Merge pull request #16 from n-takumasa/dev

dev

.github/workflows/publish.yml

@@ -12,16 +12,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
         with:
-          python-version-file: "pyproject.toml"
-
-      - name: Update pip
-        run: python -m pip install --upgrade pip
+          persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: false
 
       - name: Build a binary wheel and a source tarball
         run: uv build

.github/workflows/test.yml

@@ -1,63 +1,59 @@
 name: test
 
 on:
+  workflow_dispatch:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
 concurrency:
-  group: test-${{ github.head_ref }}
+  group: test-${{ github.ref }}
   cancel-in-progress: true
 
 env:
   PYTHONUNBUFFERED: "1"
   FORCE_COLOR: "1"
 
 jobs:
-  check:
-    name: Static analysis
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version-file: "pyproject.toml"
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
-      - run: uv venv
-      - name: Install tox
-        run: uv pip install tox tox-uv
-      - name: Run static analysis
-        run: uv run tox run -e lint
-      - name: Run mypy
-        run: uv run tox run -e type
-
   run:
-    needs: check
-    name: Python ${{ matrix.python-version }} on ${{ startsWith(matrix.os, 'macos-') && 'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }}
+    name: test with ${{ matrix.env }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        env: ["3.13", "3.12", "3.11", "3.10", "3.9", "3.8"]
         include:
           - os: windows-latest
-            python-version: 3.12
+            env: "3.13"
           - os: macos-latest
-            python-version: 3.12
+            env: "3.13"
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
-      - run: uv venv
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@v5
       - name: Install tox
-        run: uv pip install tox tox-uv tox-gh-actions
-      - name: Run tests
-        run: uv run tox
+        run: >-
+          uv tool install
+          --python-preference only-managed
+          --python 3.13
+          tox
+          --with tox-uv
+          --with tox-gh
+      - name: Install Python
+        if: matrix.env != '3.13'
+        run: >-
+          uv python install
+          --python-preference only-managed
+          ${{ matrix.env }}
+      - name: Setup test suite
+        run: tox run -vv --notest --skip-missing-interpreters false
+        env:
+          TOX_GH_MAJOR_MINOR: ${{ matrix.env }}
+      - name: Run test suite
+        run: tox run --skip-pkg-install
+        env:
+          TOX_GH_MAJOR_MINOR: ${{ matrix.env }}

.github/workflows/zizmor.yml

@@ -0,0 +1,38 @@
+name: GitHub Actions Security Analysis with zizmor 🌈
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+  schedule:
+    - cron: "0 23 * * 2"
+
+jobs:
+  zizmor:
+    name: zizmor latest via PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+      # required for workflows in private repositories
+      contents: read
+      actions: read
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Run zizmor 🌈
+        run: uvx zizmor --format sarif . > results.sarif
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload SARIF file
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: results.sarif
+          category: zizmor

example/water.py

@@ -8,8 +8,6 @@
 # ]
 # ///
 
-import os
-
 import matplotlib.pyplot as plt
 import polars as pl
 from matplotlib.axes import Axes
@@ -39,5 +37,5 @@
 
 fig.suptitle(f"{t.name} {t.formula}")
 fig.tight_layout()
-if not os.getenv("CI"):
-    plt.show()
+
+plt.show()

tests/test_example.py

@@ -2,9 +2,18 @@
 import subprocess
 import sys
 from pathlib import Path
+from tempfile import NamedTemporaryFile
 
 import pytest
 
+_patch = """\
+import matplotlib.pyplot as plt
+def _show(*args, **kwargs):
+    ...
+plt.show = _show
+
+"""
+
 
 def get_example_scripts():
     return [
@@ -19,9 +28,15 @@ def get_example_scripts():
 )
 def test_example(fp: Path):
     env = os.environ.copy()
-    env["CI"] = "true"
-    ret = subprocess.run(
-        [sys.executable, fp.absolute()],
-        env=env,
-    )
+    env["MPLBACKEND"] = "agg"
+    with NamedTemporaryFile("w", suffix=".py", delete=False) as tmp:
+        # python >= 3.12
+        # with TemporaryFile("w", suffix=".py", delete_on_close=False) as tmp:
+        tmp.write(_patch + fp.read_text())
+        tmp.close()
+        ret = subprocess.run(
+            [sys.executable, tmp.name],
+            env=env,
+        )
+        os.unlink(tmp.name)
     assert ret.returncode == 0

tests/test_table.py

@@ -14,8 +14,9 @@ def get_index() -> list[str]:
 
