diff --git a/.github/workflows/check_for_api_break.yaml b/.github/workflows/check_for_api_break.yaml index e3d74f141..661ea52dd 100644 --- a/.github/workflows/check_for_api_break.yaml +++ b/.github/workflows/check_for_api_break.yaml @@ -27,8 +27,8 @@ jobs: id: check run: | pip install griffe - griffe check "openfe" --verbose -a origin/main - griffe check "openfecli" --verbose -a origin/main + griffe check "src/openfe" --verbose -a origin/main + griffe check "src/openfecli" --verbose -a origin/main - name: Manage PR Comments uses: actions/github-script@v7 diff --git a/.github/workflows/cpu-long-tests.yaml b/.github/workflows/cpu-long-tests.yaml index 346e3a934..8cc1e480f 100644 --- a/.github/workflows/cpu-long-tests.yaml +++ b/.github/workflows/cpu-long-tests.yaml @@ -92,7 +92,7 @@ jobs: DUECREDIT_ENABLE: 'yes' OFE_INTEGRATION_TESTS: FALSE run: | - pytest -n logical -vv --durations=10 --runslow openfecli/tests/ openfe/tests/ + pytest -n logical -vv --durations=10 --runslow src/openfecli/tests/ src/openfe/tests/ stop-aws-runner: runs-on: ubuntu-latest diff --git a/.github/workflows/gpu-integration-tests.yaml b/.github/workflows/gpu-integration-tests.yaml index 22db41163..535e526fa 100644 --- a/.github/workflows/gpu-integration-tests.yaml +++ b/.github/workflows/gpu-integration-tests.yaml @@ -96,7 +96,7 @@ jobs: OFE_INTEGRATION_TESTS: TRUE run: | # The -m flag will only run tests with @pytest.mark.integration - pytest -n logical -vv --durations=10 -m integration openfecli/tests/ openfe/tests/ + pytest -n logical -vv --durations=10 -m integration src/openfecli/tests/ src/openfe/tests/ stop-aws-runner: runs-on: ubuntu-latest diff --git a/MANIFEST.in b/MANIFEST.in index 6e18d4c72..d2479fcec 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,18 +1,18 @@ -recursive-include openfe/tests/data/ *.sdf -recursive-include openfe/tests/data/ *.bz2 -recursive-include openfe/tests/data/ *.csv -recursive-include openfe/tests/data/ *.pdb -recursive-include openfe/tests/data/ *.mol2 -recursive-include openfe/tests/data/ *.xml -recursive-include openfe/tests/data/ *.graphml -recursive-include openfe/tests/data/ *.edge -recursive-include openfe/tests/data/ *.dat -recursive-include openfe/tests/data/ *.txt -recursive-include openfe/tests/data/ *.gz -recursive-include openfe/tests/data/ *json_results.gz -include openfecli/tests/data/*.json -include openfecli/tests/data/*.tar.gz -include openfecli/tests/commands/test_gather/*.tsv -recursive-include openfecli/tests/ *.sdf -recursive-include openfecli/tests/ *.pdb -include openfe/tests/data/openmm_rfe/vacuum_nocoord.nc +recursive-include src/openfe/tests/data/ *.sdf +recursive-include src/openfe/tests/data/ *.bz2 +recursive-include src/openfe/tests/data/ *.csv +recursive-include src/openfe/tests/data/ *.pdb +recursive-include src/openfe/tests/data/ *.mol2 +recursive-include src/openfe/tests/data/ *.xml +recursive-include src/openfe/tests/data/ *.graphml +recursive-include src/openfe/tests/data/ *.edge +recursive-include src/openfe/tests/data/ *.dat +recursive-include src/openfe/tests/data/ *.txt +recursive-include src/openfe/tests/data/ *.gz +recursive-include src/openfe/tests/data/ *json_results.gz +include src/openfecli/tests/data/*.json +include src/openfecli/tests/data/*.tar.gz +include src/openfecli/tests/commands/test_gather/*.tsv +recursive-include src/openfecli/tests/ *.sdf +recursive-include src/openfecli/tests/ *.pdb +include src/openfe/tests/data/openmm_rfe/vacuum_nocoord.nc diff --git a/pyproject.toml b/pyproject.toml index 784d16912..8f995c09e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,11 +38,12 @@ scripts.openfe = "openfecli.cli:main" zip-safe = false include-package-data = true -[tool.setuptools.packages] -find = { namespaces = false } +[tool.setuptools.packages.find] +where = [ "src" ] +namespaces = false [tool.setuptools.package-data] -openfe = [ '"./openfe/tests/data/lomap_basic/toluene.mol2"' ] +openfe = [ '"./src/openfe/tests/data/lomap_basic/toluene.mol2"' ] [tool.setuptools_scm] fallback_version = "0.0.0" @@ -71,9 +72,9 @@ lint.isort.known-first-party = [ "openfe" ] [tool.coverage.run] omit = [ - "openfe/due.py", - "*/tests/dev/*py", - "*/tests/protocols/test_openmm_rfe_slow.py", + "src/openfe/due.py", + "src/*/tests/dev/*py", + "src/*/tests/protocols/test_openmm_rfe_slow.py", ] [tool.coverage.report] @@ -86,6 +87,6 @@ exclude_lines = [ ] [tool.mypy] -files = "openfe" +files = "src/openfe" # TODO: add src/openfecli ignore_missing_imports = true warn_unused_ignores = true diff --git a/openfe/__init__.py b/src/openfe/__init__.py similarity index 100% rename from openfe/__init__.py rename to src/openfe/__init__.py diff --git a/openfe/analysis/__init__.py b/src/openfe/analysis/__init__.py similarity index 100% rename from openfe/analysis/__init__.py rename to src/openfe/analysis/__init__.py diff --git a/openfe/analysis/plotting.py b/src/openfe/analysis/plotting.py similarity index 100% rename from openfe/analysis/plotting.py rename to src/openfe/analysis/plotting.py diff --git a/openfe/due.py b/src/openfe/due.py similarity index 100% rename from openfe/due.py rename to src/openfe/due.py diff --git a/openfe/orchestration/__init__.py b/src/openfe/orchestration/__init__.py similarity index 100% rename from openfe/orchestration/__init__.py rename to src/openfe/orchestration/__init__.py diff --git a/openfe/protocols/__init__.py b/src/openfe/protocols/__init__.py similarity index 100% rename from openfe/protocols/__init__.py rename to src/openfe/protocols/__init__.py diff --git a/openfe/protocols/openmm_afe/__init__.py b/src/openfe/protocols/openmm_afe/__init__.py similarity index 100% rename from openfe/protocols/openmm_afe/__init__.py rename to src/openfe/protocols/openmm_afe/__init__.py diff --git a/openfe/protocols/openmm_afe/base.py b/src/openfe/protocols/openmm_afe/base.py similarity index 100% rename from openfe/protocols/openmm_afe/base.py rename to src/openfe/protocols/openmm_afe/base.py diff --git a/openfe/protocols/openmm_afe/equil_afe_settings.py b/src/openfe/protocols/openmm_afe/equil_afe_settings.py similarity index 100% rename from openfe/protocols/openmm_afe/equil_afe_settings.py rename to src/openfe/protocols/openmm_afe/equil_afe_settings.py diff --git a/openfe/protocols/openmm_afe/equil_binding_afe_method.py b/src/openfe/protocols/openmm_afe/equil_binding_afe_method.py similarity index 100% rename from openfe/protocols/openmm_afe/equil_binding_afe_method.py rename to src/openfe/protocols/openmm_afe/equil_binding_afe_method.py diff --git a/openfe/protocols/openmm_afe/equil_solvation_afe_method.py b/src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py similarity index 100% rename from openfe/protocols/openmm_afe/equil_solvation_afe_method.py rename to src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py diff --git a/openfe/protocols/openmm_md/__init__.py b/src/openfe/protocols/openmm_md/__init__.py similarity index 100% rename from openfe/protocols/openmm_md/__init__.py rename to src/openfe/protocols/openmm_md/__init__.py diff --git a/openfe/protocols/openmm_md/plain_md_methods.py b/src/openfe/protocols/openmm_md/plain_md_methods.py similarity index 100% rename from openfe/protocols/openmm_md/plain_md_methods.py rename to src/openfe/protocols/openmm_md/plain_md_methods.py diff --git a/openfe/protocols/openmm_md/plain_md_settings.py b/src/openfe/protocols/openmm_md/plain_md_settings.py similarity index 100% rename from openfe/protocols/openmm_md/plain_md_settings.py rename to src/openfe/protocols/openmm_md/plain_md_settings.py diff --git a/openfe/protocols/openmm_rfe/__init__.py b/src/openfe/protocols/openmm_rfe/__init__.py similarity index 100% rename from openfe/protocols/openmm_rfe/__init__.py rename to src/openfe/protocols/openmm_rfe/__init__.py diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/__init__.py b/src/openfe/protocols/openmm_rfe/_rfe_utils/__init__.py similarity index 100% rename from openfe/protocols/openmm_rfe/_rfe_utils/__init__.py rename to src/openfe/protocols/openmm_rfe/_rfe_utils/__init__.py diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py b/src/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py similarity index 100% rename from openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py rename to src/openfe/protocols/openmm_rfe/_rfe_utils/lambdaprotocol.py diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py b/src/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py similarity index 100% rename from