Add scientific research tool detectors

detect/research_test.go

@@ -0,0 +1,98 @@
+package detect
+
+import (
+	"slices"
+	"testing"
+
+	"github.com/git-pkgs/brief"
+)
+
+func TestResearchToolDetectors(t *testing.T) {
+	dir := t.TempDir()
+	files := map[string]string{
+		"analysis/notebook.ipynb":  "{}\n",
+		"report.qmd":               "---\ntitle: Analysis\n---\n",
+		"workflow/Snakefile":       "rule all:\n    input: []\n",
+		"nextflow.config":          "manifest { name = 'research-pipeline' }\n",
+		"main.nf":                  "workflow { }\n",
+		"pyproject.toml":           "[project]\nname = \"research-tools\"\nversion = \"0.1.0\"\n",
+		"tox.ini":                  "[tox]\nenv_list = py312\n",
+		"benchmarks/asv.conf.json": `{"repo": "."}`,
+		"DESCRIPTION": `Package: researchtools
+Version: 0.1.0
+Suggests:
+    covr,
+    knitr,
+    pkgdown,
+    rmarkdown,
+    testthat
+Config/roxygen2/version: 7.3.3
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+`,
+		"README.Rmd":                   "---\ntitle: Research tools\n---\n",
+		"_pkgdown.yml":                 "url: https://example.com\n",
+		"renv.lock":                    `{"R":{"Version":"4.5.0"}}`,
+		"Project.toml":                 "name = \"ResearchTools\"\nuuid = \"11111111-1111-1111-1111-111111111111\"\n",
+		"src/ResearchTools.jl":         "module ResearchTools\nend\n",
+		"docs/Project.toml":            "[deps]\nDocumenter = \"e30172f5-a6a5-5a46-863b-614d45cd2de4\"\n",
+		"docs/make.jl":                 "using Documenter\n",
+		".JuliaFormatter.toml":         "margin = 92\n",
+		".github/workflows/format.yml": "name: format\non: push\njobs:\n  format:\n    runs-on: ubuntu-latest\n    steps:\n      - uses: fredrikekre/runic-action@v1\n",
+		"model.f90":                    "program model\nend program model\n",
+		"fortitude.toml":               "line-length = 100\n",
+	}
+	for path, content := range files {
+		writeProjectFile(t, dir, path, content)
+	}
+
+	report := runOn(t, dir)
+	want := []struct {
+		category string
+		name     string
+	}{
+		{category: "environment", name: "Jupyter"},
+		{category: "docs", name: "Quarto"},
+		{category: "build", name: "Snakemake"},
+		{category: "build", name: "Nextflow"},
+		{category: "test", name: "tox"},
+		{category: "test", name: "ASV"},
+		{category: "test", name: "testthat"},
+		{category: "coverage", name: "covr"},
+		{category: "docs", name: "pkgdown"},
+		{category: "docs", name: "roxygen2"},
+		{category: "docs", name: "knitr"},
+		{category: "docs", name: "R Markdown"},
+		{category: "docs", name: "Documenter.jl"},
+		{category: "format", name: "JuliaFormatter"},
+		{category: "format", name: "Runic"},
+		{category: "lint", name: "Fortitude"},
+	}
+	for _, item := range want {
+		assertToolDetected(t, report, item.category, item.name)
+	}
+	if !slices.ContainsFunc(report.PackageManagers, func(d brief.Detection) bool {
+		return d.Name == "renv"
+	}) {
+		t.Error("expected renv package manager")
+	}
+}
+
+func TestSnakemakeSmkConfigFile(t *testing.T) {
+	dir := t.TempDir()
+	const path = "workflow/rules/common.smk"
+	const configPattern = "**/*.smk"
+	writeProjectFile(t, dir, path, "rule all:\n    input: []\n")
+
+	report := runOn(t, dir)
+	for _, tool := range report.Tools["build"] {
+		if tool.Name != "Snakemake" {
+			continue
+		}
+		if !slices.Contains(tool.ConfigFiles, configPattern) {
+			t.Errorf("Snakemake config files = %v, want %q", tool.ConfigFiles, configPattern)
+		}
+		return
+	}
+	t.Fatal("expected Snakemake in build category")
+}

knowledge/_shared/jupyter.toml

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+[tool]
+name = "Jupyter"
+category = "environment"
+homepage = "https://jupyter.org"
+docs = "https://docs.jupyter.org/en/latest/"
+repo = "https://github.com/jupyter/jupyter"
+description = "Interactive computing environment for notebook documents"
+
+[detect]
+files = ["*.ipynb", "**/*.ipynb"]
+dependencies = ["jupyter", "jupyterlab", "notebook"]
+dev_dependencies = ["jupyter", "jupyterlab", "notebook"]
+
+[commands]
+run = "jupyter lab"
+alternatives = ["jupyter notebook"]
+
+[config]
+files = ["jupyter_server_config.py", "jupyter_notebook_config.py", "jupyter_lab_config.py"]
+
+[taxonomy]
+role = ["application"]

