Merge branch 'develop' into dependabot/github_actions/pypa/cibuildwhe…

…el-2.16.1
scikit-hep · Dec 7, 2023 · 9df7ad3 · 9df7ad3
2 parents 18aed0d + 86c5201
commit 9df7ad3
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Showing 12 changed files with 194 additions and 71 deletions.
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
     - uses: hendrikmuhs/[email protected]

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
     - uses: hendrikmuhs/[email protected]

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -16,7 +16,7 @@ jobs:
     outputs:
       tag: ${{ steps.tag.outputs.tag }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
@@ -56,12 +56,12 @@ jobs:
       CIBW_BUILD: ${{ matrix.py }}-*
       CIBW_ARCHS_LINUX: ${{ matrix.arch }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
       - if: ${{ matrix.arch == 'aarch64' }}
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - uses: pypa/[email protected]
         env:
@@ -77,7 +77,7 @@ jobs:
     name: source package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
@@ -111,7 +111,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.ref == 'refs/heads/main' }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: softprops/action-gh-release@v1
         with:
           name: v${{ needs.release_check.outputs.tag }}

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -29,7 +29,7 @@ jobs:
             python-version: "pypy-3.8"
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: true
     # must come after checkout
@@ -51,7 +51,7 @@ jobs:
   #     py: /opt/python/cp309-cp309/bin/python
   #     img: quay.io/pypa/manylinux2014_aarch64
   #   steps:
-  #   - uses: actions/checkout@v3
+  #   - uses: actions/checkout@v4
   #     with:
   #       submodules: true
   #   - uses: docker/setup-qemu-action@v2

diff --git a/.gitignore b/.gitignore
@@ -22,6 +22,8 @@ __pycache__
 
 pip-wheel-metadata
 
+bench/*.svg
+
 .benchmarks
 .DS_Store
 .idea

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@
 repos:
 # Standard hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-case-conflict
   - id: check-docstring-first
@@ -34,20 +34,20 @@ repos:
 
 # Python formatting
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.7.0
+  rev: 23.11.0
   hooks:
   - id: black
 
 # Ruff linter, replacement for flake8, pydocstyle, isort
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.0.286'
+  rev: 'v0.1.6'
   hooks:
     - id: ruff
       args: [--fix, --show-fixes]
 
 # C++ formatting
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v16.0.6
+  rev: v17.0.6
   hooks:
   - id: clang-format
 
@@ -62,7 +62,7 @@ repos:
 
 # Python type checking
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.5.1'
+  rev: 'v1.7.1'
   hooks:
   - id: mypy
     additional_dependencies: [numpy]

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -92,5 +92,6 @@ else()
 endif()
 target_include_directories(_core PRIVATE extern/root/math/minuit2/inc)
 set_target_properties(_core PROPERTIES VISIBILITY_INLINES_HIDDEN ON)
+target_compile_definitions(_core PUBLIC PYBIND11_DETAILED_ERROR_MESSAGES=1)
 
 install(TARGETS _core DESTINATION iminuit)
diff --git a/bench/plot.ipynb b/bench/plot.ipynb
diff --git a/bench/test_cost.py b/bench/test_cost.py
@@ -35,9 +35,12 @@ def logsumexp(a, b):
     r = np.empty_like(a)
     for i in nb.prange(len(r)):
         if a[i] > b[i]:
-            r[i] = a[i] + np.log(1 + np.exp(b[i] - a[i]))
+            c = a[i]
+            d = b[i]
         else:
-            r[i] = b[i] + np.log(1 + np.exp(a[i] - b[i]))
+            c = b[i]
+            d = a[i]
+        r[i] = c + np.log1p(np.exp(d - c))
     return r
 
 
@@ -210,34 +213,77 @@ def run():
     assert_allclose(m.values[:-1], ARGS[:-1], atol=2 / n**0.5)
 
 
-@pytest.mark.parametrize("n", N)
-@pytest.mark.parametrize("BatchMode", [False, True])
-@pytest.mark.parametrize("NumCPU", [0, nb.get_num_threads()])
-def test_RooFit(benchmark, n, BatchMode, NumCPU):
+try:
     import ROOT as R
 
