Camera ready

.github/workflows/tests.yml

@@ -0,0 +1,47 @@
+name: tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  # Formulas, numerical solvers and the per-call generators. These import
+  # nothing that needs SageMath, so they run on a plain Python and are the
+  # fast guard against a formula changing without the paper changing.
+  formulas:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install numpy scipy lmfit pytest
+      - name: Run the tests that do not need SageMath
+        run: python -m pytest -v
+        # Tests marked needs_sage skip themselves; see tests/conftest.py.
+
+  # The command line and the refitting of fastparameterselection/const.py both
+  # go through fastparameterselection/nd.py, which imports sage.all.
+  #
+  # Sage runs through `docker run` rather than a job-level `container:`. The
+  # image runs as the unprivileged `sage` user while the runner owns its
+  # workspace as root, so actions/checkout fails inside it with EACCES on
+  # /__w/_temp. Running the container as root is not a way out either: Sage
+  # ignores `--python3` as root and drops into its REPL. Checking out on the
+  # host and mounting the tree read-only avoids both.
+  full:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run the whole suite inside SageMath
+        run: |
+          docker run --rm -v "$PWD":/src:ro sagemath/sagemath:10.3 bash -lc '
+            cp -r /src /tmp/repo && cd /tmp/repo &&
+            sage --pip install --quiet lmfit pytest &&
+            sage --python3 -m pytest -v
+          '
+          # The copy keeps writes (output.csv) inside the container, where the
+          # sage user owns the tree.

.gitignore

@@ -169,3 +169,13 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+# Tool output written into the repo root by every run
+output.csv
+compiled_output.csv
+debug_log.txt
+
+# packaging
+build/
+dist/
+*.egg-info/

.readthedocs.yaml

@@ -1,27 +1,16 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Set the OS, Python version, and other tools you might need
 build:
   os: ubuntu-24.04
   tools:
     python: "3.13"
 
-# Build documentation in the "docs/" directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  configuration: docs/conf.py
 
 python:
   install:
     - requirements: docs/requirements.txt
-
-# Optionally, but recommended,
-# declare the Python requirements required to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-   install:
-   - requirements: docs/requirements.txt
-