From 958a0eb56d07a7a809c69bade44cdbc075d54446 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 21:27:24 +0200 Subject: [PATCH 01/24] update changelog --- CHANGES.txt | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/CHANGES.txt b/CHANGES.txt index 5f0bf0f0cb..9f02f9395f 100755 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -1,3 +1,30 @@ +4.0.0 +* new Rust-backed core for bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations for these five tools; the previous Python implementations remain available as bamCoverage_old, bamCompare_old, computeMatrix_old, alignmentSieve_old and multiBamSummary_old during the transition, but will be removed in a future release +* gtf, bed and blacklist can be compressed in mbs, computematrix, alsieve, bamcompare and bamcoverage +* --exactScaling is removed as this is the only scaling option available with the new backend +* --ignoreDuplicates has been deprecated from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) +* plotPCA re-implemented with a lightweight scipy/numpy SVD backend. Proper handling of --transpose, --log2/--rowCenter and --ntop options. +* plotly backend from plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment in favor of matplotlib, with a new optional --ggplot theme +* removed the standalone cm.py colormap module; colormap handling now lives in the plotting tools directly +* plot labels now show sample names only per default (dropped .filtered.bam/.bed suffixes) +* prebuilt wheels now cover Linux manylinux_2_28 and musllinux_1_2 (x86_64 + aarch64) and macOS (Intel + Apple Silicon), built via maturin +* CI overhauled: pytest/rust/planemo test workflows split up (test_pytest.yml, test_rust.yml, test_planemo.yml), zizmor hardening for GitHub Actions, dependabot enabled +* extensive new pytest/cargo test coverage across the Rust-backed tools and plotCorrelation/plotPCA/plotFingerprint data outputs +* nanafterend doesn't rescale inner region anymore in reference-point mode +* BED output doesn't show wrong blockstart values anymore +* blacklist filtering is done at bp level instead of genome chunk level for rewritten tools +* alignmentsieve output order matches input order exactly +* missingdataszero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins +* large scale values precision slightly altered with new backend (f32 vs f64) + +3.5.6 +* minimal supported python version raised to 3.9 (numpy >= 2 support); NaN handling switched to np.nan +* drop conda usage in pypi/test/planemo CI in favor of pip installs; samtools now pulled from conda-forge/bioconda where still needed in CI +* include GRCm39 in the effective genome size docs +* add ARM/osx specific installation instructions +* computeMatrix: ensure --beforeRegionStartLength/-b and --afterRegionStartLength/-a are always treated as positive values +* minor --version output fixes in plotCoverage and multiBigwigSummary + 3.5.5 * drop support for python 3.7 * doc fixes (argparse properly displayed, minor changes in installation instructions) From 5c3b42fc1a2dfba5a76f268aefa86d5b157aff8b Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 21:32:04 +0200 Subject: [PATCH 02/24] mend --- CHANGES.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGES.txt b/CHANGES.txt index 9f02f9395f..cb70071a2f 100755 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -1,8 +1,8 @@ 4.0.0 * new Rust-backed core for bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations for these five tools; the previous Python implementations remain available as bamCoverage_old, bamCompare_old, computeMatrix_old, alignmentSieve_old and multiBamSummary_old during the transition, but will be removed in a future release -* gtf, bed and blacklist can be compressed in mbs, computematrix, alsieve, bamcompare and bamcoverage +* gzipped GTF/BED region files are now supported in multiBamSummary, computeMatrix and alignmentSieve; gzipped blacklist files are supported in all five Rust-backed tools (multiBamSummary, computeMatrix, alignmentSieve, bamCompare, bamCoverage) * --exactScaling is removed as this is the only scaling option available with the new backend -* --ignoreDuplicates has been deprecated from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) +* --ignoreDuplicates has been removed from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) * plotPCA re-implemented with a lightweight scipy/numpy SVD backend. Proper handling of --transpose, --log2/--rowCenter and --ntop options. * plotly backend from plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment in favor of matplotlib, with a new optional --ggplot theme * removed the standalone cm.py colormap module; colormap handling now lives in the plotting tools directly @@ -10,11 +10,11 @@ * prebuilt wheels now cover Linux manylinux_2_28 and musllinux_1_2 (x86_64 + aarch64) and macOS (Intel + Apple Silicon), built via maturin * CI overhauled: pytest/rust/planemo test workflows split up (test_pytest.yml, test_rust.yml, test_planemo.yml), zizmor hardening for GitHub Actions, dependabot enabled * extensive new pytest/cargo test coverage across the Rust-backed tools and plotCorrelation/plotPCA/plotFingerprint data outputs -* nanafterend doesn't rescale inner region anymore in reference-point mode +* --nanAfterEnd doesn't rescale the inner region anymore in reference-point mode * BED output doesn't show wrong blockstart values anymore * blacklist filtering is done at bp level instead of genome chunk level for rewritten tools -* alignmentsieve output order matches input order exactly -* missingdataszero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins +* alignmentSieve output order matches input order exactly +* --missingDataAsZero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins * large scale values precision slightly altered with new backend (f32 vs f64) 3.5.6 From 51637eafdbe11d3ea5b6cb74a697abc14338ce87 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 22:29:50 +0200 Subject: [PATCH 03/24] docs orphan for warnings --- docs/content/feature/blacklist.rst | 2 ++ docs/content/feature/effectiveGenomeSize.rst | 2 ++ docs/content/feature/metagene.rst | 2 ++ docs/content/feature/plotFingerprint_QC_metrics.rst | 2 ++ docs/content/feature/plotly.rst | 2 ++ docs/content/feature/read_extension.rst | 2 ++ docs/content/feature/read_offsets.rst | 2 ++ docs/content/feature/unscaled_regions.rst | 2 ++ docs/content/tools/alignmentSieve.rst | 4 +++- docs/content/tools/bamCompare.rst | 4 +++- docs/content/tools/bamCoverage.rst | 4 +++- docs/content/tools/bamPEFragmentSize.rst | 2 ++ docs/content/tools/bigwigAverage.rst | 2 ++ docs/content/tools/bigwigCompare.rst | 2 ++ docs/content/tools/computeGCBias.rst | 2 ++ docs/content/tools/computeMatrix.rst | 4 +++- docs/content/tools/computeMatrixOperations.rst | 2 ++ docs/content/tools/correctGCBias.rst | 2 ++ docs/content/tools/estimateReadFiltering.rst | 2 ++ docs/content/tools/multiBamSummary.rst | 4 +++- docs/content/tools/multiBigwigSummary.rst | 2 ++ docs/content/tools/plotCorrelation.rst | 2 ++ docs/content/tools/plotCoverage.rst | 2 ++ docs/content/tools/plotEnrichment.rst | 2 ++ docs/content/tools/plotFingerprint.rst | 2 ++ docs/content/tools/plotHeatmap.rst | 2 ++ docs/content/tools/plotPCA.rst | 2 ++ docs/content/tools/plotProfile.rst | 2 ++ docs/source/deeptools.rst | 8 -------- docs/source/modules.rst | 2 ++ 30 files changed, 63 insertions(+), 13 deletions(-) diff --git a/docs/content/feature/blacklist.rst b/docs/content/feature/blacklist.rst index 78562ab930..56af5ec559 100644 --- a/docs/content/feature/blacklist.rst +++ b/docs/content/feature/blacklist.rst @@ -1,3 +1,5 @@ +:orphan: + Blacklist Regions ================= diff --git a/docs/content/feature/effectiveGenomeSize.rst b/docs/content/feature/effectiveGenomeSize.rst index 73c41ffaaf..32095bc6d7 100644 --- a/docs/content/feature/effectiveGenomeSize.rst +++ b/docs/content/feature/effectiveGenomeSize.rst @@ -1,3 +1,5 @@ +:orphan: + Effective Genome Size ===================== diff --git a/docs/content/feature/metagene.rst b/docs/content/feature/metagene.rst index 202ff22ab9..5120abdc9d 100644 --- a/docs/content/feature/metagene.rst +++ b/docs/content/feature/metagene.rst @@ -1,3 +1,5 @@ +:orphan: + Metagene analyses ================= diff --git a/docs/content/feature/plotFingerprint_QC_metrics.rst b/docs/content/feature/plotFingerprint_QC_metrics.rst index 7d84a56e9e..09074f1413 100644 --- a/docs/content/feature/plotFingerprint_QC_metrics.rst +++ b/docs/content/feature/plotFingerprint_QC_metrics.rst @@ -1,3 +1,5 @@ +:orphan: + plotFingerprint QC metrics ========================== diff --git a/docs/content/feature/plotly.rst b/docs/content/feature/plotly.rst index 1d9cf8ff94..7325731972 100644 --- a/docs/content/feature/plotly.rst +++ b/docs/content/feature/plotly.rst @@ -1,3 +1,5 @@ +:orphan: + Plotly ====== diff --git a/docs/content/feature/read_extension.rst b/docs/content/feature/read_extension.rst index 80c8328262..42ce019a2e 100644 --- a/docs/content/feature/read_extension.rst +++ b/docs/content/feature/read_extension.rst @@ -1,3 +1,5 @@ +:orphan: + Read extension ============== diff --git a/docs/content/feature/read_offsets.rst b/docs/content/feature/read_offsets.rst index 295ba39280..be8d8a1b4e 100644 --- a/docs/content/feature/read_offsets.rst +++ b/docs/content/feature/read_offsets.rst @@ -1,3 +1,5 @@ +:orphan: + Offsetting signal to a given position ===================================== diff --git a/docs/content/feature/unscaled_regions.rst b/docs/content/feature/unscaled_regions.rst index 5cbb0a6591..e3a98bdd25 100644 --- a/docs/content/feature/unscaled_regions.rst +++ b/docs/content/feature/unscaled_regions.rst @@ -1,3 +1,5 @@ +:orphan: + Unscaled regions ================ diff --git a/docs/content/tools/alignmentSieve.rst b/docs/content/tools/alignmentSieve.rst index d9f6dd19d6..9c8e5d58f5 100644 --- a/docs/content/tools/alignmentSieve.rst +++ b/docs/content/tools/alignmentSieve.rst @@ -1,3 +1,5 @@ +:orphan: + alignmentSieve ============== @@ -5,7 +7,7 @@ alignmentSieve :local: .. argparse:: - :ref: deeptools.alignmentSieve.parseArguments + :ref: deeptools.alignmentSieve2.parseArguments :prog: alignmentSieve :nodefault: diff --git a/docs/content/tools/bamCompare.rst b/docs/content/tools/bamCompare.rst index a0522a88c4..1daf32935d 100644 --- a/docs/content/tools/bamCompare.rst +++ b/docs/content/tools/bamCompare.rst @@ -1,3 +1,5 @@ +:orphan: + bamCompare =========== @@ -22,6 +24,6 @@ The basic algorithm works proceeds in two steps: .. argparse:: - :ref: deeptools.bamCompare.parseArguments + :ref: deeptools.bamCompare2.parseArguments :prog: bamCompare :nodefault: diff --git a/docs/content/tools/bamCoverage.rst b/docs/content/tools/bamCoverage.rst index e5420ea16f..3507c62d9d 100644 --- a/docs/content/tools/bamCoverage.rst +++ b/docs/content/tools/bamCoverage.rst @@ -1,3 +1,5 @@ +:orphan: + bamCoverage =========== @@ -9,7 +11,7 @@ bamCoverage If you are not familiar with BAM, bedGraph and bigWig formats, you can read up on that in our :doc:`../help_glossary` .. argparse:: - :ref: deeptools.bamCoverage.parseArguments + :ref: deeptools.bamCoverage2.parseArguments :prog: bamCoverage :nodefault: diff --git a/docs/content/tools/bamPEFragmentSize.rst b/docs/content/tools/bamPEFragmentSize.rst index 85f16e07d0..ad2db10e79 100644 --- a/docs/content/tools/bamPEFragmentSize.rst +++ b/docs/content/tools/bamPEFragmentSize.rst @@ -1,3 +1,5 @@ +:orphan: + bamPEFragmentSize ================= diff --git a/docs/content/tools/bigwigAverage.rst b/docs/content/tools/bigwigAverage.rst index 7772219240..86a8f343e0 100644 --- a/docs/content/tools/bigwigAverage.rst +++ b/docs/content/tools/bigwigAverage.rst @@ -1,3 +1,5 @@ +:orphan: + bigwigAverage ============= diff --git a/docs/content/tools/bigwigCompare.rst b/docs/content/tools/bigwigCompare.rst index e0a8610354..86d78a2f63 100644 --- a/docs/content/tools/bigwigCompare.rst +++ b/docs/content/tools/bigwigCompare.rst @@ -1,3 +1,5 @@ +:orphan: + bigwigCompare ============= diff --git a/docs/content/tools/computeGCBias.rst b/docs/content/tools/computeGCBias.rst index c3ba679f58..3d794aceaf 100644 --- a/docs/content/tools/computeGCBias.rst +++ b/docs/content/tools/computeGCBias.rst @@ -1,3 +1,5 @@ +:orphan: + computeGCBias ============= diff --git a/docs/content/tools/computeMatrix.rst