Merge pull request #1356 from deeptools/develop

Develop - 3.5.6

.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
@@ -20,56 +16,40 @@ jobs:
       matrix:
         chunk: [1, 2, 3]
     steps:
-    - uses: actions/checkout@v3
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@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@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
   planemo_combine_outputs:
     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@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache .cache/pip
-      uses: actions/cache@v3
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
     - name: Combine outputs
       uses: galaxyproject/planemo-ci-action@v1
       id: combine
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload

.github/workflows/pypi.yml

@@ -15,21 +15,19 @@ jobs:
     name: upload to pypi
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: mamba-org/setup-micromamba@main
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@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
       env:
         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@v3
+    - uses: actions/checkout@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@v3
-    - uses: mamba-org/setup-micromamba@main
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@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@v3
+    - uses: actions/upload-artifact@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@v3
-      - uses: actions/download-artifact@v3
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
         with:
           name: "distfiles"
           path: ~/dist/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@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@v3
-    - uses: mamba-org/setup-micromamba@main
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@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 @@ def compute_sub_matrix_worker(self, chrom, start, end, score_file_list, paramete
 
         # 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 @@ def parse_arguments(args=None):
             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 @@ def parse_arguments(args=None):
                   '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 signalAndBinDist(x):
 
     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

docs/content/feature/effectiveGenomeSize.rst

@@ -23,6 +23,8 @@ The effective genome size for a number of genomes using this method is given bel
 +---------------+------------------+
 |GRCm38         |    2652783500    |
 +---------------+------------------+
+|GRCm39         |    2654621783    |
++---------------+------------------+
 |dm3            |    162367812     |
 +---------------+------------------+
 |dm6            |    142573017     |
@@ -44,18 +46,18 @@ These are then based on the read length.
 We can approximate these values for various read lengths using the `khmer program <https://khmer.readthedocs.io/en/latest/>`__ program and ``unique-kmers.py`` in particular.
 A table of effective genome sizes given a read length using this method is provided below:
 
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|Read length      | GRCh37          | GRCh38          | T2T/CHM13CAT_v2 | GRCm37          | GRCm38          | dm3             | dm6             | GRCz10          | GRCz11          | WBcel235        | TAIR10          |
-+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
-|50               | 2685511454      | 2701495711      | 2725240337      | 2304947876      | 2308125299      | 130428510       | 125464678       | 1195445541      | 1197575653      | 95159402        | 114339094       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|75               | 2736124898      | 2747877702      | 2786136059      | 2404646149      | 2407883243      | 135004387       | 127324557       | 1251132611      | 1250812288      | 96945370        | 115317469       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|100              | 2776919708      | 2805636231      | 2814334875      | 2462480910      | 2467481008      | 139647132       | 129789773       | 1280188944      | 1280354977      | 98259898        | 118459858       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|150              | 2827436883      | 2862010428      | 2931551487      | 2489384085      | 2494787038      | 144307658       | 129940985       | 1312207019      | 1311832909      | 98721103        | 118504138       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|200              | 2855463800      | 2887553103      | 2936403235      | 2513019076      | 2520868989      | 148523810       | 132508963       | 1321355041      | 1322366338      | 98672558        | 117723393       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
-|250              | 2855044784      | 2898802627      | 2960856300      | 2528988583      | 2538590322      | 151901455       | 132900923       | 1339205109      | 1342093482      | 101271756       | 119585546       |
-+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|Read length      | GRCh37          | GRCh38          | T2T/CHM13CAT_v2 | GRCm37          | GRCm38          | GRCm39          | dm3             | dm6             | GRCz10          | GRCz11          | WBcel235        | TAIR10          |
++=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
+|50               | 2685511454      | 2701495711      | 2725240337      | 2304947876      | 2308125299      | 2309746861      | 130428510       | 125464678       | 1195445541      | 1197575653      | 95159402        | 114339094       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|75               | 2736124898      | 2747877702      | 2786136059      | 2404646149      | 2407883243      | 2410055689      | 135004387       | 127324557       | 1251132611      | 1250812288      | 96945370        | 115317469       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|100              | 2776919708      | 2805636231      | 2814334875      | 2462480910      | 2467481008      | 2468088461      | 139647132       | 129789773       | 1280188944      | 1280354977      | 98259898        | 118459858       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|150              | 2827436883      | 2862010428      | 2931551487      | 2489384085      | 2494787038      | 2495461690      | 144307658       | 129940985       | 1312207019      | 1311832909      | 98721103        | 118504138       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|200              | 2855463800      | 2887553103      | 2936403235      | 2513019076      | 2520868989      | 2521902382      | 148523810       | 132508963       | 1321355041      | 1322366338      | 98672558        | 117723393       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+|250              | 2855044784      | 2898802627      | 2960856300      | 2528988583      | 2538590322      | 2538633971      | 151901455       | 132900923       | 1339205109      | 1342093482      | 101271756       | 119585546       |
++-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+

docs/content/installation.rst

@@ -14,7 +14,14 @@ The recommended way to install deepTools (including its requirements) is via `mi
 
 .. code:: bash
 
-    $ conda install -c bioconda deeptools
+    $ conda install -c conda-forge -c bioconda deeptools
+
+Note that for ARM architecture (e.g. M1 on OSX) you could go via the pip installation (see below), or install via the osx-64 env:
+
+.. code:: bash
+
+    $ CONDA_SUBDIR=osx-64 conda create -c conda-forge -c bioconda -n deeptools deeptools
+
 
 Command line installation using ``pip``
 ---------------------------------------

docs/content/tools/plotFingerprint.rst

@@ -21,7 +21,7 @@ It determines how well the signal in the ChIP-seq sample can be differentiated f
 For factors that will enrich well-defined, rather narrow regions (e.g. transcription factors such as p300), the resulting plot can be used to assess the strength of a ChIP, but the broader the enrichments are to be expected, the less clear the plot will be.
 Vice versa, if you do not know what kind of signal to expect, the fingerprint plot will give you a straight-forward indication of how careful you will have to be during your downstream analyses to separate biological noise from meaningful signal.
 
-Similar to ``multiBamSummary``, ``plotFingerprint`` randomly samples genome regions (bins) of a specified length and sums the per-base coverage in indexed [BAM][] (or bigWig) files that overlap with those regions.
+Similar to ``multiBamSummary``, ``plotFingerprint`` randomly samples genome regions (bins) of a specified length and sums the per-base coverage in indexed BAM files that overlap with those regions.
 These values are then sorted according to their rank and the cumulative sum of read counts is plotted.