5 pipeline with unit tests (#10)

---------

Co-authored-by: Julian Piribauer <julian.piribauer@gmail.com>
Co-authored-by: julian <julian.piribauer@gmail.com>
Reviewed-on: #10

.gitea/ci-image/Dockerfile

@@ -0,0 +1,17 @@
+# Custom CI image for the arm64 (Raspberry Pi) Gitea Actions runner,
+# since the official sagemath/sagemath image is amd64-only.
+#
+# Build & push commands:
+#   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
+
+FROM condaforge/miniforge3:latest
+
+RUN mamba install -y -c conda-forge sage ruff pytest \
+    && mamba clean -afy
+
+RUN mamba install -y -c conda-forge nodejs \
+    && mamba clean -afy
+
+WORKDIR /workspace

.gitea/preparse.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+# This script is run in the CI container to preparse all .sage files into .sage.py files
+# and can also be run locally for local linting/testing.
+
+set -e
+
+if command -v python >/dev/null 2>&1 && python -c "import sage.repl" >/dev/null 2>&1; then
+  run_python() { python "$@"; }
+else
+  run_python() { sage --python "$@"; }
+fi
+
+for f in $(find . -name "*.sage" -not -path "./playground/*"); do
+  run_python -c "
+import sys
+from sage.repl.preparse import preparse_file
+
+path = sys.argv[1]
+with open(path) as fh:
+    src = fh.read()
+with open(path + '.py', 'w') as fh:
+    fh.write('from sage.all import *  # noqa: F401,F403\n')
+    fh.write(preparse_file(src))
+" "$f"
+done

.gitea/workflows/ci.yml

@@ -0,0 +1,37 @@
+name: CI
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+    branches: ["**"]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    # Custom image (see .gitea/ci-image/Dockerfile)
+    container:
+      image: gitea.piribauer.ch/julian/sage-ci:latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Preparse .sage files
+        run: .gitea/preparse.sh
+
+      - name: ruff check
+        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 +1,17 @@
+[tool.ruff]
+line-length = 120
+target-version = "py311"
+
+[tool.ruff.lint]
+# E: pycodestyle errors, F: pyflakes (undefined/unused names), I: isort (import order), W: pycodestyle warnings
+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 preparser output: star-import globals, semicolon preamble, and literal-substitution artifacts trip static analysis.
+"*.sage.py" = ["F403", "F405", "F821", "E741", "E402", "E702", "I001", "W291", "W293", "W292"]
+
+# test_smoke.py star-imports sage.all and loads a .sage file, so ruff can't see where its names come from.
+"tests/test_topdata_and_disc.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
@@ -102,6 +101,7 @@ class ToricPolytope(Polytope):
         if no_triangulation < 0 or no_triangulation >= len(self.triangulations):
             raise IndexError("Invalid triangulation index {} (available: 0..{}).".format(no_triangulation, len(self.triangulations) - 1))
         
+        if len(self.triangulations) > 1:
             logger.info("Using triangulation index %d of [0..%d].", no_triangulation, len(self.triangulations) - 1)
         self.triangulation = self.triangulations[no_triangulation]
     
@@ -233,7 +233,7 @@ 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 +275,7 @@ 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 +289,7 @@ 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_models.sage

