mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #11192 from nsoranzo/update_dependencies
Replace pipenv with poetry. Update all dependencies
This commit is contained in:
Dannon
@@ -1,7 +1,7 @@
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# Location of virtualenv used for development.
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VENV?=.venv
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# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
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IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
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IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
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RELEASE_CURR:=16.01
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RELEASE_CURR_MINOR_NEXT:=$(shell $(IN_VENV) python scripts/bootstrap_history.py --print-next-minor-version)
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RELEASE_NEXT:=16.04
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@@ -55,9 +55,6 @@ open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in bro
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open-project: ## open project on github
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$(OPEN_RESOURCE) $(PROJECT_URL)
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lint: ## check style using tox and flake8 for Python 2 and Python 3
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$(IN_VENV) tox -e py27-lint && tox -e py34-lint
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uwsgi-rebuild-validation: ## rebuild uwsgi_config.yml kwalify schema against latest uwsgi master.
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$(CONFIG_MANAGE) build_uwsgi_yaml
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@@ -132,14 +129,11 @@ release-check-blocking-prs: ## Check github for release blocking PRs
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release-bootstrap-history: ## bootstrap history for a new release
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$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
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build-dependencies-docker: ## Builds the docker container used for dependency updates
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$(MAKE) -C lib/galaxy/dependencies/pipfiles/docker
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update-lint-requirements:
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./lib/galaxy/dependencies/update_lint_requirements.sh
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update-dependencies: build-dependencies-docker ## update linting + dev dependencies
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sh lib/galaxy/dependencies/pipfiles/update.sh -d
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update-and-commit-dependencies: build-dependencies-docker ## update and commit linting + dev dependencies
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sh lib/galaxy/dependencies/pipfiles/update.sh -d -c
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update-dependencies: update-lint-requirements ## update pinned and dev dependencies
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$(IN_VENV) ./lib/galaxy/dependencies/update.sh
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node-deps: ## Install NodeJS dependencies.
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ifndef YARN
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@@ -77,7 +77,7 @@ class CustosAuthnz(IdentityProvider):
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# Get nonce from token['id_token'] and validate. 'nonce' in the
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# id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
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# cookie.
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id_token_decoded = jwt.decode(id_token, verify=False)
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id_token_decoded = jwt.decode(id_token, options={"verify_signature": False})
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nonce_hash = id_token_decoded['nonce']
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self._validate_nonce(trans, nonce_hash)
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@@ -144,7 +144,7 @@ class CustosAuthnz(IdentityProvider):
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# Get nonce from token['id_token'] and validate. 'nonce' in the
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# id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME
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# cookie.
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userinfo = jwt.decode(id_token, verify=False)
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userinfo = jwt.decode(id_token, options={"verify_signature": False})
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# Get userinfo and create Galaxy user record
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email = userinfo['email']
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@@ -180,7 +180,7 @@ class CustosAuthnz(IdentityProvider):
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raise Exception("User is not associated with provider {}".format(self.config["provider"]))
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if len(provider_tokens) > 1:
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for idx, token in enumerate(provider_tokens):
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id_token_decoded = jwt.decode(token.id_token, verify=False)
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id_token_decoded = jwt.decode(token.id_token, options={"verify_signature": False})
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if (id_token_decoded['email'] == email):
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index = idx
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trans.sa_session.delete(provider_tokens[index])
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@@ -1,26 +0,0 @@
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#!/bin/bash
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#
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# Conda does not have all of Galaxy's dependencies, and the list of which ones it does is always changing. As a result,
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# it's not possible to keep a conda requirements file up to date. However, with Conda >= 4.4, we can use Conda itself to
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# determine which dependencies it can install. Pip will be used (upon Galaxy startup) to install the rest.
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#
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# You should use this script like so:
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#
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# conda create --override-channels -c conda-forge -c bioconda -c defaults \
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# -n <env> --file <(lib/galaxy/dependencies/conda-file.sh) python=2.7
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here=$(dirname $0)
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if ! command -v conda >/dev/null; then
