OpenFreeEnergy · atravitz · Dec 16, 2025 · Dec 16, 2025 · Dec 16, 2025 · Dec 16, 2025
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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 → src/openfe/__init__.py b/openfe/__init__.py → src/openfe/__init__.py
diff --git a/openfe/analysis/__init__.py → src/openfe/analysis/__init__.py b/openfe/analysis/__init__.py → src/openfe/analysis/__init__.py
diff --git a/openfe/analysis/plotting.py → src/openfe/analysis/plotting.py b/openfe/analysis/plotting.py → src/openfe/analysis/plotting.py
diff --git a/openfe/due.py → src/openfe/due.py b/openfe/due.py → src/openfe/due.py
diff --git a/openfe/orchestration/__init__.py → src/openfe/orchestration/__init__.py b/openfe/orchestration/__init__.py → src/openfe/orchestration/__init__.py
diff --git a/openfe/protocols/__init__.py → src/openfe/protocols/__init__.py b/openfe/protocols/__init__.py → src/openfe/protocols/__init__.py
diff --git a/openfe/protocols/openmm_afe/__init__.py → src/openfe/protocols/openmm_afe/__init__.py b/openfe/protocols/openmm_afe/__init__.py → src/openfe/protocols/openmm_afe/__init__.py
diff --git a/openfe/protocols/openmm_afe/base.py → src/openfe/protocols/openmm_afe/base.py b/openfe/protocols/openmm_afe/base.py → src/openfe/protocols/openmm_afe/base.py
diff --git a/...rotocols/openmm_afe/equil_afe_settings.py → ...rotocols/openmm_afe/equil_afe_settings.py b/...rotocols/openmm_afe/equil_afe_settings.py → ...rotocols/openmm_afe/equil_afe_settings.py
diff --git a/...ls/openmm_afe/equil_binding_afe_method.py → ...ls/openmm_afe/equil_binding_afe_method.py b/...ls/openmm_afe/equil_binding_afe_method.py → ...ls/openmm_afe/equil_binding_afe_method.py
diff --git a/.../openmm_afe/equil_solvation_afe_method.py → .../openmm_afe/equil_solvation_afe_method.py b/.../openmm_afe/equil_solvation_afe_method.py → .../openmm_afe/equil_solvation_afe_method.py
diff --git a/openfe/protocols/openmm_md/__init__.py → src/openfe/protocols/openmm_md/__init__.py b/openfe/protocols/openmm_md/__init__.py → src/openfe/protocols/openmm_md/__init__.py
diff --git a/...e/protocols/openmm_md/plain_md_methods.py → ...e/protocols/openmm_md/plain_md_methods.py b/...e/protocols/openmm_md/plain_md_methods.py → ...e/protocols/openmm_md/plain_md_methods.py
diff --git a/.../protocols/openmm_md/plain_md_settings.py → .../protocols/openmm_md/plain_md_settings.py b/.../protocols/openmm_md/plain_md_settings.py → .../protocols/openmm_md/plain_md_settings.py
diff --git a/openfe/protocols/openmm_rfe/__init__.py → src/openfe/protocols/openmm_rfe/__init__.py b/openfe/protocols/openmm_rfe/__init__.py → src/openfe/protocols/openmm_rfe/__init__.py
diff --git a/...otocols/openmm_rfe/_rfe_utils/__init__.py → ...otocols/openmm_rfe/_rfe_utils/__init__.py b/...otocols/openmm_rfe/_rfe_utils/__init__.py → ...otocols/openmm_rfe/_rfe_utils/__init__.py
diff --git a/...s/openmm_rfe/_rfe_utils/lambdaprotocol.py → ...s/openmm_rfe/_rfe_utils/lambdaprotocol.py b/...s/openmm_rfe/_rfe_utils/lambdaprotocol.py → ...s/openmm_rfe/_rfe_utils/lambdaprotocol.py
