Compile reference library

.github/workflows/ci.yml

@@ -10,13 +10,13 @@ on:
 jobs:
   test_glibc_gcc:
     runs-on: ubuntu-latest
-    container: gcc:latest
+    container: gcc:12
 
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
       - uses: ./.github/actions/regression_tests
         with:
           artifact-name: regression-test-results_glibc_gcc

INCHI-1-TEST/Dockerfile

@@ -1,6 +1,12 @@
-FROM python:3.12
-
-# Python image includes the dependencies we need for building InChI (gcc, make, etc.)
+FROM python:3.12-bookworm
+# Python image includes the dependencies we need for building InChI (gcc, make, etc.).
 
 RUN pip install --upgrade pip && \
     pip install git+https://github.com/TUCAN-nest/SDF-pipeline.git
+
+# On Debian bookworm (12) only GCC versions 11 and 12 are available.
+# For GCC versions 9 and 10, use Debian bullseye (11).
+ARG GCC_VERSION=12
+RUN apt-get update && apt-get install gcc-$GCC_VERSION -y
+RUN update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-$GCC_VERSION 42
+RUN update-alternatives --set gcc /usr/bin/gcc-$GCC_VERSION

INCHI-1-TEST/compile_reference_inchi_lib.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+reference_version="v1.06"
+
+if ! git diff-index --quiet HEAD --; then
+    echo "There are uncommitted changes on the current branch."
+    echo "Please commit or stash them before checking out the reference tag."
+    exit 1
+fi
+git checkout tags/$reference_version
+
+(cd INCHI-1-SRC/INCHI_API/libinchi/gcc &&
+make -j LIB_DIR=../../../../INCHI-1-TEST VERSION=.$reference_version)
+
+# Switch back to the branch that was checked out prior to checking out the tag.
+git switch -

INCHI-1-TEST/compute_regression_reference.py

@@ -19,9 +19,7 @@
 if __name__ == "__main__":
     dataset = get_dataset_arg()
 
-    subprocess.run(
-        f"{TEST_PATH}/download_inchi_regression_reference_lib.sh", check=True
-    )
+    subprocess.run(f"{TEST_PATH}/compile_reference_inchi_lib.sh", check=True)
 
     exit_code = 0
     sdf_paths = DATASETS[dataset]["sdf_paths"]

INCHI-1-TEST/config.py

@@ -59,7 +59,7 @@ def get_progress(current: int, total: int) -> str:
 INCHI_API_PARAMETERS: Final[str] = ""
 TEST_PATH: Final[Path] = Path(__file__).parent.absolute()
 INCHI_LIB_PATH: Final[Path] = TEST_PATH.joinpath("libinchi.so.dev")
-INCHI_REFERENCE_LIB_PATH: Final[Path] = TEST_PATH.joinpath("libinchi.so.1.06.00")
+INCHI_REFERENCE_LIB_PATH: Final[Path] = TEST_PATH.joinpath("libinchi.so.v1.06")
 N_PROCESSES: Final[int] = len(
     os.sched_getaffinity(0)
 )  # https://docs.python.org/3/library/multiprocessing.html#multiprocessing.cpu_count

INCHI-1-TEST/docs/README.md

@@ -53,7 +53,7 @@ Note that validation isn't available for `pubchem_compound3d`.
 ```Shell
 python -m INCHI-1-TEST.compute_regression_reference <dataset>
 ```
-downloads `libinchi.so.1.06.00`, the shared library belonging to the current stable InChI release,
+compiles `libinchi.so.v1.06`, the shared library belonging to the current stable InChI release,
 and generates an `<SDF>.regression_reference.sqlite` file for each SDF under `INCHI-1-TEST/data/<dataset>`.
 The `sqlite` file contains a table with the results for each molfile.