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Merge pull request #15264 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
Dannon
2023-01-03 08:52:34 -05:00
committed by GitHub
parent 9ca8a7ec06 f9de592a4d
commit c8b4904da2
11 changed files with 25 additions and 30 deletions
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lib/galaxy/datatypes/binary.py
+5 -5
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@@ -749,13 +749,13 @@ class Bam(BamNative):
cmd = [
"python",
"-c",
f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')",
f"import pysam; pysam.set_verbosity(0); pysam.index('-o', '{index_name}', '{file_name}')",
]
else:
cmd = [
"python",
"-c",
f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')",
f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '-o', '{index_name}', '{file_name}')",
]
with open(os.devnull, "w") as devnull:
subprocess.check_call(cmd, stderr=devnull, shell=False)
@@ -786,9 +786,9 @@ class Bam(BamNative):
)
if index_flag == "-b":
# IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
pysam.index(dataset.file_name, index_file.file_name) # type: ignore [attr-defined]
pysam.index("-o", index_file.file_name, dataset.file_name) # type: ignore [attr-defined]
else:
pysam.index(index_flag, dataset.file_name, index_file.file_name) # type: ignore [attr-defined]
pysam.index(index_flag, "-o", index_file.file_name, dataset.file_name) # type: ignore [attr-defined]
dataset.metadata.bam_index = index_file
def sniff(self, filename: str) -> bool:
@@ -979,7 +979,7 @@ class CRAM(Binary):
def set_index_file(self, dataset: "DatasetInstance", index_file) -> bool:
try:
pysam.index(dataset.file_name, index_file.file_name) # type: ignore [attr-defined]
pysam.index("-o", index_file.file_name, dataset.file_name) # type: ignore [attr-defined]
return True
except Exception as exc:
log.warning("%s, set_index_file Exception: %s", self, exc)
lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
+1 -1
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@@ -16,7 +16,7 @@ python '$__tool_directory__/cram_to_bam.py' '$input' '$output'
<param name="input" ftype="cram" value="2.cram"/>
<output name="output" ftype="bam">
<assert_contents>
<has_size value="57232"/>
<has_size value="60331"/>
</assert_contents>
</output>
</test>
lib/galaxy/dependencies/dev-requirements.txt
+2 -2
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@@ -27,7 +27,7 @@ commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.11"
coverage[toml]==7.0.1 ; python_version >= "3.7" and python_version < "3.11"
cwltest==2.2.20210901154959 ; python_version >= "3.7" and python_version < "3.11"
cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.11"
darker==1.6.0 ; python_version >= "3.7" and python_version < "3.11"
darker==1.6.1 ; python_version >= "3.7" and python_version < "3.11"
defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11"
deprecated==1.2.13 ; python_version >= "3.7" and python_version < "3.11"
docutils==0.16 ; python_version >= "3.7" and python_version < "3.11"
@@ -66,7 +66,7 @@ packaging==21.3 ; python_version >= "3.7" and python_version < "3.11"
pathspec==0.10.3 ; python_version >= "3.7" and python_version < "3.11"
pillow==9.3.0 ; python_version >= "3.7" and python_version < "3.11"
pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.11"
platformdirs==2.6.0 ; python_version >= "3.7" and python_version < "3.11"
platformdirs==2.6.2 ; python_version >= "3.7" and python_version < "3.11"
pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.11"
port-for==0.6.3 ; python_version >= "3.7" and python_version < "3.11"
prettytable==3.5.0 ; python_version >= "3.7" and python_version < "3.11"
lib/galaxy/dependencies/pinned-requirements.txt
+6 -6
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@@ -77,7 +77,7 @@ h5py==3.7.0 ; python_version >= "3.7" and python_version < "3.11"
humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.11"
idna==3.4 ; python_version >= "3.7" and python_version < "3.11"
importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.10"
importlib-resources==5.10.1 ; python_version >= "3.7" and python_version < "3.11"
importlib-resources==5.10.2 ; python_version >= "3.7" and python_version < "3.11"
isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.11"
isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.11"
jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.11"
@@ -118,8 +118,8 @@ pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.11"
pycparser==2.21 ; python_version >= "3.7" and python_version < "3.11"
pycryptodome==3.16.0 ; python_version >= "3.7" and python_version < "3.11"
pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.11"
pydantic==1.10.2 ; python_version >= "3.7" and python_version < "3.11"
pydantic[email]==1.10.2 ; python_version >= "3.7" and python_version < "3.11"
pydantic==1.10.4 ; python_version >= "3.7" and python_version < "3.11"
pydantic[email]==1.10.4 ; python_version >= "3.7" and python_version < "3.11"
pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.11"
pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.11"
pyfaidx==0.7.1 ; python_version >= "3.7" and python_version < "3.11"
@@ -131,8 +131,8 @@ pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.11"
pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.11"
pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.11"
pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7"
pyrsistent==0.19.2 ; python_version >= "3.7" and python_version < "3.11"
pysam==0.19.1 ; python_version >= "3.7" and python_version < "3.11"
pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.11"
pysam==0.20.0 ; python_version >= "3.7" and python_version < "3.11"
python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.11"
python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.11"
python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.11"
@@ -147,7 +147,7 @@ repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.11"
requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.11"
requests-toolbelt==0.10.1 ; python_version >= "3.7" and python_version < "3.11"
requests==2.28.1 ; python_version >= "3.7" and python_version < "3.11"
rich==12.6.0 ; python_version >= "3.7" and python_version < "3.11"
rich==13.0.0 ; python_version >= "3.7" and python_version < "3.11"
rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.11"
routes==2.5.1 ; python_version >= "3.7" and python_version < "3.11"
rsa==4.9 ; python_version >= "3.7" and python_version < "3.11"
lib/galaxy/tool_util/deps/mulled/get_tests.py
+5 -6
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@@ -142,6 +142,7 @@ def find_anaconda_versions(name, anaconda_channel="bioconda"):
Find a list of available anaconda versions for a given container name
"""
r = requests.get(f"https://anaconda.org/{anaconda_channel}/{name}/files", timeout=MULLED_SOCKET_TIMEOUT)
r.raise_for_status()
urls = []
for line in r.text.split("\n"):
if "download/linux" in line:
@@ -173,12 +174,9 @@ def get_alternative_versions(filepath, filename, recipes_path=None, github_repo=
return [n.replace(f"{recipes_path}/", "") for n in glob(f"{recipes_path}/{filepath}/*/{filename}")]
# else use the GitHub API:
versions = []
r = json.loads(
requests.get(
f"https://api.github.com/repos/{github_repo}/contents/{filepath}", timeout=MULLED_SOCKET_TIMEOUT
).text
)
for subfile in r:
r = requests.get(f"https://api.github.com/repos/{github_repo}/contents/{filepath}", timeout=MULLED_SOCKET_TIMEOUT)
r.raise_for_status()
for subfile in json.loads(r.text):
if subfile["type"] == "dir":
if (
requests.get(
@@ -295,6 +293,7 @@ def hashed_test_search(
containers = []
for package in packages:
r = requests.get(f"https://anaconda.org/bioconda/{package[0]}/files", timeout=MULLED_SOCKET_TIMEOUT)
r.raise_for_status()
p = "-".join(package)
for line in r.text.split("\n"):
if p in line:
packages/app/setup.cfg
+1 -1
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@@ -60,7 +60,7 @@ install_requires =
pebble
pulsar-galaxy-lib>=0.15.0.dev0
pydantic
pysam
pysam>=0.20
PyJWT
PyYAML
refgenconf>=0.12.0
packages/data/setup.cfg
+1 -1
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@@ -49,7 +49,7 @@ install_requires =
pydantic[email]
pylibmagic
python-magic
pysam
pysam>=0.20
rocrate
social-auth-core[openidconnect]==4.0.3
SQLAlchemy>=1.4.25,<2
pyproject.toml
+1 -1
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@@ -83,7 +83,7 @@ PyJWT = "*"
pykwalify = "*"
pylibmagic = "*"
pyparsing = "*"
pysam = "*"
pysam = ">=0.20"
python = ">=3.7,<3.11" # Keep maximum version strict to appease numpy and scipy
python-dateutil = "*"
python-magic = "*"
test-data/2.cram
BIN
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Binary file not shown.
test/unit/data/datatypes/test_cram.py
+1 -5
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@@ -1,5 +1,3 @@
import os
import pysam
from galaxy.datatypes.binary import CRAM
@@ -12,9 +10,7 @@ from .util import (
def test_cram():
c = CRAM()
with get_input_files("2.cram") as input_files, get_dataset(input_files[0], index_attr="cram_index") as dataset:
assert os.path.exists(dataset.metadata.cram_index.file_name) is False
c.set_index_file(dataset=dataset, index_file=dataset.metadata.cram_index)
assert os.path.exists(dataset.metadata.cram_index.file_name) is True
assert c.set_index_file(dataset=dataset, index_file=dataset.metadata.cram_index) is True
c.set_meta(dataset)
pysam.AlignmentFile(dataset.file_name, index_filename=dataset.metadata.cram_index.file_name)
assert dataset.metadata.cram_version == "3.0"
test/unit/data/datatypes/util.py
+2 -2
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@@ -36,7 +36,7 @@ class MockDataset:
@contextmanager
def get_dataset(filename, index_attr="bam_index", dataset_id=1, has_data=True):
dataset = MockDataset(dataset_id)
with get_input_files(filename) as input_files, get_tmp_path() as index_path:
with get_input_files(filename) as input_files, get_tmp_path(should_exist=True) as index_path:
dataset.file_name = input_files[0]
index = MockMetadata()
index.file_name = index_path
@@ -64,6 +64,6 @@ def get_input_files(*args):
yield test_files
new_md5_sums = [md5_hash_file(f) for f in test_files]
for old_hash, new_hash, f in zip(md5_sums, new_md5_sums, test_files):
assert old_hash == new_hash, "Unexpected change of content for file %s" % f
assert old_hash == new_hash, f"Unexpected change of content for file {f}"
finally:
shutil.rmtree(temp_dir, ignore_errors=True)