diff --git a/...ocols/openmm_rfe/_rfe_utils/multistate.py → ...ocols/openmm_rfe/_rfe_utils/multistate.py b/...ocols/openmm_rfe/_rfe_utils/multistate.py → ...ocols/openmm_rfe/_rfe_utils/multistate.py
diff --git a/...otocols/openmm_rfe/_rfe_utils/relative.py → ...otocols/openmm_rfe/_rfe_utils/relative.py b/...otocols/openmm_rfe/_rfe_utils/relative.py → ...otocols/openmm_rfe/_rfe_utils/relative.py
diff --git a/.../openmm_rfe/_rfe_utils/topologyhelpers.py → .../openmm_rfe/_rfe_utils/topologyhelpers.py b/.../openmm_rfe/_rfe_utils/topologyhelpers.py → .../openmm_rfe/_rfe_utils/topologyhelpers.py
diff --git a/...protocols/openmm_rfe/equil_rfe_methods.py → ...protocols/openmm_rfe/equil_rfe_methods.py b/...protocols/openmm_rfe/equil_rfe_methods.py → ...protocols/openmm_rfe/equil_rfe_methods.py
diff --git a/...rotocols/openmm_rfe/equil_rfe_settings.py → ...rotocols/openmm_rfe/equil_rfe_settings.py b/...rotocols/openmm_rfe/equil_rfe_settings.py → ...rotocols/openmm_rfe/equil_rfe_settings.py
diff --git a/openfe/protocols/openmm_septop/__init__.py → ...penfe/protocols/openmm_septop/__init__.py b/openfe/protocols/openmm_septop/__init__.py → ...penfe/protocols/openmm_septop/__init__.py
diff --git a/openfe/protocols/openmm_septop/base.py → src/openfe/protocols/openmm_septop/base.py b/openfe/protocols/openmm_septop/base.py → src/openfe/protocols/openmm_septop/base.py
diff --git a/...cols/openmm_septop/equil_septop_method.py → ...cols/openmm_septop/equil_septop_method.py b/...cols/openmm_septop/equil_septop_method.py → ...cols/openmm_septop/equil_septop_method.py
diff --git a/...ls/openmm_septop/equil_septop_settings.py → ...ls/openmm_septop/equil_septop_settings.py b/...ls/openmm_septop/equil_septop_settings.py → ...ls/openmm_septop/equil_septop_settings.py
diff --git a/openfe/protocols/openmm_septop/utils.py → src/openfe/protocols/openmm_septop/utils.py b/openfe/protocols/openmm_septop/utils.py → src/openfe/protocols/openmm_septop/utils.py
diff --git a/openfe/protocols/openmm_utils/__init__.py → ...openfe/protocols/openmm_utils/__init__.py b/openfe/protocols/openmm_utils/__init__.py → ...openfe/protocols/openmm_utils/__init__.py
diff --git a/...otocols/openmm_utils/charge_generation.py → ...otocols/openmm_utils/charge_generation.py b/...otocols/openmm_utils/charge_generation.py → ...otocols/openmm_utils/charge_generation.py
diff --git a/...ocols/openmm_utils/multistate_analysis.py → ...ocols/openmm_utils/multistate_analysis.py b/...ocols/openmm_utils/multistate_analysis.py → ...ocols/openmm_utils/multistate_analysis.py
diff --git a/openfe/protocols/openmm_utils/omm_compute.py → ...nfe/protocols/openmm_utils/omm_compute.py b/openfe/protocols/openmm_utils/omm_compute.py → ...nfe/protocols/openmm_utils/omm_compute.py
diff --git a/...fe/protocols/openmm_utils/omm_settings.py → ...fe/protocols/openmm_utils/omm_settings.py b/...fe/protocols/openmm_utils/omm_settings.py → ...fe/protocols/openmm_utils/omm_settings.py
