Replace setup.py with pyproject.toml (#2353)

* Replace setup.py with pyproject.toml * [automated] Update CHANGELOG.md * Add myself as author --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io>
MultiQC · Feb 23, 2024 · 2bda311 · 2bda311
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diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -2,10 +2,10 @@
 
 This checklist is for my own reference, as I forget the steps every time.
 
-1. Check that everything is up to date and ready to go
+1. Check that everything is up-to-date and ready to go
 2. Figure out what this release should be called
-3. Update version numbers in code: `setup.py`, `CHANGELOG.md`
-4. Link the changelog subheading to the as yet non-existant release URL. Add date.
+3. Update version numbers in code: `pyproject.toml`, `CHANGELOG.md`
+4. Link the changelog subheading to the as yet non-existent release URL. Add date.
 5. Install the package again in `install` mode:
 
    ```bash

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@
 - MegaQC: dump `pconfig` ([#2344](https://github.com/MultiQC/MultiQC/pull/2344))
 - Catch non-hashable values in table data ([#2348](https://github.com/MultiQC/MultiQC/pull/2348))
 - Prevent parsing numerical sample names in heatmap ([#2349](https://github.com/MultiQC/MultiQC/pull/2349))
+- Replace `setup.py` with `pyproject.toml` ([#2353](https://github.com/MultiQC/MultiQC/pull/2353))
 - Infinite dmax or dmin fail JSON dump load in JavaScript ([#2354](https://github.com/MultiQC/MultiQC/pull/2354))
 - Wrap `full_figure_for_development` in try to handle Kaleido error ([#2359](https://github.com/MultiQC/MultiQC/pull/2359))
 - Add box plot ([#2358](https://github.com/MultiQC/MultiQC/pull/2358))