b/docs/content/tools/computeMatrix.rst index 60aaf8cb55..bbfe2a7dd4 100644 --- a/docs/content/tools/computeMatrix.rst +++ b/docs/content/tools/computeMatrix.rst @@ -1,3 +1,5 @@ +:orphan: + computeMatrix ============= @@ -5,7 +7,7 @@ computeMatrix :local: .. argparse:: - :ref: deeptools.computeMatrix.parse_arguments + :ref: deeptools.computeMatrix2.parse_arguments :prog: computeMatrix :nodefault: diff --git a/docs/content/tools/computeMatrixOperations.rst b/docs/content/tools/computeMatrixOperations.rst index e06db04cf0..07f20f97d4 100644 --- a/docs/content/tools/computeMatrixOperations.rst +++ b/docs/content/tools/computeMatrixOperations.rst @@ -1,3 +1,5 @@ +:orphan: + computeMatrixOperations ======================= diff --git a/docs/content/tools/correctGCBias.rst b/docs/content/tools/correctGCBias.rst index 7432fb7562..460561f35d 100644 --- a/docs/content/tools/correctGCBias.rst +++ b/docs/content/tools/correctGCBias.rst @@ -1,3 +1,5 @@ +:orphan: + correctGCBias ============= diff --git a/docs/content/tools/estimateReadFiltering.rst b/docs/content/tools/estimateReadFiltering.rst index f57fd386a4..70e7b93db3 100644 --- a/docs/content/tools/estimateReadFiltering.rst +++ b/docs/content/tools/estimateReadFiltering.rst @@ -1,3 +1,5 @@ +:orphan: + estimateReadFiltering ===================== diff --git a/docs/content/tools/multiBamSummary.rst b/docs/content/tools/multiBamSummary.rst index e39ed3ab0b..71231905fe 100644 --- a/docs/content/tools/multiBamSummary.rst +++ b/docs/content/tools/multiBamSummary.rst @@ -1,3 +1,5 @@ +:orphan: + multiBamSummary ================ @@ -5,7 +7,7 @@ multiBamSummary :local: .. argparse:: - :ref: deeptools.multiBamSummary.parse_arguments + :ref: deeptools.multiBamSummary2.parse_arguments :prog: multiBamSummary :nodefault: diff --git a/docs/content/tools/multiBigwigSummary.rst b/docs/content/tools/multiBigwigSummary.rst index 1c9af5520c..4beb65ca2c 100644 --- a/docs/content/tools/multiBigwigSummary.rst +++ b/docs/content/tools/multiBigwigSummary.rst @@ -1,3 +1,5 @@ +:orphan: + multiBigwigSummary ================== diff --git a/docs/content/tools/plotCorrelation.rst b/docs/content/tools/plotCorrelation.rst index d42244687c..bafc163a5b 100644 --- a/docs/content/tools/plotCorrelation.rst +++ b/docs/content/tools/plotCorrelation.rst @@ -1,3 +1,5 @@ +:orphan: + plotCorrelation =============== diff --git a/docs/content/tools/plotCoverage.rst b/docs/content/tools/plotCoverage.rst index 82e8558dda..1d203351d5 100644 --- a/docs/content/tools/plotCoverage.rst +++ b/docs/content/tools/plotCoverage.rst @@ -1,3 +1,5 @@ +:orphan: + plotCoverage ============ diff --git a/docs/content/tools/plotEnrichment.rst b/docs/content/tools/plotEnrichment.rst index c9815edfe1..536f56e0e9 100644 --- a/docs/content/tools/plotEnrichment.rst +++ b/docs/content/tools/plotEnrichment.rst @@ -1,3 +1,5 @@ +:orphan: + plotEnrichment ============== diff --git a/docs/content/tools/plotFingerprint.rst b/docs/content/tools/plotFingerprint.rst index 1be0d17cfc..c5718b9cfa 100644 --- a/docs/content/tools/plotFingerprint.rst +++ b/docs/content/tools/plotFingerprint.rst @@ -1,3 +1,5 @@ +:orphan: + plotFingerprint =============== diff --git a/docs/content/tools/plotHeatmap.rst b/docs/content/tools/plotHeatmap.rst index 3920ef0ec9..320d79efd6 100644 --- a/docs/content/tools/plotHeatmap.rst +++ b/docs/content/tools/plotHeatmap.rst @@ -1,3 +1,5 @@ +:orphan: + plotHeatmap =========== diff --git a/docs/content/tools/plotPCA.rst b/docs/content/tools/plotPCA.rst index abef919485..bcf1b01146 100644 --- a/docs/content/tools/plotPCA.rst +++ b/docs/content/tools/plotPCA.rst @@ -1,3 +1,5 @@ +:orphan: + plotPCA ======= diff --git a/docs/content/tools/plotProfile.rst b/docs/content/tools/plotProfile.rst index fb0a1a41cb..28900bd2f2 100644 --- a/docs/content/tools/plotProfile.rst +++ b/docs/content/tools/plotProfile.rst @@ -1,3 +1,5 @@ +:orphan: + plotProfile =========== diff --git a/docs/source/deeptools.rst b/docs/source/deeptools.rst index 97d9689941..d792ff0ac2 100644 --- a/docs/source/deeptools.rst +++ b/docs/source/deeptools.rst @@ -28,14 +28,6 @@ deeptools.correlation module :undoc-members: :show-inheritance: -deeptools.correlation_heatmap module ------------------------------------- - -.. automodule:: deeptools.correlation_heatmap - :members: - :undoc-members: - :show-inheritance: - deeptools.countReadsPerBin module --------------------------------- diff --git a/docs/source/modules.rst b/docs/source/modules.rst index 06391abc61..c2cf26a96a 100644 --- a/docs/source/modules.rst +++ b/docs/source/modules.rst @@ -1,3 +1,5 @@ +:orphan: + deeptools ========= From b9d17f264cacb710a0d458554fc41e40a77df0ab Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 22:32:07 +0200 Subject: [PATCH 04/24] drop doc reqs, fix python docstring --- docs/requirements.txt | 4 - pydeeptools/deeptools/correlation_heatmap.py | 106 ------------------ .../deeptools/getFragmentAndReadSize.py | 31 +++-- pydeeptools/deeptools/getScorePerBigWigBin.py | 47 ++++---- pydeeptools/deeptools/heatmapper.py | 12 +- 5 files changed, 46 insertions(+), 154 deletions(-) delete mode 100644 docs/requirements.txt delete mode 100644 pydeeptools/deeptools/correlation_heatmap.py diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index f330fe4e6a..0000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -sphinx==7.2.6 -mock==5.1.0 -sphinx_rtd_theme==2.0.0 -sphinx-argparse==0.4.0 \ No newline at end of file diff --git a/pydeeptools/deeptools/correlation_heatmap.py b/pydeeptools/deeptools/correlation_heatmap.py deleted file mode 100644 index 690717ee95..0000000000 --- a/pydeeptools/deeptools/correlation_heatmap.py +++ /dev/null @@ -1,106 +0,0 @@ -from deeptools import matplotlib_defaults -from deeptools import cm # noqa: F401 -import matplotlib.pyplot as plt -import numpy as np -import scipy.cluster.hierarchy as sch -import matplotlib.colors as pltcolors -import copy - -old_settings = np.seterr(all='ignore') - - -def plot_correlation(corr_matrix, labels, plotFileName, vmax=None, - vmin=None, colormap='jet', image_format=None, - plot_numbers=False, plot_title=''): - - num_rows = corr_matrix.shape[0] - - # set a font size according to figure length - if num_rows < 6: - font_size = 14 - elif num_rows > 40: - font_size = 5 - else: - font_size = int(14 - 0.25 * num_rows) - matplotlib.rcParams.update({'font.size': font_size}) - # set the minimum and maximum values - if vmax is None: - vmax = 1 - if vmin is None: - vmin = 0 if corr_matrix.min() >= 0 else -1 - - # Compute and plot dendrogram. - fig = plt.figure(figsize=(11, 9.5)) - if plot_title: - plt.suptitle(plot_title) - axdendro = fig.add_axes([0.02, 0.12, 0.1, 0.66]) - axdendro.set_axis_off() - y_var = sch.linkage(corr_matrix, method='complete') - z_var = sch.dendrogram(y_var, orientation='right', - link_color_func=lambda k: 'darkred') - axdendro.set_xticks([]) - axdendro.set_yticks([]) - cmap = copy.copy(plt.get_cmap(colormap)) - - # this line simply makes a new cmap, based on the original - # colormap that goes from 0.0 to 0.9 - # This is done to avoid colors that - # are too dark at the end of the range that do not offer - # a good contrast between the correlation numbers that are - # plotted on black. - if plot_numbers: - cmap = pltcolors.LinearSegmentedColormap.from_list(colormap + "clipped", - cmap(np.linspace(0, 0.9, 10))) - - cmap.set_under((0., 0., 1.)) - # Plot distance matrix. - axmatrix = fig.add_axes([0.13, 0.1, 0.6, 0.7]) - index = z_var['leaves'] - corr_matrix = corr_matrix[index, :] - corr_matrix = corr_matrix[:, index] - img_mat = axmatrix.pcolormesh(corr_matrix, - edgecolors='black', - cmap=cmap, - vmax=vmax, - vmin=vmin) - axmatrix.set_xlim(0, num_rows) - axmatrix.set_ylim(0, num_rows) - - axmatrix.yaxis.tick_right() - axmatrix.set_yticks(np.arange(corr_matrix.shape[0]) + 0.5) - axmatrix.set_yticklabels(np.array(labels).astype('str')[index]) - -# axmatrix.xaxis.set_label_position('top') - axmatrix.xaxis.set_tick_params(labeltop=True) - axmatrix.xaxis.set_tick_params(labelbottom=False) - axmatrix.set_xticks(np.arange(corr_matrix.shape[0]) + 0.5) - axmatrix.set_xticklabels(np.array(labels).astype('str')[index], - rotation=45, - ha='left') - - axmatrix.tick_params( - axis='x', - which='both', - bottom=False, - top=False) - - axmatrix.tick_params( - axis='y', - which='both', - left=False, - right=False) - - # axmatrix.set_xticks([]) - # Plot colorbar. - axcolor = fig.add_axes([0.13, 0.065, 0.6, 0.02]) - cobar = plt.colorbar(img_mat, cax=axcolor, orientation='horizontal') - cobar.solids.set_edgecolor("face") - if plot_numbers: - for row in range(num_rows): - for col in range(num_rows): - axmatrix.text(row + 0.5, col + 0.5, - "{:.2f}".format(corr_matrix[row, col]), - ha='center', va='center') - - fig.savefig(plotFileName, format=image_format) - fig.close() diff --git a/pydeeptools/deeptools/getFragmentAndReadSize.py b/pydeeptools/deeptools/getFragmentAndReadSize.py index 0cf2dc8eba..e80d4f3323 100644 --- a/pydeeptools/deeptools/getFragmentAndReadSize.py +++ b/pydeeptools/deeptools/getFragmentAndReadSize.py @@ -62,22 +62,21 @@ def get_read_and_fragment_length(bamFile, return_lengths=False, blackListFileNam """ Estimates the fragment length and read length through sampling - Parameters - ---------- - bamFile : str - BAM file name - return_lengths : bool - numberOfProcessors : int - verbose : bool - binSize : int - distanceBetweenBins : int - - Returns - ------- - d : dict - tuple of two dictionaries, one for the fragment length and the other -for the read length. The dictionaries summarise the mean, median etc. values - + :param bamFile: BAM file name + :type bamFile: str + :param return_lengths: + :type return_lengths: bool + :param numberOfProcessors: + :type numberOfProcessors: int + :param verbose: + :type verbose: bool + :param binSize: + :type binSize: int + :param distanceBetweenBins: + :type distanceBetweenBins: int + :returns: tuple of two dictionaries, one for the fragment length and the other + for the read length. The dictionaries summarise the mean, median etc. values + :rtype: dict """ bam_handle = bamHandler.openBam(bamFile) diff --git a/pydeeptools/deeptools/getScorePerBigWigBin.py b/pydeeptools/deeptools/getScorePerBigWigBin.py index 6f0ff45eae..34a11ea17c 100644 --- a/pydeeptools/deeptools/getScorePerBigWigBin.py +++ b/pydeeptools/deeptools/getScorePerBigWigBin.py @@ -33,24 +33,27 @@ def countFragmentsInRegions_worker(chrom, start, end, If a list of bedRegions is given, then the number of reads that overlaps with each region is counted. - Test dataset with two samples covering 200 bp. - >>> test = Tester() + Test dataset with two samples covering 200 bp:: + + >>> test = Tester() + + Fragment coverage:: + + >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200, [test.bwFile1, test.bwFile2], 50, 25, False)[0]) + array([[1., 1., 2., 2.], + [1., 1., 1., 3.]]) - Fragment coverage. - >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200, [test.bwFile1, test.bwFile2], 50, 25, False)[0]) - array([[1., 1., 2., 2.], - [1., 1., 1., 3.]]) - - >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200, [test.bwFile1, test.bwFile2], 200, 200, False)[0]) - array([[1.5], - [1.5]]) - - BED regions: - >>> bedRegions = [[test.chrom, [(45, 55)]], [test.chrom, [(95, 105)]], [test.chrom, [(145, 155)]]] - >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200,[test.bwFile1, test.bwFile2], 200, 200, False, - ... bedRegions=bedRegions)[0]) - array([[1. , 1.5, 2. ], - [1. , 1. , 2. ]]) + >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200, [test.bwFile1, test.bwFile2], 200, 200, False)[0]) + array([[1.5], + [1.5]]) + + BED regions:: + + >>> bedRegions = [[test.chrom, [(45, 55)]], [test.chrom, [(95, 105)]], [test.chrom, [(145, 155)]]] + >>> np.transpose(countFragmentsInRegions_worker(test.chrom, 0, 200,[test.bwFile1, test.bwFile2], 200, 200, False, + ... bedRegions=bedRegions)[0]) + array([[1. , 1.5, 2. ], + [1. , 1. , 2. ]]) """ assert start < end, "start {} bigger that end {}".format(start, end) @@ -208,12 +211,12 @@ def getScorePerBin(bigWigFiles, binLength, of fragments within a region. Each row corresponds to a sampled region. Likewise, each column corresponds to a bigwig file. - Test dataset with two samples covering 200 bp. - >>> test = Tester() - >>> np.transpose(getScorePerBin([test.bwFile1, test.bwFile2], 50, 3)) - array([[1., 1., 2., 2.], - [1., 1., 1., 3.]]) + Test dataset with two samples covering 200 bp:: + >>> test = Tester() + >>> np.transpose(getScorePerBin([test.bwFile1, test.bwFile2], 50, 3)) + array([[1., 1., 2., 2.], + [1., 1., 1., 3.]]) """ # Try to determine an optimal fraction of the genome (chunkSize) # that is sent to workers for analysis. If too short, too much time diff --git a/pydeeptools/deeptools/heatmapper.py b/pydeeptools/deeptools/heatmapper.py index f86b85e234..5b70ec74fa 100644 --- a/pydeeptools/deeptools/heatmapper.py +++ b/pydeeptools/deeptools/heatmapper.py @@ -72,12 +72,12 @@ def chopRegionsFromMiddle(exonsInput, left=0, right=0): The steps are as follow: - 1) Find the center point of the set of exons (e.g., [(0, 200), (300, 400), (800, 900)] would be centered at 200) - * If a given exon spans the center point then the exon is split - 2) The given number of bases at the end of the left-of-center list are extracted - * If the set of exons don't contain enough bases, then padLeft is incremented accordingly - 3) As above but for the right-of-center list - 4) A tuple of (#2, #3, pading on the left, and padding on the right) is returned + 1. Find the center point of the set of exons (e.g., [(0, 200), (300, 400), (800, 900)] + would be centered at 200). If a given exon spans the center point then the exon is split. + 2. The given number of bases at the end of the left-of-center list are extracted. If the + set of exons don't contain enough bases, then padLeft is incremented accordingly. + 3. As above but for the right-of-center list. + 4. A tuple of (#2, #3, padding on the left, and padding on the right) is returned. """ leftBins = [] rightBins = [] From 071c90f5f21cf1fb0a5cc11356e23d193206a377 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 22:55:53 +0200 Subject: [PATCH 05/24] drop unused code from new entrypoints --- pydeeptools/deeptools/bamCompare2.py | 2 +- pydeeptools/deeptools/bamCoverage2.py | 12 ------------ pydeeptools/deeptools/multiBamSummary2.py | 6 ------ 3 files changed, 1 insertion(+), 19 deletions(-) diff --git a/pydeeptools/deeptools/bamCompare2.py b/pydeeptools/deeptools/bamCompare2.py index df19b9cf85..048a148f87 100644 --- a/pydeeptools/deeptools/bamCompare2.py +++ b/pydeeptools/deeptools/bamCompare2.py @@ -215,7 +215,7 @@ def main(args=None): if args.scaleFactors: if len(args.scaleFactors.split(":")) == 2: args.sf1 = float(args.scaleFactors.split(":")[0]) - args.sf2 = float(args.scaleFactors.split(":")[0]) + args.sf2 = float(args.scaleFactors.split(":")[1]) elif len(args.scaleFactors.split(":")) == 1: args.sf1 = float(args.scaleFactors.split(":")[0]) args.sf2 = float(args.scaleFactors.split(":")[0]) diff --git a/pydeeptools/deeptools/bamCoverage2.py b/pydeeptools/deeptools/bamCoverage2.py index 64f4ecfb72..963835ca42 100644 --- a/pydeeptools/deeptools/bamCoverage2.py +++ b/pydeeptools/deeptools/bamCoverage2.py @@ -110,18 +110,6 @@ def get_optional_args(): return parser -def scaleFactor(string): - try: - scalefactor1, scalefactor2 = string.split(":") - scalefactors = (float(scalefactor1), float(scalefactor2)) - except: - raise argparse.ArgumentTypeError( - "Format of scaleFactors is factor1:factor2. " - "The value given ( {} ) is not valid".format(string)) - - return scalefactors - - def process_args(args=None): args = parseArguments().parse_args(args) if not args.smoothLength: diff --git a/pydeeptools/deeptools/multiBamSummary2.py b/pydeeptools/deeptools/multiBamSummary2.py index 376d768c81..dc60db2ab0 100644 --- a/pydeeptools/deeptools/multiBamSummary2.py +++ b/pydeeptools/deeptools/multiBamSummary2.py @@ -7,14 +7,8 @@ import sys from importlib.metadata import version -import numpy as np - -import deeptools.countReadsPerBin as countR from deeptools import parserCommon from deeptools.utilities import smartLabels - -old_settings = np.seterr(all="ignore") - from deeptools.hp import r_mbams From 38a9fbb6f6bfb41aa0093ab3a4b4af0049810884 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 22:56:23 +0200 Subject: [PATCH 06/24] point rtd to docs req --- .readthedocs.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml 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"matplotlib >= 3.10.5, < 3.12", +] +docs = [ + "sphinx >= 7.2.6", + "mock >= 5.1.0", + "sphinx_rtd_theme >= 2.0.0", + "sphinx-argparse >= 0.4.0", ] [project.urls] homepage = "https://pypi.python.org/pypi/deepTools/" @@ -109,7 +109,7 @@ openssl = "*" pkg-config = "*" py-spy = "*" [tool.pixi.pypi-dependencies] -deeptools = { path = ".", editable = true, extras = ['actions'] } +deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] } [tool.pixi.activation.env] LIBCLANG_PATH = "$CONDA_PREFIX/lib" # Link conda-forge's OpenSSL instead of building the vendored copy from source @@ -119,3 +119,4 @@ OPENSSL_DIR = "$CONDA_PREFIX" [tool.pixi.tasks] build = "maturin develop --release" test = "pytest pydeeptools/deeptools/test/" +docs = "sphinx-build -b html docs docs/_build/html -W --keep-going" From 90eac523db103e219c46f28465eec85155eb851b Mon Sep 17 00:00:00 2001 From: WardDeb Date: Thu, 3 Sep 2026 23:24:23 +0200 Subject: [PATCH 08/24] action to test docs --- .github/workflows/test_docs.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/workflows/test_docs.yml diff --git a/.github/workflows/test_docs.yml b/.github/workflows/test_docs.yml new file mode 100644 index 0000000000..9e9562b2f2 --- /dev/null +++ b/.github/workflows/test_docs.yml @@ -0,0 +1,19 @@ +name: tests_docs +on: [push, pull_request, workflow_dispatch] + +permissions: + contents: read + +jobs: + build-docs: + name: Build Sphinx documentation + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 + with: + persist-credentials: false + - uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2 + with: + environments: default + - name: build docs + run: pixi run docs From 76855ff3adae0dcd0a2a76cd4fba2332054fc0b9 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 07:13:44 +0200 Subject: [PATCH 09/24] minimal versions, include lock --- .gitignore | 1 - 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[dependencies] -openssl-sys = { version = "*", features = ["vendored"] } +openssl-sys = { version = "0.9.117", features = ["vendored"] } pyo3 = { version = ">= 0.28.2", features = ["extension-module"] } -rust-htslib = "*" -rayon = "*" -tokio = "*" -itertools = "*" -bigtools = "*" -flate2 = "*" -tempfile = "*" -ndarray = "*" -ndarray-npy = "*" +rust-htslib = "1.0.1" +rayon = "1.12.0" +tokio = "1.53.0" +itertools = "0.15.0" +bigtools = "0.5.8" +flate2 = "1.1.9" +tempfile = "3.27.0" +ndarray = "0.17.2" +ndarray-npy = "0.10.0" From c75609feb0ff3dc9b844d7e15cc7f2ea9d615816 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 07:29:22 +0200 Subject: [PATCH 10/24] centralize version check deeptools/galaxy, rust version in docs/deeptools --- .github/workflows/test_pytest.yml | 32 +++---------- .pre-commit-config.yaml | 8 ++++ .readthedocs.yaml | 2 +- scripts/check_version_sync.py | 74 +++++++++++++++++++++++++++++++ 4 files changed, 89 insertions(+), 27 deletions(-) create mode 100644 scripts/check_version_sync.py diff --git a/.github/workflows/test_pytest.yml b/.github/workflows/test_pytest.yml index 775d4b9890..f1ecd961d0 100644 --- a/.github/workflows/test_pytest.yml +++ b/.github/workflows/test_pytest.yml @@ -10,37 +10,17 @@ defaults: jobs: check_versions_matches: - name: Check deeptools version matches galaxy tools + name: Check deeptools/galaxy/Rust versions stay in sync runs-on: ubuntu-latest - if: github.base_ref == 'master' steps: - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - - name: Check path - run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml" - - name: Get Version of Deeptools - run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV - - name: Get Version of Galaxy tools - run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV - - name: Versions - run: | - echo deeptools version=${deeptools_version} - echo deeptools version in galaxy=${galaxy_deeptools_version} - - name: Fail PR if versions not matching - run: | - if [ -z $galaxy_deeptools_version ]; then - echo "galaxy_deeptools_version not defined change the github action" - exit 1 - fi - if [ -z $deeptools_version ]; then - echo "deeptools_version not defined change the github action" - exit 1 - fi - if [ "$galaxy_deeptools_version" != "$deeptools_version" ]; then - echo "versions do not match" - exit 1 - fi + - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + with: + python-version: "3.x" + - name: Check version sync + run: python3 scripts/check_version_sync.py build-linux: name: Test on Linux runs-on: ubuntu-latest diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4b60e1a43e..6dde3a7162 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,3 +3,11 @@ repos: rev: v1.11.0 hooks: - id: zizmor + - repo: local + hooks: + - id: check-version-sync + name: check Rust versions (docs - toml) and deeptools versions (toml - galaxy) to stay in sync + entry: python3 scripts/check_version_sync.py + language: system + files: ^(Cargo\.toml|pyproject\.toml|\.readthedocs\.yaml|galaxy/wrapper/deepTools_macros\.xml)$ + pass_filenames: false diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 598bf14c74..bc3018ec80 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,7 +4,7 @@ build: os: ubuntu-22.04 tools: python: "3.12" - rust: "1.82" + rust: "1.85" apt_packages: - clang diff --git a/scripts/check_version_sync.py b/scripts/check_version_sync.py new file mode 100644 index 0000000000..5e2d349e17 --- /dev/null +++ b/scripts/check_version_sync.py @@ -0,0 +1,74 @@ +import re +import sys +import tomllib +from pathlib import Path + +REPO_ROOT = Path(__file__).resolve().parent.parent + + +def cargo_rust_version() -> str: + data = tomllib.loads((REPO_ROOT / "Cargo.toml").read_text()) + return data["package"]["rust-version"] + + +def pixi_rust_version() -> str: + data = tomllib.loads((REPO_ROOT / "pyproject.toml").read_text()) + spec = data["tool"]["pixi"]["dependencies"]["rust"] + match = re.fullmatch(r">=\s*([\d.]+)", spec) + if not match: + sys.exit(f"pyproject.toml: unexpected [tool.pixi.dependencies] rust spec {spec!r}, " + "expected '>=X.Y' so it can be compared to Cargo.toml's rust-version") + return match.group(1) + + +def readthedocs_rust_version() -> str: + text = (REPO_ROOT / ".readthedocs.yaml").read_text() + match = re.search(r'^\s*rust:\s*"([\d.]+)"', text, re.MULTILINE) + if not match: + sys.exit("could not find a 'rust: \"X.Y\"' line under build.tools in .readthedocs.yaml") + return match.group(1) + + +def deeptools_version() -> str: + data = tomllib.loads((REPO_ROOT / "pyproject.toml").read_text()) + return data["project"]["version"] + + +def galaxy_tool_version() -> str: + text = (REPO_ROOT / "galaxy/wrapper/deepTools_macros.xml").read_text() + match = re.search(r'([^<]+)', text) + if not match: + sys.exit("could not find a '' line in " + "galaxy/wrapper/deepTools_macros.xml") + return match.group(1) + + +def main() -> None: + cargo_version = cargo_rust_version() + rust_checks = { + "pyproject.toml [tool.pixi.dependencies] rust": pixi_rust_version(), + ".readthedocs.yaml build.tools.rust": readthedocs_rust_version(), + } + mismatches = { + f"rust: {name}": (cargo_version, version) + for name, version in rust_checks.items() + if version != cargo_version + } + + pkg_version = deeptools_version() + galaxy_version = galaxy_tool_version() + if galaxy_version != pkg_version: + mismatches["deeptools: galaxy/wrapper/deepTools_macros.xml @TOOL_VERSION@"] = ( + pkg_version, + galaxy_version, + ) + + if mismatches: + print("Version mismatch detected:", file=sys.stderr) + for name, (expected, actual) in mismatches.items(): + print(f" {name}: expected {expected!r}, found {actual!r}", file=sys.stderr) + sys.exit(1) + + +if __name__ == "__main__": + main() From 0f1d3946da8a79681c8b835497836c4c2e6a7e87 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 08:13:48 +0200 Subject: [PATCH 11/24] include authors --- pyproject.toml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 88e99b9e75..e07adf3ce6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,16 +14,25 @@ bindings = "pyo3" name = "deeptools" version = "4.0.0" authors = [ - {name="Fidel Ramirez"}, - {name="Devon P