knowledge/_shared/nextflow.toml

@@ -0,0 +1,21 @@
+[tool]
+name = "Nextflow"
+category = "build"
+homepage = "https://www.nextflow.io"
+docs = "https://www.nextflow.io/docs/latest/"
+repo = "https://github.com/nextflow-io/nextflow"
+description = "Workflow system for portable data pipelines"
+
+[detect]
+files = ["nextflow.config", "main.nf", "*.nf", "**/*.nf"]
+
+[commands]
+run = "nextflow run main.nf"
+
+[config]
+files = ["nextflow.config"]
+
+[taxonomy]
+role = ["orchestrator"]
+function = ["automation"]
+domain = ["scientific-computing"]

knowledge/_shared/quarto.toml

@@ -0,0 +1,22 @@
+[tool]
+name = "Quarto"
+category = "docs"
+homepage = "https://quarto.org"
+docs = "https://quarto.org/docs/get-started/"
+repo = "https://github.com/quarto-dev/quarto-cli"
+description = "Scientific and technical publishing system"
+
+[detect]
+files = ["_quarto.yml", "_quarto.yaml", "*.qmd", "**/*.qmd"]
+dependencies = ["quarto", "quarto-dev/quarto-actions/setup"]
+dev_dependencies = ["quarto"]
+
+[commands]
+run = "quarto render"
+alternatives = ["quarto preview"]
+
+[config]
+files = ["_quarto.yml", "_quarto.yaml"]
+
+[taxonomy]
+function = ["documentation", "site-generation"]

knowledge/_shared/snakemake.toml

@@ -0,0 +1,23 @@
+[tool]
+name = "Snakemake"
+category = "build"
+homepage = "https://snakemake.github.io"
+docs = "https://snakemake.readthedocs.io/en/stable/"
+repo = "https://github.com/snakemake/snakemake"
+description = "Workflow system for reproducible data analysis"
+
+[detect]
+files = ["Snakefile", "**/Snakefile", "*.smk", "**/*.smk"]
+dependencies = ["snakemake"]
+dev_dependencies = ["snakemake"]
+
+[commands]
+run = "snakemake"
+
+[config]
+files = ["Snakefile", "**/Snakefile", "*.smk", "**/*.smk"]
+
+[taxonomy]
+role = ["orchestrator"]
+function = ["automation"]
+domain = ["scientific-computing"]

knowledge/fortran/fortitude.toml

@@ -0,0 +1,26 @@
+[tool]
+name = "Fortitude"
+category = "lint"
+homepage = "https://fortitude.readthedocs.io/"
+docs = "https://fortitude.readthedocs.io/"
+repo = "https://github.com/PlasmaFAIR/fortitude"
+description = "Linter for Fortran"
+
+[detect]
+files = ["fortitude.toml", ".fortitude.toml"]
+dependencies = ["fortitude", "fortitude-lint"]
+dev_dependencies = ["fortitude", "fortitude-lint"]
+ecosystems = ["fortran"]
+[detect.key_exists]
+"fpm.toml" = ["extra.fortitude"]
+"pyproject.toml" = ["tool.fortitude"]
+
+[commands]
+run = "fortitude check"
+alternatives = ["fortitude check --fix"]
+
+[config]
+files = ["fortitude.toml", ".fortitude.toml", "fpm.toml", "pyproject.toml"]
+
+[taxonomy]
+role = ["linter"]

knowledge/julia/documenter.toml

@@ -0,0 +1,24 @@
+[tool]
+name = "Documenter.jl"
+category = "docs"
+homepage = "https://documenter.juliadocs.org/stable/"
+docs = "https://documenter.juliadocs.org/stable/"
+repo = "https://github.com/JuliaDocs/Documenter.jl"
+description = "Documentation generator for Julia packages"
+
+[detect]
+dependencies = ["Documenter"]
+dev_dependencies = ["Documenter"]
+ecosystems = ["julia"]
+[detect.file_contains]
+"docs/Project.toml" = ["Documenter"]
+"docs/make.jl" = ["Documenter"]
+
+[commands]
+run = "julia --project=docs docs/make.jl"
+
+[config]
+files = ["docs/Project.toml", "docs/make.jl"]
+
+[taxonomy]
+function = ["documentation", "site-generation"]

