Detect PyMoDAQ dependencies (#241)

Recognise declared `pymodaq` dependencies as PyMoDAQ, the scientific instrument acquisition and control software. Include its research taxonomy in the report and update the generated tool list.

Author: andrew

README.md

@@ -324,7 +324,7 @@ Language ecosystems and development tools across multiple categories.
 
 **Native Ext:** Maturin, Neon, Rustler, cffi, meson-python, mkmf, nanobind, napi-rs, node-gyp, phpize, pybind11, rb-sys, scikit-build-core, setuptools Extension, setuptools-rust.
 
-**Library:** Akka, Akka HTTP, Apache Flink, Apache Pekko, Apache Pekko HTTP, Apache Spark, Authlib, Busboy, CarrierWave, Cats Effect, Celery, Chi, Circe, Devise, Doobie, EJS, Fabric, Faraday, Finagle, Finatra, Formidable, FreeMarker, Gson, Guzzle, HTTParty, Haml, Handlebars, JDOM, Jackson, Jinja2, Kafka Streams, Laravel Sanctum, Liquid, Magnus, Mako, Monix, Multer, Mustache, Newtonsoft.Json, NextAuth.js, Nokogiri, Nunjucks, OkHttp, OmniAuth, Ox, PHP LDAP, Passport, Play, Pug, PyCryptodome, PyJWT, PyYAML, Quill, React, RestClient, Resty, ShellJS, Shrine, Slick, Slim, SnakeYAML, SolidJS, Spring Security, Tailwind CSS, Tapir, Tera, Thymeleaf, Twig, UnoCSS, Velocity, XStream, ZIO, ZIO HTTP, aiohttp, axios, bcrypt, bcrypt-ruby, cross-spawn, crypto-js, cryptography, defusedxml, dom4j, execa, fast-xml-parser, fs2, golang-jwt, got, http4s, httpx, js-yaml, jsonwebtoken, ldap3, ldapjs, lxml, net-ldap, node-fetch, python-jose, python-multipart, requests, reqwest, ruamel.yaml, ruby-jwt, sh, undici, urllib3, xml2js.
+**Library:** Akka, Akka HTTP, Apache Flink, Apache Pekko, Apache Pekko HTTP, Apache Spark, Authlib, Busboy, CarrierWave, Cats Effect, Celery, Chi, Circe, Devise, Doobie, EJS, Fabric, Faraday, Finagle, Finatra, Formidable, FreeMarker, Gson, Guzzle, HTTParty, Haml, Handlebars, JDOM, Jackson, Jinja2, Kafka Streams, Laravel Sanctum, Liquid, Magnus, Mako, Monix, Multer, Mustache, Newtonsoft.Json, NextAuth.js, Nokogiri, Nunjucks, OkHttp, OmniAuth, Ox, PHP LDAP, Passport, Play, Pug, PyCryptodome, PyJWT, PyMoDAQ, PyYAML, Quill, React, RestClient, Resty, ShellJS, Shrine, Slick, Slim, SnakeYAML, SolidJS, Spring Security, Tailwind CSS, Tapir, Tera, Thymeleaf, Twig, UnoCSS, Velocity, XStream, ZIO, ZIO HTTP, aiohttp, axios, bcrypt, bcrypt-ruby, cross-spawn, crypto-js, cryptography, defusedxml, dom4j, execa, fast-xml-parser, fs2, golang-jwt, got, http4s, httpx, js-yaml, jsonwebtoken, ldap3, ldapjs, lxml, net-ldap, node-fetch, python-jose, python-multipart, requests, reqwest, ruamel.yaml, ruby-jwt, sh, undici, urllib3, xml2js.
 
 **Codegen:** Buf, GraphQL Code Generator, OpenAPI, Protobuf, Thrift, Wire, ent, gRPC, mockgen, sqlc.
 

detect/pymodaq_test.go

@@ -0,0 +1,35 @@
+package detect
+
+import "testing"
+
+func TestPyMoDAQProject(t *testing.T) {
+	assertToolDetected(t, runOn(t, "../testdata/pymodaq-project"), "library", "PyMoDAQ")
+}
+
+func TestPyMoDAQDependencySignals(t *testing.T) {
+	for _, tt := range []struct{ path, content string }{
+		{"pyproject.toml", "[project]\nname = 'spectrometer'\ndependencies = ['pymodaq>=4']\n"},
+		{"requirements.txt", "pymodaq\n"},
+	} {
+		t.Run(tt.path, func(t *testing.T) {
+			dir := t.TempDir()
+			writeFile(t, dir, tt.path, tt.content)
+			assertToolDetected(t, runOn(t, dir), "library", "PyMoDAQ")
+		})
+	}
+}
+
+func TestPyMoDAQRequiresDeclaredDependency(t *testing.T) {
+	for _, tt := range []struct{ path, content string }{
+		{"requirements.txt", "pymodaq-plugins\n"},
+		{"README.md", "Install pymodaq to control the spectrometer.\n"},
+		{"instrument.py", "from pymodaq import utils\n"},
+		{"fixtures/requirements.txt", "pymodaq\n"},
+	} {
+		t.Run(tt.path, func(t *testing.T) {
+			dir := t.TempDir()
+			writeFile(t, dir, tt.path, tt.content)
+			assertToolNotDetected(t, runOn(t, dir), "library", "PyMoDAQ")
+		})
+	}
+}

kb/kb_test.go

@@ -380,6 +380,7 @@ func TestResearchToolTaxonomy(t *testing.T) {
 		"targets":           {"role:build-tool", "role:orchestrator", "function:workflow-orchestration", "domain:data-science", "domain:research", "domain:scientific-computing", "audience:data-scientist", "audience:researcher"},
 		"R Markdown":        {"function:documentation", "function:literate-programming", "function:report-generation"},
 		"knitr":             {"function:documentation", "function:literate-programming", "function:report-generation"},
+		"PyMoDAQ":           {"role:application", "domain:research", "domain:scientific-computing"},
 	}
 	for name, tags := range want {
 		tool := base.ByName[name]

knowledge/python/pymodaq.toml

@@ -0,0 +1,15 @@
+[tool]
+name = "PyMoDAQ"
+category = "library"
+homepage = "https://pymodaq.cnrs.fr/"
+docs = "https://pymodaq.cnrs.fr/en/latest/"
+repo = "https://github.com/PyMoDAQ/PyMoDAQ"
+description = "Modular data acquisition and control for scientific instruments"
+
+[detect]
+dependencies = ["pymodaq"]
+ecosystems = ["python"]
+
+[taxonomy]
+role = ["application"]
+domain = ["research", "scientific-computing"]

testdata/pymodaq-project/setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup(name="spectrometer", install_requires=["pymodaq"])