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printf "$0: command not found: conda\n" >&2
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printf "hint: did you run 'conda activate base'?\n" >&2
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exit 1
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fi
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printf "Filtering out Galaxy requirements not available from Conda:" >&2
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egrep -iv $( \
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conda create --override-channels -c conda-forge -c bioconda -c defaults \
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-n _gx_test_env --dry-run --file <(sed 's/;.*//' $here/pinned-requirements.txt) python=2.7 2>&1 \
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| grep '^\s*-' | grep -v https: | awk '{print $NF}' | paste -s -d'|' \
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) $here/pinned-requirements.txt | sed 's/;.*//'
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printf " done\n" >&2
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@@ -1 +0,0 @@
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pipfiles/default/pinned-dev-requirements.txt
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@@ -0,0 +1,232 @@
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--extra-index-url https://wheels.galaxyproject.org/simple
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|
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adal==1.2.5
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aiofiles==0.6.0
|
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alabaster==0.7.12; python_version >= "3.5"
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amqp==5.0.3; python_version >= "3.6"
|
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appdirs==1.4.4; python_version >= "3.6"
|
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argcomplete==1.12.2; python_version >= "3.6" and python_version < "4"
|
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atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
|
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attmap==0.12.11
|
||||
attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
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babel==2.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
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bagit==1.7.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.6"
|
||||
bcrypt==3.2.0; python_version >= "3.6"
|
||||
bdbag==1.5.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4")
|
||||
beaker==1.11.0
|
||||
bioblend==0.14.0; python_version >= "3.5"
|
||||
bleach==3.2.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
boltons==20.2.1
|
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boto3==1.16.57
|
||||
boto==2.49.0
|
||||
botocore==1.19.57
|
||||
bx-python==0.8.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
|
||||
cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
|
||||
cachetools==4.2.0; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
|
||||
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
cffi==1.14.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
|
||||
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
cheetah3==3.2.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
click==7.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
|
||||
cliff==3.6.0; python_version >= "3.6"
|
||||
cloudauthz==0.6.0
|
||||
cloudbridge==2.1.0
|
||||
cmd2==1.4.0; python_version >= "3.6"
|
||||
colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
|
||||
coloredlogs==15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
|
||||
commonmark==0.9.1
|
||||
coverage==5.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
cryptography==3.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
|
||||
cwltool==3.0.20201109103151; python_version >= "3.6" and python_version < "4"
|
||||
dataclasses==0.8; python_version >= "3.6" and python_version < "3.7"
|
||||
debtcollector==2.2.0; python_version >= "3.6"
|
||||
decorator==4.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.6"
|
||||
defusedxml==0.7.0rc2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.0"
|
||||
deprecated==1.2.11; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
|
||||
deprecation==2.1.0
|
||||
dictobj==0.4
|
||||
docopt==0.6.2
|
||||
docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
dogpile.cache==1.1.1; python_version >= "3.6"
|
||||
ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
|
||||
fabric3==1.14.post1
|
||||
fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
|
||||
fastapi==0.63.0; python_version >= "3.6"
|
||||
funcsigs==1.0.2
|
||||
future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
galaxy-sequence-utils==1.1.5
|
||||
google-api-core==1.25.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
google-api-python-client==1.12.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
google-auth-httplib2==0.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
google-auth==1.24.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
googleapis-common-protos==1.52.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
gunicorn==20.0.4; python_version >= "3.4"
|
||||
gxformat2==0.15.0
|
||||
h11==0.12.0; python_version >= "3.6"
|
||||
h5py==3.1.0; python_version >= "3.6"
|
||||
httplib2==0.18.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
humanfriendly==9.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
|
||||
idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
imagesize==1.2.0; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.5"
|
||||
importlib-metadata==3.4.0; python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6")
|
||||
importlib-resources==5.1.0; python_version < "3.7" and python_version >= "3.6"
|
||||
iniconfig==1.1.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
isa-rwval==0.10.9
|
||||
iso8601==0.1.13; python_version >= "3.6"
|
||||
isodate==0.6.0; python_version >= "3.6" and python_version < "4"
|
||||
jinja2==2.11.2; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.5"
|
||||
jmespath==0.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
|
||||
jsonpatch==1.28; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
jsonpointer==2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
keystoneauth1==4.3.0; python_version >= "3.6"
|
||||
kombu==5.0.2; python_version >= "3.6"
|
||||
lockfile==0.12.2; python_version >= "3.6" and python_version < "4"
|
||||
lxml==4.6.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
mako==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
markdown==3.3.3; python_version >= "3.6"
|
||||
markupsafe==1.1.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
mercurial==5.6.1
|
||||
mirakuru==2.3.0; python_version >= "3.6"
|
||||
mistune==0.8.4; python_version >= "3.6" and python_version < "4"
|
||||
msgpack==1.0.2; python_version >= "3.6"
|
||||
munch==2.5.0; python_version >= "3.6"
|
||||
mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4"
|
||||
netaddr==0.8.0; python_version >= "3.6"
|
||||
netifaces==0.10.9; python_version >= "3.6"
|
||||
networkx==1.11; python_version >= "3.6" and python_version < "4"
|
||||
nodeenv==1.5.0
|
||||
nose==1.3.7
|
||||
nosehtml==0.4.6
|
||||
numpy==1.19.5; python_version >= "3.6"
|
||||
oauth2client==4.1.3
|
||||