knowledge/julia/juliaformatter.toml

@@ -0,0 +1,22 @@
+[tool]
+name = "JuliaFormatter"
+category = "format"
+homepage = "https://juliaeditorsupport.github.io/JuliaFormatter.jl/stable/"
+docs = "https://juliaeditorsupport.github.io/JuliaFormatter.jl/stable/"
+repo = "https://github.com/JuliaEditorSupport/JuliaFormatter.jl"
+description = "Code formatter for Julia"
+
+[detect]
+files = [".JuliaFormatter.toml"]
+dependencies = ["JuliaFormatter"]
+dev_dependencies = ["JuliaFormatter"]
+ecosystems = ["julia"]
+
+[commands]
+run = "julia -e 'using JuliaFormatter; format(\".\")'"
+
+[config]
+files = [".JuliaFormatter.toml"]
+
+[taxonomy]
+role = ["formatter"]

knowledge/julia/runic.toml

@@ -0,0 +1,15 @@
+[tool]
+name = "Runic"
+category = "format"
+homepage = "https://github.com/fredrikekre/Runic.jl"
+docs = "https://github.com/fredrikekre/Runic.jl"
+repo = "https://github.com/fredrikekre/Runic.jl"
+description = "Code formatter for Julia"
+
+[detect]
+dependencies = ["Runic", "fredrikekre/runic-action"]
+dev_dependencies = ["Runic"]
+ecosystems = ["julia"]
+
+[taxonomy]
+role = ["formatter"]

knowledge/python/asv.toml

@@ -0,0 +1,23 @@
+[tool]
+name = "ASV"
+category = "test"
+homepage = "https://asv.readthedocs.io/en/stable/"
+docs = "https://asv.readthedocs.io/en/stable/"
+repo = "https://github.com/airspeed-velocity/asv"
+description = "Python benchmarking tool for tracking performance across revisions"
+
+[detect]
+files = ["asv.conf.json", "**/asv.conf.json"]
+dependencies = ["asv"]
+dev_dependencies = ["asv"]
+ecosystems = ["python"]
+
+[commands]
+run = "asv run"
+alternatives = ["asv publish", "asv preview"]
+
+[config]
+files = ["asv.conf.json", "**/asv.conf.json"]
+
+[taxonomy]
+function = ["benchmarking"]

knowledge/python/tox.toml

@@ -0,0 +1,25 @@
+[tool]
+name = "tox"
+category = "test"
+homepage = "https://tox.wiki/en/stable/"
+docs = "https://tox.wiki/en/stable/"
+repo = "https://github.com/tox-dev/tox"
+description = "Python test environment orchestrator"
+
+[detect]
+files = ["tox.ini"]
+dependencies = ["tox"]
+dev_dependencies = ["tox"]
+ecosystems = ["python"]
+[detect.key_exists]
+"pyproject.toml" = ["tool.tox"]
+
+[commands]
+run = "tox"
+
+[config]
+files = ["tox.ini", "pyproject.toml"]
+
+[taxonomy]
+role = ["orchestrator"]
+function = ["testing"]

knowledge/r/covr.toml

@@ -0,0 +1,23 @@
+[tool]
+name = "covr"
+category = "coverage"
+homepage = "https://covr.r-lib.org"
+docs = "https://covr.r-lib.org"
+repo = "https://github.com/r-lib/covr"
+description = "Test coverage reporting for R packages"
+
+[detect]
+files = [".covrignore"]
+dependencies = ["covr"]
+dev_dependencies = ["covr"]
+ecosystems = ["r"]
+
+[commands]
+run = "Rscript -e 'covr::package_coverage()'"
+alternatives = ["Rscript -e 'covr::report()'"]
+
+[config]
+files = [".covrignore"]
+
+[taxonomy]
+function = ["coverage"]

knowledge/r/knitr.toml

@@ -0,0 +1,17 @@
+[tool]
+name = "knitr"
+category = "docs"
+homepage = "https://yihui.org/knitr/"
+docs = "https://yihui.org/knitr/"
+repo = "https://github.com/yihui/knitr"
+description = "Literate programming engine for R documents"
+
+[detect]
+dependencies = ["knitr"]
+dev_dependencies = ["knitr"]
+ecosystems = ["r"]
+[detect.file_contains]
+"DESCRIPTION" = ["VignetteBuilder: knitr"]
+
+[taxonomy]
+function = ["documentation"]

knowledge/r/pkgdown.toml

@@ -0,0 +1,22 @@
+[tool]
+name = "pkgdown"
+category = "docs"
+homepage = "https://pkgdown.r-lib.org"
+docs = "https://pkgdown.r-lib.org"
+repo = "https://github.com/r-lib/pkgdown"
+description = "Static documentation sites for R packages"
+
+[detect]
+files = ["_pkgdown.yml", "_pkgdown.yaml"]
+dependencies = ["pkgdown"]
+dev_dependencies = ["pkgdown"]
+ecosystems = ["r"]
+
+[commands]
+run = "Rscript -e 'pkgdown::build_site()'"
+
+[config]
+files = ["_pkgdown.yml", "_pkgdown.yaml"]
+
+[taxonomy]
+function = ["documentation", "site-generation"]