ci: fix sage CLI invocations for conda-forge's sage (no --preparse/--python flags)

.gitea/ci-image/Dockerfile

@@ -0,0 +1,27 @@
+# Custom CI image for the arm64 (Raspberry Pi) Gitea Actions runner.
+#
+# The official sagemath/sagemath image is amd64-only; conda-forge's `sage`
+# package is the one place SageMath is actually published for linux-aarch64,
+# so this bakes it (plus the lint/test tools) into a single image, built and
+# pushed once rather than reinstalled on every CI run.
+#
+# Build & push (run directly on the Pi, or any arm64 machine with Docker):
+#   docker build -t gitea.piribauer.ch/julian/sage-ci:latest -f .gitea/ci-image/Dockerfile .
+#   docker login gitea.piribauer.ch -u julian
+#   docker push gitea.piribauer.ch/julian/sage-ci:latest
+#
+# Rebuild and re-push whenever this Dockerfile changes (e.g. bumping the sage
+# version) or the pinned tool versions need updating.
+
+FROM condaforge/miniforge3:latest
+
+RUN mamba install -y -c conda-forge sage ruff pytest \
+    && mamba clean -afy
+
+# actions/checkout@v4 (and other JS-based actions) run via `node` inside this
+# container -- act_runner doesn't inject a runtime of its own when a custom
+# `container:` image is set, so one has to be present here.
+RUN mamba install -y -c conda-forge nodejs \
+    && mamba clean -afy
+
+WORKDIR /workspace

.gitea/workflows/ci.yml

@@ -0,0 +1,64 @@
+name: CI
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+    branches: ["**"]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    # Custom image (see .gitea/ci-image/Dockerfile): the official
+    # sagemath/sagemath image is amd64-only and this runner is arm64, and
+    # ruff/pytest are baked in here so jobs don't reinstall them every run.
+    container:
+      image: gitea.piribauer.ch/julian/sage-ci:latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Preparse .sage files
+        # Turns each *.sage file into real Python (*.sage.py) so ruff can
+        # parse it, and prepends the `from sage.all import *` that `sage`
+        # normally injects at runtime, so Sage's globals (ZZ, var, matrix, ...)
+        # resolve instead of looking like undefined names.
+        #
+        # The conda-forge `sage` CLI has no `--preparse` flag (unlike the
+        # classical sage script the image was originally written against), so
+        # this calls the same preparser Sage itself uses, directly in Python.
+        run: |
+          python - <<'PYEOF'
+          import pathlib
+          from sage.repl.preparse import preparse_file
+
+          for f in pathlib.Path(".").rglob("*.sage"):
+              if f.parts and f.parts[0] == "playground":
+                  continue
+              out = preparse_file(f.read_text())
+              f.with_suffix(f.suffix + ".py").write_text(
+                  "from sage.all import *  # noqa: F401,F403\n" + out
+              )
+          PYEOF
+
+      - name: ruff check
+        # --no-respect-gitignore: *.sage.py is gitignored (it's generated, see
+        # the previous step) but that's exactly what we need to lint here.
+        # `python` here is the conda env's own interpreter -- it already has
+        # sage/ruff/pytest importable, `sage --python` isn't a real flag on
+        # the conda-forge sage CLI.
+        run: python -m ruff check --no-respect-gitignore .
+
+  test:
+    runs-on: ubuntu-latest
+    needs: lint
+    container:
+      image: gitea.piribauer.ch/julian/sage-ci:latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Run tests
+        run: python -m pytest tests/

.gitignore

@@ -0,0 +1,10 @@
+# Sage preparser output (regenerated from .sage sources, not hand-maintained)
+*.sage.py
+
+# Python / tooling caches
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+.pytest_cache/
+
+.venv/