openfe/protocols/openmm_rfe/_rfe_utils/multistate.py rename to src/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/relative.py b/src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py similarity index 100% rename from openfe/protocols/openmm_rfe/_rfe_utils/relative.py rename to src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py diff --git a/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py b/src/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py similarity index 100% rename from openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py rename to src/openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py diff --git a/openfe/protocols/openmm_rfe/equil_rfe_methods.py b/src/openfe/protocols/openmm_rfe/equil_rfe_methods.py similarity index 100% rename from openfe/protocols/openmm_rfe/equil_rfe_methods.py rename to src/openfe/protocols/openmm_rfe/equil_rfe_methods.py diff --git a/openfe/protocols/openmm_rfe/equil_rfe_settings.py b/src/openfe/protocols/openmm_rfe/equil_rfe_settings.py similarity index 100% rename from openfe/protocols/openmm_rfe/equil_rfe_settings.py rename to src/openfe/protocols/openmm_rfe/equil_rfe_settings.py diff --git a/openfe/protocols/openmm_septop/__init__.py b/src/openfe/protocols/openmm_septop/__init__.py similarity index 100% rename from openfe/protocols/openmm_septop/__init__.py rename to src/openfe/protocols/openmm_septop/__init__.py diff --git a/openfe/protocols/openmm_septop/base.py b/src/openfe/protocols/openmm_septop/base.py similarity index 100% rename from openfe/protocols/openmm_septop/base.py rename to src/openfe/protocols/openmm_septop/base.py diff --git a/openfe/protocols/openmm_septop/equil_septop_method.py b/src/openfe/protocols/openmm_septop/equil_septop_method.py similarity index 100% rename from openfe/protocols/openmm_septop/equil_septop_method.py rename to src/openfe/protocols/openmm_septop/equil_septop_method.py diff --git a/openfe/protocols/openmm_septop/equil_septop_settings.py b/src/openfe/protocols/openmm_septop/equil_septop_settings.py similarity index 100% rename from openfe/protocols/openmm_septop/equil_septop_settings.py rename to src/openfe/protocols/openmm_septop/equil_septop_settings.py diff --git a/openfe/protocols/openmm_septop/utils.py b/src/openfe/protocols/openmm_septop/utils.py similarity index 100% rename from openfe/protocols/openmm_septop/utils.py rename to src/openfe/protocols/openmm_septop/utils.py diff --git a/openfe/protocols/openmm_utils/__init__.py b/src/openfe/protocols/openmm_utils/__init__.py similarity index 100% rename from openfe/protocols/openmm_utils/__init__.py rename to src/openfe/protocols/openmm_utils/__init__.py diff --git a/openfe/protocols/openmm_utils/charge_generation.py b/src/openfe/protocols/openmm_utils/charge_generation.py similarity index 100% rename from openfe/protocols/openmm_utils/charge_generation.py rename to src/openfe/protocols/openmm_utils/charge_generation.py diff --git a/openfe/protocols/openmm_utils/multistate_analysis.py b/src/openfe/protocols/openmm_utils/multistate_analysis.py similarity index 100% rename from openfe/protocols/openmm_utils/multistate_analysis.py rename to src/openfe/protocols/openmm_utils/multistate_analysis.py diff --git a/openfe/protocols/openmm_utils/omm_compute.py b/src/openfe/protocols/openmm_utils/omm_compute.py similarity index 100% rename from openfe/protocols/openmm_utils/omm_compute.py rename to src/openfe/protocols/openmm_utils/omm_compute.py diff --git a/openfe/protocols/openmm_utils/omm_settings.py b/src/openfe/protocols/openmm_utils/omm_settings.py similarity index 100% rename from openfe/protocols/openmm_utils/omm_settings.py rename to src/openfe/protocols/openmm_utils/omm_settings.py diff --git a/openfe/protocols/openmm_utils/settings_validation.py b/src/openfe/protocols/openmm_utils/settings_validation.py similarity index 100% rename from openfe/protocols/openmm_utils/settings_validation.py rename to src/openfe/protocols/openmm_utils/settings_validation.py diff --git a/openfe/protocols/openmm_utils/system_creation.py b/src/openfe/protocols/openmm_utils/system_creation.py similarity index 100% rename from openfe/protocols/openmm_utils/system_creation.py rename to src/openfe/protocols/openmm_utils/system_creation.py