Add tests for executable

IUPAC-InChI · Sep 25, 2024 · 290f547 · 290f547
1 parent 08dcd9c
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Showing 11 changed files with 273 additions and 5 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -3,5 +3,4 @@ INCHI-1-TEST/data/
 INCHI-1-TEST/docs/
 INCHI-1-TEST/libs/
 INCHI-1-TEST/exes/
-INCHI-1-TEST/tests/
 **/__pycache__/
diff --git a/.github/actions/compile_inchi_exe/action.yml b/.github/actions/compile_inchi_exe/action.yml
@@ -0,0 +1,13 @@
+name: Compile InChI executable from triggering commit
+
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        git config --global --add safe.directory "$GITHUB_WORKSPACE" # https://github.com/actions/runner-images/issues/6775
+        mkdir "$GITHUB_WORKSPACE/$EXE_DIR"
+        ./INCHI-1-TEST/compile_inchi.sh $COMMIT "$GITHUB_WORKSPACE/$EXE_DIR" exe
+      shell: bash
+      env:
+        COMMIT: ${{ github.sha }}
+        EXE_DIR: INCHI-1-TEST/exes
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -21,6 +21,11 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e INCHI-1-TEST[invariance-tests]
+
+      - uses: ./.github/actions/compile_inchi_exe
+      - name: Run executable tests
+        run: pytest INCHI-1-TEST/tests/test_executable
+
       - uses: ./.github/actions/compile_inchi_lib
       - uses: ./.github/actions/regression_tests
         with:
@@ -41,7 +46,7 @@ jobs:
     steps:
       - name: Install build and test environment
         run: |
-          apk add bash git musl-dev gcc make python3 py-pip
+          apk add bash git musl-dev gcc g++ make python3 py-pip
       # We need to install git before checking out the repository.
       # Otherwise, the repository will be downloaded using the GitHub REST API instead of git.
       - uses: actions/checkout@v4
@@ -59,6 +64,11 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install -e INCHI-1-TEST
+
+      - uses: ./.github/actions/compile_inchi_exe
+      - name: Run executable tests
+        run: pytest INCHI-1-TEST/tests/test_executable
+
       - uses: ./.github/actions/compile_inchi_lib
       - uses: ./.github/actions/regression_tests
         with:

diff --git a/INCHI-1-TEST/Dockerfile b/INCHI-1-TEST/Dockerfile
@@ -32,13 +32,22 @@ RUN mkdir $lib_dir && for version in $inchi_versions; do \
     /inchi/INCHI-1-TEST/compile_inchi.sh "$version" "$lib_dir" lib || exit 1; \
     done
 
+ENV exe_dir="/inchi/INCHI-1-TEST/exes"
+RUN for version in $inchi_versions; do \
+    version_dir="${exe_dir}/${version}"; \
+    mkdir -p $version_dir; \
+    /inchi/INCHI-1-TEST/compile_inchi.sh "$version" "$version_dir" exe || exit 1; \
+    done
+
 FROM gcc:14-bookworm AS inchi_test
 
 WORKDIR /inchi
 
 # Include only what's necessary for running the tests.
 COPY --from=inchi_compilation /inchi/INCHI-1-TEST/src /inchi/INCHI-1-TEST/src
 COPY --from=inchi_compilation /inchi/INCHI-1-TEST/libs /inchi/INCHI-1-TEST/libs
+COPY --from=inchi_compilation /inchi/INCHI-1-TEST/exes /inchi/INCHI-1-TEST/exes
+COPY --from=inchi_compilation /inchi/INCHI-1-TEST/tests /inchi/INCHI-1-TEST/tests
 COPY --from=inchi_compilation /inchi/INCHI-1-TEST/pyproject.toml /inchi/INCHI-1-TEST/pyproject.toml
 COPY --from=inchi_compilation /inchi/INCHI-1-TEST/install.sh /inchi/INCHI-1-TEST/install.sh
 