oauthlib==3.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
openstacksdk==0.52.0; python_version >= "3.6"
|
||||
os-client-config==2.1.0; python_version >= "3.6"
|
||||
os-service-types==1.7.0; python_version >= "3.6"
|
||||
osc-lib==2.3.1; python_version >= "3.6"
|
||||
oslo.config==8.4.0; python_version >= "3.6"
|
||||
oslo.context==3.1.1; python_version >= "3.6"
|
||||
oslo.i18n==5.0.1; python_version >= "3.6"
|
||||
oslo.log==4.4.0; python_version >= "3.6"
|
||||
oslo.serialization==4.0.1; python_version >= "3.6"
|
||||
oslo.utils==4.7.0; python_version >= "3.6"
|
||||
oyaml==1.0
|
||||
packaging==20.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
paramiko==2.7.2
|
||||
parsley==1.3
|
||||
paste==3.5.0
|
||||
pastedeploy==2.1.1
|
||||
pastescript==3.2.0
|
||||
pbr==5.5.1; python_version >= "3.6"
|
||||
pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
port-for==0.4; python_version >= "3.6"
|
||||
prettytable==0.7.2; python_version >= "3.6"
|
||||
protobuf==3.14.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
prov==1.5.1; python_version >= "3.6" and python_version < "4"
|
||||
psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
pulsar-galaxy-lib==0.14.0.dev4
|
||||
py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
|
||||
pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
|
||||
pycryptodome==3.9.9; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
|
||||
pydot==1.4.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
|
||||
pyeventsystem==0.1.0
|
||||
pyfaidx==0.5.9.2
|
||||
pygithub==1.54.1; python_version >= "3.6"
|
||||
pygments==2.7.4; python_version >= "3.5"
|
||||
pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
|
||||
pyjwt==1.7.1; python_version >= "3.6"
|
||||
pykwalify==1.8.0
|
||||
pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
pyperclip==1.8.1; python_version >= "3.6"
|
||||
pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" and sys_platform == "win32" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" and sys_platform == "win32"
|
||||
pysam==0.16.0.1
|
||||
pytest-cov==2.11.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
pytest-html==3.1.1; python_version >= "3.6"
|
||||
pytest-metadata==1.11.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
|
||||
pytest-mock==3.5.1; python_version >= "3.5"
|
||||
pytest-postgresql==2.5.2; python_version >= "3.6"
|
||||
pytest-pythonpath==0.7.3
|
||||
pytest-shard==0.1.2; python_version >= "3.6"
|
||||
pytest==6.2.1; python_version >= "3.6"
|
||||
python-dateutil==2.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
|
||||
python-irodsclient==0.8.5
|
||||
python-jose==3.2.0
|
||||
python-keystoneclient==4.1.1; python_version >= "3.6"
|
||||
python-neutronclient==7.2.1; python_version >= "3.6"
|
||||
python-novaclient==17.2.1; python_version >= "3.6"
|
||||
python-swiftclient==3.10.1
|
||||
python3-openid==3.2.0; python_version >= "3.0"
|
||||
pytz==2020.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
|
||||
pyuwsgi==2.0.19.1.post0
|
||||
pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
|
||||
rdflib-jsonld==0.5.0; python_version >= "3.6" and python_version < "4"
|
||||
rdflib==4.2.2; python_version >= "3.6" and python_version < "4"
|
||||
recommonmark==0.7.1
|
||||
refgenconf==0.9.3
|
||||
repoze.lru==0.7
|
||||
requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
requests-toolbelt==0.9.1; python_version >= "3.5"
|
||||
requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
requestsexceptions==1.4.0; python_version >= "3.6"
|
||||
responses==0.12.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
rfc3986==1.4.0; python_version >= "3.6"
|
||||
routes==2.5.1
|
||||
rsa==4.7; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
|
||||
ruamel.yaml.clib==0.2.2; platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"
|
||||
ruamel.yaml==0.16.5; python_version >= "3.6" and python_version < "4"
|
||||
s3transfer==0.3.4
|
||||
schema-salad==7.0.20201119201711; python_version >= "3.6" and python_version < "4"
|
||||
selenium==3.141.0
|
||||
setuptools-scm==5.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
shellescape==3.4.1; python_version >= "3.6" and python_version < "4"
|
||||
simplejson==3.17.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
|
||||
six==1.15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version >= "3.6" and python_version < "4"
|
||||
snowballstemmer==2.1.0; python_version >= "3.5"
|
||||
social-auth-core==3.3.0
|
||||
sortedcontainers==2.3.0
|
||||
sphinx-markdown-tables==0.0.15
|
||||
sphinx-rtd-theme==0.5.1
|
||||
sphinx==3.4.3; python_version >= "3.5"
|
||||
sphinxcontrib-applehelp==1.0.2; python_version >= "3.5"
|
||||
sphinxcontrib-devhelp==1.0.2; python_version >= "3.5"
|
||||
sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5"
|
||||
sphinxcontrib-jsmath==1.0.1; python_version >= "3.5"
|
||||
sphinxcontrib-qthelp==1.0.3; python_version >= "3.5"
|
||||
sphinxcontrib-serializinghtml==1.1.4; python_version >= "3.5"
|
||||
sqlalchemy-migrate==0.13.0
|
||||
sqlalchemy-utils==0.36.7
|
||||
sqlalchemy==1.3.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
sqlitedict==1.7.0
|
||||
sqlparse==0.4.1; python_version >= "3.5"
|
||||
starlette==0.13.6; python_version >= "3.6" and python_version < "4.0"
|
||||
stevedore==3.3.0; python_version >= "3.6"
|
||||
svgwrite==1.4.1; python_version >= "3.6"
|
||||
tempita==0.5.2
|
||||
tenacity==6.3.1
|
||||
testfixtures==6.17.1
|
||||
toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
tqdm==4.56.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
twill==2.0.1
|
||||
typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"
|
||||
tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version < "4"
|
||||
ubiquerg==0.6.1
|
||||
unidecode==1.1.2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
|
||||
uritemplate==3.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
urllib3==1.26.2; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
|
||||
uvicorn==0.13.3
|
||||
vine==5.0.0; python_version >= "3.6"
|
||||
watchdog==1.0.2; python_version >= "3.6"
|
||||
wcwidth==0.2.5; python_version >= "3.6"
|
||||
webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
|
||||
webob==1.8.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
whoosh==2.7.4
|
||||
wrapt==1.12.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
|
||||
xmlrunner==1.7.7
|
||||
yacman==0.7.0
|
||||
zipp==3.4.0; python_version < "3.7" and python_version >= "3.6"
|
||||
zipstream-new==1.1.8
|
||||
@@ -0,0 +1,4 @@
|
||||
flake8
|
||||
flake8-bugbear
|
||||
flake8-import-order
|
||||
mypy
|
||||
@@ -0,0 +1,11 @@
|
||||
attrs==20.3.0
|
||||
flake8==3.8.4
|
||||
flake8-bugbear==20.11.1
|
||||
flake8-import-order==0.18.1
|
||||
mccabe==0.6.1
|
||||
mypy==0.790
|
||||
mypy-extensions==0.4.3
|
||||
pycodestyle==2.6.0
|
||||
pyflakes==2.2.0
|
||||
typed-ast==1.4.2
|
||||
typing-extensions==3.7.4.3
|
||||
@@ -1 +0,0 @@
|
||||
pipfiles/default/pinned-requirements.txt
|
||||
@@ -0,0 +1,189 @@
|
||||
--extra-index-url https://wheels.galaxyproject.org/simple
|
||||
|
||||
adal==1.2.5
|
||||
aiofiles==0.6.0
|
||||
amqp==5.0.3; python_version >= "3.6"
|
||||
appdirs==1.4.4; python_version >= "3.6"
|
||||
argcomplete==1.12.2; python_version >= "3.6" and python_version < "4"
|
||||
attmap==0.12.11
|
||||
attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
|
||||