-    x = R.RooRealVar("x", "x", 0, 1)
-    z = R.RooRealVar("z", "z", 0.5, 0, 1)
-    mu = R.RooRealVar("mu", "mu", 0.5, 0, 1)
-    sigma = R.RooRealVar("sigma", "sigma", 0.1, 0, 10)
-    slope = R.RooRealVar("slope", "slope", 1.0, 0, 10)
-    pdf1 = R.RooGaussian("gauss", "gauss", x, mu, sigma)
-    pdf2 = R.RooExponential("expon", "expon", x, slope)
-    pdf = R.RooAddPdf("pdf", "pdf", [pdf1, pdf2], [z])
+    if R.__version__ >= "6.30":
+
+        @pytest.mark.parametrize("n", N)
+        @pytest.mark.parametrize("NumCPU", [0, nb.get_num_threads()])
+        @pytest.mark.parametrize(
+            "EvalBackend", ["legacy", "cpu", "codegen", "codegen_no_grad"]
+        )
+        def test_RooFit(benchmark, n, NumCPU, EvalBackend):
+            x = R.RooRealVar("x", "x", 0, 1)
+            z = R.RooRealVar("z", "z", 0.5, 0, 1)
+            mu = R.RooRealVar("mu", "mu", 0.5, 0, 1)
+            sigma = R.RooRealVar("sigma", "sigma", 0.1, 0, 10)
+            slope = R.RooRealVar("slope", "slope", 1.0, 0, 10)
+            pdf1 = R.RooGaussian("gauss", "gauss", x, mu, sigma)
+            pdf2 = R.RooExponential("expon", "expon", x, slope)
+            pdf = R.RooAddPdf("pdf", "pdf", [pdf1, pdf2], [z])
+
+            data = pdf.generate(x, n)
+
+            args = [R.RooFit.PrintLevel(-1), R.RooFit.EvalBackend(EvalBackend)]
+            if NumCPU:
+                args.append(R.RooFit.NumCPU(NumCPU))
+
+            def run():
+                mu.setVal(0.5)
+                sigma.setVal(0.1)
+                slope.setVal(1)
+                z.setVal(0.5)
+                pdf.fitTo(data, *args)
+
+            benchmark(run)
+            assert_allclose(z.getVal(), 0.5, atol=5 / n**0.5)
+            assert_allclose(mu.getVal(), 0.5, atol=5 / n**0.5)
+            assert_allclose(sigma.getVal(), 0.1, atol=5 / n**0.5)
 
-    data = pdf.generate(x, n)
+    else:
 
-    def run():
-        mu.setVal(0.5)
-        sigma.setVal(0.1)
-        slope.setVal(1)
-        z.setVal(0.5)
-        args = [R.RooFit.PrintLevel(-1), R.RooFit.BatchMode(BatchMode)]
-        if NumCPU:
-            args.append(R.RooFit.NumCPU(NumCPU))
-        pdf.fitTo(data, *args)
-
-    benchmark(run)
-    assert_allclose(z.getVal(), 0.5, atol=5 / n**0.5)
-    assert_allclose(mu.getVal(), 0.5, atol=5 / n**0.5)
-    assert_allclose(sigma.getVal(), 0.1, atol=5 / n**0.5)
+        @pytest.mark.parametrize("n", N)
+        @pytest.mark.parametrize("NumCPU", [0, nb.get_num_threads()])
+        @pytest.mark.parametrize("BatchMode", [False, True])
+        def test_RooFit(benchmark, n, NumCPU, BatchMode):
+            x = R.RooRealVar("x", "x", 0, 1)
+            z = R.RooRealVar("z", "z", 0.5, 0, 1)
+            mu = R.RooRealVar("mu", "mu", 0.5, 0, 1)
+            sigma = R.RooRealVar("sigma", "sigma", 0.1, 0, 10)
+            slope = R.RooRealVar("slope", "slope", 1.0, 0, 10)
+            pdf1 = R.RooGaussian("gauss", "gauss", x, mu, sigma)
+            pdf2 = R.RooExponential("expon", "expon", x, slope)
+            pdf = R.RooAddPdf("pdf", "pdf", [pdf1, pdf2], [z])
+
+            data = pdf.generate(x, n)
+
+            args = [R.RooFit.PrintLevel(-1), R.RooFit.BatchMode(BatchMode)]
+            if NumCPU:
+                args.append(R.RooFit.NumCPU(NumCPU, 1))
+                args.append(R.RooFit.Parallelize(NumCPU))
+
+            def run():
+                mu.setVal(0.5)
+                sigma.setVal(0.1)
+                slope.setVal(1)
+                z.setVal(0.5)
+                pdf.fitTo(data, *args)
+
+            benchmark(run)
+            assert_allclose(z.getVal(), 0.5, atol=5 / n**0.5)
+            assert_allclose(mu.getVal(), 0.5, atol=5 / n**0.5)
+            assert_allclose(sigma.getVal(), 0.1, atol=5 / n**0.5)
+
+except ModuleNotFoundError:
+    pass
diff --git a/src/iminuit/util.py b/src/iminuit/util.py
@@ -236,7 +236,7 @@ def _set(self, i: int, arg: UserBound) -> None:
         state.set_error(i, err)
 