diff --git a/INCHI-1-TEST/install.sh b/INCHI-1-TEST/install.sh
@@ -2,6 +2,6 @@
 
 apt update && apt install -y python3-pip cmake
 python3 -m pip install --upgrade --break-system-packages pip
-python3 -m pip install --break-system-packages -e .[invariance-tests,development]
+python3 -m pip install --break-system-packages -e .[invariance-tests]
 # Make `python3` available as `python`.
 update-alternatives --install /usr/bin/python python /usr/bin/python3 10
diff --git a/INCHI-1-TEST/pyproject.toml b/INCHI-1-TEST/pyproject.toml
@@ -2,12 +2,11 @@
 name = "inchi_tests"
 version = "1.0.0"
 requires-python = ">=3.11"
-dependencies = ["pydantic == 2.7.1"]
+dependencies = ["pydantic == 2.7.1", "pytest == 8.3.3"]
 
 [project.optional-dependencies]
 # FIXME: We're forcing numpy major version for now until https://github.com/kuelumbus/rdkit-pypi/issues/102 is resolved.
 invariance-tests = ["rdkit == 2023.9.6", "numpy < 2.0.0"]
-development = ["pytest"]
 
 [project.scripts]
 run-tests = "inchi_tests.run_tests:main"

diff --git a/INCHI-1-TEST/tests/test_executable/README.md b/INCHI-1-TEST/tests/test_executable/README.md
@@ -0,0 +1,19 @@
+# Executable tests
+
+Test specific behaviors of the executable.
+Ensure that specific input (molfile and arguments) elicits specific output (e.g., error).
+
+Where possible, stick to the following principles:
+- Define input inline rather than using external files (having entire test scenario on screen is nice).
+- Keep number of tests per file to a minimum.
+- When replicating a bug, reference the (GitHub) issue number in the file name (e.g., `test_github_42.py`).
+
+Have a look at the existing tests for examples on how to write a test.
+
+Run with `pytest INCHI-1-TEST/tests/test_executable`.
+Note that by default, the tests expect the InChI executable to live at `INCHI-1-TEST/exes/inchi-1`.
+You can specify another InChI executable like so:
+
+```shell
+pytest INCHI-1-TEST/tests/test_executable --exe-path=path/to/executable
+```
diff --git a/INCHI-1-TEST/tests/test_executable/conftest.py b/INCHI-1-TEST/tests/test_executable/conftest.py
@@ -0,0 +1,31 @@
+import pytest
+import subprocess
+from typing import Callable
+from pathlib import Path
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--exe-path",
+        action="store",
+        default="INCHI-1-TEST/exes/inchi-1",
+        help="Absolute path to the InChI executable.",
+    )
+
+
+@pytest.fixture
+def run_inchi_exe(request) -> Callable:
+    def _run_inchi_exe(
+        molfile_path: str, args: str = ""
+    ) -> subprocess.CompletedProcess:
+
+        exe_path: str = request.config.getoption("--exe-path")
+        if not Path(exe_path).exists():
+            raise FileNotFoundError(f"InChI executable not found at {exe_path}.")
+
+        return subprocess.run(
+            [exe_path, molfile_path, args],
+            capture_output=True,
+        )
+
+    return _run_inchi_exe
diff --git a/INCHI-1-TEST/tests/test_executable/helpers.py b/INCHI-1-TEST/tests/test_executable/helpers.py
@@ -0,0 +1,18 @@
+from typing import Callable
+from pathlib import Path
+
+
+def tmp_molfile(molfile: Callable) -> Callable:
+    """
+    Creates a temporary molfile and returns its path.
+
+    `molfile` must return a string.
+    """
+
+    def get_molfile_path(tmp_path: Path) -> str:
+        molfile_path = tmp_path.joinpath("tmp.mol")
+        molfile_path.write_text(molfile())
+
+        return str(molfile_path)
+
+    return get_molfile_path
diff --git a/INCHI-1-TEST/tests/test_executable/test_github_40.py b/INCHI-1-TEST/tests/test_executable/test_github_40.py
@@ -0,0 +1,113 @@
+import pytest
+from helpers import tmp_molfile
+
+
+@pytest.fixture
+@tmp_molfile
+def molfile():
+    return """(R)-SDP
+  ChemDraw08122419562D
+
+ 43 50  0  0  1  0  0  0  0  0999 V2000
+   -0.7846   -1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4991   -1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.2136   -1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.2136   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4991    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7813    0.9328    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2510    1.5648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5331    2.3400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0028    2.9720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1904    2.8288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0918    2.0535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4385    1.4215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5937    1.0761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.1240    0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9365    0.