diff --git a/openfe/protocols/openmm_utils/system_validation.py b/src/openfe/protocols/openmm_utils/system_validation.py similarity index 100% rename from openfe/protocols/openmm_utils/system_validation.py rename to src/openfe/protocols/openmm_utils/system_validation.py diff --git a/openfe/protocols/restraint_utils/__init__.py b/src/openfe/protocols/restraint_utils/__init__.py similarity index 100% rename from openfe/protocols/restraint_utils/__init__.py rename to src/openfe/protocols/restraint_utils/__init__.py diff --git a/openfe/protocols/restraint_utils/geometry/__init__.py b/src/openfe/protocols/restraint_utils/geometry/__init__.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/__init__.py rename to src/openfe/protocols/restraint_utils/geometry/__init__.py diff --git a/openfe/protocols/restraint_utils/geometry/base.py b/src/openfe/protocols/restraint_utils/geometry/base.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/base.py rename to src/openfe/protocols/restraint_utils/geometry/base.py diff --git a/openfe/protocols/restraint_utils/geometry/boresch/__init__.py b/src/openfe/protocols/restraint_utils/geometry/boresch/__init__.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/boresch/__init__.py rename to src/openfe/protocols/restraint_utils/geometry/boresch/__init__.py diff --git a/openfe/protocols/restraint_utils/geometry/boresch/geometry.py b/src/openfe/protocols/restraint_utils/geometry/boresch/geometry.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/boresch/geometry.py rename to src/openfe/protocols/restraint_utils/geometry/boresch/geometry.py diff --git a/openfe/protocols/restraint_utils/geometry/boresch/guest.py b/src/openfe/protocols/restraint_utils/geometry/boresch/guest.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/boresch/guest.py rename to src/openfe/protocols/restraint_utils/geometry/boresch/guest.py diff --git a/openfe/protocols/restraint_utils/geometry/boresch/host.py b/src/openfe/protocols/restraint_utils/geometry/boresch/host.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/boresch/host.py rename to src/openfe/protocols/restraint_utils/geometry/boresch/host.py diff --git a/openfe/protocols/restraint_utils/geometry/flatbottom.py b/src/openfe/protocols/restraint_utils/geometry/flatbottom.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/flatbottom.py rename to src/openfe/protocols/restraint_utils/geometry/flatbottom.py diff --git a/openfe/protocols/restraint_utils/geometry/harmonic.py b/src/openfe/protocols/restraint_utils/geometry/harmonic.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/harmonic.py rename to src/openfe/protocols/restraint_utils/geometry/harmonic.py diff --git a/openfe/protocols/restraint_utils/geometry/utils.py b/src/openfe/protocols/restraint_utils/geometry/utils.py similarity index 100% rename from openfe/protocols/restraint_utils/geometry/utils.py rename to src/openfe/protocols/restraint_utils/geometry/utils.py diff --git a/openfe/protocols/restraint_utils/openmm/__init__.py b/src/openfe/protocols/restraint_utils/openmm/__init__.py similarity index 100% rename from openfe/protocols/restraint_utils/openmm/__init__.py rename to src/openfe/protocols/restraint_utils/openmm/__init__.py diff --git a/openfe/protocols/restraint_utils/openmm/omm_forces.py b/src/openfe/protocols/restraint_utils/openmm/omm_forces.py similarity index 100% rename from openfe/protocols/restraint_utils/openmm/omm_forces.py rename to src/openfe/protocols/restraint_utils/openmm/omm_forces.py diff --git a/openfe/protocols/restraint_utils/openmm/omm_restraints.py b/src/openfe/protocols/restraint_utils/openmm/omm_restraints.py similarity index 100% rename from openfe/protocols/restraint_utils/openmm/omm_restraints.py rename to src/openfe/protocols/restraint_utils/openmm/omm_restraints.py diff --git a/openfe/protocols/restraint_utils/settings.py b/src/openfe/protocols/restraint_utils/settings.py similarity index 100% rename from openfe/protocols/restraint_utils/settings.py rename to src/openfe/protocols/restraint_utils/settings.py diff --git a/openfe/setup/__init__.py b/src/openfe/setup/__init__.py similarity index 100% rename from openfe/setup/__init__.py rename to src/openfe/setup/__init__.py diff --git