Ryan"}, - {name="Björn Grüning"}, - {name="Friederike Dündar"}, - {name="Sarah Diehl"}, {name="Vivek Bhardwaj"}, - {name="Fabian Kilpert"}, - {name="Andreas S Richter"}, + {name="Ward Deboutte"}, + {name="Lucille Delisle"}, + {name="Sarah Diehl"}, + {name="Galina Erikson"}, + {name="Friederike Dündar"}, + {name="Björn Grüning"}, {name="Steffen Heyne"}, + {name="Fabian Kilpert"}, + {name="Wolfgang Maier"}, {name="Thomas Manke"}, + {name="Saim Momin"}, + {name="Mohit Navander"}, + {name="Juan Perez Caballero"}, + {name="Fidel Ramirez"}, + {name="Adrian Salatino"}, + {name="Andreas S Richter"}, + {name="Devon P Ryan"}, + {name="Pavankumar Videm"}, {email="bioinfo-core@ie-freiburg.mpg.de"} ] requires-python = ">= 3.12" From 0906566ed651c98a0eedb44a6b1438ec806ff756 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 08:57:20 +0200 Subject: [PATCH 12/24] ensure rust in rtd yaml is an allowed rust version --- .readthedocs.yaml | 4 +- scripts/check_version_sync.py | 81 ++++++++++++++++++++++++++++++----- 2 files changed, 73 insertions(+), 12 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index bc3018ec80..858ccf8b17 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -3,8 +3,8 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.12" - rust: "1.85" + python: "3.14" + rust: "1.86" apt_packages: - clang diff --git a/scripts/check_version_sync.py b/scripts/check_version_sync.py index 5e2d349e17..0d721174a4 100644 --- a/scripts/check_version_sync.py +++ b/scripts/check_version_sync.py @@ -1,10 +1,65 @@ +import json import re import sys import tomllib +import urllib.error +import urllib.request from pathlib import Path REPO_ROOT = Path(__file__).resolve().parent.parent +# RTD only ships specific Rust toolchains, so build.tools.rust can't be set to an +# arbitrary version string the way Cargo.toml's rust-version can. The allowed set +# is published as the JSON schema RTD uses to validate .readthedocs.yaml. +READTHEDOCS_SCHEMA_URL = ( + "https://raw.githubusercontent.com/readthedocs/readthedocs.org/main/" + "readthedocs/rtd_tests/fixtures/spec/v2/schema.json" +) + + +def _version_tuple(version: str) -> tuple[int, ...]: + return tuple(int(part) for part in version.split(".")) + + +def _find_rust_enum(node: object) -> list[str] | None: + """Walk the RTD JSON schema looking for the `rust` tool's `enum` list.""" + if isinstance(node, dict): + rust = node.get("rust") + if isinstance(rust, dict) and isinstance(rust.get("enum"), list): + return rust["enum"] + for value in node.values(): + found = _find_rust_enum(value) + if found is not None: + return found + elif isinstance(node, list): + for item in node: + found = _find_rust_enum(item) + if found is not None: + return found + return None + + +def fetch_readthedocs_allowed_rust_versions() -> list[str] | None: + """Return RTD's allowed build.tools.rust values, or None if unreachable/unparseable.""" + try: + with urllib.request.urlopen(READTHEDOCS_SCHEMA_URL, timeout=5) as response: + schema = json.load(response) + except (urllib.error.URLError, TimeoutError, json.JSONDecodeError) as exc: + print( + f"warning: could not fetch RTD's schema ({READTHEDOCS_SCHEMA_URL}) to validate " + f"build.tools.rust ({exc}); skipping the allowed-toolchain check", + file=sys.stderr, + ) + return None + versions = _find_rust_enum(schema) + if versions is None: + print( + f"warning: RTD's schema ({READTHEDOCS_SCHEMA_URL}) no longer has the expected " + "build.tools.rust enum shape; skipping the allowed-toolchain check", + file=sys.stderr, + ) + return versions + def cargo_rust_version() -> str: data = tomllib.loads((REPO_ROOT / "Cargo.toml").read_text()) @@ -23,7 +78,7 @@ def pixi_rust_version() -> str: def readthedocs_rust_version() -> str: text = (REPO_ROOT / ".readthedocs.yaml").read_text() - match = re.search(r'^\s*rust:\s*"([\d.]+)"', text, re.MULTILINE) + match = re.search(r'^\s*rust:\s*"([\w.]+)"', text, re.MULTILINE) if not match: sys.exit("could not find a 'rust: \"X.Y\"' line under build.tools in .readthedocs.yaml") return match.group(1) @@ -45,15 +100,21 @@ def galaxy_tool_version() -> str: def main() -> None: cargo_version = cargo_rust_version() - rust_checks = { - "pyproject.toml [tool.pixi.dependencies] rust": pixi_rust_version(), - ".readthedocs.yaml build.tools.rust": readthedocs_rust_version(), - } - mismatches = { - f"rust: {name}": (cargo_version, version) - for name, version in rust_checks.items() - if version != cargo_version - } + mismatches: dict[str, tuple[str, str]] = {} + + pixi_version = pixi_rust_version() + if pixi_version != cargo_version: + mismatches["rust: pyproject.toml [tool.pixi.dependencies] rust"] = (cargo_version, pixi_version) + + rtd_version = readthedocs_rust_version() + allowed_rtd_versions = fetch_readthedocs_allowed_rust_versions() + if allowed_rtd_versions is not None and rtd_version not in allowed_rtd_versions: + mismatches["rust: .readthedocs.yaml build.tools.rust (not an RTD-provided toolchain)"] = ( + f"one of {allowed_rtd_versions}", + rtd_version, + ) + elif rtd_version != "latest" and _version_tuple(rtd_version) < _version_tuple(cargo_version): + mismatches["rust: .readthedocs.yaml build.tools.rust"] = (f">= {cargo_version}", rtd_version) pkg_version = deeptools_version() galaxy_version = galaxy_tool_version() From 467dd2ff40c703243c42bc3330e93bbb8898ef6b Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 09:00:14 +0200 Subject: [PATCH 13/24] cleanup readme, https --- README.md | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index f3f614c210..615f906061 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating **normalized coverage files** in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready **visualizations** to identify enrichments and for functional annotations of the genome. -For support or questions please post to [Biostars](http://biostars.org). For bug reports and feature requests please open an issue [on github](http://github.com/deeptools/deeptools). +For bug reports and feature requests please open an issue [on github](https://github.com/deeptools/deeptools). ### Citation: @@ -19,12 +19,10 @@ Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dü ### Documentation: -Our [documentation](http://deeptools.readthedocs.org/) contains more details on the [individual tool scopes and usages](http://deeptools.readthedocs.org/en/latest/content/list_of_tools.html) and an [introduction to our deepTools Galaxy web server](http://deeptools.readthedocs.org/en/latest/content/help_galaxy_intro.html) including [step-by-step protocols](http://deeptools.readthedocs.org/en/latest/content/example_usage.html). +Our [documentation](https://deeptools.readthedocs.org/) contains more details on the [individual tool scopes and usages](https://deeptools.readthedocs.org/en/latest/content/list_of_tools.html) and an [introduction to our deepTools Galaxy web server](https://deeptools.readthedocs.org/en/latest/content/help_galaxy_intro.html) including [step-by-step protocols](https://deeptools.readthedocs.org/en/latest/content/example_usage.html). ->Please see also the [FAQ](http://deeptools.readthedocs.org/en/latest/content/help_faq.html), which we update regularly. -Our [Gallery](http://deeptools.readthedocs.org/en/latest/content/example_gallery.html) may give you some more ideas about the scope of deepTools. - ->For more specific **troubleshooting, feedback, and tool suggestions**, please post [to Biostars](http://biostars.org). +>Please see also the [FAQ](https://deeptools.readthedocs.org/en/latest/content/help_faq.html), which we update regularly. +Our [Gallery](https://deeptools.readthedocs.org/en/latest/content/example_gallery.html) may give you some more ideas about the scope of deepTools. ------------------------------------------------------------------------------------------------------------------- @@ -57,12 +55,8 @@ In Brief: ### Galaxy Installation -deepTools can be easily integrated into [Galaxy](http://galaxyproject.org). Please see the [installation instructions in our documentation](http://deeptools.readthedocs.io/en/latest/content/installation.html#galaxy-installation) for further details. - -**Note:** From version 2.3 onwards, deepTools support **python3**. +deepTools can be easily integrated into [Galaxy](https://galaxyproject.org). Please see the [installation instructions in our documentation](https://deeptools.readthedocs.io/en/latest/content/installation.html#galaxy-installation) for further details. ------------------------------------ -This tool suite is developed by the [Bioinformatics Facility](http://www1.ie-freiburg.mpg.de/bioinformaticsfac) at the [Max Planck Institute for Immunobiology and Epigenetics, Freiburg](http://www1.ie-freiburg.mpg.de/). - -[Documentation](http://deeptools.readthedocs.org/en/latest/index.html) | [deepTools Galaxy](http://deeptools.ie-freiburg.mpg.de) | [FAQ](http://deeptools.readthedocs.org/en/latest/content/help_faq.html) +[Documentation](https://deeptools.readthedocs.org/en/latest/index.html) | [FAQ](https://deeptools.readthedocs.org/en/latest/content/help_faq.html) From 35e6b1b6c9c75980e138ab9ad4612c1e0947291a Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 09:52:33 +0200 Subject: [PATCH 14/24] docs overhauls, remove plotly refs, update parser --- CHANGES.txt | 2 +- docs/conf.py | 2 +- docs/content/changelog.rst | 13 ++++-- docs/content/feature/plotly.rst | 8 ---- docs/content/list_of_tools.rst | 12 ++--- docs/content/tools/alignmentSieve.rst | 2 + docs/content/tools/bamCompare.rst | 4 +- docs/content/tools/bamCoverage.rst | 4 +- docs/content/tools/computeGCBias.rst | 1 - docs/content/tools/computeMatrix.rst | 2 + docs/content/tools/multiBamSummary.rst | 2 + pydeeptools/deeptools/alignmentSieve2.py | 2 +- pydeeptools/deeptools/bamPEFragmentSize.py | 2 +- pydeeptools/deeptools/computeGCBias.py | 53 ++-------------------- pydeeptools/deeptools/computeMatrix2.py | 4 +- pydeeptools/deeptools/parserCommon.py | 4 +- pydeeptools/deeptools/plotPCA.py | 2 +- 17 files changed, 38 insertions(+), 81 deletions(-) delete mode 100644 docs/content/feature/plotly.rst diff --git a/CHANGES.txt b/CHANGES.txt index cb70071a2f..56dfe7914d 100755 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -4,7 +4,7 @@ * --exactScaling is removed as this is the only scaling option available with the new backend * --ignoreDuplicates has been removed from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) * plotPCA re-implemented with a lightweight scipy/numpy SVD backend. Proper handling of --transpose, --log2/--rowCenter and --ntop options. -* plotly backend from plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment in favor of matplotlib, with a new optional --ggplot theme +* plotly backend removed entirely; plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment now use matplotlib, with a new optional --ggplot theme, and computeGCBias's --plotFileFormat plotly option has also been removed * removed the standalone cm.py colormap module; colormap handling now lives in the plotting tools directly * plot labels now show sample names only per default (dropped .filtered.bam/.bed suffixes) * prebuilt wheels now cover Linux manylinux_2_28 and musllinux_1_2 (x86_64 + aarch64) and macOS (Intel + Apple Silicon), built via maturin diff --git a/docs/conf.py b/docs/conf.py index 5a741a451e..e8f62a607f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -20,7 +20,7 @@ import mock # MOCK_MODULES = ['numpy', 'numpy.ma', 'scipy', 'pyBigWig'] -MOCK_MODULES = ['pyBigWig', 'py2bit', 'plotly', 'plotly.offline', 'plotly.graph_objs', 'plotly.figure_factory'] +MOCK_MODULES = ['pyBigWig', 'py2bit'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = mock.Mock() diff --git a/docs/content/changelog.rst b/docs/content/changelog.rst index 72f7b6c2d8..0985a445a1 100644 --- a/docs/content/changelog.rst +++ b/docs/content/changelog.rst @@ -20,7 +20,7 @@ Plotting - Retained only sample names, when provided with the complete file path and name. * plotPCA: - - Using scikit-learn for computing PCA. + - Re-implemented with a lightweight scipy/numpy SVD backend (mirroring scikit-learn's PCA), instead of the previous plotly-based implementation. - New option to add labels for each point (--addLabels). - Expander for colors and markers, for example ``--colors red:3 blue:3`` is expanded as ``[red, red, red, blue, blue, blue]``. - Scree plot is showing lines for individual and accumulated variation. @@ -33,7 +33,6 @@ Core - --no_collapse flag to not merge bins with equal coverage values together. * computeMatrix - - --sortRegions 'no' option no longer exists - Sorting ascend / descend no longer has subsorting by position. - --quiet / -q option no longer exists. - bed files in computeMatrix no longer support '#' to define groups. @@ -47,8 +46,14 @@ Core - blackList filtering is now performed on a position-based level. Meaning reads that overlap partially with the blacklist can still contribute to the signal. * alignmentSieve - - options label, smartLabels, genomeChunkLength are removed. - - ignoreDuplicates is removed, and (if wanted) should be set by the SamFlagExclude setting. + - --genomeChunkLength is removed; --label, --smartLabels and --ignoreDuplicates are still available. + - output order now exactly matches input order. + +* new Rust-backed core + - bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary are now backed by a Rust core (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations. + - the previous Python implementations remain available as ``bamCoverage_old``, ``bamCompare_old``, ``computeMatrix_old``, ``alignmentSieve_old`` and ``multiBamSummary_old`` during the transition, but will be removed in a future release. + - gzipped GTF/BED region files are now supported in multiBamSummary, computeMatrix and alignmentSieve; gzipped blacklist files are supported in all five Rust-backed tools. + - large scale values have slightly different precision than before (f32 vs f64 internally). Testing ------- diff --git a/docs/content/feature/plotly.rst b/docs/content/feature/plotly.rst deleted file mode 100644 index 7325731972..0000000000 --- a/docs/content/feature/plotly.rst +++ /dev/null @@ -1,8 +0,0 @@ -:orphan: - -Plotly -====== - -`Plotly `__ is a tool for interactive visualization of datasets that deepTools has supported since version 2.6. The output of this "image format" is a web page that you can load in your browser of choice. Generally the resulting webpages will look essentially like the default images, but you can do things such as mouse-over an area to get the sample label or value and zoom in/pan around images. These web pages can grow to be **very** large, particularly for `plotHeatmap`. Further, not all deepTools options will be supported. In particular, in `plotHeatmap`, only a single colorbar is supported. These limitations are due to limitations in plotly itself and may be removed as plotly itself matures. - -Note that plotly output is saved locally and remote servers are not used. This is due to most users likely wishing to keep their data private. If you would like to edit the resulting pages and export them to plot.ly then click on the link in the bottom-right corner of the plotly output. diff --git a/docs/content/list_of_tools.rst b/docs/content/list_of_tools.rst index 2191f3c235..1a370e957d 100644 --- a/docs/content/list_of_tools.rst +++ b/docs/content/list_of_tools.rst @@ -54,8 +54,8 @@ A typical deepTools command could look like this: $ bamCoverage --bam myAlignedReads.bam \ --outFileName myCoverageFile.bigWig \ --outFileFormat bigwig \ - --fragmentLength 200 \ - --ignoreDuplicates \ + --extendReads 200 \ + --samFlagExclude 1024 \ --scaleFactor 0.5 You can always see all available command-line options via --help or -h: @@ -95,17 +95,17 @@ Filtering BAMs while processing Several deepTools modules allow for efficient processing of BAM files, e.g. ``bamCoverage`` and ``bamCompare``. We offer several ways to filter those BAM files on the fly so that you don't need to pre-process them using other tools such as `samtools `_ -- ``ignoreDuplicates`` - Reads with the same orientation and start position will be considered only once. If reads are paired, the mate is also evaluated - ``minMappingQuality`` Only reads with a mapping quality score of at least this are considered - ``samFlagInclude`` Include reads based on the SAM flag, e.g. ``--samFlagInclude 64`` gets reads that are first in a pair. For translating SAM flags into English, go to: `https://broadinstitute.github.io/picard/explain-flags.html `_ -- ` `samFlagExclude`` - Exclude reads based on the SAM flags - see previous explanation. +- ``samFlagExclude`` + Exclude reads based on the SAM flags - see previous explanation. E.g. ``--samFlagExclude 1024`` excludes reads marked as duplicates. These parameters are optional and available throughout deepTools. +.. note:: ``ignoreDuplicates`` is still available in tools that were not rewritten in 4.0.0 (e.g. ``plotCoverage``, ``estimateReadFiltering``), but was removed from ``bamCoverage`` and ``bamCompare``. For those two tools, use ``--samFlagExclude`` against a BAM file with duplicates marked instead. + .. note:: In version 2.3 we introduced a sampling method to correct the effect of filtering when normalizing using ``bamCoverage`` or ``bamCompare``. For previous versions, if you know that your files will be strongly affected by the filtering of duplicates or reads of low quality then consider removing those reads *before* using ``bamCoverage`` or ``bamCompare``, as the filtering by deepTools is done *after* the scaling factors are calculated! diff --git a/docs/content/tools/alignmentSieve.rst b/docs/content/tools/alignmentSieve.rst index 9c8e5d58f5..88d78d4357 100644 --- a/docs/content/tools/alignmentSieve.rst +++ b/docs/content/tools/alignmentSieve.rst @@ -11,6 +11,8 @@ alignmentSieve :prog: alignmentSieve :nodefault: +.. note:: As of deepTools 4.0.0, ``alignmentSieve`` uses a new Rust-backed core. Region files (BED/GTF) and ``--blackListFileName`` may be gzip-compressed, blacklist filtering is done at base-pair resolution rather than by rejecting whole genomic chunks, output order now exactly matches input order, and ``--genomeChunkLength`` has been removed. The previous pure-Python implementation is still available as ``alignmentSieve_old`` during the transition period, but will be removed in a future release. + Background ^^^^^^^^^^ diff --git a/docs/content/tools/bamCompare.rst b/docs/content/tools/bamCompare.rst index 1daf32935d..30ea5b7ea6 100644 --- a/docs/content/tools/bamCompare.rst +++ b/docs/content/tools/bamCompare.rst @@ -13,7 +13,7 @@ The basic algorithm works proceeds in two steps: 1. Per-sample scaling / depth Normalization: - - If scaling is used (using the SES or read counts method), appropriate scaling + - If scaling is used (via the read counts method), appropriate scaling factors are determined to account for sequencing depth differences. - Optionally scaling can be turned off and individual samples normalized using the RPKM, BPM or CPM methods (or no normalization at all) @@ -27,3 +27,5 @@ The basic algorithm works proceeds in two steps: :ref: deeptools.bamCompare2.parseArguments :prog: bamCompare :nodefault: + +.. note:: As of deepTools 4.0.0, ``bamCompare`` uses a new Rust-backed core. ``--blackListFileName`` may be gzip-compressed and blacklist filtering is done at base-pair resolution rather than by rejecting whole genomic chunks. The SES scaling method and ``--ignoreDuplicates`` have both been removed; for duplicate removal use ``--samFlagExclude`` against a BAM file with duplicates marked. The previous pure-Python implementation is still available as ``bamCompare_old`` during the transition period, but will be removed in a future release. diff --git a/docs/content/tools/bamCoverage.rst b/docs/content/tools/bamCoverage.rst index 3507c62d9d..7894ba70fd 100644 --- a/docs/content/tools/bamCoverage.rst +++ b/docs/content/tools/bamCoverage.rst @@ -26,10 +26,10 @@ Usage hints Other data, e.g. Chip-seq, where fragments are known to map contiguously, should be processed with read extension (``--extendReads [INTEGER]``). * For paired-end data, the fragment length is generally defined by the two read mates. The user provided fragment length is only used as a fallback for singletons or mate reads that map too far apart (with a distance greater than four times the fragment length or are located on different chromosomes). -.. warning:: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``! - .. note:: Like BAM files, bigWig files are compressed, binary files. If you would like to see the coverage values, choose the bedGraph output via ``--outFileFormat``. +.. note:: As of deepTools 4.0.0, ``bamCoverage`` uses a new Rust-backed core. ``--blackListFileName`` may be gzip-compressed and blacklist filtering is done at base-pair resolution rather than by rejecting whole genomic chunks. ``--ignoreDuplicates`` has been removed; use ``--samFlagExclude`` against a BAM file with duplicates marked instead. The previous pure-Python implementation is still available as ``bamCoverage_old`` during the transition period, but will be removed in a future release. + Usage example for ChIP-seq ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/content/tools/computeGCBias.rst b/docs/content/tools/computeGCBias.rst index 3d794aceaf..a9f381f5bc 100644 --- a/docs/content/tools/computeGCBias.rst +++ b/docs/content/tools/computeGCBias.rst @@ -11,7 +11,6 @@ computeGCBias :prog: computeGCBias :nodefault: - Background ^^^^^^^^^^^ diff --git a/docs/content/tools/computeMatrix.rst b/docs/content/tools/computeMatrix.rst index bbfe2a7dd4..c9ac108dfb 100644 --- a/docs/content/tools/computeMatrix.rst +++ b/docs/content/tools/computeMatrix.rst @@ -11,6 +11,8 @@ computeMatrix :prog: computeMatrix :nodefault: +.. note:: As of deepTools 4.0.0, ``computeMatrix`` uses a new Rust-backed core. Region files (BED/GTF) and ``--blackListFileName`` may be gzip-compressed, and blacklist filtering is done at base-pair resolution rather than by rejecting whole genomic chunks. The previous pure-Python implementation is still available as ``computeMatrix_old`` during the transition period, but will be removed in a future release. + Details ^^^^^^^ diff --git a/docs/content/tools/multiBamSummary.rst b/docs/content/tools/multiBamSummary.rst index 71231905fe..623652991f 100644 --- a/docs/content/tools/multiBamSummary.rst +++ b/docs/content/tools/multiBamSummary.rst @@ -11,6 +11,8 @@ multiBamSummary :prog: multiBamSummary :nodefault: +.. note:: As of deepTools 4.0.0, ``multiBamSummary`` uses a new Rust-backed core. Region files (BED/GTF) and ``--blackListFileName`` may be gzip-compressed, and blacklist filtering is done at base-pair resolution rather than by rejecting whole genomic chunks. The previous pure-Python implementation is still available as ``multiBamSummary_old`` during the transition period, but will be removed in a future release. + Example ^^^^^^^ diff --git a/pydeeptools/deeptools/alignmentSieve2.py b/pydeeptools/deeptools/alignmentSieve2.py index d230f7cd22..b55918bd6c 100644 --- a/pydeeptools/deeptools/alignmentSieve2.py +++ b/pydeeptools/deeptools/alignmentSieve2.py @@ -118,7 +118,7 @@ def parseArguments(): required=False) filtering.add_argument('--blackListFileName', '-bl', - help="A BED or GTF file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. Please note that you should adjust the effective genome size, if relevant.", + help="A BED or GTF file (optionally gzip-compressed) containing regions that should be excluded from all analyses. Filtering is performed at base-pair resolution, so only the portion of a read/fragment that overlaps a blacklisted region is excluded. Please note that you should adjust the effective genome size, if relevant.", metavar="BED file", nargs="+", default="None", diff --git a/pydeeptools/deeptools/bamPEFragmentSize.py b/pydeeptools/deeptools/bamPEFragmentSize.py index 3f6db136c1..eb65b565cb 100755 --- a/pydeeptools/deeptools/bamPEFragmentSize.py +++ b/pydeeptools/deeptools/bamPEFragmentSize.py @@ -49,7 +49,7 @@ def parse_arguments(): help="Image format type. If given, this option " "overrides the image format based on the plotFile " "ending. The available options are: png, " - "eps, pdf, svg and plotly.", + "eps, pdf and svg.", default=None, choices=["png", "pdf", "svg", "eps"], ) diff --git a/pydeeptools/deeptools/computeGCBias.py b/pydeeptools/deeptools/computeGCBias.py index 2e20e6d8cf..151ee050c7 100755 --- a/pydeeptools/deeptools/computeGCBias.py +++ b/pydeeptools/deeptools/computeGCBias.py @@ -119,8 +119,8 @@ def