diff --git a/...ocols/openmm_utils/settings_validation.py → ...ocols/openmm_utils/settings_validation.py b/...ocols/openmm_utils/settings_validation.py → ...ocols/openmm_utils/settings_validation.py
diff --git a/...protocols/openmm_utils/system_creation.py → ...protocols/openmm_utils/system_creation.py b/...protocols/openmm_utils/system_creation.py → ...protocols/openmm_utils/system_creation.py
diff --git a/...otocols/openmm_utils/system_validation.py → ...otocols/openmm_utils/system_validation.py b/...otocols/openmm_utils/system_validation.py → ...otocols/openmm_utils/system_validation.py
diff --git a/openfe/protocols/restraint_utils/__init__.py → ...nfe/protocols/restraint_utils/__init__.py b/openfe/protocols/restraint_utils/__init__.py → ...nfe/protocols/restraint_utils/__init__.py
diff --git a/...cols/restraint_utils/geometry/__init__.py → ...cols/restraint_utils/geometry/__init__.py b/...cols/restraint_utils/geometry/__init__.py → ...cols/restraint_utils/geometry/__init__.py
diff --git a/...rotocols/restraint_utils/geometry/base.py → ...rotocols/restraint_utils/geometry/base.py b/...rotocols/restraint_utils/geometry/base.py → ...rotocols/restraint_utils/geometry/base.py
diff --git a/...traint_utils/geometry/boresch/__init__.py → ...traint_utils/geometry/boresch/__init__.py b/...traint_utils/geometry/boresch/__init__.py → ...traint_utils/geometry/boresch/__init__.py
diff --git a/...traint_utils/geometry/boresch/geometry.py → ...traint_utils/geometry/boresch/geometry.py b/...traint_utils/geometry/boresch/geometry.py → ...traint_utils/geometry/boresch/geometry.py
diff --git a/...restraint_utils/geometry/boresch/guest.py → ...restraint_utils/geometry/boresch/guest.py b/...restraint_utils/geometry/boresch/guest.py → ...restraint_utils/geometry/boresch/guest.py
diff --git a/.../restraint_utils/geometry/boresch/host.py → .../restraint_utils/geometry/boresch/host.py b/.../restraint_utils/geometry/boresch/host.py → .../restraint_utils/geometry/boresch/host.py
diff --git a/...ls/restraint_utils/geometry/flatbottom.py → ...ls/restraint_utils/geometry/flatbottom.py b/...ls/restraint_utils/geometry/flatbottom.py → ...ls/restraint_utils/geometry/flatbottom.py
diff --git a/...cols/restraint_utils/geometry/harmonic.py → ...cols/restraint_utils/geometry/harmonic.py b/...cols/restraint_utils/geometry/harmonic.py → ...cols/restraint_utils/geometry/harmonic.py
diff --git a/...otocols/restraint_utils/geometry/utils.py → ...otocols/restraint_utils/geometry/utils.py b/...otocols/restraint_utils/geometry/utils.py → ...otocols/restraint_utils/geometry/utils.py
diff --git a/...tocols/restraint_utils/openmm/__init__.py → ...tocols/restraint_utils/openmm/__init__.py b/...tocols/restraint_utils/openmm/__init__.py → ...tocols/restraint_utils/openmm/__init__.py
diff --git a/...cols/restraint_utils/openmm/omm_forces.py → ...cols/restraint_utils/openmm/omm_forces.py b/...cols/restraint_utils/openmm/omm_forces.py → ...cols/restraint_utils/openmm/omm_forces.py
diff --git a/.../restraint_utils/openmm/omm_restraints.py → .../restraint_utils/openmm/omm_restraints.py b/.../restraint_utils/openmm/omm_restraints.py → .../restraint_utils/openmm/omm_restraints.py