pyproject.toml

@@ -0,0 +1,32 @@
+[tool.ruff]
+line-length = 120
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "W"]
+ignore = [
+    "E501", # symbolic-math expressions routinely exceed a "normal" line length
+]
+
+[tool.ruff.lint.per-file-ignores]
+# *.sage.py is generated by `sage --preparse` from *.sage sources.
+# - F403/F405/F821/E741: Sage's runtime injects hundreds of globals (ZZ, var,
+#   matrix, LatticePolytope, ...) via `from sage.all import *` before
+#   executing these files, so plain static analysis can't see where names
+#   come from.
+# - E402/E702/I001: Sage's preparser itself emits an import-then-semicolon-
+#   joined-constants preamble (e.g. `_sage_const_1 = Integer(1); ...`) ahead
+#   of the file's own imports; that's Sage's boilerplate, not this project's
+#   code style.
+# - W291/W293: the preparser replaces every integer literal with
+#   `_sage_const_N ` (trailing space included) to preserve token boundaries,
+#   so trailing-whitespace warnings fire mechanically on almost every line
+#   with a number in it -- not something `ruff format` could fix anyway,
+#   since it wouldn't change the .sage source that generated it.
+"*.sage.py" = ["F403", "F405", "F821", "E741", "E402", "E702", "I001", "W291", "W293"]
+
+# tests/test_smoke.py does `from sage.all import *` and `load(...)` a .sage
+# file to get at its classes -- the same dynamic-namespace situation as
+# *.sage.py above, just in a hand-written file: ruff can't see that
+# Polytope/ToricPolytope/etc. come from the loaded file.
+"tests/test_smoke.py" = ["F403", "F405"]

sage/toric_topdata.sage

@@ -2,7 +2,6 @@ import numpy as np
 import logging
 import os
 import json
-from datetime import datetime, timezone
 import re
 
 # Logger
@@ -233,7 +232,7 @@ class ToricPolytope(Polytope):
     def _setup_discriminant_symbols(self):
         mori_rays = self.Mori_cone.rays()
 
-        a_vars = [var("a_{}".format(u), latex_name="a_{{}}".format(u)) for u in (1..len(mori_rays))]
+        a_vars = [var("a_{}".format(u), latex_name="a_{{{}}}".format(u)) for u in (1..len(mori_rays))]
         z_vars = var('z', n=len(mori_rays)+1, latex_name='z') # z[0] is superfluous
         lambda_vars = var('l', n=len(mori_rays)+1, latex_name='l') # l[0] is superfluous
         a_row = matrix(a_vars)
@@ -275,7 +274,7 @@ class ToricPolytope(Polytope):
             if polynomials[0] == 0:
                 polynomials = maxima.eliminate(equation_system, lambda_symbols[:-1]).sage()
                 reverse_solve = True
-        except:
+        except Exception:
             # In one-parameter cases there may be nothing to eliminate.
             polynomials = equation_system
             logger.debug("No elimination needed for the equation system: %s", equation_system)
@@ -289,7 +288,7 @@ class ToricPolytope(Polytope):
             else:
                 last_lambda = lambda_symbols[-1]
                 polynomials = [poly / last_lambda ** (poly.degree(last_lambda)) for poly in polynomials]
-        except:
+        except Exception:
             pass
 
         return polynomials

tests/test_smoke.py

@@ -0,0 +1,32 @@
+import os
+
+import pytest
+from sage.all import *  # noqa: F401,F403
+
+load(os.path.join(os.path.dirname(__file__), "..", "sage", "toric_topdata.sage"))
+
+
+def test_polytope_rejects_too_few_points():
+    with pytest.raises(ValueError):
+        Polytope([[0, 0], [1, 0]])  # 2 points in dimension 2: not enough
+
+
+def test_mirror_quintic_topdata():
+    # Vertices e_1, ..., e_4, -e_1-...-e_4 -- the worked example from
+    # ToricPolytope's own docstring.
+    points = [
+        [1, 0, 0, 0],
+        [0, 1, 0, 0],
+        [0, 0, 1, 0],
+        [0, 0, 0, 1],
+        [-1, -1, -1, -1],
+    ]
+
+    polytope = ToricPolytope(points, model_name="ci_smoke_test_quintic")
+    assert polytope.dimension == 4
+    assert len(polytope.triangulations) >= 1
+
+    polytope.topdata()
+    assert polytope.cy_dimension == 3
+    assert polytope.no_divs == 1  # P^4 has Picard rank 1
+    assert polytope.intersection_numbers_CY == {(0, 0, 0): 5}  # classical quintic self-intersection