getRequiredArgs(): 'option overrides the ' 'image format based on the plotFile ending. ' 'The available options are: "png", ' - '"eps", "pdf", "plotly" and "svg"', - choices=['png', 'pdf', 'svg', 'eps', 'plotly']) + '"eps", "pdf" and "svg"', + choices=['png', 'pdf', 'svg', 'eps']) plot.add_argument('--regionSize', metavar='INT', @@ -534,50 +534,6 @@ def bin_by(x, y, nbins=10): return output, bins -def plotlyGCbias(file_name, frequencies, reads_per_gc, region_size): - import plotly.offline as py - import plotly.graph_objs as go - import matplotlib.cbook as cbook - - fig = go.Figure() - fig['layout']['xaxis1'] = dict(domain=[0.0, 1.0], anchor="y1", title="GC fraction") - fig['layout']['yaxis1'] = dict(domain=[0.55, 1.0], anchor="x1", title="Number of reads") - fig['layout']['xaxis2'] = dict(domain=[0.0, 1.0], anchor="y2", title="GC fraction", range=[0.2, 0.7]) - fig['layout']['yaxis2'] = dict(domain=[0.0, 0.45], anchor="x2", title="log2(observed/expected)") - text = "reads per {} base region".format(region_size) - annos = [{'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': text, 'y': 1.0, 'x': 0.5, 'font': {'size': 16}, 'showarrow': False}] - text = "normalized observed/expected read counts" - annos.append({'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': text, 'y': 0.5, 'x': 0.5, 'font': {'size': 16}, 'showarrow': False}) - - # prepare data for boxplot - reads, GC = reads_per_gc.T - reads_per_gc, bin_labels = bin_by(reads, GC, nbins=100) - to_keep = [idx for idx, x in enumerate(bin_labels) if 0.2 <= x <= 0.7] - reads_per_gc = [reads_per_gc[x] for x in to_keep] - bin_labels = [bin_labels[x] for x in to_keep] - - # produce the same boxplot as matplotlib as vastly reduce the output file size - bins = [] - for b in reads_per_gc: - s = cbook.boxplot_stats(b)[0] - bins.append([s['whislo'], s['q1'], s['q1'], s['med'], s['med'], s['med'], s['q3'], s['q3'], s['whishi']]) - - data = [] - - # top plot - for x, y in zip(bin_labels, bins): - trace = go.Box(x=x, y=y, xaxis='x1', yaxis='y1', boxpoints='outliers', showlegend=False, name="{}".format(x), line=dict(color='rgb(107,174,214)')) - data.append(trace) - - # bottom plot - x = np.linspace(0, 1, frequencies.shape[0]) - trace = go.Scatter(x=x, y=np.log2(frequencies[:, 2]), xaxis='x2', yaxis='y2', showlegend=False, line=dict(color='rgb(107,174,214)')) - data.append(trace) - fig.add_traces(data) - fig['layout']['annotations'] = annos - py.plot(fig, filename=file_name, auto_open=False) - - def plotGCbias(file_name, frequencies, reads_per_gc, region_size, image_format=None): import matplotlib matplotlib.use('Agg') @@ -718,10 +674,7 @@ def main(args=None): numberOfProcessors=args.numberOfProcessors, verbose=args.verbose, region=args.region) - if args.plotFileFormat == "plotly": - plotlyGCbias(args.biasPlot, data, reads_per_gc, args.regionSize) - else: - plotGCbias(args.biasPlot, data, reads_per_gc, args.regionSize, image_format=args.plotFileFormat) + plotGCbias(args.biasPlot, data, reads_per_gc, args.regionSize, image_format=args.plotFileFormat) class Tester(): diff --git a/pydeeptools/deeptools/computeMatrix2.py b/pydeeptools/deeptools/computeMatrix2.py index d972a6e71a..0a609a20d6 100644 --- a/pydeeptools/deeptools/computeMatrix2.py +++ b/pydeeptools/deeptools/computeMatrix2.py @@ -367,7 +367,7 @@ def computeMatrixOptArgs(case=["scale-regions", "reference-point"][0]): optional.add_argument( "--blackListFileName", "-bl", - help="A BED file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered.", + help="A BED file (optionally gzip-compressed) containing regions that should be excluded from all analyses. Filtering is performed at base-pair resolution, so only the portion of a region that overlaps a blacklisted region is excluded.", metavar="BED file", default='none', required=False, @@ -385,7 +385,7 @@ def computeMatrixOptArgs(case=["scale-regions", "reference-point"][0]): optional.add_argument( "--verbose", - help="Being VERY verbose in the status messages. --quiet will disable this.", + help="Being VERY verbose in the status messages.", action="store_true", ) diff --git a/pydeeptools/deeptools/parserCommon.py b/pydeeptools/deeptools/parserCommon.py index e3c68183ab..927c50f863 100755 --- a/pydeeptools/deeptools/parserCommon.py +++ b/pydeeptools/deeptools/parserCommon.py @@ -329,7 +329,7 @@ def getParentArgParse(args=None, binSize=True, blackList=True): if blackList: optional.add_argument('--blackListFileName', '-bl', - help="A BED or GTF file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. Please note that you should adjust the effective genome size, if relevant.", + help="A BED or GTF file (optionally gzip-compressed) containing regions that should be excluded from all analyses. Filtering is performed at base-pair resolution, so only the portion of a read/fragment that overlaps a blacklisted region is excluded. Please note that you should adjust the effective genome size, if relevant.", metavar="BED file", nargs="+", required=False) @@ -878,7 +878,7 @@ def heatmapperOptionalArgs(mode=['heatmap', 'profile'][0]): 'option overrides the ' 'image format based on the plotFile ending. ' 'The available options are: "png", ' - '"eps", "pdf", "plotly" and "svg"', + '"eps", "pdf" and "svg"', choices=['png', 'pdf', 'svg', 'eps']) optional.add_argument('--ggplot', diff --git a/pydeeptools/deeptools/plotPCA.py b/pydeeptools/deeptools/plotPCA.py index 24260b2c79..49bb3de622 100644 --- a/pydeeptools/deeptools/plotPCA.py +++ b/pydeeptools/deeptools/plotPCA.py @@ -70,7 +70,7 @@ def plotCorrelationArgs(): help='Image format type. If given, this option ' 'overrides the image format based on the plotFile ' 'ending. The available options are: png, ' - 'eps, pdf, plotly and svg.', + 'eps, pdf and svg.', choices=['png', 'pdf', 'svg', 'eps']) optional.add_argument('--plotHeight', From 75ef38887273d5ef426caf96890ac5ae3637afc1 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 09:55:59 +0200 Subject: [PATCH 15/24] rust 1.87 minimum --- .readthedocs.yaml | 2 +- Cargo.toml | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 858ccf8b17..35d094d6e1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,7 +4,7 @@ build: os: ubuntu-22.04 tools: python: "3.14" - rust: "1.86" + rust: "1.91" apt_packages: - clang diff --git a/Cargo.toml b/Cargo.toml index 129cececb4..3df301e998 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -2,7 +2,7 @@ name = "hp" version = "0.1.0" edition = "2024" -rust-version = "1.85" +rust-version = "1.87" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [lib] diff --git a/pyproject.toml b/pyproject.toml index e07adf3ce6..cbd7c77b43 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -112,7 +112,7 @@ libclang = "<22" clangdev = "<22" htslib = "<=1.19" zlib = "*" -rust = ">=1.85" +rust = ">=1.87" maturin = ">=1.0,<2.0" openssl = "*" pkg-config = "*" From 39774ad30eeede60f5f47474085074403983b61d Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 12:39:05 +0200 Subject: [PATCH 16/24] ignore venv --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 1665f89622..500462cbf6 100755 --- a/.gitignore +++ b/.gitignore @@ -72,3 +72,5 @@ target* # pixi .pixi* + +.venv From 3a25f4534360110ea5c3bd703fe7438b4c86b29c Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 12:54:31 +0200 Subject: [PATCH 17/24] move pytest action over to pixi --- .github/workflows/test_pytest.yml | 58 +- pixi.lock | 7497 ++++++++++++++++++++++++++++- pyproject.toml | 12 + 3 files changed, 7361 insertions(+), 206 deletions(-) diff --git a/.github/workflows/test_pytest.yml b/.github/workflows/test_pytest.yml index f1ecd961d0..10459403af 100644 --- a/.github/workflows/test_pytest.yml +++ b/.github/workflows/test_pytest.yml @@ -4,10 +4,6 @@ on: [push, pull_request, workflow_dispatch] permissions: contents: read -defaults: - run: - shell: bash -l {0} - jobs: check_versions_matches: name: Check deeptools/galaxy/Rust versions stay in sync @@ -26,66 +22,40 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.12", "3.13", "3.14"] + pixi-env: [py312, py313, py314] steps: - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2 with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - name: Install Rust - uses: actions-rust-lang/setup-rust-toolchain@166cdcfd11aee3cb47222f9ddb555ce30ddb9659 # v1.17.0 + environments: ${{ matrix.pixi-env }} - name: build deeptools - run: | - python -m venv venv - source venv/bin/activate - pip install maturin - maturin develop --release --extras actions + run: pixi run -e ${{ matrix.pixi-env }} build - name: test deeptools - run: | - source venv/bin/activate - pytest -v + run: pixi run -e ${{ matrix.pixi-env }} test -v - name: build wheel - run: | - source venv/bin/activate - python -m build + run: pixi run -e ${{ matrix.pixi-env }} python -m build - name: test wheel - run: | - source venv/bin/activate - pip install dist/*whl + run: pixi run -e ${{ matrix.pixi-env }} bash -c "pip install dist/*.whl" build-osx: name: Test on OSX runs-on: macOS-latest strategy: matrix: - python-version: ["3.12", "3.13", "3.14"] + pixi-env: [py312, py313, py314] steps: - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: persist-credentials: false - - uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0 + - uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2 with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - name: Install Rust - uses: actions-rust-lang/setup-rust-toolchain@166cdcfd11aee3cb47222f9ddb555ce30ddb9659 # v1.17.0 + environments: ${{ matrix.pixi-env }} - name: build deeptools - run: | - python -m venv venv - source venv/bin/activate - pip install maturin - maturin develop --release --extras actions + run: pixi run -e ${{ matrix.pixi-env }} build - name: test deeptools - run: | - source venv/bin/activate - pytest -v + run: pixi run -e ${{ matrix.pixi-env }} test -v - name: build wheel - run: | - source venv/bin/activate - python -m build + run: pixi run -e ${{ matrix.pixi-env }} python -m build - name: test wheel - run: | - source venv/bin/activate - pip install dist/*whl + run: pixi run -e ${{ matrix.pixi-env }} bash -c "pip install dist/*.whl" diff --git a/pixi.lock b/pixi.lock index f514dc1366..cfd6ea38ba 100644 --- a/pixi.lock +++ b/pixi.lock @@ -673,6 +673,2024 @@ environments: - pypi: https://files.pythonhosted.org/packages/fd/99/757a48b4ace0097b63550597db28f58da0b91d89889f98b34b30f272c0bf/ct3-3.4.0.post5-cp314-cp314-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/fd/e1/3542a9cb596cadd76fcef413f19c79216e002623158befe6daa03dbfa88c/contourpy-1.3.3-cp314-cp314-macosx_11_0_arm64.whl - pypi: https://files.pythonhosted.org/packages/ff/9a/9afaade874b2fa6c752c36f1548f718b5b83af81ed9b76628329dab81c1b/rfc3986-2.0.0-py2.py3-none-any.whl + py312: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/bioconda/linux-64/htslib-1.10-hc616636_2.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.8.0-hcd8ed7f_7.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.8.0-he70792b_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.10.0-hb9d3cd8_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.0-hba2fe39_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.5.0-h127f702_4.