babel==2.9.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
bagit==1.7.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.4.0" and python_version < "4" and python_version >= "3.6"
|
||||
bcrypt==3.2.0; python_version >= "3.6"
|
||||
bdbag==1.5.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4")
|
||||
beaker==1.11.0
|
||||
bioblend==0.14.0; python_version >= "3.5"
|
||||
bleach==3.2.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
boltons==20.2.1
|
||||
boto3==1.16.57
|
||||
boto==2.49.0
|
||||
botocore==1.19.57
|
||||
bx-python==0.8.9; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
cachecontrol==0.11.7; python_version >= "3.6" and python_version < "4"
|
||||
cached-property==1.5.2; python_version < "3.8" and python_version >= "3.6"
|
||||
cachetools==4.2.0; python_version >= "3.5" and python_version < "4.0" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0")
|
||||
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
cffi==1.14.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
|
||||
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
cheetah3==3.2.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
click==7.1.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
|
||||
cliff==3.6.0; python_version >= "3.6"
|
||||
cloudauthz==0.6.0
|
||||
cloudbridge==2.1.0
|
||||
cmd2==1.4.0; python_version >= "3.6"
|
||||
colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
coloredlogs==15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
|
||||
cryptography==3.3.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
|
||||
cwltool==3.0.20201109103151; python_version >= "3.6" and python_version < "4"
|
||||
dataclasses==0.8; python_version >= "3.6" and python_version < "3.7"
|
||||
debtcollector==2.2.0; python_version >= "3.6"
|
||||
decorator==4.4.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0" and python_version >= "3.6"
|
||||
defusedxml==0.7.0rc2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.0"
|
||||
deprecation==2.1.0
|
||||
dictobj==0.4
|
||||
docopt==0.6.2
|
||||
docutils==0.16; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
dogpile.cache==1.1.1; python_version >= "3.6"
|
||||
ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
|
||||
fabric3==1.14.post1
|
||||
fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
|
||||
fastapi==0.63.0; python_version >= "3.6"
|
||||
funcsigs==1.0.2
|
||||
future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
galaxy-sequence-utils==1.1.5
|
||||
google-api-core==1.25.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
google-api-python-client==1.12.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
google-auth-httplib2==0.0.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
google-auth==1.24.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
googleapis-common-protos==1.52.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
gxformat2==0.15.0
|
||||
h11==0.12.0; python_version >= "3.6"
|
||||
h5py==3.1.0; python_version >= "3.6"
|
||||
httplib2==0.18.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
humanfriendly==9.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
|
||||
idna==2.10; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
importlib-metadata==3.4.0; python_version < "3.8" and python_version >= "3.6" and (python_version == "3.6" or python_version == "3.7")
|
||||
importlib-resources==5.1.0; python_version < "3.7" and python_version >= "3.6"
|
||||
isa-rwval==0.10.9
|
||||
iso8601==0.1.13; python_version >= "3.6"
|
||||
isodate==0.6.0; python_version >= "3.6" and python_version < "4"
|
||||
jmespath==0.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
|
||||
jsonpatch==1.28; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
jsonpointer==2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
keystoneauth1==4.3.0; python_version >= "3.6"
|
||||
kombu==5.0.2; python_version >= "3.6"
|
||||
lockfile==0.12.2; python_version >= "3.6" and python_version < "4"
|
||||
lxml==4.6.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
mako==1.1.4; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
markdown==3.3.3; python_version >= "3.6"
|
||||
markupsafe==1.1.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
mercurial==5.6.1
|
||||
mistune==0.8.4; python_version >= "3.6" and python_version < "4"
|
||||
msgpack==1.0.2; python_version >= "3.6"
|
||||
munch==2.5.0; python_version >= "3.6"
|
||||
mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4"
|
||||
netaddr==0.8.0; python_version >= "3.6"
|
||||
netifaces==0.10.9; python_version >= "3.6"
|
||||
networkx==1.11; python_version >= "3.6" and python_version < "4"
|
||||
nodeenv==1.5.0
|
||||
nose==1.3.7
|
||||
numpy==1.19.5; python_version >= "3.6"
|
||||
oauth2client==4.1.3
|
||||
oauthlib==3.1.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
openstacksdk==0.52.0; python_version >= "3.6"
|
||||
os-client-config==2.1.0; python_version >= "3.6"
|
||||
os-service-types==1.7.0; python_version >= "3.6"
|
||||
osc-lib==2.3.1; python_version >= "3.6"
|
||||
oslo.config==8.4.0; python_version >= "3.6"
|
||||
oslo.context==3.1.1; python_version >= "3.6"
|
||||
oslo.i18n==5.0.1; python_version >= "3.6"
|
||||
oslo.log==4.4.0; python_version >= "3.6"
|
||||
oslo.serialization==4.0.1; python_version >= "3.6"
|
||||
oslo.utils==4.7.0; python_version >= "3.6"
|
||||
oyaml==1.0
|
||||
packaging==20.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
|
||||
paramiko==2.7.2
|
||||
parsley==1.3
|
||||
paste==3.5.0
|
||||
pastedeploy==2.1.1
|
||||
pastescript==3.2.0
|
||||
pbr==5.5.1; python_version >= "3.6"
|
||||
prettytable==0.7.2; python_version >= "3.6"
|
||||
protobuf==3.14.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
prov==1.5.1; python_version >= "3.6" and python_version < "4"
|
||||
psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
pulsar-galaxy-lib==0.14.0.dev4
|
||||
pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
|
||||
pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
|
||||
pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
|
||||
pycryptodome==3.9.9; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
|
||||
pydot==1.4.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
|
||||
pyeventsystem==0.1.0
|
||||
pyfaidx==0.5.9.2
|
||||
pyinotify==0.9.6; sys_platform != "win32" and sys_platform != "darwin" and sys_platform != "sunos5" and python_version >= "3.6"
|
||||
pyjwt==1.7.1
|
||||
pykwalify==1.8.0
|
||||
pynacl==1.4.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
pyparsing==2.4.7; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
pyperclip==1.8.1; python_version >= "3.6"
|
||||
pyreadline==2.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" and sys_platform == "win32" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0" and sys_platform == "win32"
|
||||
pysam==0.16.0.1
|
||||
python-dateutil==2.8.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
|
||||
python-jose==3.2.0
|
||||
python-keystoneclient==4.1.1; python_version >= "3.6"
|
||||
python-neutronclient==7.2.1; python_version >= "3.6"
|
||||
python-novaclient==17.2.1; python_version >= "3.6"
|
||||
python-swiftclient==3.10.1
|
||||
python3-openid==3.2.0; python_version >= "3.0"
|
||||
pytz==2020.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
|
||||
pyuwsgi==2.0.19.1.post0
|
||||
pyyaml==5.4.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
|
||||