diff --git a/openfe/protocols/restraint_utils/settings.py → ...nfe/protocols/restraint_utils/settings.py b/openfe/protocols/restraint_utils/settings.py → ...nfe/protocols/restraint_utils/settings.py
diff --git a/openfe/setup/__init__.py → src/openfe/setup/__init__.py b/openfe/setup/__init__.py → src/openfe/setup/__init__.py
diff --git a/...up/alchemical_network_planner/__init__.py → ...up/alchemical_network_planner/__init__.py b/...up/alchemical_network_planner/__init__.py → ...up/alchemical_network_planner/__init__.py
diff --git a/...er/abstract_alchemical_network_planner.py → ...er/abstract_alchemical_network_planner.py b/...er/abstract_alchemical_network_planner.py → ...er/abstract_alchemical_network_planner.py
diff --git a/...er/relative_alchemical_network_planner.py → ...er/relative_alchemical_network_planner.py b/...er/relative_alchemical_network_planner.py → ...er/relative_alchemical_network_planner.py
diff --git a/openfe/setup/atom_mapping/__init__.py → src/openfe/setup/atom_mapping/__init__.py b/openfe/setup/atom_mapping/__init__.py → src/openfe/setup/atom_mapping/__init__.py
diff --git a/...fe/setup/atom_mapping/ligandatommapper.py → ...fe/setup/atom_mapping/ligandatommapper.py b/...fe/setup/atom_mapping/ligandatommapper.py → ...fe/setup/atom_mapping/ligandatommapper.py
diff --git a/openfe/setup/atom_mapping/lomap_mapper.py → ...openfe/setup/atom_mapping/lomap_mapper.py b/openfe/setup/atom_mapping/lomap_mapper.py → ...openfe/setup/atom_mapping/lomap_mapper.py
diff --git a/openfe/setup/atom_mapping/lomap_scorers.py → ...penfe/setup/atom_mapping/lomap_scorers.py b/openfe/setup/atom_mapping/lomap_scorers.py → ...penfe/setup/atom_mapping/lomap_scorers.py
diff --git a/openfe/setup/atom_mapping/perses_mapper.py → ...penfe/setup/atom_mapping/perses_mapper.py b/openfe/setup/atom_mapping/perses_mapper.py → ...penfe/setup/atom_mapping/perses_mapper.py
diff --git a/openfe/setup/atom_mapping/perses_scorers.py → ...enfe/setup/atom_mapping/perses_scorers.py b/openfe/setup/atom_mapping/perses_scorers.py → ...enfe/setup/atom_mapping/perses_scorers.py
diff --git a/...etup/chemicalsystem_generator/__init__.py → ...etup/chemicalsystem_generator/__init__.py b/...etup/chemicalsystem_generator/__init__.py → ...etup/chemicalsystem_generator/__init__.py
diff --git a/...ator/abstract_chemicalsystem_generator.py → ...ator/abstract_chemicalsystem_generator.py b/...ator/abstract_chemicalsystem_generator.py → ...ator/abstract_chemicalsystem_generator.py
diff --git a/...enerator/easy_chemicalsystem_generator.py → ...enerator/easy_chemicalsystem_generator.py b/...enerator/easy_chemicalsystem_generator.py → ...enerator/easy_chemicalsystem_generator.py
diff --git a/openfe/setup/ligand_network_planning.py → src/openfe/setup/ligand_network_planning.py b/openfe/setup/ligand_network_planning.py → src/openfe/setup/ligand_network_planning.py
diff --git a/openfe/storage/__init__.py → src/openfe/storage/__init__.py b/openfe/storage/__init__.py → src/openfe/storage/__init__.py