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.9.0-h8a7d7e2_5.conda + - 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hypothesis>=6.30 ; extra == 'test' + - array-api-strict>=2.3.1 ; extra == 'test' + - cython ; extra == 'test' + - meson ; extra == 'test' + - ninja ; sys_platform != 'emscripten' and extra == 'test' + - scipy-doctest>=2.0.0 ; extra == 'test' + - sphinx>=5.0.0,<8.2.0 ; extra == 'doc' + - intersphinx-registry ; extra == 'doc' + - pydata-sphinx-theme>=0.15.2 ; extra == 'doc' + - sphinx-copybutton ; extra == 'doc' + - sphinx-design>=0.4.0 ; extra == 'doc' + - matplotlib>=3.5 ; extra == 'doc' + - numpydoc ; extra == 'doc' + - jupytext ; extra == 'doc' + - myst-nb>=1.2.0 ; extra == 'doc' + - pooch ; extra == 'doc' + - jupyterlite-sphinx>=0.19.1 ; extra == 'doc' + - jupyterlite-pyodide-kernel ; extra == 'doc' + - linkify-it-py ; extra == 'doc' + - tabulate ; extra == 'doc' + - click<8.3.0 ; extra == 'dev' + - spin ; extra == 'dev' + - mypy==1.19.1 ; extra == 'dev' + - pyrefly==0.63.0 ; extra == 'dev' + - typing-extensions ; extra == 'dev' + - types-psutil ; extra == 'dev' + - pycodestyle ; extra == 'dev' + - 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colorama>=0.4.6 ; extra == 'windows-terminal' requires_python: '>=3.9' -- pypi: https://files.pythonhosted.org/packages/f4/c4/b3e049d2aa3766180c78507110543d9d50894cc97f57de543f1be521dcdc/charset_normalizer-3.4.9-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl - name: charset-normalizer - version: 3.4.9 - sha256: c25fe15c70c59eb7c5ce8c06a1f3fa1da0ecc5ea1e7a5922c40fd2fa9b0d5046 - requires_python: '>=3.7' - pypi: https://files.pythonhosted.org/packages/f5/37/5abe39a8372a61d3dc3c1338fc504281c01b32fdb3169cd7187153b56d3e/pydantic_core-2.46.5-cp313-cp313-macosx_10_12_x86_64.whl name: pydantic-core version: 2.46.5 diff --git a/pyproject.toml b/pyproject.toml index c6b3e2cb9d..015b23d85f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -114,6 +114,7 @@ htslib = "<=1.19" zlib = "*" rust = ">=1.87" maturin = ">=1.0,<2.0" +pip = "*" openssl = "*" pkg-config = "*" py-spy = "*" From 2096fc121cc92742819ee53e0f7ffe36181c5ac9 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 14:04:11 +0200 Subject: [PATCH 19/24] of course dist upload needs mussllinux builds --- .github/workflows/wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 5de16c0709..dc3dbc7053 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -188,7 +188,7 @@ jobs: name: Release runs-on: ubuntu-latest if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }} - needs: [linux, macos, sdist] + needs: [linux, musllinux, macos, sdist] permissions: id-token: write contents: write From 9548b458b6c5958f2e5493f2f24619c0de309f27 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 14:11:44 +0200 Subject: [PATCH 20/24] set stack min for osx build in pixi env --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 015b23d85f..2563a054ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -122,10 +122,9 @@ py-spy = "*" deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] } [tool.pixi.activation.env] LIBCLANG_PATH = "$CONDA_PREFIX/lib" -# Link conda-forge's OpenSSL instead of building the vendored copy from source -# (the from-source build needs a full perl toolchain, e.g. FindBin.pm). OPENSSL_NO_VENDOR = "1" OPENSSL_DIR = "$CONDA_PREFIX" +RUST_MIN_STACK = "16777216" [tool.pixi.tasks] build = "maturin develop --release" test = "pytest pydeeptools/deeptools/test/" From a37ce354c67833882d552e3d18e3b8baaf932816 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 14:14:44 +0200 Subject: [PATCH 21/24] up stack --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2563a054ed..03d60cfc96 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,7 +124,7 @@ deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] } LIBCLANG_PATH = "$CONDA_PREFIX/lib" OPENSSL_NO_VENDOR = "1" OPENSSL_DIR = "$CONDA_PREFIX" -RUST_MIN_STACK = "16777216" +RUST_MIN_STACK = "50000000" [tool.pixi.tasks] build = "maturin develop --release" test = "pytest pydeeptools/deeptools/test/" From 38b1ec448b1c23e1242f73ece6bbab039ab37456 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 14:27:28 +0200 Subject: [PATCH 22/24] 100MB stack for osx build ? --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 03d60cfc96..9513165be1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,7 +124,7 @@ deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] } LIBCLANG_PATH = "$CONDA_PREFIX/lib" OPENSSL_NO_VENDOR = "1" OPENSSL_DIR = "$CONDA_PREFIX" -RUST_MIN_STACK = "50000000" +RUST_MIN_STACK = "100000000" [tool.pixi.tasks] build = "maturin develop --release" test = "pytest pydeeptools/deeptools/test/" From 4c4a2d10d9ce1fa61ca26cf2b28b539cc3546715 Mon Sep 17 00:00:00 2001 From: WardDeb Date: Fri, 4 Sep 2026 14:50:17 +0200 Subject: [PATCH 23/24] strip wheels, cap rust version to avoid conda-forge rust build error for osx --- .github/workflows/wheels.yml | 41 +------------ pixi.lock | 108 +++++++++++++++++----------------- pyproject.toml | 5 +- scripts/check_version_sync.py | 5 +- 4 files changed, 61 insertions(+), 98 deletions(-) diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index dc3dbc7053..937e63c114 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -1,6 +1,4 @@ -name: build wheels -# maturin generate-ci github > .github/workflows/maturin.yml -# Also, see: https://github.com/jackh726/bigtools/blob/master/.github/workflows/release-python.yml +name: build_wheels on: push: @@ -103,41 +101,6 @@ jobs: name: wheels-musllinux-${{ matrix.platform.target }} path: dist - # windows: - # runs-on: ${{ matrix.platform.runner }} - # strategy: - # matrix: - # platform: - # - runner: windows-latest - # target: x64 - # - runner: windows-latest - # target: x86 - # steps: - # - uses: actions/checkout@v4 - # - uses: actions/setup-python@v5 - # with: - # python-version: 3.x - # architecture: ${{ matrix.platform.target }} - # - name: Install And Configure Dependencies - # env: - # VCPKG_DEFAULT_TRIPLET: ${{ matrix.platform.target }}-windows - # OPENSSL_DIR: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows - # OPENSSL_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows - # LZMA_ROOT: ${{ github.workspace }}/vcpkg/installed/${{ matrix.platform.target }}-windows - # run: | - # vcpkg install openssl liblzma - # - name: Build wheels - # uses: PyO3/maturin-action@v1 - # with: - # target: ${{ matrix.platform.target }} - # args: --release --out dist --find-interpreter - # # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }} - # - name: Upload wheels - # uses: actions/upload-artifact@v4 - # with: - # name: wheels-windows-${{ matrix.platform.target }} - # path: dist - macos: runs-on: ${{ matrix.platform.runner }} strategy: @@ -159,7 +122,6 @@ jobs: with: target: ${{ matrix.platform.target }} args: --release --out dist --find-interpreter - # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }} - name: Upload wheels uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 with: @@ -177,7 +139,6 @@ jobs: with: command: sdist args: --out dist - # sccache: ${{ !startsWith(github.ref, 'refs/tags/') }} - name: Upload sdist uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 with: diff --git a/pixi.lock b/pixi.lock index 76f6f54b8b..a754315244 100644 --- a/pixi.lock +++ b/pixi.lock @@ -759,7 +759,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/py-spy-0.4.2-hbe0e3b8_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.14-h5f976f7_3_cpython.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-hd6e31c0_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/rust-1.98.0-hc89c8c8_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/rust-1.97.1-hc89c8c8_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/s2n-1.5.7-hd3e8b83_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h1df4ec4_4.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_3.conda @@ -772,7 +772,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-16.2.0-h86e191b_104.conda - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.2.1-pyh8b19718_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-unknown-linux-gnu-1.98.0-h2c6d0dc_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-unknown-linux-gnu-1.97.1-h2c6d0dc_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-84.0.0-pyh332efcf_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.28-h4ee821c_9.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda @@ -927,7 +927,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/libcxx-headers-21.1.8-h707e725_3.conda - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.2.1-pyh8b19718_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-apple-darwin-1.98.0-h38e4360_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-x86_64-apple-darwin-1.97.1-h38e4360_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-84.0.0-pyh332efcf_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda @@ -988,7 +988,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-64/py-spy-0.4.2-he704061_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/python-3.12.14-h6907cb8_3_cpython.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/readline-8.3-h000c2f7_1.conda - - conda: https://conda.anaconda.org/conda-forge/osx-64/rust-1.98.0-h5655b98_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-64/rust-1.97.1-h5655b98_2.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/sigtool-codesign-0.1.3-h8c25ef7_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/tapi-1600.0.11.8-h44950e2_3.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/tk-8.6.13-ha6c374e_4.conda @@ -1141,7 +1141,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/libcxx-headers-21.1.8-h707e725_3.conda - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.3-pyhc364b38_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.2.1-pyh8b19718_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-aarch64-apple-darwin-1.98.0-hf6ec828_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/rust-std-aarch64-apple-darwin-1.97.1-hf6ec828_2.conda - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-84.0.0-pyh332efcf_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.4.1-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2026c-h151e31d_0.conda @@ -1202,7 +1202,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/py-spy-0.4.2-hc2d82ec_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.14-hd05a0c4_3_cpython.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/readline-8.3-h8b90a29_1.conda - - conda: https://conda.anaconda.org/conda-forge/osx-arm64/rust-1.98.0-h4ff7c5d_0.conda + - conda: https://conda.anaconda.org/conda-forge/osx-arm64/rust-1.97.1-h4ff7c5d_2.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/sigtool-codesign-0.1.3-h98dc951_1.conda - conda: 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https://conda.anaconda.org/conda-forge/osx-arm64/rust-1.98.0-h4ff7c5d_0.conda - sha256: d414006a1803d04d42a3723cb2fbd620a4df9e703754ac4bc2cf36cafaad249e - md5: 918602a058733aba81876ecbf1d28005 +- conda: https://conda.anaconda.org/conda-forge/osx-arm64/rust-1.97.1-h4ff7c5d_2.conda + sha256: 5181f582c32bdd39926cd8eb03957d7eb355c32bac889b6dcbd3d91b839f3c66 + md5: 4a33cc4400d259e297e60416cd4a8927 depends: - - rust-std-aarch64-apple-darwin 1.98.0 hf6ec828_0 + - rust-std-aarch64-apple-darwin 1.97.1 hf6ec828_2 license: MIT license_family: MIT purls: [] run_exports: {} - size: 105937676 - timestamp: 1787578529591 + size: 181267329 + timestamp: 1787152435071 - conda: https://conda.anaconda.org/conda-forge/osx-arm64/sigtool-codesign-0.1.3-h98dc951_1.conda sha256: 7efd6d7d18bf9cc5788bfe1c1e1620d9dbbe00a81c646814929a82ff31944cf3 md5: a322c0a0d3b5be99ee11f9ccec99b60e diff --git a/pyproject.toml b/pyproject.toml index 9513165be1..9120d46e13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -112,7 +112,9 @@ libclang = "<22" clangdev = "<22" htslib = "<=1.19" zlib = "*" -rust = ">=1.87" +# conda-forge's rust 1.98.0 build segfaults in LLVM target init on osx-arm64 +# (reproducible even after a clean env reinstall); capped until that's fixed upstream. +rust = ">=1.87,<1.98" maturin = ">=1.0,<2.0" pip = "*" openssl = "*" @@ -124,7 +126,6 @@ deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] } LIBCLANG_PATH = "$CONDA_PREFIX/lib" OPENSSL_NO_VENDOR = "1" OPENSSL_DIR = "$CONDA_PREFIX" -RUST_MIN_STACK = "100000000" [tool.pixi.tasks] build = "maturin develop --release" test = "pytest pydeeptools/deeptools/test/" diff --git a/scripts/check_version_sync.py b/scripts/check_version_sync.py index 0d721174a4..5ff64a70d2 100644 --- a/scripts/check_version_sync.py +++ b/scripts/check_version_sync.py @@ -69,10 +69,11 @@ def cargo_rust_version() -> str: def pixi_rust_version() -> str: data = tomllib.loads((REPO_ROOT / "pyproject.toml").read_text()) spec = data["tool"]["pixi"]["dependencies"]["rust"] - match = re.fullmatch(r">=\s*([\d.]+)", spec) + match = re.fullmatch(r">=\s*([\d.]+)(?:\s*,\s*<\s*[\d.]