[med-svn] [Git][med-team/python-deeptools][master] 2 commits: New upstream version 3.5.6+dfsg
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sat Feb 8 21:01:48 GMT 2025
Alexandre Detiste pushed to branch master at Debian Med / python-deeptools
Commits:
63101d35 by Alexandre Detiste at 2025-02-08T21:59:31+01:00
New upstream version 3.5.6+dfsg
- - - - -
844fb99f by Alexandre Detiste at 2025-02-08T21:59:42+01:00
Update upstream source from tag 'upstream/3.5.6+dfsg'
Update to upstream version '3.5.6+dfsg'
with Debian dir 42e7690bf12079f55751b8d1f4f7362a5272599a
- - - - -
14 changed files:
- − .github/test_and_build.yml
- .github/workflows/planemo.yml
- .github/workflows/pypi.yml
- .github/workflows/test.yml
- deeptools/bigwigAverage.py
- deeptools/bigwigCompare.py
- deeptools/computeMatrix.py
- deeptools/computeMatrixOperations.py
- deeptools/heatmapper.py
- deeptools/multiBigwigSummary.py
- deeptools/plotCoverage.py
- deeptools/plotFingerprint.py
- galaxy/wrapper/deepTools_macros.xml
- pyproject.toml
Changes:
=====================================
.github/test_and_build.yml deleted
=====================================
@@ -1,20 +0,0 @@
-channels:
- - conda-forge
- - bioconda
-dependencies:
- - python > 3.7
- - numpy
- - scipy
- - flake8
- - pysam
- - deeptoolsintervals
- - pytest
- - samtools
- - py2bit
- - pyBigWig
- - twine
- - pip
- - tomli # remove dependency when lowest supported version is py 3.11
- - pip:
- - build
- - planemo
\ No newline at end of file
=====================================
.github/workflows/planemo.yml
=====================================
@@ -2,16 +2,12 @@ name: Planemo
on: [push, pull_request]
env:
- GALAXY_BRANCH: release_23.1
+ GALAXY_BRANCH: release_24.1
defaults:
run:
shell: bash -l {0}
-# setup micromamba doesn't work as galaxy setup by planemo requires conda.
-# installing conda over into micromamba built env screws up the PATH
-# setup-miniconda + changing over to libmamba to solve is the easiest workaround
-
jobs:
planemo_test:
name: Planemo test
@@ -20,26 +16,22 @@ jobs:
matrix:
chunk: [1, 2, 3]
steps:
- - uses: actions/checkout at v3
- - uses: conda-incubator/setup-miniconda at v2
+ - uses: actions/checkout at v4
+ - uses: conda-incubator/setup-miniconda at v3
with:
miniconda-version: "latest"
auto-activate-base: true
- - name: setup env
+ python-version: "3.12"
+ - name: get samtools
run: |
- conda env list
- conda install -n base conda-libmamba-solver
- conda config --set solver libmamba
- conda env create -f .github/test_and_build.yml -n test_and_build
+ conda install -c conda-forge -c bioconda samtools
- name: pip install
run: |
- conda activate test_and_build
- pip install .
+ pip install .[actions]
- name: planemo
run: |
- conda activate test_and_build
./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
- - uses: actions/upload-artifact at v3
+ - uses: actions/upload-artifact at v4
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
@@ -47,29 +39,17 @@ jobs:
name: Combine chunked test results
needs: planemo_test
runs-on: ubuntu-latest
- strategy:
- matrix:
- python-version: ['3.8', '3.11']
steps:
- - uses: actions/download-artifact at v3
+ - uses: actions/download-artifact at v4
with:
path: artifacts
- - uses: actions/setup-python at v4
- with:
- python-version: ${{ matrix.python-version }}
- - name: Cache .cache/pip
- uses: actions/cache at v3
- id: cache-pip
- with:
- path: ~/.cache/pip
- key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
- name: Combine outputs
uses: galaxyproject/planemo-ci-action at v1
id: combine
with:
mode: combine
html-report: true
- - uses: actions/upload-artifact at v3
+ - uses: actions/upload-artifact at v4
with:
name: 'All tool test results'
path: upload
=====================================
.github/workflows/pypi.yml
=====================================
@@ -15,15 +15,14 @@ jobs:
name: upload to pypi
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v3
- - uses: mamba-org/setup-micromamba at main
+ - uses: actions/checkout at v4
+ - uses: actions/setup-python at v5
with:
- environment-file: .github/test_and_build.yml
- cache-downloads: true
- environment-name: test_and_build
+ python-version: '3.12'
+ cache: 'pip'
- name: build
run: |
- micromamba activate test_and_build
+ pip install .[actions]
rm -f dist/*
python -m build
- name: upload
@@ -31,5 +30,4 @@ jobs:
TWINE_USERNAME: "__token__"
TWINE_PASSWORD: ${{ secrets.pypi_password }}
run: |
- micromamba activate test_and_build
twine upload dist/*
=====================================
.github/workflows/test.yml
=====================================
@@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
if: github.base_ref == 'master'
steps:
- - uses: actions/checkout at v3
+ - uses: actions/checkout at v4
- name: Check path
run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
- name: Get Version of Deeptools
@@ -40,30 +40,26 @@ jobs:
name: Test on Linux
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout at v3
- - uses: mamba-org/setup-micromamba at main
+ - uses: actions/checkout at v4
+ - uses: actions/setup-python at v5
with:
- environment-file: .github/test_and_build.yml
- cache-downloads: true
- environment-name: test_and_build
+ python-version: '3.12'
+ cache: 'pip'
- name: pip install
run: |
- micromamba activate test_and_build
- pip install .