 
-def _normalize_limit(lim: UserBound) -> Tuple[float, float]:
+def _normalize_limit(lim: Optional[Iterable]) -> Tuple[float, float]:
     if lim is None:
         return (-np.inf, np.inf)
     a, b = lim

diff --git a/tests/test_cost.py b/tests/test_cost.py
@@ -1164,7 +1164,7 @@ def grad2(x, b, a):
         return g
 
     def model3(x, c):
-        return c
+        return c * np.ones_like(x)
 
     def grad3(x, c):
         return np.ones((1, len(x)))
@@ -1201,7 +1201,7 @@ def grad3(x, c):
         a = 2
         b = 3
         ref = np.zeros(2)
-        ref[0] += lsq1.grad(a)
+        ref[0] += lsq1.grad(a)[0]
         ref[[1, 0]] += lsq2.grad(b, a)
         assert_allclose(lsq12.grad(a, b), ref)
 
@@ -1214,9 +1214,9 @@ def grad3(x, c):
         a = 2
         b = 3
         ref = np.zeros(2)
-        ref[0] += lsq1.grad(a)
+        ref[0] += lsq1.grad(a)[0]
         ref[[1, 0]] += lsq2.grad(b, a)
-        ref[0] += lsq1.grad(a)
+        ref[0] += lsq1.grad(a)[0]
         assert_allclose(lsq121.grad(a, b), ref)
 
     lsq312 = lsq3 + lsq12
@@ -1229,8 +1229,8 @@ def grad3(x, c):
         b = 3
         c = 4
         ref = np.zeros(3)
-        ref[0] += lsq3.grad(c)
-        ref[1] += lsq1.grad(a)
+        ref[0] += lsq3.grad(c)[0]
+        ref[1] += lsq1.grad(a)[0]
         ref[[2, 1]] += lsq2.grad(b, a)
         assert_allclose(lsq312.grad(c, a, b), ref)
 

diff --git a/tests/test_minimize.py b/tests/test_minimize.py
@@ -63,9 +63,9 @@ def rosen(par):
 
 
 def test_disp(capsys):
-    minimize(lambda x: x**2, 0)
+    minimize(lambda x: np.sum(x**2), 0)
     assert capsys.readouterr()[0] == ""
-    minimize(lambda x: x**2, 0, options={"disp": True})
+    minimize(lambda x: np.sum(x**2), 0, options={"disp": True})
     assert capsys.readouterr()[0] != ""
 
 
@@ -115,7 +115,7 @@ class Fcn:
 
         def __call__(self, x):
             self.n += 1
-            return x**2 + 1e-2 * (self.n % 3)
+            return np.sum(x**2 + 1e-2 * (self.n % 3))
 
     r = minimize(Fcn(), [1], options={"maxfun": 100000000})
     assert not r.success