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JanCBrammerJanCBrammer
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Add tests for executable
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‎.dockerignore‎

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@@ -3,5 +3,4 @@ INCHI-1-TEST/data/
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INCHI-1-TEST/docs/
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INCHI-1-TEST/libs/
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INCHI-1-TEST/exes/
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INCHI-1-TEST/tests/
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**/__pycache__/

‎.github/actions/compile_inchi_exe/action.yml‎

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name: Compile InChI executable from triggering commit
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runs:
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using: "composite"
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steps:
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- run: |
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git config --global --add safe.directory "$GITHUB_WORKSPACE" # https://github.com/actions/runner-images/issues/6775
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mkdir "$GITHUB_WORKSPACE/$EXE_DIR"
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./INCHI-1-TEST/compile_inchi.sh $COMMIT "$GITHUB_WORKSPACE/$EXE_DIR" exe
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shell: bash
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env:
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COMMIT: ${{ github.sha }}
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EXE_DIR: INCHI-1-TEST/exes

‎.github/workflows/ci.yml‎

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@@ -21,6 +21,11 @@ jobs:
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e INCHI-1-TEST[invariance-tests]
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- uses: ./.github/actions/compile_inchi_exe
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- name: Run executable tests
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run: pytest INCHI-1-TEST/tests/test_executable
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- uses: ./.github/actions/compile_inchi_lib
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- uses: ./.github/actions/regression_tests
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with:
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run: |
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python -m pip install --upgrade pip
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python -m pip install -e INCHI-1-TEST
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- uses: ./.github/actions/compile_inchi_exe
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- name: Run executable tests
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run: pytest INCHI-1-TEST/tests/test_executable
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- uses: ./.github/actions/compile_inchi_lib
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- uses: ./.github/actions/regression_tests
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with:

‎INCHI-1-TEST/Dockerfile‎

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

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apt update && apt install -y python3-pip cmake
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python3 -m pip install --upgrade --break-system-packages pip
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python3 -m pip install --break-system-packages -e .[invariance-tests,development]
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python3 -m pip install --break-system-packages -e .[invariance-tests]
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# Make `python3` available as `python`.
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update-alternatives --install /usr/bin/python python /usr/bin/python3 10

‎INCHI-1-TEST/pyproject.toml‎

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name = "inchi_tests"
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version = "1.0.0"
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requires-python = ">=3.11"
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dependencies = ["pydantic == 2.7.1"]
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dependencies = ["pydantic == 2.7.1", "pytest == 8.3.3"]
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[project.optional-dependencies]
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# FIXME: We're forcing numpy major version for now until https://github.com/kuelumbus/rdkit-pypi/issues/102 is resolved.
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invariance-tests = ["rdkit == 2023.9.6", "numpy < 2.0.0"]
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development = ["pytest"]
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[project.scripts]
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run-tests = "inchi_tests.run_tests:main"

‎INCHI-1-TEST/tests/test_executable/README.md‎

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# Executable tests
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Test specific behaviors of the executable.
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Ensure that specific input (molfile and arguments) elicits specific output (e.g., error).
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Where possible, stick to the following principles:
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- Define input inline rather than using external files (having entire test scenario on screen is nice).
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- Keep number of tests per file to a minimum.
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- When replicating a bug, reference the (GitHub) issue number in the file name (e.g., `test_github_42.py`).
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Have a look at the existing tests for examples on how to write a test.
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Run with `pytest INCHI-1-TEST/tests/test_executable`.
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Note that by default, the tests expect the InChI executable to live at `INCHI-1-TEST/exes/inchi-1`.
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You can specify another InChI executable like so:
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```shell
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pytest INCHI-1-TEST/tests/test_executable --exe-path=path/to/executable
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```