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,243 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "multiqc"
+version = "1.21dev"
+dependencies = [
+    "click",
+    "coloredlogs",
+    "humanize",
+    "importlib-metadata",
+    "jinja2>=3.0.0",
+    "kaleido",  # for flat plot export
+    "markdown",
+    "numpy",
+    "packaging",
+    "requests",
+    "Pillow>=10",  # to add a logo into flat plots
+    "plotly>=5.18",
+    "pyyaml>=4",
+    "pyaml-env",
+    "rich>=10",
+    "rich-click",
+    "spectra>=0.0.10",
+]
+requires-python = ">=3.8"
+authors = [
+    {name = "Phil Ewels", email = "phil.ewels@seqera.io"},
+    {name = "Vlad Savelyev", email = "vladislav.savelyev@seqera.io"},
+]
+description = "Create aggregate bioinformatics analysis reports across many samples and tools"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["bioinformatics", "biology", "sequencing", "NGS", "next generation sequencing", "quality control"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Environment :: Web Environment",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: JavaScript",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+
+[project.optional-dependencies]
+matplotlib = [
+    "matplotlib>=2.1.1",
+]
+dev = [
+    "pre-commit",
+    "ruff",
+]
+
+[project.urls]
+Homepage = "https://multiqc.info"
+Repository = "https://github.com/MultiQC/MultiQC"
+Issues = "https://github.com/MultiQC/MultiQC/issues"
+Documentation = "https://multiqc.info/docs"
+Changelog = "https://github.com/MultiQC/MultiQC/blob/main/CHANGELOG.md"
+
+[project.entry-points.console_scripts]
+multiqc = "multiqc.__main__:run_multiqc"
+
+[project.entry-points."multiqc.modules.v1"]
+adapterRemoval = "multiqc.modules.adapterRemoval:MultiqcModule"
+afterqc = "multiqc.modules.afterqc:MultiqcModule"
+anglerfish = "multiqc.modules.anglerfish:MultiqcModule"
+bakta = "multiqc.modules.bakta:MultiqcModule"
+bamdst = "multiqc.modules.bamdst:MultiqcModule"
+bamtools = "multiqc.modules.bamtools:MultiqcModule"
+bbduk = "multiqc.modules.bbduk:MultiqcModule"
+bbmap = "multiqc.modules.bbmap:MultiqcModule"
+bcftools = "multiqc.modules.bcftools:MultiqcModule"
+bcl2fastq = "multiqc.modules.bcl2fastq:MultiqcModule"
+bclconvert = "multiqc.modules.bclconvert:MultiqcModule"
+biobambam2 = "multiqc.modules.biobambam2:MultiqcModule"
+biobloomtools = "multiqc.modules.biobloomtools:MultiqcModule"
+biscuit = "multiqc.modules.biscuit:MultiqcModule"
+bismark = "multiqc.modules.bismark:MultiqcModule"
+bowtie1 = "multiqc.modules.bowtie1:MultiqcModule"
+bowtie2 = "multiqc.modules.bowtie2:MultiqcModule"
+bracken = "multiqc.modules.bracken:MultiqcModule"
+busco = "multiqc.modules.busco:MultiqcModule"
+bustools = "multiqc.modules.bustools:MultiqcModule"
+ccs = "multiqc.modules.ccs:MultiqcModule"
+cellranger = "multiqc.modules.cellranger:MultiqcModule"
+checkqc = "multiqc.modules.checkqc:MultiqcModule"
+clipandmerge = "multiqc.modules.clipandmerge:MultiqcModule"
+clusterflow = "multiqc.modules.clusterflow:MultiqcModule"
+conpair = "multiqc.modules.conpair:MultiqcModule"
+custom_content = "multiqc.modules.custom_content:custom_module_classes"  # special case
+cutadapt = "multiqc.modules.cutadapt:MultiqcModule"
+damageprofiler = "multiqc.modules.damageprofiler:MultiqcModule"
+dedup = "multiqc.modules.dedup:MultiqcModule"
+deeptools = "multiqc.modules.deeptools:MultiqcModule"
+diamond = "multiqc.modules.diamond:MultiqcModule"
+disambiguate = "multiqc.modules.disambiguate:MultiqcModule"
+dragen = "multiqc.modules.dragen:MultiqcModule"
+dragen_fastqc = "multiqc.modules.dragen_fastqc:MultiqcModule"
+eigenstratdatabasetools = "multiqc.modules.eigenstratdatabasetools:MultiqcModule"
+fastp = "multiqc.modules.fastp:MultiqcModule"
+fastq_screen = "multiqc.modules.fastq_screen:MultiqcModule"
+fastqc = "multiqc.modules.fastqc:MultiqcModule"
+featureCounts = "multiqc.modules.featureCounts:MultiqcModule"
+fgbio = "multiqc.modules.fgbio:MultiqcModule"
+flash = "multiqc.modules.flash:MultiqcModule"
+flexbar = "multiqc.modules.flexbar:MultiqcModule"
+filtlong = "multiqc.modules.filtlong:MultiqcModule"
+freyja = "multiqc.modules.freyja:MultiqcModule"
+gffcompare = "multiqc.modules.gffcompare:MultiqcModule"
+gatk = "multiqc.modules.gatk:MultiqcModule"
+goleft_indexcov = "multiqc.modules.goleft_indexcov:MultiqcModule"
+gopeaks = "multiqc.modules.gopeaks:MultiqcModule"
+happy = "multiqc.modules.happy:MultiqcModule"
+hicexplorer = "multiqc.modules.hicexplorer:MultiqcModule"
+hicpro = "multiqc.modules.hicpro:MultiqcModule"
+hicup = "multiqc.modules.hicup:MultiqcModule"
+hifiasm = "multiqc.modules.hifiasm:MultiqcModule"
+hisat2 = "multiqc.modules.hisat2:MultiqcModule"
+homer = "multiqc.modules.homer:MultiqcModule"
+hops = "multiqc.modules.hops:MultiqcModule"
+htseq = "multiqc.modules.htseq:MultiqcModule"
+humid = "multiqc.modules.humid:MultiqcModule"
+interop = "multiqc.modules.interop:MultiqcModule"
+ivar = "multiqc.modules.ivar:MultiqcModule"
+jcvi = "multiqc.modules.jcvi:MultiqcModule"
+jellyfish = "multiqc.modules.jellyfish:MultiqcModule"
+kaiju = "multiqc.modules.kaiju:MultiqcModule"