 
 @pytest.mark.parametrize("index", get_index())
-def test_columns(index: str):
+def test_table(index: str):
     table = janaf.Table(index)
+
     assert table.df.columns == [
         "T(K)",
         "Cp",
@@ -27,6 +28,7 @@ def test_columns(index: str):
         "log Kf",
         "Note",
     ]
+
     assert table.df.dtypes == [
         pl.Float64,
         pl.Float64,
@@ -38,3 +40,78 @@ def test_columns(index: str):
         pl.Float64,
         pl.String,
     ]
+
+    # S(Tr) = -[G(Tr) - H(Tr)] / Tr
+    if index not in {"S-016", "S-017", "S-018", "S-019", "S-020"}:
+        assert (
+            table.df.filter(pl.col("T(K)") == 298.15)
+            .select(pl.col("S") - pl.col("-[G-H(Tr)]/T"))
+            .item()
+            == 0
+        )
+
+    # At constant pressure, enthalpy is a monotonically increasing function of temperature
+    # TODO: https://github.com/n-takumasa/py-janaf/issues/13
+    if index not in {"C-066", "Cl-121"}:
+        assert table.df.select((pl.col("H-H(Tr)").diff() >= 0).all()).item()
+
+    R = 8.31446261815324
+    atol = 1e-3
+    rtol = 1e-3
+    # ΔG(T) = ΔfG°(T) + R T ln(Kf) = 0
+    # ΔfG°(T) = - R T ln(Kf)
+    # log10(Kf) = - ΔfG°(T) / (ln(10) * R * T)
+    # TODO: https://github.com/n-takumasa/py-janaf/issues/13
+    if index not in {"B-123", "B-133"}:
+        assert (
+            table.df.select(
+                a="log Kf",
+                b=(
+                    (-1e3 * pl.col("delta-f G"))
+                    / (pl.lit(10).log() * R * pl.col("T(K)"))
+                ).fill_nan(0),
+            )
+            .with_columns(
+                eq=(pl.col("a") == pl.col("b")),
+                er_a=(pl.col("a") - pl.col("b")).abs(),
+                er_r=(pl.col("a") - pl.col("b")).abs() / pl.col("b").abs(),
+            )
+            .with_columns(
+                is_close=(pl.col("er_a") <= (atol + rtol * pl.col("b").abs())),
+            )
+            .select(
+                q=(pl.col("eq") | pl.col("is_close")).all(),
+            )
+            .item()
+        )
+
+    # G-H-S relation
+    # G°(T) = H°(T) - T S°(T)
+    # S°(T) = [H°(T) - H°(Tr)]/T - [G°(T) - H°(Tr)]/T
+    # TODO: https://github.com/n-takumasa/py-janaf/issues/13
+    # fmt: off
+    if index not in {
+        "B-065", "B-116", "B-133", "Be-044", "Be-047", "C-002", "C-008", "C-010",
+        "H-014", "H-016", "Hf-001", "Hf-002", "Hf-004", "Hf-005", "Li-014", "Li-016",
+        "Mg-008", "Mg-010", "S-016", "S-017", "S-018", "S-019", "S-020",
+    }:
+        # fmt: on
+        assert (
+            table.df.select(
+                "T(K)",
+                a="S",
+                b=(pl.col("H-H(Tr)") * 1e3 / pl.col("T(K)") + pl.col("-[G-H(Tr)]/T")),
+            )
+            .with_columns(
+                eq=(pl.col("a") == pl.col("b")),
+                er_a=(pl.col("a") - pl.col("b")).abs(),
+                er_r=(pl.col("a") - pl.col("b")).abs() / pl.col("b").abs(),
+            )
+            .with_columns(
+                is_close=(pl.col("er_a") <= (atol + rtol * pl.col("b").abs())),
+            )
+            .select(
+                q=(pl.col("eq") | pl.col("is_close")).all(),
+            )
+            .item()
+        )

tox.toml

@@ -0,0 +1,41 @@
+requires = [
+    "tox>=4.21",
+    "tox-uv",
+]
+env_list = [
+    "lint", "type",
+    "3.13", "3.12", "3.11", "3.10", "3.9", "3.8",
+]
+
+[gh.python]
+"3.13" = ["3.13", "lint", "type"]
+"3.12" = ["3.12"]
+"3.11" = ["3.11"]
+"3.10" = ["3.10"]
+"3.9" = ["3.9"]
+"3.8" = ["3.8"]
+
+[env_run_base]
+package = "wheel"
+wheel_build_env = ".pkg"
+extras = ["test"]
+commands = [
+    ["pytest", "-p", "no:faulthandler", { replace = "posargs", default = ["tests"], extend = true }],
+]
+
+[env.lint]
+package = "skip"
+deps = [
+    "ruff",
+]
+commands = [
+    ["ruff", "format", "--check", { replace = "posargs", default = ["."], extend = true }],
+    ["ruff", "check", "--no-fix", { replace = "posargs", default = ["."], extend = true }],
+]
+
+[env.type]
+package = "wheel"
+extras = ["type"]
+commands = [
+    ["mypy", "--install-types", "--non-interactive", { replace = "posargs", default = [], extend = true }],
+]