‎INCHI-1-TEST/tests/test_executable/conftest.py‎

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import pytest
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import subprocess
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from typing import Callable
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from pathlib import Path
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def pytest_addoption(parser):
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parser.addoption(
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"--exe-path",
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action="store",
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default="INCHI-1-TEST/exes/inchi-1",
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help="Absolute path to the InChI executable.",
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)
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@pytest.fixture
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def run_inchi_exe(request) -> Callable:
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def _run_inchi_exe(
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molfile_path: str, args: str = ""
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) -> subprocess.CompletedProcess:
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exe_path: str = request.config.getoption("--exe-path")
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if not Path(exe_path).exists():
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raise FileNotFoundError(f"InChI executable not found at {exe_path}.")
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return subprocess.run(
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[exe_path, molfile_path, args],
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capture_output=True,
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)
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return _run_inchi_exe

‎INCHI-1-TEST/tests/test_executable/helpers.py‎

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from typing import Callable
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from pathlib import Path
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def tmp_molfile(molfile: Callable) -> Callable:
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"""
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Creates a temporary molfile and returns its path.
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`molfile` must return a string.
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"""
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def get_molfile_path(tmp_path: Path) -> str:
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molfile_path = tmp_path.joinpath("tmp.mol")
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molfile_path.write_text(molfile())
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return str(molfile_path)
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return get_molfile_path

‎INCHI-1-TEST/tests/test_executable/test_github_40.py‎

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import pytest
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from helpers import tmp_molfile
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@pytest.fixture
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@tmp_molfile
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def molfile():
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return """(R)-SDP
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ChemDraw08122419562D
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43 50 0 0 1 0 0 0 0 0999 V2000
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-0.7846 -1.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4991 -1.4924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.2136 -1.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.2136 -0.2549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4991 0.1576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7813 0.9328 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
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-1.2510 1.5648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.5331 2.3400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.0028 2.9720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1904 2.8288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0918 2.0535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4385 1.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.5937 1.0761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.1240 0.4441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.9365 0.5873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-4.2187 1.3626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.6884 1.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.8759 1.8513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.7846 -0.2549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4849 0.6674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 1.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7846 1.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7846 0.2549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.4991 -0.1576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7813 -0.9328 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
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2.5937 -1.0761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.8759 -1.8513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.6884 -1.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.2187 -1.3626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.9365 -0.5873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.1240 -0.4441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.2510 -1.5648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.4385 -1.4215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0918 -2.0535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.1904 -2.8288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.0028 -2.9720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.5331 -2.3400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.2136 0.2549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.2136 1.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.4991 1.4924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.4849 -0.6674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 -1.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0
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2 3 1 0 0
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3 4 2 0 0
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4 5 1 0 0
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5 6 1 0 0
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6 7 1 0 0
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7 8 2 0 0
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8 9 1 0 0
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9 10 2 0 0
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10 11 1 0 0
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11 12 2 0 0
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7 12 1 0 0
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6 13 1 0 0
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13 14 2 0 0
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14 15 1 0 0
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15 16 2 0 0
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16 17 1 0 0
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17 18 2 0 0
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13 18 1 0 0
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5 19 2 0 0
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1 19 1 0 0
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20 19 1 1 0
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20 21 1 0 0
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21 22 1 0 0
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22 23 1 0 0
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23 24 2 0 0
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20 24 1 0 0
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24 25 1 0 0
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25 26 1 0 0
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26 27 1 0 0
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27 28 2 0 0
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28 29 1 0 0
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29 30 2 0 0
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30 31 1 0 0
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31 32 2 0 0
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27 32 1 0 0
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26 33 1 0 0
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33 34 2 0 0
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34 35 1 0 0
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35 36 2 0 0
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36 37 1 0 0
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37 38 2 0 0
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33 38 1 0 0
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25 39 2 0 0
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39 40 1 0 0
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40 41 2 0 0
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23 41 1 0 0
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20 42 1 6 0
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42 43 1 0 0
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1 43 1 0 0
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M END
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"""
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@pytest.mark.xfail(strict=True, raises=AssertionError)
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def test_spiro_compound_chiral(molfile, run_inchi_exe):
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result = run_inchi_exe(molfile)
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assert "Warning (Not chiral) structure #1." not in result.stderr.decode()

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