scrap setup.py, move entirely to pyproject.toml

.bumpversion.cfg

@@ -5,7 +5,7 @@ tag = False
 
 [bumpversion:file:README.md]
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:.github/workflows/index_page_builder.yaml]
 

Dockerfile

@@ -27,7 +27,7 @@ RUN bash install_glcoud.sh --disable-prompts --install-dir=/opt && \
 ENV PATH=$PATH:/opt/google-cloud-sdk/bin
 
 # Add in the additional requirements that are most likely to change.
-COPY requirements*.txt README.md setup.py ./
+COPY README.md pyproject.toml ./
 COPY src src/
 RUN pip install --upgrade pip && pip install .[cpg]
 
@@ -36,6 +36,6 @@ FROM base AS talos_none
 RUN echo "Skipping cloud dependency installation"
 
 # Add in the additional requirements that are most likely to change.
-COPY requirements*.txt README.md setup.py ./
+COPY README.md pyproject.toml ./
 COPY src src/
-RUN pip install .[cpg]
+RUN pip install ".[cpg]"

pyproject.toml

@@ -1,3 +1,106 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name='talos'
+description='Centre for Population Genomics Variant Prioritisation'
+readme = "README.md"
+version='6.6.1'
+license={ "file" = "LICENSE" }
+classifiers=[
+    'Environment :: Console',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Natural Language :: English',
+    'Operating System :: MacOS :: MacOS X',
+    'Operating System :: POSIX',
+    'Operating System :: Unix',
+    'Programming Language :: Python',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+]
+
+dependencies=[
+    "cloudpathlib[all]>=0.16.0",
+    "cyvcf2>=0.30.18",
+    "dill>=0.3.7",
+    "hail==0.2.133",
+    "httpx>=0.27.0",
+    "Jinja2>=3.1.3",
+    "networkx>=3",
+    "obonet>=1",
+    "pandas>=2",
+    "peds>=1.2.0",
+    "phenopackets>=2",
+    "protobuf==3.20.2",
+    "pydantic>=2.5.2",
+    "pyspark>=3.5.1",
+    "python-dateutil>=2",
+    "semsimian",
+    "tabulate>=0.8.9",
+    "tenacity>=9.0.0",
+    "toml==0.10.2",
+]
+
+
+[project.optional-dependencies]
+cpg = [
+    "gql",
+    "metamist>=7.4.0",
+]
+test = [
+    "bump2version>=1.0.1",
+    "pytest>=8",
+    "pytest-cov>=3.0.0",
+    "pytest-httpx",
+    "pytest-xdist>=3.6.0",
+]
+
+[project.scripts]
+# for use in translating a VEP annotated VCF to a MatrixTable
+VcfToMt = 'talos.VcfToMt:cli_main'
+# turns the SVDB TSV into a Hail Table
+ConvertSpliceVarDb = 'talos.ConvertSpliceVarDb:cli_main'
+# CPG internal, scans database for published reports, collects into an index page
+BuildReportIndexPage = 'talos.CPG.BuildReportIndexPage:main'
+# CPG implementation, builds cohort phenopackets
+MakePhenopackets = 'talos.CPG.MakePhenopackets:cli_main'
+# CPG implementation, builds cohort phenopackets from a pedigree with HPO terms
+ConvertPedToPhenopackets = 'talos.CPG.convert_ePED_to_phenopackets:cli_main'
+# use the HPO terms to select panels for this analysis
+GeneratePanelData = 'talos.GeneratePanelData:cli_main'
+# query PanelApp for those selected panels
+QueryPanelapp = 'talos.QueryPanelapp:cli_main'
+# use API queries to find the gene symbol for each gene ID
+FindGeneSymbolMap = 'talos.FindGeneSymbolMap:cli_main'
+# Filter and label a small-variant MatrixTable
+RunHailFiltering = 'talos.RunHailFiltering:cli_main'
+# Filter and label a SV MatrixTable
+RunHailFilteringSV = 'talos.RunHailFilteringSV:cli_main'
+# Run each of the category-labelled variants through MOI filters
+ValidateMOI = 'talos.ValidateMOI:cli_main'
+# catch variants which have strong phenotypic matches
+HPOFlagging = 'talos.HPOFlagging:cli_main'
+# CPG internal (?), publish those results as an HTML report
+CreateTalosHTML = 'talos.CreateTalosHTML:cli_main'
+# CPG internal (?), generate a file for ingestion by Seqr
+MinimiseOutputForSeqr = 'talos.MinimiseOutputForSeqr:cli_main'
+# CPG internal (?), generate a JSON summary of an existing report
+SummariseReport = 'talos.SummariseReport:cli_main'
+
+[project.urls]
+Repository = "https://github.com/populationgenomics/talos"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[options]
+include_package_data = true
+
+[options.package_data]
+'talos'=  ['templates/*.jinja', 'example_config.toml']
+
 [tool.black]
 line-length = 120
 skip-string-normalization = true