Merge pull request #163 from naik-aakash/debug_test

Fix tests

.github/workflows/python-package.yml

@@ -31,7 +31,7 @@ jobs:
           python -m pip install --upgrade pip && \
           python -m uv pip install .[strict,tests] && \
           python -m uv pip install ase==3.23.0 && \
-          pytest --cov=autoplex --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} -vv --durations-path /workspace/tests/test_data/.pytest-split-durations
+          OMP_NUM_THREADS=1 pytest --cache-clear --cov=autoplex --cov-report term-missing --cov-append --splits 5 --group ${{ matrix.split }} -vv --durations-path /workspace/tests/test_data/.pytest-split-durations
         "
     - name: Upload coverage
       uses: actions/upload-artifact@v3

pyproject.toml

@@ -77,7 +77,7 @@ strict = [
      "torchdata==0.7.1",
 ]
 dev = ["pre-commit>=2.12.1"]
-tests = ["pytest", "pytest-mock", "pytest-split", "pytest-cov", "types-setuptools"]
+tests = ["pytest", "pytest-mock", "pytest-split==0.9.0", "pytest-cov", "types-setuptools"]
 
 [tool.versioningit.vcs]
 method = "git"

tests/auto/test_auto_flows.py

@@ -1,14 +1,9 @@
 from __future__ import annotations
-import os
 import pytest
 from monty.serialization import loadfn
 from atomate2.common.schemas.phonons import PhononBSDOSDoc
 from pymatgen.core.structure import Structure
 from autoplex.auto.phonons.flows import CompleteDFTvsMLBenchmarkWorkflow
-from jobflow.core.job import Response
-
-os.environ["OMP_NUM_THREADS"] = "4"  # export OMP_NUM_THREADS=4
-os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=1
 
 
 @pytest.fixture(scope="class")

tests/auto/test_auto_jobs.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 from jobflow import Flow
 from pymatgen.core.structure import Structure
 from autoplex.auto.phonons.jobs import (
@@ -18,8 +17,6 @@
 import pytest
 from pytest import approx
 
-os.environ["OMP_NUM_THREADS"] = "4"  # export OMP_NUM_THREADS=4
-os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=1
 
 
 @pytest.fixture(scope="class")

tests/data/test_datagen_flows.py

@@ -14,9 +14,6 @@
 from autoplex.data.common.flows import GenerateTrainingDataForTesting
 from autoplex.data.phonons.flows import IsoAtomMaker, RandomStructuresDataGenerator, MLPhononMaker
 
-os.environ["OMP_NUM_THREADS"] = "4"  # export OMP_NUM_THREADS=4
-os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=1
-
 
 def test_ml_phonon_maker(test_dir, clean_dir, memory_jobstore):
     from jobflow import run_locally

tests/data/test_datagen_utils.py

@@ -11,10 +11,7 @@
     filter_outlier_energy,
     filter_outlier_forces,
 )
-from autoplex.data.phonons.utils import update_phonon_displacement_maker
 
-os.environ["OMP_NUM_THREADS"] = "4"  # export OMP_NUM_THREADS=4
-os.environ["OPENBLAS_NUM_THREADS"] = "1"  # export OPENBLAS_NUM_THREADS=1
 
 fig, ax_list = plt.subplots(nrows=1, ncols=1)
 fig.set_size_inches(15, 20)

tests/fitting/test_fitting_flows.py

@@ -73,15 +73,9 @@ def fit_input_dict(vasp_test_dir):
 
 
 def test_mlip_fit_maker(test_dir, clean_dir, memory_jobstore, vasp_test_dir, fit_input_dict):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
-
     # Test to check if gap fit runs with default hyperparameter sets (i.e. two_body and soap is True)
     gapfit = MLIPFitMaker().make(
         species_list=["Li", "Cl"],
@@ -93,28 +87,16 @@ def test_mlip_fit_maker(test_dir, clean_dir, memory_jobstore, vasp_test_dir, fit
         gapfit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    test_files_dir = Path(test_dir / "fitting").resolve()
-    path_to_job_files = list(test_files_dir.glob("job*"))
     # check if gap fit file is generated
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
-
 
 def test_mlip_fit_maker_with_kwargs(
         test_dir, clean_dir, memory_jobstore, vasp_test_dir, fit_input_dict
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
 