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.2187    1.3626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.6884    1.9946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8759    1.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4849    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7846    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7846    0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4991   -0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7813   -0.9328    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+    2.5937   -1.0761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8759   -1.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6884   -1.9946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.2187   -1.3626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9365   -0.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.1240   -0.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2510   -1.5648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.4385   -1.4215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0918   -2.0535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1904   -2.8288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0028   -2.9720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5331   -2.3400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2136    0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2136    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4991    1.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.4849   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0        0
+  2  3  1  0        0
+  3  4  2  0        0
+  4  5  1  0        0
+  5  6  1  0        0
+  6  7  1  0        0
+  7  8  2  0        0
+  8  9  1  0        0
+  9 10  2  0        0
+ 10 11  1  0        0
+ 11 12  2  0        0
+  7 12  1  0        0
+  6 13  1  0        0
+ 13 14  2  0        0
+ 14 15  1  0        0
+ 15 16  2  0        0
+ 16 17  1  0        0
+ 17 18  2  0        0
+ 13 18  1  0        0
+  5 19  2  0        0
+  1 19  1  0        0
+ 20 19  1  1        0
+ 20 21  1  0        0
+ 21 22  1  0        0
+ 22 23  1  0        0
+ 23 24  2  0        0
+ 20 24  1  0        0
+ 24 25  1  0        0
+ 25 26  1  0        0
+ 26 27  1  0        0
+ 27 28  2  0        0
+ 28 29  1  0        0
+ 29 30  2  0        0
+ 30 31  1  0        0
+ 31 32  2  0        0
+ 27 32  1  0        0
+ 26 33  1  0        0
+ 33 34  2  0        0
+ 34 35  1  0        0
+ 35 36  2  0        0
+ 36 37  1  0        0
+ 37 38  2  0        0
+ 33 38  1  0        0
+ 25 39  2  0        0
+ 39 40  1  0        0
+ 40 41  2  0        0
+ 23 41  1  0        0
+ 20 42  1  6        0
+ 42 43  1  0        0
+  1 43  1  0        0
+M  END
+"""
+
+
+@pytest.mark.xfail(strict=True, raises=AssertionError)
+def test_spiro_compound_chiral(molfile, run_inchi_exe):
+    result = run_inchi_exe(molfile)
+
+    assert "Warning (Not chiral) structure #1." not in result.stderr.decode()
diff --git a/INCHI-1-TEST/tests/test_executable/test_github_52.py b/INCHI-1-TEST/tests/test_executable/test_github_52.py
@@ -0,0 +1,57 @@
+import pytest
+from helpers import tmp_molfile
+
+
+@pytest.fixture
+@tmp_molfile
+def molfile_empty_bondblock():
+    return """
+  -INDIGO-08292417452D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 1 0 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 9.35 -4.8 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+"""
+
+
+@pytest.fixture
+@tmp_molfile
+def molfile_no_bondblock():
+    return """
+  -INDIGO-08292417452D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 1 0 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 9.35 -4.8 0.0 0
+M  V30 END ATOM
+M  V30 END CTAB
+M  END
+"""
+
+
+@pytest.mark.xfail(strict=True, raises=AssertionError)
+def test_empty_bondblock(molfile_empty_bondblock, run_inchi_exe):
+    result = run_inchi_exe(molfile_empty_bondblock)
+
+    assert (
+        "Error 71 (no InChI; Error: No V3000 CTAB end marker) inp structure #1."
+        not in result.stderr.decode()
+    )
+
+
+def test_no_bondblock(molfile_no_bondblock, run_inchi_exe):
+    result = run_inchi_exe(molfile_no_bondblock)
+
+    assert (
+        "Error 71 (no InChI; Error: No V3000 CTAB end marker) inp structure #1."
+        not in result.stderr.decode()
+    )