rdflib-jsonld==0.5.0; python_version >= "3.6" and python_version < "4"
|
||||
rdflib==4.2.2; python_version >= "3.6" and python_version < "4"
|
||||
refgenconf==0.9.3
|
||||
repoze.lru==0.7
|
||||
requests-oauthlib==1.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
requests-toolbelt==0.9.1; python_version >= "3.5"
|
||||
requests==2.25.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
|
||||
requestsexceptions==1.4.0; python_version >= "3.6"
|
||||
rfc3986==1.4.0; python_version >= "3.6"
|
||||
routes==2.5.1
|
||||
rsa==4.7; python_version >= "3.5" and python_version < "4" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6")
|
||||
ruamel.yaml.clib==0.2.2; platform_python_implementation == "CPython" and python_version < "3.8" and python_version >= "3.6"
|
||||
ruamel.yaml==0.16.5; python_version >= "3.6" and python_version < "4"
|
||||
s3transfer==0.3.4
|
||||
schema-salad==7.0.20201119201711; python_version >= "3.6" and python_version < "4"
|
||||
setuptools-scm==5.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
|
||||
shellescape==3.4.1; python_version >= "3.6" and python_version < "4"
|
||||
simplejson==3.17.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6"
|
||||
six==1.15.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version >= "3.6" and python_version < "4"
|
||||
social-auth-core==3.3.0
|
||||
sortedcontainers==2.3.0
|
||||
sqlalchemy-migrate==0.13.0
|
||||
sqlalchemy-utils==0.36.7
|
||||
sqlalchemy==1.3.22; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
|
||||
sqlitedict==1.7.0
|
||||
sqlparse==0.4.1; python_version >= "3.5"
|
||||
starlette==0.13.6; python_version >= "3.6" and python_version < "4.0"
|
||||
stevedore==3.3.0; python_version >= "3.6"
|
||||
svgwrite==1.4.1; python_version >= "3.6"
|
||||
tempita==0.5.2
|
||||
tenacity==6.3.1
|
||||
tqdm==4.56.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8"
|
||||
tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version < "4"
|
||||
ubiquerg==0.6.1
|
||||
unidecode==1.1.2; python_version >= "3.0" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.0"
|
||||
uritemplate==3.0.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
|
||||
urllib3==1.26.2; python_version >= "2.7" and python_full_version < "3.0.0" and python_version != "3.4" or python_full_version >= "3.5.0" and python_version < "4" and python_version != "3.4"
|
||||
uvicorn==0.13.3
|
||||
vine==5.0.0; python_version >= "3.6"
|
||||
wcwidth==0.2.5; python_version >= "3.6"
|
||||
webencodings==0.5.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
|
||||
webob==1.8.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
|
||||
whoosh==2.7.4
|
||||
wrapt==1.12.1; python_version >= "3.6"
|
||||
yacman==0.7.0
|
||||
zipp==3.4.0; python_version < "3.7" and python_version >= "3.6"
|
||||
zipstream-new==1.1.8
|
||||
@@ -1,74 +0,0 @@
|
||||
#
|
||||
# These requirements were autogenerated by pipenv
|
||||
# To regenerate from the project's Pipfile, run:
|
||||
#
|
||||
# pipenv lock --requirements --dev-only
|
||||
#
|
||||
|
||||
-i https://wheels.galaxyproject.org/simple
|
||||
--extra-index-url https://pypi.python.org/simple
|
||||
alabaster==0.7.12
|
||||
attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
babel==2.9.0
|
||||
certifi==2020.12.5
|
||||
chardet==3.0.4
|
||||
commonmark==0.9.1
|
||||
coverage==5.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
|
||||
deprecated==1.2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
docutils==0.16
|
||||
gunicorn==20.0.4
|
||||
idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
imagesize==1.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
|
||||
iniconfig==1.1.1
|
||||
jinja2==2.11.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
markdown==3.3.3
|
||||
markupsafe==1.1.1
|
||||
mirakuru==2.3.0; python_version >= '3.6'
|
||||
nose==1.3.7
|
||||
nosehtml==0.4.6
|
||||
packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pluggy==0.13.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
port-for==0.4
|
||||
prettytable==0.7.2
|
||||
psutil==5.7.3
|
||||
py==1.9.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pygithub==1.54
|
||||
pygments==2.7.3; python_version >= '3.5'
|
||||
pyjwt==1.7.1
|
||||
pyparsing==2.4.7
|
||||
pytest-cov==2.10.1
|
||||
pytest-html==3.1.0
|
||||
pytest-metadata==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
|
||||
pytest-mock==3.3.1
|
||||
pytest-postgresql==2.5.2
|
||||
pytest-pythonpath==0.7.3
|
||||
pytest-shard==0.1.1
|
||||
pytest==6.1.2
|
||||
python-irodsclient==0.8.5
|
||||
pytz==2020.4
|
||||
recommonmark==0.6.0
|
||||
requests==2.24.0
|
||||
responses==0.12.1
|
||||
selenium==3.141.0
|
||||
six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
snowballstemmer==2.0.0
|
||||
sphinx-markdown-tables==0.0.15
|
||||
sphinx-rtd-theme==0.5.0
|
||||
sphinx==3.3.1
|
||||
sphinxcontrib-applehelp==1.0.2; python_version >= '3.5'
|
||||
sphinxcontrib-devhelp==1.0.2; python_version >= '3.5'
|
||||
sphinxcontrib-htmlhelp==1.0.3; python_version >= '3.5'
|
||||
sphinxcontrib-jsmath==1.0.1; python_version >= '3.5'
|
||||
sphinxcontrib-qthelp==1.0.3; python_version >= '3.5'
|
||||
sphinxcontrib-serializinghtml==1.1.4; python_version >= '3.5'
|
||||
testfixtures==6.16.0
|
||||
toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
twill==2.0.1
|
||||
urllib3==1.25.11; python_version != '3.4'
|
||||
watchdog==1.0.0
|
||||
wcwidth==0.2.5; sys_platform != 'win32'
|
||||
wrapt==1.12.1
|
||||
xmlrunner==1.7.7
|
||||
zipp==3.4.0; python_version < '3.8'
|
||||
@@ -1,194 +0,0 @@
|
||||
#
|
||||
# These requirements were autogenerated by pipenv
|
||||
# To regenerate from the project's Pipfile, run:
|
||||
#
|
||||
# pipenv lock --requirements
|
||||
#
|
||||
|
||||
-i https://wheels.galaxyproject.org/simple
|
||||
--extra-index-url https://pypi.python.org/simple
|
||||
adal==1.2.5
|
||||
aiofiles==0.6.0
|
||||
amqp==5.0.2; python_version >= '3.6'
|
||||
appdirs==1.4.4
|
||||
argcomplete==1.12.2
|
||||
attmap==0.12.11
|
||||
attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
babel==2.9.0
|
||||
bagit==1.7.0
|
||||
bcrypt==3.2.0; python_version >= '3.6'
|
||||
bdbag==1.5.6
|
||||
beaker==1.11.0
|
||||
bioblend==0.14.0
|
||||
bleach==3.2.1
|
||||
boltons==20.2.1
|
||||
boto3==1.16.33
|
||||
boto==2.49.0
|
||||
botocore==1.19.33
|
||||
bx-python==0.8.9
|
||||
cachecontrol==0.11.7
|
||||
cached-property==1.5.2; python_version < '3.8'
|
||||
cachetools==4.1.1; python_version ~= '3.5'
|
||||
certifi==2020.12.5
|
||||
cffi==1.14.4
|
||||
chardet==3.0.4
|
||||
cheetah3==3.2.6
|
||||
click==7.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
cliff==3.5.0; python_version >= '3.6'
|
||||
cloudauthz==0.6.0
|
||||
cloudbridge==2.1.0
|
||||
cmd2==1.4.0; python_version >= '3.5'
|
||||
colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
coloredlogs==14.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
cryptography==3.3.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
|
||||
cwltool==3.0.20201109103151
|
||||
dataclasses==0.8; python_version < '3.7'
|
||||
debtcollector==2.2.0; python_version >= '3.6'
|
||||
decorator==4.4.2
|
||||
defusedxml==0.6.0; python_version >= '3.0'
|
||||
deprecation==2.1.0
|
||||
dictobj==0.4
|
||||
docopt==0.6.2
|
||||
docutils==0.16
|
||||
dogpile.cache==1.1.1; python_version >= '3.6'
|
||||
ecdsa==0.14.1; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
fabric3==1.14.post1
|
||||