     # Test to check if gap fit runs with default hyperparameter sets (i.e. include_two_body and include_soap is True)
     gapfit = MLIPFitMaker().make(
@@ -135,30 +117,16 @@ def test_mlip_fit_maker_with_kwargs(
         gapfit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    test_files_dir = Path(test_dir / "fitting").resolve()
-    path_to_job_files = list(test_files_dir.glob("job*"))
-
     # check if gap fit file is generated
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
-
 
 def test_mlip_fit_maker_with_pre_database_dir(
         test_dir, memory_jobstore, vasp_test_dir, fit_input_dict, clean_dir
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
-
     test_files_dir = Path(test_dir / "fitting").resolve()
 
     # Test if gap fit runs with pre_database_dir
@@ -172,28 +140,16 @@ def test_mlip_fit_maker_with_pre_database_dir(
 
     run_locally(gapfit, ensure_success=True, create_folders=True, store=memory_jobstore)
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
-
     # check if gap potential file is generated
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
-
 
 def test_mlip_fit_maker_jace(
         test_dir, memory_jobstore, vasp_test_dir, fit_input_dict, clean_dir
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
 
     test_files_dir = Path(test_dir / "fitting").resolve()
 
@@ -217,29 +173,18 @@ def test_mlip_fit_maker_jace(
         jacefit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
-
     # check if julia-ACE potential file is generated
     assert Path(jacefit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
 
 
 def test_mlip_fit_maker_nequip(
         test_dir, memory_jobstore, vasp_test_dir, fit_input_dict, clean_dir
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
-
+
     test_files_dir = Path(test_dir / "fitting").resolve()
 
     # Test NEQUIP fit runs with pre_database_dir
@@ -261,28 +206,18 @@ def test_mlip_fit_maker_nequip(
         nequipfit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
 
     # check if NEQUIP potential file is generated
     assert Path(nequipfit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
 
 
 def test_mlip_fit_maker_m3gnet(
         test_dir, memory_jobstore, vasp_test_dir, fit_input_dict, clean_dir
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
 
     test_files_dir = Path(test_dir / "fitting").resolve()
 
@@ -313,28 +248,16 @@ def test_mlip_fit_maker_m3gnet(
         m3gnetfit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
-
     # check if M3GNET potential file is generated
     assert Path(m3gnetfit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
-
 
 def test_mlip_fit_maker_mace(
         test_dir, memory_jobstore, vasp_test_dir, fit_input_dict, clean_dir
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
 
     test_files_dir = Path(test_dir / "fitting").resolve()
 
@@ -365,15 +288,10 @@ def test_mlip_fit_maker_mace(
         macefit, ensure_success=True, create_folders=True, store=memory_jobstore
     )
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
 
     # check if MACE potential file is generated
     assert Path(macefit.output["mlip_path"].resolve(memory_jobstore)).exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)
 
 
 def test_mlip_fit_maker_glue_xml(
@@ -385,7 +303,6 @@ def test_mlip_fit_maker_glue_xml(
     from jobflow import run_locally
 
     parent_dir = os.getcwd()
-
     os.chdir(test_dir / "fitting")
 
     fit_input_dict = {
@@ -470,17 +387,13 @@ def test_mlip_fit_maker_glue_xml(
     os.chdir(parent_dir)
 
 
+
 def test_mlip_fit_maker_with_automated_separated_dataset(
         test_dir, memory_jobstore, vasp_test_dir, clean_dir, fit_input_dict
 ):
-    import os
-    import shutil
     from pathlib import Path
     from jobflow import run_locally
 
-    parent_dir = os.getcwd()
-
-    os.chdir(test_dir / "fitting")
 
     test_files_dir = Path(test_dir / "fitting").resolve()
 
@@ -497,14 +410,9 @@ def test_mlip_fit_maker_with_automated_separated_dataset(
 
     run_locally(gapfit, ensure_success=True, create_folders=True, store=memory_jobstore)
 
-    path_to_job_files = list(test_files_dir.glob("job*"))
 
     # check if gap potential file is generated
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore)).exists()
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore) + "/train_phonon.extxyz").exists()
     assert Path(gapfit.output["mlip_path"].resolve(memory_jobstore) + "/train_rand_struc.extxyz").exists()
 
-    for job_dir in path_to_job_files:
-        shutil.rmtree(job_dir)
-
-    os.chdir(parent_dir)