a/openfe/setup/alchemical_network_planner/__init__.py b/src/openfe/setup/alchemical_network_planner/__init__.py similarity index 100% rename from openfe/setup/alchemical_network_planner/__init__.py rename to src/openfe/setup/alchemical_network_planner/__init__.py diff --git a/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py b/src/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py similarity index 100% rename from openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py rename to src/openfe/setup/alchemical_network_planner/abstract_alchemical_network_planner.py diff --git a/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py b/src/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py similarity index 100% rename from openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py rename to src/openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py diff --git a/openfe/setup/atom_mapping/__init__.py b/src/openfe/setup/atom_mapping/__init__.py similarity index 100% rename from openfe/setup/atom_mapping/__init__.py rename to src/openfe/setup/atom_mapping/__init__.py diff --git a/openfe/setup/atom_mapping/ligandatommapper.py b/src/openfe/setup/atom_mapping/ligandatommapper.py similarity index 100% rename from openfe/setup/atom_mapping/ligandatommapper.py rename to src/openfe/setup/atom_mapping/ligandatommapper.py diff --git a/openfe/setup/atom_mapping/lomap_mapper.py b/src/openfe/setup/atom_mapping/lomap_mapper.py similarity index 100% rename from openfe/setup/atom_mapping/lomap_mapper.py rename to src/openfe/setup/atom_mapping/lomap_mapper.py diff --git a/openfe/setup/atom_mapping/lomap_scorers.py b/src/openfe/setup/atom_mapping/lomap_scorers.py similarity index 100% rename from openfe/setup/atom_mapping/lomap_scorers.py rename to src/openfe/setup/atom_mapping/lomap_scorers.py diff --git a/openfe/setup/atom_mapping/perses_mapper.py b/src/openfe/setup/atom_mapping/perses_mapper.py similarity index 100% rename from openfe/setup/atom_mapping/perses_mapper.py rename to src/openfe/setup/atom_mapping/perses_mapper.py diff --git a/openfe/setup/atom_mapping/perses_scorers.py b/src/openfe/setup/atom_mapping/perses_scorers.py similarity index 100% rename from openfe/setup/atom_mapping/perses_scorers.py rename to src/openfe/setup/atom_mapping/perses_scorers.py diff --git a/openfe/setup/chemicalsystem_generator/__init__.py b/src/openfe/setup/chemicalsystem_generator/__init__.py similarity index 100% rename from openfe/setup/chemicalsystem_generator/__init__.py rename to src/openfe/setup/chemicalsystem_generator/__init__.py diff --git a/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py b/src/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py similarity index 100% rename from openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py rename to src/openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py diff --git a/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py b/src/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py similarity index 100% rename from openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py rename to src/openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py diff --git a/openfe/setup/ligand_network_planning.py b/src/openfe/setup/ligand_network_planning.py similarity index 100% rename from openfe/setup/ligand_network_planning.py rename to src/openfe/setup/ligand_network_planning.py diff --git a/openfe/storage/__init__.py b/src/openfe/storage/__init__.py similarity index 100% rename from openfe/storage/__init__.py rename to src/openfe/storage/__init__.py diff --git a/openfe/storage/metadatastore.py b/src/openfe/storage/metadatastore.py similarity index 100% rename from openfe/storage/metadatastore.py rename to src/openfe/storage/metadatastore.py diff --git a/openfe/storage/resultclient.py b/src/openfe/storage/resultclient.py similarity index 100% rename from openfe/storage/resultclient.py rename to src/openfe/storage/resultclient.py diff --git a/openfe/storage/resultserver.py b/src/openfe/storage/resultserver.py similarity index 100% rename from openfe/storage/resultserver.py rename to src/openfe/storage/resultserver.py diff --git a/openfe/tests/__init__.py b/src/openfe/tests/__init__.py 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