fastapi-utils==0.2.1
|
||||
fastapi==0.62.0
|
||||
future==0.18.2
|
||||
galaxy-sequence-utils==1.1.5
|
||||
google-api-core==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
google-api-python-client==1.12.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
google-auth-httplib2==0.0.4
|
||||
google-auth==1.23.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
googleapis-common-protos==1.52.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
gxformat2==0.15.0
|
||||
h11==0.11.0
|
||||
h5py==3.1.0
|
||||
httplib2==0.18.1
|
||||
humanfriendly==9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
idna==2.10; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
importlib-metadata==3.1.1; python_version == '3.6' and python_version < '3.8'
|
||||
importlib-resources==3.3.0; python_version < '3.7'
|
||||
isa-rwval==0.10.9
|
||||
iso8601==0.1.13
|
||||
isodate==0.6.0
|
||||
jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
jsonpatch==1.28; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
jsonpointer==2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
keystoneauth1==4.3.0; python_version >= '3.6'
|
||||
kombu==5.0.2
|
||||
lockfile==0.12.2
|
||||
lxml==4.6.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
mako==1.1.3
|
||||
markdown==3.3.3
|
||||
markupsafe==1.1.1
|
||||
mercurial==5.6.1
|
||||
mistune==0.8.4
|
||||
msgpack==1.0.0
|
||||
munch==2.5.0
|
||||
mypy-extensions==0.4.3
|
||||
netaddr==0.8.0
|
||||
netifaces==0.10.9
|
||||
networkx==1.11
|
||||
nodeenv==1.5.0
|
||||
nose==1.3.7
|
||||
numpy==1.19.4
|
||||
oauth2client==4.1.3
|
||||
oauthlib==3.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
openstacksdk==0.52.0; python_version >= '3.6'
|
||||
os-client-config==2.1.0
|
||||
os-service-types==1.7.0
|
||||
osc-lib==2.3.0; python_version >= '3.6'
|
||||
oslo.config==8.4.0; python_version >= '3.6'
|
||||
oslo.context==3.1.1; python_version >= '3.6'
|
||||
oslo.i18n==5.0.1; python_version >= '3.6'
|
||||
oslo.log==4.4.0; python_version >= '3.6'
|
||||
oslo.serialization==4.0.1; python_version >= '3.6'
|
||||
oslo.utils==4.7.0; python_version >= '3.6'
|
||||
oyaml==1.0
|
||||
packaging==20.7; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
paramiko==2.7.2
|
||||
parsley==1.3
|
||||
paste==3.5.0
|
||||
pastedeploy==2.1.1
|
||||
pastescript==3.2.0
|
||||
pbr==5.5.1; python_version >= '2.6'
|
||||
prettytable==0.7.2
|
||||
protobuf==3.14.0
|
||||
prov==1.5.1
|
||||
psutil==5.7.3
|
||||
pulsar-galaxy-lib==0.14.0.dev4
|
||||
pyasn1-modules==0.2.8
|
||||
pyasn1==0.4.8
|
||||
pycparser==2.20; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pycryptodome==3.9.9
|
||||
pydantic==1.7.3; python_version >= '3.6'
|
||||
pydot==1.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pyeventsystem==0.1.0
|
||||
pyfaidx==0.5.9.2
|
||||
pyinotify==0.9.6; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
|
||||
pyjwt==1.7.1
|
||||
pykwalify==1.7.0
|
||||
pynacl==1.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pyparsing==2.4.7
|
||||
pyperclip==1.8.1
|
||||
pysam==0.16.0.1
|
||||
python-dateutil==2.8.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
python-jose==3.2.0
|
||||
python-keystoneclient==4.1.1; python_version >= '3.6'
|
||||
python-neutronclient==7.2.1; python_version >= '3.6'
|
||||
python-novaclient==17.2.1; python_version >= '3.6'
|
||||
python-swiftclient==3.10.1
|
||||
python3-openid==3.2.0; python_version >= '3.0'
|
||||
pytz==2020.4
|
||||
pyuwsgi==2.0.19.1.post0
|
||||
pyyaml==5.3.1
|
||||
rdflib-jsonld==0.5.0
|
||||
rdflib==4.2.2
|
||||
refgenconf==0.9.3
|
||||
repoze.lru==0.7
|
||||
requests-oauthlib==1.3.0
|
||||
requests-toolbelt==0.9.1
|
||||
requests==2.24.0
|
||||
requestsexceptions==1.4.0
|
||||
rfc3986==1.4.0
|
||||
routes==2.5.1
|
||||
rsa==4.6; python_version >= '3.5'
|
||||
ruamel.yaml.clib==0.2.2; python_version < '3.8' and platform_python_implementation == 'CPython'
|
||||
ruamel.yaml==0.16.5
|
||||
s3transfer==0.3.3
|
||||
schema-salad==7.0.20201119201711; python_version >= '3.6'
|
||||
setuptools-scm==4.1.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
|
||||
shellescape==3.4.1
|
||||
simplejson==3.17.2; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
six==1.15.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
social-auth-core[openidconnect]==3.3.0
|
||||
sortedcontainers==2.3.0
|
||||
sqlalchemy-migrate==0.13.0
|
||||
sqlalchemy-utils==0.36.7
|
||||
sqlalchemy==1.3.20
|
||||
sqlitedict==1.7.0
|
||||
sqlparse==0.4.1
|
||||
starlette==0.13.6; python_version >= '3.6'
|
||||
stevedore==3.3.0; python_version >= '3.6'
|
||||
svgwrite==1.4
|
||||
tempita==0.5.2
|
||||
tenacity==6.2.0
|
||||
tqdm==4.54.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
typing-extensions==3.7.4.3; python_version < '3.8'
|
||||
tzlocal==2.1
|
||||
ubiquerg==0.6.1
|
||||
unidecode==1.1.1; python_version >= '3.0'
|
||||
uritemplate==3.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
urllib3==1.25.11; python_version != '3.4'
|
||||
uvicorn==0.13.0
|
||||
vine==5.0.0; python_version >= '3.6'
|
||||
wcwidth==0.2.5; sys_platform != 'win32'
|
||||
webencodings==0.5.1
|
||||
webob==1.8.6
|
||||
whoosh==2.7.4
|
||||
wrapt==1.12.1
|
||||
yacman==0.7.0
|
||||
zipp==3.4.0; python_version < '3.8'
|
||||
zipstream-new==1.1.8
|
||||
@@ -1,15 +0,0 @@
|
||||
FROM python:3.6
|
||||
|
||||
ENV DEBIAN_FRONTEND noninteractive
|
||||
ENV LC_ALL C.UTF-8
|
||||
ENV LANG C.UTF-8
|
||||
|
||||
# Install Pipenv
|
||||
RUN apt-get update && apt-get -y upgrade
|
||||
RUN pip install pipenv
|
||||
|
||||
ADD docker_script.sh /docker_script.sh
|
||||
|
||||
WORKDIR /working
|
||||
|
||||
CMD bash /docker_script.sh
|
||||
@@ -1,7 +0,0 @@
|
||||
all:
|
||||
if ! docker inspect galaxy/update-python-dependencies >/dev/null 2>&1; then \
|
||||
docker build --no-cache -t galaxy/update-python-dependencies .; \
|
||||
fi
|
||||
|
||||
clean:
|
||||
docker rmi --force galaxy/update-python-dependencies
|
||||
@@ -1,5 +0,0 @@
|
||||
#!/bin/sh
|
||||
|
||||
pipenv lock -v
|
||||
pipenv lock -r > pinned-requirements.txt
|
||||
pipenv lock -r --dev-only > pinned-dev-requirements.txt
|
||||
@@ -1,15 +0,0 @@
|
||||
[[source]]
|
||||
url = "https://pypi.python.org/simple"
|
||||
verify_ssl = true
|
||||
name = "pypi"
|
||||
|
||||
[dev-packages]
|
||||
|
||||
|
||||
[packages]
|
||||
flake8 = "*"
|
||||
flake8-bugbear = "*"
|
||||
flake8-import-order = "*"
|
||||
|
||||
[requires]
|
||||
python_version = "3.6"
|
||||
@@ -1,18 +0,0 @@
|
||||
#
|
||||
# These requirements were autogenerated by pipenv
|
||||
# To regenerate from the project's Pipfile, run:
|
||||
#
|
||||
# pipenv lock --requirements
|
||||
#
|
||||
|
||||
-i https://pypi.python.org/simple
|
||||
attrs==20.3.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
flake8-bugbear==20.11.1
|
||||
flake8-import-order==0.18.1
|
||||
flake8==3.8.4
|
||||
importlib-metadata==3.1.1; python_version < '3.8'
|
||||
mccabe==0.6.1
|
||||
pycodestyle==2.6.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
pyflakes==2.2.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
|
||||
typing-extensions==3.7.4.3; python_version < '3.8'
|
||||
zipp==3.4.0; python_version >= '3.6'
|
||||
@@ -1,60 +0,0 @@
|
||||
#!/bin/sh
|
||||
set -e
|
||||
|
||||
usage() {
|
||||
cat << EOF
|
||||
Usage: ${0##*/} [-c] [-d]
|
||||
|
||||
Use pipenv to regenerate locked and hashed versions of Galaxy dependencies.