+)?", spec) if not match: sys.exit(f"pyproject.toml: unexpected [tool.pixi.dependencies] rust spec {spec!r}, " - "expected '>=X.Y' so it can be compared to Cargo.toml's rust-version") + "expected '>=X.Y' or '>=X.Y, Date: Fri, 4 Sep 2026 18:37:28 +0200 Subject: [PATCH 24/24] https in docs, clarify installation instructions, delete rst --- README.md | 41 ++++++++++++++++++++-------- README.rst | 29 -------------------- docs/content/help_faq.rst | 2 +- docs/content/help_glossary.rst | 2 +- docs/content/installation.rst | 25 +++++++++-------- docs/content/tools/computeMatrix.rst | 2 +- docs/content/tools/plotHeatmap.rst | 4 +-- pyproject.toml | 2 +- 8 files changed, 50 insertions(+), 57 deletions(-) delete mode 100644 README.rst diff --git a/README.md b/README.md index 615f906061..5db677e3f2 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,12 @@ # deepTools -[![Documentation Status](https://readthedocs.org/projects/deeptools/badge/)](http://deeptools.readthedocs.org/) +[![Documentation Status](https://readthedocs.org/projects/deeptools/badge/)](https://deeptools.readthedocs.io/) [![PyPI Version](https://img.shields.io/pypi/v/deeptools.svg?style=plastic)](https://pypi.org/project/deepTools/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/deeptools/README.html) [![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,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)](https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix) -![test](https://github.com/deeptools/deepTools/actions/workflows/test.yml/badge.svg) +![pytest](https://github.com/deeptools/deepTools/actions/workflows/test_pytest.yml/badge.svg) +![docs](https://github.com/deeptools/deepTools/actions/workflows/test_docs.yml/badge.svg) +![rust](https://github.com/deeptools/deepTools/actions/workflows/test_rust.yml/badge.svg) +![planemo](https://github.com/deeptools/deepTools/actions/workflows/test_planemo.yml/badge.svg) ## User-friendly tools for exploring deep-sequencing data @@ -19,10 +22,10 @@ Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dü ### Documentation: -Our [documentation](https://deeptools.readthedocs.org/) contains more details on the [individual tool scopes and usages](https://deeptools.readthedocs.org/en/latest/content/list_of_tools.html) and an [introduction to our deepTools Galaxy web server](https://deeptools.readthedocs.org/en/latest/content/help_galaxy_intro.html) including [step-by-step protocols](https://deeptools.readthedocs.org/en/latest/content/example_usage.html). +Our [documentation](https://deeptools.readthedocs.io/) contains more details on the [individual tool scopes and usages](https://deeptools.readthedocs.io/en/latest/content/list_of_tools.html) and an [introduction to our deepTools Galaxy web server](https://deeptools.readthedocs.io/en/latest/content/help_galaxy_intro.html) including [step-by-step protocols](https://deeptools.readthedocs.io/en/latest/content/example_usage.html). ->Please see also the [FAQ](https://deeptools.readthedocs.org/en/latest/content/help_faq.html), which we update regularly. -Our [Gallery](https://deeptools.readthedocs.org/en/latest/content/example_gallery.html) may give you some more ideas about the scope of deepTools. +>Please see also the [FAQ](https://deeptools.readthedocs.io/en/latest/content/help_faq.html), which we update regularly. +Our [Gallery](https://deeptools.readthedocs.io/en/latest/content/example_gallery.html) may give you some more ideas about the scope of deepTools. ------------------------------------------------------------------------------------------------------------------- @@ -34,23 +37,39 @@ deepTools are available for: * Command line usage (via pip / conda / github) * Integration into Galaxy servers (via toolshed/API/web-browser) -There are many easy ways to install deepTools. More details can be found [here](https://deeptools.readthedocs.io/en/latest/content/installation.html). +There are many ways to install deepTools. More details can be found [here](https://deeptools.readthedocs.io/en/latest/content/installation.html). -In Brief: +In Brief, to install stable released version: -**Install through pypi** +**Install via pip** $ pip install deeptools **Install via conda** - $ conda install -c bioconda deeptools + $ conda install -c conda-forge -c bioconda deeptools + +**Install via uv / pipx / pixi** + + $ uv tool install deeptools + $ pipx install deeptools + $ pixi global install -c conda-forge -c bioconda deeptools + +You can also install the latest development version (if you want to contribute or have the latest features). +The easiest way to do this is clone the repository and install with pixi (which will take care of the system dependencies via conda for you): **Install by cloning the repository** $ git clone https://github.com/deeptools/deepTools $ cd deepTools - $ pip install . + $ pixi install + +`pixi install` pins the whole build toolchain (Rust, `maturin`, `libclang`, HTSlib, ...) via +conda -- see [`pyproject.toml`](pyproject.toml)'s `[tool.pixi.dependencies]` for exactly what's +pinned. Building without pixi (via uv / pip / pipx) is possible too, but then you're responsible +for providing that same toolchain yourself; see the ["Building from +source"](https://deeptools.readthedocs.io/en/latest/content/installation.html#building-from-source) +section of the docs. ### Galaxy Installation @@ -59,4 +78,4 @@ deepTools can be easily integrated into [Galaxy](https://galaxyproject.org). Ple ------------------------------------ -[Documentation](https://deeptools.readthedocs.org/en/latest/index.html) | [FAQ](https://deeptools.readthedocs.org/en/latest/content/help_faq.html) +[Documentation](https://deeptools.readthedocs.io/en/latest/index.html) | [FAQ](https://deeptools.readthedocs.io/en/latest/content/help_faq.html) diff --git a/README.rst b/README.rst deleted file mode 100644 index d0231e8416..0000000000 --- a/README.rst +++ /dev/null @@ -1,29 +0,0 @@ -====================================================================== -deepTools -====================================================================== - -User-friendly tools for exploring deep-sequencing data -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -deepTools addresses the challenge of handling the large amounts of data -that are now routinely generated from DNA sequencing centers. deepTools -contains useful modules to process the mapped reads data for multiple -quality checks, creating **normalized coverage files** in standard -bedGraph and bigWig file formats, that allow comparison between -different files (for example, treatment and control). Finally, using -such normalized and standardized files, deepTools can create many -publication-ready **visualizations** to identify enrichments and for -functional annotations of the genome. - -For support or questions please make a post on `Biostars `__. For feature requests, please open an issue on `github `__. - -For further documentation, please see our `read the docs page `__. - -Citation: -^^^^^^^^^ - -Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne -S, Dündar F, Manke T. `deepTools2: a next generation web server for -deep-sequencing data -analysis. `__ -Nucleic Acids Research. 2016 Apr 13:gkw257. diff --git a/docs/content/help_faq.rst b/docs/content/help_faq.rst index b6e397e6dc..1f615a06da 100644 --- a/docs/content/help_faq.rst +++ b/docs/content/help_faq.rst @@ -288,7 +288,7 @@ Use ``genomeCoverageBed`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``genomeCoverageBed`` from the BEDtools suite can be used to calculate the number of bases in the genome for which 0 overlapping reads can be found. -As described on the `BEDtools website `__ (go to genomeCov description), you need: +As described on the `BEDtools website `__ (go to genomeCov description), you need: * a file with the chromosome sizes of your sample's organism * a position-sorted BAM file diff --git a/docs/content/help_glossary.rst b/docs/content/help_glossary.rst index c5de0cf48e..a35668b609 100644 --- a/docs/content/help_glossary.rst +++ b/docs/content/help_glossary.rst @@ -95,7 +95,7 @@ Follow the links for more information on the different tool collections mentione `samtools `__ | `UCSCtools `__ | -`BEDtools `__ | +`BEDtools `__ | .. _2bit: diff --git a/docs/content/installation.rst b/docs/content/installation.rst index 4c1e32f9f3..4b882bf2d8 100644 --- a/docs/content/installation.rst +++ b/docs/content/installation.rst @@ -37,7 +37,7 @@ or a specific version with: .. code:: bash - $ pip install deeptools==3.5.3 + $ pip install deeptools==3.5.6 In case you would like to install an unreleased or development version, deepTools can also be installed from the repository: @@ -99,8 +99,9 @@ which ships prebuilt binaries (no compiler needed): $ pixi global install -c conda-forge -c bioconda deeptools To hack on deepTools from a checkout, the repository ships a pixi workspace that pins the -build toolchain (Rust, ``maturin``, ``libclang``, ``htslib``). This builds the Rust -extension from source and installs deepTools in editable mode: +build toolchain (Rust, ``maturin``, ``libclang``, ``htslib``, ``pkg-config``, ``openssl`` -- +see ``pyproject.toml``'s ``[tool.pixi.dependencies]``). This builds the Rust extension from +source and installs deepTools in editable mode: .. code:: bash @@ -117,19 +118,21 @@ Installs from `pypi `_ (``pip``, ``uv``, ``pipx``) use a preb when one is available for your platform, so **no compiler is needed**. deepTools is only built from source when no matching wheel exists (an unsupported platform, or a git checkout / source distribution). In that case its Rust extension has to be compiled, which -needs a build toolchain: **Rust (>= 1.85)**, ``maturin``, ``libclang``, ``perl`` (to build -the vendored OpenSSL) and the usual HTSlib system libraries (``zlib``, ``bzip2``, -``liblzma``, ``libcurl``). +needs a build toolchain: Rust (see ``Cargo.toml``'s ``rust-version`` for the minimum +supported version), ``maturin``, ``libclang``, ``pkg-config``, ``perl`` (to build the +vendored OpenSSL) and the usual HTSlib system libraries (``zlib``, ``bzip2``, ``liblzma``, +``libcurl``). There are two equally supported ways to provide that toolchain -- pick whichever suits your setup: 1. **Self-contained, via the pixi workspace (recommended for reproducible builds).** - ``pixi install`` pins Rust, ``maturin``, ``libclang`` and ``htslib`` from conda-forge, - so nothing has to be present on the host -- it works identically on Linux and macOS. - The workspace also links conda-forge's OpenSSL (``OPENSSL_NO_VENDOR``), so no ``perl`` - toolchain is needed on this route. Use the ``pixi install`` / ``pixi run build`` steps - shown above. + ``pixi install`` pins Rust, ``maturin``, ``libclang``, ``htslib``, ``pkg-config`` and + ``openssl`` from conda-forge -- see ``pyproject.toml``'s ``[tool.pixi.dependencies]`` + for the exact pins -- so nothing has to be present on the host, and it works identically + on Linux and macOS. The workspace also links conda-forge's OpenSSL + (``OPENSSL_NO_VENDOR``), so no ``perl`` toolchain is needed on this route. Use the + ``pixi install`` / ``pixi run build`` steps shown above. 2. **System toolchain, via ``pip`` / ``uv`` / ``pipx``.** Install Rust yourself (for example with `rustup `_ or Homebrew) plus the system libraries diff --git a/docs/content/tools/computeMatrix.rst b/docs/content/tools/computeMatrix.rst index c9ac108dfb..0c202410b0 100644 --- a/docs/content/tools/computeMatrix.rst +++ b/docs/content/tools/computeMatrix.rst @@ -133,4 +133,4 @@ The groups of regions supplied by two individual files will be merged into one: #genes_chr19_secondHalf -.. tip:: **More examples** can be found in our `Gallery `_. +.. tip:: **More examples** can be found in our `Gallery `_. diff --git a/docs/content/tools/plotHeatmap.rst b/docs/content/tools/plotHeatmap.rst index 320d79efd6..a4e6cc271d 100644 --- a/docs/content/tools/plotHeatmap.rst +++ b/docs/content/tools/plotHeatmap.rst @@ -74,7 +74,7 @@ As mentioned above, ``plotHeatmap`` has many options, including the ability to d .. image:: ../../images/test_plots/ExampleHeatmap2.png -.. tip:: **More examples** can be found in our `Gallery `_. +.. tip:: **More examples** can be found in our `Gallery `_. Multiple colors for heatmaps @@ -121,4 +121,4 @@ we combine different colormap colors, different scales and the new `--boxAround .. image:: ../../images/test_plots/ExampleHeatmap4.png -.. tip:: **More examples** can be found in our `Gallery `_. +.. tip:: **More examples** can be found in our `Gallery `_. diff --git a/pyproject.toml b/pyproject.toml index 9120d46e13..02bd3ebf90 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,7 +52,7 @@ classifiers = [ "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: Bio-Informatics" ] -readme = "README.rst" +readme = "README.md" [project.optional-dependencies] actions = [ "flake8",