Move data to tests/test_library

.dockerignore

@@ -1,6 +1,5 @@
 INCHI-1-TEST/tests/test_library/config/
-INCHI-1-TEST/data/
-INCHI-1-TEST/docs/
+INCHI-1-TEST/tests/test_library/data/
 INCHI-1-TEST/libs/
 INCHI-1-TEST/exes/
 **/__pycache__/

.github/actions/invariance_tests/action.yml

@@ -34,5 +34,5 @@ runs:
       with:
         name: ${{ inputs.artifact-name }}
         path: |
-          ./INCHI-1-TEST/data/ci/*_invariance_ci.log
-          ./INCHI-1-TEST/data/ci/*_invariance_ci_*.html
+          ./INCHI-1-TEST/tests/test_library/data/ci/*_invariance_ci.log
+          ./INCHI-1-TEST/tests/test_library/data/ci/*_invariance_ci_*.html

.github/actions/regression_tests/action.yml

@@ -34,5 +34,5 @@ runs:
       with:
         name: ${{ inputs.artifact-name }}
         path: |
-          ./INCHI-1-TEST/data/ci/*_regression_ci.log
-          ./INCHI-1-TEST/data/ci/*_regression_ci_*.html
+          ./INCHI-1-TEST/tests/test_library/data/ci/*_regression_ci.log
+          ./INCHI-1-TEST/tests/test_library/data/ci/*_regression_ci_*.html

.gitignore

@@ -1,11 +1,8 @@
-INCHI-1-TEST/**/*.so*
 INCHI-1-TEST/exes
-INCHI-1-TEST/data/**/*.html
-INCHI-1-TEST/data/**/*.log
-INCHI-1-TEST/data/pubchem/compound
-INCHI-1-TEST/data/pubchem/compound3d
-INCHI-1-TEST/data/pubchem/substance
-INCHI-1-TEST/legacy.bak/
+INCHI-1-TEST/libs
+INCHI-1-TEST/tests/test_library/data/**/*.html
+INCHI-1-TEST/tests/test_library/data/**/*.log
+INCHI-1-TEST/tests/test_library/data/pubchem/**
 .listing
 *.o
 __pycache__
@@ -14,4 +11,3 @@ __pycache__
 *.egg-info/
 # Ignore core dump files
 core.*[0-9]
-gcc_crash_report.txt

INCHI-1-TEST/docker-compose.yml

@@ -7,7 +7,7 @@ services:
       # `source` paths are relative to the `docker-compose.yml` file, not the build context.
       # `target` paths are absolute paths in the container. The `/inchi/INCHI-1-TEST` directory already exists in the container.
       - type: bind
-        source: data
+        source: tests/test_library/data
         target: /inchi/INCHI-1-TEST/data
       - type: bind
         source: tests/test_library/config

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

@@ -32,19 +32,19 @@ The test pipeline expects the library under `INCHI-1-TEST/libs`, see `INCHI-1-TE
 In this README, `<dataset>` refers to either `ci`
 (i.e, continuous integration, aka the tests running on GitHub), or a `<subset>` of PubChem.
 `<subset>` can be either `compound`, `compound3d`, or `substance`.
-The `ci` data already lives in the repository (i.e., `mcule.sdf.gz` and `inchi.sdf.gz` under `INCHI-1-TEST/data/ci`).
+The `ci` data already lives in the repository (i.e., `mcule.sdf.gz` and `inchi.sdf.gz` under `INCHI-1-TEST/tests/test_library/data/ci`).
 The PubChem `<subset>` data doesn't live in the repository since it's too large.
 You can download the `<subset>` data from <https://ftp.ncbi.nlm.nih.gov/pubchem/> by running
 
 ```Shell
-python -m INCHI-1-TEST.data.pubchem.download <subset>
+python -m INCHI-1-TEST.tests.test_library.data.pubchem.download <subset>
 ```
 
-On completion of the download you'll find the data in `INCHI-1-TEST/data/pubchem/<subset>`.
+On completion of the download you'll find the data in `INCHI-1-TEST/tests/test_library/data/pubchem/<subset>`.
 Validate the integrity of `<subset>` (i.e., make sure the downloads aren't corrupted) by running
 
 ```Shell
-python -m INCHI-1-TEST.data.pubchem.validate <subset>
+python -m INCHI-1-TEST.tests.test_library.data.pubchem.validate <subset>
 ```
 
 Note that validation isn't available for `compound3d` (PubChem doesn't provide file hashes).
@@ -84,7 +84,7 @@ run-tests --test-config=INCHI-1-TEST/tests/test_library/config/config.regression
 ```
 
 uses `libinchi.so.<version>`, the shared library specified with `--test-config`,
-and generates an `<SDF>.regression_reference.sqlite` file for each SDF under `INCHI-1-TEST/data/<dataset>`.
+and generates an `<SDF>.regression_reference.sqlite` file for each SDF under `INCHI-1-TEST/tests/test_library/data/<dataset>`.
 The `sqlite` file contains a table with the results for each molfile.
 
 ### Run tests against the references
@@ -94,7 +94,7 @@ run-tests --test-config=INCHI-1-TEST/tests/test_library/config/config.regression
 ```
 
 uses `libinchi.so.main`, a shared library compiled from the `main` branch,
-to compute the results (e.g., InChI strings and keys) for each molfile in each SDF under `INCHI-1-TEST/data/<dataset>`.
+to compute the results (e.g., InChI strings and keys) for each molfile in each SDF under `INCHI-1-TEST/tests/test_library/data/<dataset>`.
 Those results are compared with the corresponding reference.
 Failed comparisons are logged to `<datetime>.regression_<dataset>.log` (where `<datetime>` reflects the start of the test run).
 