diff --git a/openfe/storage/metadatastore.py → src/openfe/storage/metadatastore.py b/openfe/storage/metadatastore.py → src/openfe/storage/metadatastore.py
diff --git a/openfe/storage/resultclient.py → src/openfe/storage/resultclient.py b/openfe/storage/resultclient.py → src/openfe/storage/resultclient.py
diff --git a/openfe/storage/resultserver.py → src/openfe/storage/resultserver.py b/openfe/storage/resultserver.py → src/openfe/storage/resultserver.py
diff --git a/openfe/tests/__init__.py → src/openfe/tests/__init__.py b/openfe/tests/__init__.py → src/openfe/tests/__init__.py
diff --git a/openfe/tests/analysis/__init__.py → src/openfe/tests/analysis/__init__.py b/openfe/tests/analysis/__init__.py → src/openfe/tests/analysis/__init__.py
diff --git a/openfe/tests/analysis/test_plotting.py → src/openfe/tests/analysis/test_plotting.py b/openfe/tests/analysis/test_plotting.py → src/openfe/tests/analysis/test_plotting.py
diff --git a/openfe/tests/conftest.py → src/openfe/tests/conftest.py b/openfe/tests/conftest.py → src/openfe/tests/conftest.py
diff --git a/openfe/tests/data/181l_only.pdb → src/openfe/tests/data/181l_only.pdb b/openfe/tests/data/181l_only.pdb → src/openfe/tests/data/181l_only.pdb
diff --git a/openfe/tests/data/6CZJ.pdb.gz → src/openfe/tests/data/6CZJ.pdb.gz b/openfe/tests/data/6CZJ.pdb.gz → src/openfe/tests/data/6CZJ.pdb.gz
diff --git a/openfe/tests/data/CN.sdf → src/openfe/tests/data/CN.sdf b/openfe/tests/data/CN.sdf → src/openfe/tests/data/CN.sdf
diff --git a/openfe/tests/data/__init__.py → src/openfe/tests/data/__init__.py b/openfe/tests/data/__init__.py → src/openfe/tests/data/__init__.py
diff --git a/openfe/tests/data/benzene_modifications.sdf → ...enfe/tests/data/benzene_modifications.sdf b/openfe/tests/data/benzene_modifications.sdf → ...enfe/tests/data/benzene_modifications.sdf
diff --git a/openfe/tests/data/cdk8/__init__.py → src/openfe/tests/data/cdk8/__init__.py b/openfe/tests/data/cdk8/__init__.py → src/openfe/tests/data/cdk8/__init__.py
diff --git a/openfe/tests/data/cdk8/cdk8_ligands.sdf → src/openfe/tests/data/cdk8/cdk8_ligands.sdf b/openfe/tests/data/cdk8/cdk8_ligands.sdf → src/openfe/tests/data/cdk8/cdk8_ligands.sdf
diff --git a/openfe/tests/data/cdk8/cdk8_protein.pdb → src/openfe/tests/data/cdk8/cdk8_protein.pdb b/openfe/tests/data/cdk8/cdk8_protein.pdb → src/openfe/tests/data/cdk8/cdk8_protein.pdb
diff --git a/openfe/tests/data/eg5/__init__.py → src/openfe/tests/data/eg5/__init__.py b/openfe/tests/data/eg5/__init__.py → src/openfe/tests/data/eg5/__init__.py
diff --git a/openfe/tests/data/eg5/eg5_cofactor.sdf → src/openfe/tests/data/eg5/eg5_cofactor.sdf b/openfe/tests/data/eg5/eg5_cofactor.sdf → src/openfe/tests/data/eg5/eg5_cofactor.sdf
diff --git a/openfe/tests/data/eg5/eg5_ligands.sdf → src/openfe/tests/data/eg5/eg5_ligands.sdf b/openfe/tests/data/eg5/eg5_ligands.sdf → src/openfe/tests/data/eg5/eg5_ligands.sdf