+ pip install .[actions]
- name: PEP8
run: |
micromamba activate test_and_build
flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605
- name: Test deepTools
run: |
- micromamba activate test_and_build
pytest -v
- name: make an artifact
run: |
- micromamba activate test_and_build
rm -f dist/*
python -m build
- - uses: actions/upload-artifact at v3
+ - uses: actions/upload-artifact at v4
with:
name: "distfiles"
path: "dist"
@@ -73,14 +69,14 @@ jobs:
needs: build-linux
strategy:
matrix:
- python-version: ['3.8','3.9','3.10', '3.11', '3.12']
+ python-version: ['3.9','3.10', '3.11', '3.12']
steps:
- - uses: actions/checkout at v3
- - uses: actions/download-artifact at v3
+ - uses: actions/checkout at v4
+ - uses: actions/download-artifact at v4
with:
name: "distfiles"
path: ~/dist/
- - uses: actions/setup-python at v4
+ - uses: actions/setup-python at v5
with:
python-version: ${{ matrix.python-version }}
cache: 'pip'
@@ -96,17 +92,14 @@ jobs:
name: Test on OSX
runs-on: macOS-latest
steps:
- - uses: actions/checkout at v3
- - uses: mamba-org/setup-micromamba at main
+ - uses: actions/checkout at v4
+ - uses: actions/setup-python at v5
with:
- environment-file: .github/test_and_build.yml
- cache-downloads: true
- environment-name: test_and_build
+ python-version: '3.12'
+ cache: 'pip'
- name: pip install
run: |
- micromamba activate test_and_build
- pip install .
+ pip install .[actions]
- name: Test deepTools
run: |
- micromamba activate test_and_build
pytest -v
=====================================
deeptools/bigwigAverage.py
=====================================
@@ -55,8 +55,7 @@ def parse_arguments(args=None):
def getType(fname):
"""
- Tries to determine if a file is a wiggle file a bigWig file.
- Returns 'wiggle' if the file name ends with .wig, otherwise 'bigwig'
+ Tries to determine if a file is a wiggle, a bedgraph, or a bigWig file.
"""
if fname.endswith(".wig") or fname.endswith(".wiggle"):
return "wiggle"
=====================================
deeptools/bigwigCompare.py
=====================================
@@ -99,8 +99,7 @@ def parse_arguments(args=None):
def getType(fname):
"""
- Tries to determine if a file is a wiggle file or a bigWig file.
- Returns 'wiggle' if the file name ends with .wig, otherwise 'bigwig'
+ Tries to determine if a file is a wiggle, a bedgraph or a bigWig.