@@ -111,7 +111,7 @@ parse-log --test-config=INCHI-1-TEST/tests/test_library/config/config.<test>.py
 ```
 
 where `<test>` can be `regression` or `invariance`.
-The command generates an HTML report for each SDF under `INCHI-1-TEST/data/<dataset>` that contains structures which failed the test.
+The command generates an HTML report for each SDF under `INCHI-1-TEST/tests/test_library/data/<dataset>` that contains structures which failed the test.
 You can view the HTML report in your browser.
 
 ## Inspect `.sqlite` files
@@ -130,16 +130,16 @@ via [volumes](https://docs.docker.com/compose/compose-file/05-services/#volumes)
 ```yml
 volumes:
   - type: bind
-    source: data
+    source: tests/test_library/data
     target: /inchi/INCHI-1-TEST/data
   - type: bind
-    source: config
+    source: tests/test_library/config
     target: /inchi/INCHI-1-TEST/config
 ```
 
 Note that the `source` paths are relative to the location of the `docker-compose.yml` file.
-We're mapping the `data` directory on the host machine to the `/inchi/INCHI-1-TEST/data` directory inside the container.
-Similarly we're mapping `config`, a directory containing our [configuration files](#configuration-files), into `/inchi/INCHI-1-TEST/config`.
+We're mapping the `tests/test_library/data` directory on the host machine to the `/inchi/INCHI-1-TEST/data` directory inside the container.
+Similarly we're mapping `tests/test_library/config`, a directory containing our [configuration files](#configuration-files), into `/inchi/INCHI-1-TEST/config`.
 
 To customize the tests, start by adding your own `docker-compose.custom.yml` file:
 

INCHI-1-TEST/tests/test_library/config/config.ci.py

@@ -18,7 +18,7 @@ def get_molfile_id_ci(molfile: str) -> str:
     return molfile_id
 
 
-BASEPATH = "INCHI-1-TEST/data/ci/"
+BASEPATH = "INCHI-1-TEST/tests/test_library/data/ci/"
 
 config = DataConfig(
     name="ci",

INCHI-1-TEST/tests/test_library/config/config.pubchem_compound.py

@@ -2,11 +2,11 @@
 from inchi_tests.config_models import DataConfig
 from inchi_tests.utils import get_molfile_id_pubchem
 
-BASEPATH = "INCHI-1-TEST"
+BASEPATH = "INCHI-1-TEST/tests/test_library/data/pubchem/compound"
 
 config = DataConfig(
     name="pubchem-compound",
-    path=Path(BASEPATH).joinpath("data/pubchem/compound"),
-    sdf_paths=sorted(Path(BASEPATH).joinpath("data/pubchem/compound").glob("*.sdf.gz")),
+    path=Path(BASEPATH),
+    sdf_paths=sorted(Path(BASEPATH).glob("*.sdf.gz")),
     molfile_id_getter=get_molfile_id_pubchem,
 )

INCHI-1-TEST/tests/test_library/config/config.pubchem_compound3d.py

@@ -2,13 +2,11 @@
 from inchi_tests.config_models import DataConfig
 from inchi_tests.utils import get_molfile_id_pubchem
 
-BASEPATH = "INCHI-1-TEST"
+BASEPATH = "INCHI-1-TEST/tests/test_library/data/pubchem/compound3d"
 
 config = DataConfig(
     name="pubchem-compound3d",
-    path=Path(BASEPATH).joinpath("data/pubchem/compound3d"),
-    sdf_paths=sorted(
-        Path(BASEPATH).joinpath("data/pubchem/compound3d").glob("*.sdf.gz")
-    ),
+    path=Path(BASEPATH),
+    sdf_paths=sorted(Path(BASEPATH).glob("*.sdf.gz")),
     molfile_id_getter=get_molfile_id_pubchem,
 )

INCHI-1-TEST/tests/test_library/config/config.pubchem_substance.py

@@ -2,13 +2,11 @@
 from inchi_tests.config_models import DataConfig
 from inchi_tests.utils import get_molfile_id_pubchem
 
-BASEPATH = "INCHI-1-TEST"
+BASEPATH = "INCHI-1-TEST/tests/test_library/data/pubchem/substance"
 
 config = DataConfig(
     name="pubchem-substance",
-    path=Path(BASEPATH).joinpath("data/pubchem/substance"),
-    sdf_paths=sorted(
-        Path(BASEPATH).joinpath("data/pubchem/substance").glob("*.sdf.gz")
-    ),
+    path=Path(BASEPATH),
+    sdf_paths=sorted(Path(BASEPATH).glob("*.sdf.gz")),
     molfile_id_getter=get_molfile_id_pubchem,
 )