash
# mamba env create -n weskit -f environment-minimal.yaml
# mamba activate weskit
# mamba env export > environment.yaml
# ```
#
# > NOTE: You might get widely different envs with strict and flexible channel priority.
# e.g. with strict you might get asyncssh 2.5.0 that does not support the
# `connect(env, send_env)` options
# TODO Next time, again try to build with strict channel priority.
#
# After that edit the environment.yaml and remove all paths (prefix) and check that the channels
# are exactly as specified here. You can then check in the environment.yaml and build the
# containers.
#
# When modifying this file, make sure to put packages for optional features, or for soon to be
# removed features (e.g. supporting Nextflow or Snakemake in the container!) in the dedicated
# sections.
#
name: weskit
channels:
- bioconda
- conda-forge
- nodefaults
dependencies:
- libcurl>=8.4.0
- curl>=8.4.0
# Development
- coverage>=6
- flake8
- mccabe
- mypy
- mypy_extensions
- types-setuptools
- types-six
- types-toml
- jq
- sqlalchemy
- pymysql
- reuse
# ... Pip: Some pip-packages need gcc :(. E.g. datrie, a dependency of python-kubernetes.
- gcc_linux-64
# ... integration tests with Nextflow
- openjdk=17
# WESkit core packages
- python>=3.11.4
- pip
- asyncssh>=2.12.0
- bcrypt
- bandit
- celery=5
- cerberus=1
- dataclasses
- flask=2
- flask-cors
- flask-jwt-extended
- jaraco.functools
- jinja2=3
- more-itertools
- nest-asyncio
- pymongo
- pytest
- pytest-asyncio
- pytest-celery
- pytest-cov
- werkzeug
- tempora
- cryptography
- kombu
- tenacity=8
- validators
- bson
- yaml
- zlib
- uwsgi>=2
# TRS feature
- bzip2
- flufl.lock=7
- xz
- pip:
# In Conda these were conflicting with Python 3.11.*, but not in Pip.
# Some packages (kubernetes) seem not to install correctly with Conda.
# Development
- testcontainers==3.7.1
- typing
- typing_extensions
- pip-licenses
# .. mypy packages
- types-pyyaml
- types-requests
- types-urllib3
- types-decorator
- types-pyOpenSSL
# WESkit core packages
- gevent
- redis==4
- ulid_py
- requests
- urllib3
- boto3
- requests-mock
- kubernetes==27.2.0
# TRS feature
- trs-cli==0.7.0
- pydantic==1.10.11 # Newest 1er version!
- typing-extensions
# Integration tests with Snakemake
- snakemake==7.30.2
# Integration tests with Nextflow. `nextflow info` needs to be run afterwards!
- nextflow==23.04.1
- filelock