"""
if fname.endswith(".wig") or fname.endswith(".wiggle"):
return "wiggle"
=====================================
deeptools/computeMatrix.py
=====================================
@@ -355,6 +355,14 @@ def process_args(args=None):
if args.quiet is True:
args.verbose = False
+ # Ensure before and after region length is positive
+ if args.beforeRegionStartLength < 0:
+ print(f"beforeRegionStartLength changed from {args.beforeRegionStartLength} into {abs(args.beforeRegionStartLength)}")
+ args.beforeRegionStartLength = abs(args.beforeRegionStartLength)
+ if args.afterRegionStartLength < 0:
+ print(f"afterRegionStartLength changed from {args.afterRegionStartLength} into {abs(args.afterRegionStartLength)}")
+ args.afterRegionStartLength = abs(args.afterRegionStartLength)
+
if args.command == 'scale-regions':
args.nanAfterEnd = False
args.referencePoint = None
=====================================
deeptools/computeMatrixOperations.py
=====================================
@@ -546,7 +546,7 @@ def cbindMatrices(hm, args):
# Add on additional NA initialized columns
ncol = hm.matrix.matrix.shape[1]
hm.matrix.matrix = np.hstack((hm.matrix.matrix, np.empty(hm2.matrix.matrix.shape)))
- hm.matrix.matrix[:, ncol:] = np.NAN
+ hm.matrix.matrix[:, ncol:] = np.nan
# Update the values
for idx2, group in enumerate(hm2.parameters["group_labels"]):
=====================================
deeptools/heatmapper.py
=====================================
@@ -376,7 +376,7 @@ class heatmapper(object):
# create an empty matrix to store the values
sub_matrix = np.zeros((len(regions), matrix_cols))
- sub_matrix[:] = np.NAN
+ sub_matrix[:] = np.nan
j = 0
sub_regions = []
=====================================
deeptools/multiBigwigSummary.py
=====================================
@@ -41,7 +41,7 @@ A detailed sub-commands help is available by typing:
conflict_handler='resolve')
parser.add_argument('--version', action='version',
- version='multiBigwigSummary {}'.format(version('deeptools')))
+ version='%(prog)s {}'.format(version('deeptools')))
subparsers = parser.add_subparsers(
title="commands",
dest='command',
=====================================
deeptools/plotCoverage.py
=====================================
@@ -50,7 +50,7 @@ detailed usage help:
'help: plotCoverage -h / plotCoverage --help\n')
parser.add_argument('--version', action='version',
- version='plotCoverage {}'.format(version('deeptools')))
+ version='%(prog)s {}'.format(version('deeptools')))
return parser
=====================================
deeptools/plotFingerprint.py
=====================================
@@ -203,10 +203,10 @@ def getCHANCE(args, idx, mat):
"""
# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
- return [np.NAN, np.NAN, np.NAN]
+ return [np.nan, np.nan, np.nan]
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
- return [np.NAN, np.NAN, np.NAN]
+ return [np.nan, np.nan, np.nan]
subMatrix = np.copy(mat[:, [idx, refIdx]])
subMatrix[np.isnan(subMatrix)] = 0
@@ -272,10 +272,10 @@ def getJSD(args, idx, mat):
# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
- return np.NAN
+ return np.nan
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
- return np.NAN
+ return np.nan
# These will hold the coverage histograms
chip = np.zeros(MAXLEN, dtype=int)
@@ -339,7 +339,7 @@ def getJSDcommon(chip, input):
if abs(sum(PMFinput) - 1) > 0.01 or abs(sum(PMFchip) - 1) > 0.01:
sys.stderr.write("Warning: At least one PMF integral is significantly different from 1! The JSD will not be returned")
- return np.NAN
+ return np.nan
# Compute the JSD from the PMFs
M = (PMFinput + PMFchip) / 2.0
=====================================
galaxy/wrapper/deepTools_macros.xml
=====================================
@@ -1,7 +1,7 @@
<macros>
<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
- <token name="@TOOL_VERSION@">3.5.5</token>
+ <token name="@TOOL_VERSION@">3.5.6</token>
<token name="@GALAXY_VERSION@">22.05</token>
<xml name="requirements">
<requirements>
=====================================
pyproject.toml
=====================================
@@ -5,7 +5,7 @@ requires = [
[project]
name = "deepTools"
-version = "3.5.5"
+version = "3.5.6"
authors = [
{name="Fidel Ramirez"},
{name="Devon P Ryan"},
@@ -19,9 +19,9 @@ authors = [
{name="Thomas Manke"},
{email="bioinfo-core at ie-freiburg.mpg.de"}
]
-requires-python = ">=3.8"
+requires-python = "> 3.8"
dependencies = [
- "numpy >= 1.9.0",
+ "numpy >= 2.0.0",
"scipy >= 0.17.0",
"matplotlib >= 3.5.0",
"pysam >= 0.14.0",
@@ -38,7 +38,14 @@ classifiers = [
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
readme = "README.rst"
-
+[project.optional-dependencies]
+actions = [
+ "flake8",
+ "pytest",
+ "twine",
+ "build",
+ "planemo"
+]
[project.urls]
homepage = "https://pypi.python.org/pypi/deepTools/"
documentation = "https://deeptools.readthedocs.io/en/latest/"
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/d6efda86d7d30bcefaf53087670aa68a473bd6da...844fb99f2bcb57ebc37f7a53c05523193f010136
--
View it on GitLab: https://salsa.debian.org/med-team/python-deeptools/-/compare/d6efda86d7d30bcefaf53087670aa68a473bd6da...844fb99f2bcb57ebc37f7a53c05523193f010136
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