Merge pull request #422 from light-curve/test-without-full-extras

Improve tox test configuration

Author: hombit

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: Test
 
-on: [push, pull_request, workflow_dispatch]
+on: [ push, pull_request, workflow_dispatch ]
 
 jobs:
   py_build_deps:
@@ -14,17 +14,17 @@ jobs:
         working-directory: light-curve
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: true
-    - name: Set up Python 3.12
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.12"
-    - name: Extract build deps from pyproject.toml
-      id: extract_from_toml
-      run: |
-        echo "output="$(python -c 'import tomllib; print(" ".join(tomllib.load(open("pyproject.toml", "rb"))["build-system"]["requires"]))') >> "$GITHUB_OUTPUT"
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Extract build deps from pyproject.toml
+        id: extract_from_toml
+        run: |
+          echo "output="$(python -c 'import tomllib; print(" ".join(tomllib.load(open("pyproject.toml", "rb"))["build-system"]["requires"]))') >> "$GITHUB_OUTPUT"
 
 
   test:
@@ -33,47 +33,47 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_minor: ['8', '9', '10', '11', '12']
+        python_minor: [ '8', '9', '10', '11', '12' ]
 
     defaults:
       run:
         working-directory: light-curve
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: true
-    - name: Set up Python 3.${{ matrix.python_minor }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.${{ matrix.python_minor }}"
-    - name: Install tox
-      run: pip install tox
-    - name: Run Python tests
-      run: tox -e py3${{ matrix.python_minor }}
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Set up Python 3.${{ matrix.python_minor }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.${{ matrix.python_minor }}"
+      - name: Install tox
+        run: pip install tox
+      - name: Run Python tests
+        run: tox -e py3${{ matrix.python_minor }}-base,py3${{ matrix.python_minor }}-test
 
   cargo-fmt:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - run: cargo fmt --manifest-path=light-curve/Cargo.toml -- --check
+      - uses: actions/checkout@v4
+      - run: cargo fmt --manifest-path=light-curve/Cargo.toml -- --check
 
   cargo-clippy:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - uses: Swatinem/rust-cache@v2
-      with:
-        shared-key: "${{ runner.os }}_stable-rust_cargo-clippy"
-        workspaces: "light-curve"
-    - run: cargo clippy --manifest-path=light-curve/Cargo.toml --all-targets -- -D warnings
+      - uses: actions/checkout@v4
+      - uses: Swatinem/rust-cache@v2
+        with:
+          shared-key: "${{ runner.os }}_stable-rust_cargo-clippy"
+          workspaces: "light-curve"
+      - run: cargo clippy --manifest-path=light-curve/Cargo.toml --all-targets -- -D warnings
 
   coverage:
     runs-on: ubuntu-latest
 
-    needs: [py_build_deps]
+    needs: [ py_build_deps ]
 
     defaults:
       run:
@@ -117,7 +117,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
 
-    needs: [py_build_deps]
+    needs: [ py_build_deps ]
 
     steps:
       - uses: actions/checkout@v4
@@ -147,63 +147,63 @@ jobs:
   msrv-build:
     runs-on: ubuntu-latest
 
-    needs: [py_build_deps]
+    needs: [ py_build_deps ]
 
     defaults:
       run:
         working-directory: light-curve
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.8'
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.10'
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-    - name: Set up Python 3.12
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-    - name: Get minimum supported Rust version
-      run: echo "::set-output name=msrv::$(grep '^rust-version = ' Cargo.toml | grep -o '[0-9.]\+')"
-      id: get_msrv
-    - uses: dtolnay/rust-toolchain@master
-      with:
-        toolchain: ${{ steps.get_msrv.outputs.msrv }}
-    - uses: Swatinem/rust-cache@v2
-      with:
-        shared-key: "${{ runner.os }}_msrv-rust_maturin-build"
-        workspaces: "light-curve"
-    - name: Install build_deps
-      run: pip install "${{ needs.py_build_deps.outputs.output }}"
-    - name: Build
-      run: |
-        rustup default ${{ steps.get_msrv.outputs.msrv }}
-        maturin build --find-interpreter
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Get minimum supported Rust version
+        run: echo "::set-output name=msrv::$(grep '^rust-version = ' Cargo.toml | grep -o '[0-9.]\+')"
+        id: get_msrv
+      - uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ steps.get_msrv.outputs.msrv }}
+      - uses: Swatinem/rust-cache@v2
+        with:
+          shared-key: "${{ runner.os }}_msrv-rust_maturin-build"
+          workspaces: "light-curve"
+      - name: Install build_deps
+        run: pip install "${{ needs.py_build_deps.outputs.output }}"
+      - name: Build
+        run: |
+          rustup default ${{ steps.get_msrv.outputs.msrv }}
+          maturin build --find-interpreter
 
   arm:
-    runs-on: [self-hosted, linux, ARM64]
+    runs-on: [ self-hosted, linux, ARM64 ]
 
-    needs: [py_build_deps]
+    needs: [ py_build_deps ]
 
     defaults:
       run:
         working-directory: light-curve
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Install build_deps
-      run: pip install "${{ needs.py_build_deps.outputs.output }}"
-    - name: Build
-      run: maturin build
+      - uses: actions/checkout@v4
+      - name: Install build_deps
+        run: pip install "${{ needs.py_build_deps.outputs.output }}"
+      - name: Build
+        run: maturin build