|
||||
Use -c to automatically commit these changes (be sure you have no staged git
|
||||
changes).
|
||||
Use -d to rebuild with Pipenv from the galaxy/update-python-dependencies
|
||||
container. This container can be built by running 'make' from the docker
|
||||
subdirectory.
|
||||
|
||||
EOF
|
||||
}
|
||||
|
||||
commit=0
|
||||
docker=0
|
||||
while getopts ":hcd" opt; do
|
||||
case "$opt" in
|
||||
c)
|
||||
commit=1
|
||||
;;
|
||||
d)
|
||||
docker=1
|
||||
;;
|
||||
h)
|
||||
usage
|
||||
exit 0
|
||||
;;
|
||||
*)
|
||||
usage >&2
|
||||
exit 1
|
||||
;;
|
||||
esac
|
||||
done
|
||||
|
||||
THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
|
||||
ENVS="flake8
|
||||
default"
|
||||
|
||||
export PIPENV_IGNORE_VIRTUALENVS=1
|
||||
for env in $ENVS; do
|
||||
cd "$THIS_DIRECTORY/$env"
|
||||
if [ "$docker" -eq 1 ]; then
|
||||
docker run -v "$(pwd):/working" -t 'galaxy/update-python-dependencies'
|
||||
else
|
||||
sh ../docker/docker_script.sh
|
||||
fi
|
||||
|
||||
if ! grep '==' pinned-dev-requirements.txt ; then
|
||||
rm -f pinned-dev-requirements.txt
|
||||
fi
|
||||
done
|
||||
|
||||
if [ "$commit" -eq 1 ]; then
|
||||
git add -u "$THIS_DIRECTORY"
|
||||
git commit -m "Rev and re-lock Galaxy dependencies"
|
||||
fi
|
||||
Executable
+21
@@ -0,0 +1,21 @@
|
||||
#!/bin/sh
|
||||
set -e
|
||||
|
||||
# You can pass one or more package specifications to this script to add only
|
||||
# them without updating all the rest of the requirements.
|
||||
|
||||
if [ -z "$VIRTUAL_ENV" ]; then
|
||||
echo "Please run this script inside a virtual environment!"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
|
||||
|
||||
pip install --upgrade pip setuptools poetry
|
||||
if [ $# -gt 0 ]; then
|
||||
poetry add --lock "$@"
|
||||
else
|
||||
poetry update -vv --lock
|
||||
fi
|
||||
poetry export -f requirements.txt --without-hashes --output "$THIS_DIRECTORY/pinned-requirements.txt"
|
||||
poetry export --dev -f requirements.txt --without-hashes --output "$THIS_DIRECTORY/dev-requirements.txt"
|
||||
+12
@@ -0,0 +1,12 @@
|
||||
#!/bin/sh
|
||||
set -e
|
||||
|
||||
THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
|
||||
|
||||
LINT_VENV=$(mktemp -d "${TMPDIR:-/tmp}/lint_venv.XXXXXXXXXX")
|
||||
virtualenv -p python3 "${LINT_VENV}"
|
||||
. "${LINT_VENV}/bin/activate"
|
||||
pip install --upgrade pip setuptools
|
||||
pip install -r "${THIS_DIRECTORY}/lint-requirements.txt"
|
||||
pip freeze -l > "${THIS_DIRECTORY}/pinned-lint-requirements.txt"
|
||||
rm -rf "${LINT_VENV}"
|
||||
@@ -42,7 +42,7 @@ class OIDC(JSAppLauncher):
|
||||
rtv.append({'id': trans.app.security.encode_id(authnz.id), 'provider': authnz.provider, 'email': authnz.uid})
|
||||
# Add cilogon and custos identities
|
||||
for token in trans.user.custos_auth:
|
||||
userinfo = jwt.decode(token.id_token, verify=False)
|
||||
userinfo = jwt.decode(token.id_token, options={"verify_signature": False})
|
||||
rtv.append({'id': trans.app.security.encode_id(token.id), 'provider': token.provider, 'email': userinfo['email']})
|
||||
return rtv
|
||||
|
||||
|
||||
@@ -1,14 +1,79 @@
|
||||
[[source]]
|
||||
url = "https://wheels.galaxyproject.org/simple"
|
||||
verify_ssl = true
|
||||
[tool.poetry]
|
||||
name = "galaxy"
|
||||
version = "21.01"
|
||||
description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
|
||||
authors = ["Galaxy Contributors"]
|
||||
license = "AFL-3.0"
|
||||
readme = "README.rst"
|
||||
homepage = "https://galaxyproject.org/"
|
||||
repository = "https://github.com/galaxyproject/galaxy/"
|
||||
documentation = "https://docs.galaxyproject.org/"
|
||||
|
||||
[[source]]
|
||||
url = "https://pypi.python.org/simple"
|
||||
verify_ssl = true
|
||||
name = "pypi"
|
||||
[[tool.poetry.source]]
|
||||
name = "galaxyproject"
|
||||
url = "https://wheels.galaxyproject.org/simple"
|
||||
|
||||
[dev-packages]
|
||||
[tool.poetry.dependencies]
|
||||
aiofiles = "*"
|
||||
Babel = "*"
|
||||
bdbag = "*"
|
||||
Beaker = "1.11.0"
|
||||
bioblend = "*"
|
||||
bleach = "*"
|
||||
boltons = "*"
|
||||
boto = "*"
|
||||
bx-python = "*"
|
||||
Cheetah3 = "*"
|
||||
cloudauthz = "==0.6.0"
|
||||
cloudbridge = "*"
|
||||
cwltool = "==3.0.20201109103151"
|
||||
dictobj = "*"
|
||||
docutils = "*"
|
||||
Fabric3 = "*"
|
||||
fastapi = "*"
|
||||
fastapi-utils = "*"
|
||||
future = "*"
|
||||
galaxy_sequence_utils = "*"
|
||||
gxformat2 = "*"
|
||||
h5py = "!=2.7.0, !=2.7.1"
|
||||
isa-rwval = "*"
|
||||
kombu = "*"
|
||||
Mako = "*"
|
||||
Markdown = "*"
|
||||
MarkupSafe = "*"
|
||||
Mercurial = "*"
|
||||
nodeenv = "*"
|
||||
nose = "*"
|
||||
numpy = "*"
|
||||
paramiko = "*"
|
||||
Parsley = "*"
|
||||
Paste = "*"
|
||||
psutil = "*"
|
||||
pulsar-galaxy-lib = "==0.14.0.dev4"
|
||||
pycryptodome = "*"
|
||||
pykwalify = "*"
|
||||
pyparsing = "*"
|
||||
pysam = "*"
|
||||
python = "^3.6"
|
||||
pyuwsgi = "*"
|
||||
PyYAML = "*"
|
||||
refgenconf = ">=0.7.0"
|
||||
requests = "*"
|
||||
Routes = "*"
|
||||
social-auth-core = {version = "==3.3.0", extras = ["openidconnect"]}
|
||||
sortedcontainers = "*"
|
||||
SQLAlchemy = "*"
|
||||
sqlalchemy-migrate = "*"
|
||||
SQLAlchemy-Utils = "!=0.36.8" # https://github.com/kvesteri/sqlalchemy-utils/issues/462
|
||||
sqlitedict = "*"
|
||||
sqlparse = "*"
|
||||
svgwrite = "*"
|
||||
uvicorn = "*"
|
||||
WebOb = "*"
|
||||
Whoosh = "*"
|
||||
zipstream-new = "*"
|
||||
|
||||
[tool.poetry.dev-dependencies]
|
||||
gunicorn = "*"
|
||||
lxml = "!=4.2.2"
|
||||
NoseHTML = "*"
|
||||
@@ -16,6 +81,7 @@ pygithub = "*"
|
||||
pytest = "*"
|
||||
pytest-cov = "*"
|
||||
pytest-html = "*"
|
||||
python-irodsclient = "*"
|
||||
pytest-mock = "*"
|
||||
pytest-pythonpath = "*"
|
||||
pytest-postgresql = "*"
|
||||
@@ -29,68 +95,3 @@ sphinx_rtd_theme = "*"
|
||||
testfixtures = "*"
|
||||
twill = "*"
|
||||
watchdog = "*"
|
||||
python-irodsclient = "*"
|
||||
|
||||
[packages]
|
||||
numpy = "*"
|
||||
bx-python = "*"
|
||||
MarkupSafe = "*"
|
||||
Markdown = "*"