+kallisto = "multiqc.modules.kallisto:MultiqcModule"
+kat = "multiqc.modules.kat:MultiqcModule"
+kraken = "multiqc.modules.kraken:MultiqcModule"
+leehom = "multiqc.modules.leehom:MultiqcModule"
+librarian = "multiqc.modules.librarian:MultiqcModule"
+lima = "multiqc.modules.lima:MultiqcModule"
+longranger = "multiqc.modules.longranger:MultiqcModule"
+macs2 = "multiqc.modules.macs2:MultiqcModule"
+malt = "multiqc.modules.malt:MultiqcModule"
+mapdamage = "multiqc.modules.mapdamage:MultiqcModule"
+megahit = "multiqc.modules.megahit:MultiqcModule"
+metaphlan = "multiqc.modules.metaphlan:MultiqcModule"
+methylqa = "multiqc.modules.methylqa:MultiqcModule"
+minionqc = "multiqc.modules.minionqc:MultiqcModule"
+mirtop = "multiqc.modules.mirtop:MultiqcModule"
+mirtrace = "multiqc.modules.mirtrace:MultiqcModule"
+mosdepth = "multiqc.modules.mosdepth:MultiqcModule"
+motus = "multiqc.modules.motus:MultiqcModule"
+mtnucratio = "multiqc.modules.mtnucratio:MultiqcModule"
+multivcfanalyzer = "multiqc.modules.multivcfanalyzer:MultiqcModule"
+nanostat = "multiqc.modules.nanostat:MultiqcModule"
+nextclade = "multiqc.modules.nextclade:MultiqcModule"
+ngsderive = "multiqc.modules.ngsderive:MultiqcModule"
+nonpareil = "multiqc.modules.nonpareil:MultiqcModule"
+odgi = "multiqc.modules.odgi:MultiqcModule"
+optitype = "multiqc.modules.optitype:MultiqcModule"
+pangolin = "multiqc.modules.pangolin:MultiqcModule"
+pbmarkdup = "multiqc.modules.pbmarkdup:MultiqcModule"
+peddy = "multiqc.modules.peddy:MultiqcModule"
+phantompeakqualtools = "multiqc.modules.phantompeakqualtools:MultiqcModule"
+picard = "multiqc.modules.picard:MultiqcModule"
+porechop = "multiqc.modules.porechop:MultiqcModule"
+preseq = "multiqc.modules.preseq:MultiqcModule"
+prinseqplusplus = "multiqc.modules.prinseqplusplus:MultiqcModule"
+prokka = "multiqc.modules.prokka:MultiqcModule"
+purple = "multiqc.modules.purple:MultiqcModule"
+pychopper = "multiqc.modules.pychopper:MultiqcModule"
+pycoqc = "multiqc.modules.pycoqc:MultiqcModule"
+qc3C = "multiqc.modules.qc3C:MultiqcModule"
+qorts = "multiqc.modules.qorts:MultiqcModule"
+qualimap = "multiqc.modules.qualimap:MultiqcModule"
+quast = "multiqc.modules.quast:MultiqcModule"
+rna_seqc = "multiqc.modules.rna_seqc:MultiqcModule"
+rockhopper = "multiqc.modules.rockhopper:MultiqcModule"
+rsem = "multiqc.modules.rsem:MultiqcModule"
+rseqc = "multiqc.modules.rseqc:MultiqcModule"
+seqera_cli = "multiqc.modules.seqera_cli:MultiqcModule"
+salmon = "multiqc.modules.salmon:MultiqcModule"
+sambamba = "multiqc.modules.sambamba:MultiqcModule"
+samblaster = "multiqc.modules.samblaster:MultiqcModule"
+samtools = "multiqc.modules.samtools:MultiqcModule"
+sargasso = "multiqc.modules.sargasso:MultiqcModule"
+seqyclean = "multiqc.modules.seqyclean:MultiqcModule"
+seqwho = "multiqc.modules.seqwho:MultiqcModule"
+sexdeterrmine = "multiqc.modules.sexdeterrmine:MultiqcModule"
+sickle = "multiqc.modules.sickle:MultiqcModule"
+skewer = "multiqc.modules.skewer:MultiqcModule"
+slamdunk = "multiqc.modules.slamdunk:MultiqcModule"
+snippy = "multiqc.modules.snippy:MultiqcModule"
+snpeff = "multiqc.modules.snpeff:MultiqcModule"
+snpsplit = "multiqc.modules.snpsplit:MultiqcModule"
+somalier = "multiqc.modules.somalier:MultiqcModule"
+sortmerna = "multiqc.modules.sortmerna:MultiqcModule"
+sourmash = "multiqc.modules.sourmash:MultiqcModule"
+stacks = "multiqc.modules.stacks:MultiqcModule"
+star = "multiqc.modules.star:MultiqcModule"
+supernova = "multiqc.modules.supernova:MultiqcModule"
+theta2 = "multiqc.modules.theta2:MultiqcModule"
+tophat = "multiqc.modules.tophat:MultiqcModule"
+trimmomatic = "multiqc.modules.trimmomatic:MultiqcModule"
+truvari = "multiqc.modules.truvari:MultiqcModule"
+umitools = "multiqc.modules.umitools:MultiqcModule"
+varscan2 = "multiqc.modules.varscan2:MultiqcModule"
+vcftools = "multiqc.modules.vcftools:MultiqcModule"
+vep = "multiqc.modules.vep:MultiqcModule"
+verifybamid = "multiqc.modules.verifybamid:MultiqcModule"
+whatshap = "multiqc.modules.whatshap:MultiqcModule"
+xenome = "multiqc.modules.xenome:MultiqcModule"
+xengsort = "multiqc.modules.xengsort:MultiqcModule"
+
+[project.entry-points."multiqc.templates.v1"]
+default = "multiqc.templates.default"
+sections = "multiqc.templates.sections"
+simple = "multiqc.templates.simple"
+gathered = "multiqc.templates.gathered"
+highcharts = "multiqc.templates.highcharts"
+geo = "multiqc.templates.geo"
+
+### See https://multiqc.info/docs/#multiqc-plugins for documentation
+#[project.entry-points."multiqc.cli_options.v1"]
+#my-new-option = "myplugin.cli:new_option"
+#
+#[project.entry-points."multiqc.hooks.v1"]
+#before_config = "myplugin.hooks:before_config"
+#config_loaded = "myplugin.hooks:config_loaded"
+#execution_start = "myplugin.hooks:execution_start"
+#before_modules = "myplugin.hooks:before_modules"
+#after_modules = "myplugin.hooks:after_modules"
+#before_report_generation = "myplugin.hooks:before_report_generation"
+#execution_finish = "myplugin.hooks:execution_finish"
+
+[tool.setuptools]
+packages = ["multiqc"]
+
 [tool.ruff]
 line-length = 120
 target-version = "py312"