CHANGELOG.md

@@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
---
+- Package import doesn't fail if `scipy` is missed https://github.com/light-curve/light-curve-python/pull/422
 
 ### Security
 

light-curve/light_curve/light_curve_py/features/rainbow/bolometric.py

@@ -4,7 +4,6 @@
 from typing import Dict, List, Union
 
 import numpy as np
-from scipy.special import lambertw
 
 __all__ = [
     "bolometric_terms",
@@ -225,7 +224,6 @@ def value(t, t0, amplitude, rise_time):
 
     @staticmethod
     def initial_guesses(t, m, sigma, band):
-
         A = np.ptp(m)
         med_dt = median_dt(t, band)
 
@@ -328,6 +326,11 @@ def limits(t, m, sigma, band):
 
     @staticmethod
     def peak_time(t0, p):
+        try:
+            from scipy.special import lambertw
+        except ImportError:
+            raise ImportError("scipy is required for DoublexpBolometricTerm.peak_time, please install it")
+
         return t0 + np.real(-lambertw(p * np.exp(1)) + 1)
 
 

light-curve/light_curve/light_curve_py/minuit_ml.py

@@ -3,35 +3,10 @@
 from typing import Callable, Dict, Tuple
 
 import numpy as np
-from scipy.special import erf
-
-
-def logpdf(x, mu, sigma):
-    # We do not need second term as it does not depend on parameters
-    return -(((x - mu) / sigma) ** 2) / 2  # - np.log(np.sqrt(2*np.pi) * sigma)
-
-
-def barrier(x):
-    res = np.where(x > 0, 1 / x, np.inf)  # FIXME: naive barrier function
-
-    return res
-
-
-def logcdf(x):
-    # TODO: faster (maybe not so accurate, as we do not need it) implementation
-    # return norm.logcdf(x)
-
-    result = np.zeros(len(x))
-
-    idx = x < -5
-    result[idx] = -x[idx] ** 2 / 2 - 1 / x[idx] ** 2 - 0.9189385336 - np.log(-x[idx])
-    result[~idx] = np.log(0.5) + np.log1p(erf(x[~idx] / np.sqrt(2)))
-
-    return result
-
 
 try:
     from iminuit import Minuit
+    from scipy.special import erf
 except ImportError:
     MaximumLikelihood = None
 else:
@@ -63,21 +38,47 @@ def __call__(self, *par):
             ym = self.model(self.x, *par)
 
             if self.upper_mask is None:
-                result = -np.sum(logpdf(self.y, ym, self.yerror))
+                result = -np.sum(self.logpdf(self.y, ym, self.yerror))
             else:
                 # Measurements
-                result = -np.sum(logpdf(self.y[~self.upper_mask], ym[~self.upper_mask], self.yerror[~self.upper_mask]))
+                result = -np.sum(
+                    self.logpdf(self.y[~self.upper_mask], ym[~self.upper_mask], self.yerror[~self.upper_mask])
+                )
                 # Upper limits, Tobit model
                 # https://stats.stackexchange.com/questions/49443/how-to-model-this-odd-shaped-distribution-almost-a-reverse-j
                 result += -np.sum(
-                    logcdf((self.y[self.upper_mask] - ym[self.upper_mask]) / self.yerror[self.upper_mask])
+                    self.logcdf((self.y[self.upper_mask] - ym[self.upper_mask]) / self.yerror[self.upper_mask])
                 )
 
             # Barriers around parameter ranges
             # Scale is selected so that for the most of the range it is much smaller
             # than 0.5 which corresponds to 1-sigma errors
-            result += 0.0001 * np.sum(barrier((par - self.limits0) / self.limits_scale))
-            result += 0.0001 * np.sum(barrier((self.limits1 - par) / self.limits_scale))
+            result += 0.0001 * np.sum(self.barrier((par - self.limits0) / self.limits_scale))
+            result += 0.0001 * np.sum(self.barrier((self.limits1 - par) / self.limits_scale))
+
+            return result
+
+        @staticmethod
+        def logpdf(x, mu, sigma):
+            # We do not need the second term as it does not depend on parameters
+            return -(((x - mu) / sigma) ** 2) / 2  # - np.log(np.sqrt(2*np.pi) * sigma)
+
+        @staticmethod
+        def barrier(x):
+            res = np.where(x > 0, 1 / x, np.inf)  # FIXME: naive barrier function
+
+            return res
+
+        @staticmethod
+        def logcdf(x):
+            # TODO: faster (maybe not so accurate, as we do not need it) implementation
+            # return norm.logcdf(x)
+
+            result = np.zeros(len(x))
+
+            idx = x < -5
+            result[idx] = -x[idx] ** 2 / 2 - 1 / x[idx] ** 2 - 0.9189385336 - np.log(-x[idx])
+            result[~idx] = np.log(0.5) + np.log1p(erf(x[~idx] / np.sqrt(2)))
 
             return result
 

light-curve/pyproject.toml

@@ -159,10 +159,16 @@ markers = [
 [tool.tox]
 legacy_tox_ini = """
 [tox]
-envlist = py38,py39,py310,py311,py312
+envlist = py{38,39,310,311,312}-{base,test}
 isolated_build = True
 
-[testenv]
+[testenv:py{38,39,310,311,312}-base]
+change_dir = {envtmpdir}
+extras =
+commands =
+    python -c 'import light_curve'
+
+[testenv:py{38,39,310,311,312}-test]
 extras = dev
 commands =
     pytest README.md tests/ light_curve/