|
||||
# Optional requirement for markdown export.
|
||||
# Weasyprint = "==0.42"
|
||||
PyYAML = "*"
|
||||
SQLAlchemy = "*"
|
||||
SQLAlchemy-Utils = "!=0.36.8" # https://github.com/kvesteri/sqlalchemy-utils/issues/462
|
||||
Mercurial = "*"
|
||||
nodeenv = "*"
|
||||
pycryptodome = "*"
|
||||
pyuwsgi = "*"
|
||||
pysam = "*"
|
||||
bdbag = "*"
|
||||
bleach = "*"
|
||||
cwltool = "==3.0.20201109103151"
|
||||
isa-rwval = "*"
|
||||
boltons = "*"
|
||||
Paste = "*"
|
||||
docutils = "*"
|
||||
uvicorn = "*"
|
||||
fastapi = "*"
|
||||
fastapi-utils = "*"
|
||||
aiofiles = "*"
|
||||
Routes = "*"
|
||||
WebOb = "*"
|
||||
Mako = "*"
|
||||
Babel = "*"
|
||||
Beaker = "*"
|
||||
dictobj = "*"
|
||||
nose = "*"
|
||||
Parsley = "*"
|
||||
sortedcontainers = "*"
|
||||
Whoosh = "*"
|
||||
galaxy_sequence_utils = "*"
|
||||
h5py = "!=2.7.0, !=2.7.1"
|
||||
pykwalify = "*"
|
||||
"Cheetah3" = "*"
|
||||
requests = "<2.25" # PyGitHub 1.54 requires requests < 2.25
|
||||
bioblend = "*"
|
||||
boto = "*"
|
||||
kombu = "*"
|
||||
psutil = "*"
|
||||
pulsar-galaxy-lib = "==0.14.0.dev4"
|
||||
sqlalchemy-migrate = "*"
|
||||
sqlitedict = "*"
|
||||
sqlparse = "*"
|
||||
svgwrite = "*"
|
||||
pyparsing = "*"
|
||||
"Fabric3" = "*"
|
||||
paramiko = "*"
|
||||
cloudbridge = "*"
|
||||
social-auth-core = {version = "==3.3.0", extras = ['openidconnect']}
|
||||
cloudauthz = "==0.6.0"
|
||||
gxformat2 = "*"
|
||||
refgenconf = ">=0.7.0"
|
||||
future = "*"
|
||||
zipstream-new = "*"
|
||||
|
||||
[requires]
|
||||
python_version = "3.6"
|
||||
@@ -192,7 +192,7 @@ fi
|
||||
|
||||
requirement_args="-r requirements.txt"
|
||||
if [ $DEV_WHEELS -eq 1 ]; then
|
||||
requirement_args="$requirement_args -r ${GALAXY_DEV_REQUIREMENTS}"
|
||||
requirement_args="-r ${GALAXY_DEV_REQUIREMENTS}"
|
||||
fi
|
||||
|
||||
[ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
|
||||
|
||||
@@ -15,6 +15,7 @@ import requests
|
||||
|
||||
from galaxy.authnz import custos_authnz
|
||||
from galaxy.model import CustosAuthnzToken, User
|
||||
from galaxy.util import unicodify
|
||||
from ..unittest_utils.galaxy_mock import MockTrans
|
||||
|
||||
|
||||
@@ -83,7 +84,7 @@ class CustosAuthnzTestCase(unittest.TestCase):
|
||||
|
||||
@property
|
||||
def test_id_token(self):
|
||||
return jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None).decode()
|
||||
return unicodify(jwt.encode({'nonce': self.test_nonce_hash}, key=None, algorithm=None))
|
||||
|
||||
def mock_create_oauth2_session(self, custos_authnz):
|
||||
orig_create_oauth2_session = custos_authnz._create_oauth2_session
|
||||
@@ -360,12 +361,12 @@ class CustosAuthnzTestCase(unittest.TestCase):
|
||||
)
|
||||
self.assertEqual(0, len(self.trans.sa_session.items))
|
||||
|
||||
test_id_token = jwt.encode({
|
||||
test_id_token = unicodify(jwt.encode({
|
||||
'nonce': self.test_nonce_hash,
|
||||
'email': self.test_email,
|
||||
'preferred_username': self.test_username,
|
||||
'sub': self.test_sub},
|
||||
key=None, algorithm=None).decode()
|
||||
'sub': self.test_sub
|
||||
}, key=None, algorithm=None))
|
||||
|
||||
self._raw_token = {
|
||||
"access_token": self.test_access_token,
|
||||
|
||||
@@ -28,9 +28,8 @@ setenv =
|
||||
check_indexes: GALAXY_TEST_FORCE_DATABASE_MIGRATION=1
|
||||
check_indexes: GALAXY_SKIP_CLIENT_BUILD=1
|
||||
deps =
|
||||
lint,lint_docstring,lint_docstring_include_list: -rlib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
|
||||
lint,lint_docstring,lint_docstring_include_list,mypy: -rlib/galaxy/dependencies/pinned-lint-requirements.txt
|
||||
unit: mock-ssh-server
|
||||
mypy: mypy
|
||||
|
||||
[testenv:mulled]
|
||||
commands = bash run_tests.sh --skip-venv -u test/unit/tool_util/mulled
|
||||
|
||||
Reference in New Issue
Block a user