@@ -0,0 +1,104 @@
+# Entries are (id, factory, expected_cy_dimension, expected_no_divs, expected_disc,
+# expected_intersection_numbers_CY), where expected_disc is a list of
+# (str(discriminant_factor), codimension) pairs as returned by ToricPolytope.disc().
+
+TEST_MODELS = [
+    (
+        "K3_two_parameter_family",
+        lambda: ToricPolytopeProjectiveSpace([1, 1, 2, 4], model_name="K3_two_parameter_family"),
+        2,  # cy_dimension
+        2,  # no_divs
+        [("z2 - 1/4", 2), ("4096*z1^2*(4*z2 - 1) + 128*z1 - 1", 0)],
+        {(0, 0): 4, (0, 1): 2, (1, 1): 0},
+    ),
+    (
+        "CY3_two_parameter_family",
+        lambda: ToricPolytopeProjectiveSpace([1, 1, 2, 2, 2], model_name="CY3_two_parameter_family"),
+        3,
+        2,
+        [("z2 - 1/4", 3), ("65536*z1^2*(4*z2 - 1) + 512*z1 - 1", 0)],
+        {(0, 0, 0): 8, (0, 0, 1): 4, (0, 1, 1): 0, (1, 1, 1): 0},
+    ),
+    (
+        "CY4_two_parameter_family",
+        lambda: ToricPolytopeProjectiveSpace([1, 1, 1, 1, 8, 12], model_name="CY4_two_parameter_family"),
+        4,
+        2,
+        [
+            ("z2 - 1/256", 2),
+            ("34828517376*z1^4*(256*z2 - 1) + 322486272*z1^3 - 1119744*z1^2 + 1728*z1 - 1", 0),
+        ],
+        {(0, 0, 0, 0): 64, (0, 0, 0, 1): 16, (0, 0, 1, 1): 4, (0, 1, 1, 1): 1, (1, 1, 1, 1): 0},
+    ),
+    (
+        "CICY3_one_parameter",
+        lambda: ToricPolytopeCICY([[3, 3]], model_name="CICY3_one_parameter"),
+        3,
+        1,
+        [("z1 - 1/46656", 0)],
+        {(0, 0, 0): 9},
+    ),
+    (
+        "CICY3_two_parameter",
+        lambda: ToricPolytopeCICY([[3], [3]], model_name="CICY3_two_parameter"),
+        3,
+        2,
+        [
+            (
+                "-19683*z1^3 - 2187*(27*z1 + 1)*z2^2 - 19683*z2^3 - 2187*z1^2 "
+                "- 81*(729*z1^2 - 189*z1 + 1)*z2 - 81*z1 - 1",
+                0,
+            )
+        ],
+        {(0, 0, 0): 0, (0, 0, 1): 3, (0, 1, 1): 3, (1, 1, 1): 0},
+    ),
+    (
+        "CICY5_two_parameter",
+        lambda: ToricPolytopeCICY([[6, 1], [0, 2]], model_name="CICY5_two_parameter"),
+        5,
+        2,
+        [
+            (
+                "16384*z2^7 - 28672*z2^6 + 21504*z2^5 - 448*(1647086*z1 - 5)*z2^3 - 8960*z2^4 "
+                "- 112*(8235430*z1 + 3)*z2^2 - 678223072849*z1^2 - 28*(4941258*z1 - 1)*z2 - 1647086*z1 - 1",
+                0,
+            )
+        ],
+        {
+            (0, 0, 0, 0, 0): 6,
+            (0, 0, 0, 0, 1): 12,
+            (0, 0, 0, 1, 1): 0,
+            (0, 0, 1, 1, 1): 0,
+            (0, 1, 1, 1, 1): 0,
+            (1, 1, 1, 1, 1): 0,
+        },
+    ),
+    (
+        "CICY3_two_parameter_manual",
+        lambda: ToricPolytope(
+            [
+                [1, 0, 0, 0, 0, 0],
+                [0, 1, 0, 0, 0, 0],
+                [0, 0, 1, 0, 0, 0],
+                [0, 0, 0, 1, 0, 0],
+                [0, 0, 0, 0, 1, 0],
+                [0, 0, 0, 0, 0, 1],
+                [-1, -1, 0, 0, 0, 0],
+                [0, 0, -1, -1, -1, -1],
+            ],
+            nef_partition=[[0, 1, 2, 3], [4, 5, 6, 7]],
+            model_name="CICY3_two_parameter_manual",
+        ),
+        4,
+        2,
+        [
+            (
+                "-14348907*z1^5 - 2657205*z1^4 - 196830*z1^3 - 29296875*(270*z1 + 1)*z2^2 "
+                "- 30517578125*z2^3 - 7290*z1^2 + 9375*(98415*z1^3 - 32805*z1^2 + 810*z1 - 1)*z2 "
+                "- 135*z1 - 1",
+                0,
+            )
+        ],
+        {(0, 0, 0, 0): 0, (0, 0, 0, 1): 0, (0, 0, 1, 1): 6, (0, 1, 1, 1): 8, (1, 1, 1, 1): 2},
+    ),
+]

tests/test_topdata_and_disc.py

@@ -0,0 +1,34 @@
+import os
+
+import pytest
+from sage.all import *  # noqa: F401
+from sage.geometry.lattice_polytope import set_palp_dimension
+
+load(os.path.join(os.path.dirname(__file__), "..", "sage", "toric_topdata.sage"))
+load(os.path.join(os.path.dirname(__file__), "test_models.sage"))
+
+set_palp_dimension(11)
+
+TEST_MODELS_PARAMETRISED = [pytest.param(*row[1:], id=row[0]) for row in TEST_MODELS]
+
+
+@pytest.mark.parametrize(
+    "make_model, expected_cy_dimension, expected_no_divs, expected_disc, expected_intersection_numbers_CY",
+    TEST_MODELS_PARAMETRISED,
+)
+def test_topdata_and_disc(
+    make_model,
+    expected_cy_dimension,
+    expected_no_divs,
+    expected_disc,
+    expected_intersection_numbers_CY,
+):
+    polytope = make_model()
+
+    discriminants = polytope.disc()
+    assert [(str(factor), codim) for factor, codim in discriminants] == expected_disc
+
+    polytope.topdata()
+    assert polytope.cy_dimension == expected_cy_dimension
+    assert polytope.no_divs == expected_no_divs
+    assert polytope.intersection_numbers_CY == expected_intersection_numbers_CY