diff --git a/openfe/tests/data/eg5/eg5_protein.pdb → src/openfe/tests/data/eg5/eg5_protein.pdb b/openfe/tests/data/eg5/eg5_protein.pdb → src/openfe/tests/data/eg5/eg5_protein.pdb
diff --git a/...e/tests/data/external_formats/__init__.py → ...e/tests/data/external_formats/__init__.py b/...e/tests/data/external_formats/__init__.py → ...e/tests/data/external_formats/__init__.py
diff --git a/.../external_formats/somebenzenes_edges.edge → .../external_formats/somebenzenes_edges.edge b/.../external_formats/somebenzenes_edges.edge → .../external_formats/somebenzenes_edges.edge
diff --git a/...ata/external_formats/somebenzenes_nes.dat → ...ata/external_formats/somebenzenes_nes.dat b/...ata/external_formats/somebenzenes_nes.dat → ...ata/external_formats/somebenzenes_nes.dat
diff --git a/openfe/tests/data/htf/__init__.py → src/openfe/tests/data/htf/__init__.py b/openfe/tests/data/htf/__init__.py → src/openfe/tests/data/htf/__init__.py
diff --git a/...ta/htf/t4_lysozyme_data/chlorobenzene.sdf → ...ta/htf/t4_lysozyme_data/chlorobenzene.sdf b/...ta/htf/t4_lysozyme_data/chlorobenzene.sdf → ...ta/htf/t4_lysozyme_data/chlorobenzene.sdf
diff --git a/...ta/htf/t4_lysozyme_data/fluorobenzene.sdf → ...ta/htf/t4_lysozyme_data/fluorobenzene.sdf b/...ta/htf/t4_lysozyme_data/fluorobenzene.sdf → ...ta/htf/t4_lysozyme_data/fluorobenzene.sdf
diff --git a/...lysozyme_data/t4_lysozyme_solvated.pdb.gz → ...lysozyme_data/t4_lysozyme_solvated.pdb.gz b/...lysozyme_data/t4_lysozyme_solvated.pdb.gz → ...lysozyme_data/t4_lysozyme_solvated.pdb.gz
diff --git a/...map_basic/1,3,7-trimethylnaphthalene.mol2 → ...map_basic/1,3,7-trimethylnaphthalene.mol2 b/...map_basic/1,3,7-trimethylnaphthalene.mol2 → ...map_basic/1,3,7-trimethylnaphthalene.mol2
diff --git a/.../lomap_basic/1-butyl-4-methylbenzene.mol2 → .../lomap_basic/1-butyl-4-methylbenzene.mol2 b/.../lomap_basic/1-butyl-4-methylbenzene.mol2 → .../lomap_basic/1-butyl-4-methylbenzene.mol2
diff --git a/.../lomap_basic/2,6-dimethylnaphthalene.mol2 → .../lomap_basic/2,6-dimethylnaphthalene.mol2 b/.../lomap_basic/2,6-dimethylnaphthalene.mol2 → .../lomap_basic/2,6-dimethylnaphthalene.mol2
diff --git a/...p_basic/2-methyl-6-propylnaphthalene.mol2 → ...p_basic/2-methyl-6-propylnaphthalene.mol2 b/...p_basic/2-methyl-6-propylnaphthalene.mol2 → ...p_basic/2-methyl-6-propylnaphthalene.mol2
diff --git a/...data/lomap_basic/2-methylnaphthalene.mol2 → ...data/lomap_basic/2-methylnaphthalene.mol2 b/...data/lomap_basic/2-methylnaphthalene.mol2 → ...data/lomap_basic/2-methylnaphthalene.mol2
diff --git a/...fe/tests/data/lomap_basic/2-naftanol.mol2 → ...fe/tests/data/lomap_basic/2-naftanol.mol2 b/...fe/tests/data/lomap_basic/2-naftanol.mol2 → ...fe/tests/data/lomap_basic/2-naftanol.mol2
diff --git a/openfe/tests/data/lomap_basic/README.md → src/openfe/tests/data/lomap_basic/README.md b/openfe/tests/data/lomap_basic/README.md → src/openfe/tests/data/lomap_basic/README.md
diff --git a/openfe/tests/data/lomap_basic/__init__.py → ...openfe/tests/data/lomap_basic/__init__.py b/openfe/tests/data/lomap_basic/__init__.py → ...openfe/tests/data/lomap_basic/__init__.py
diff --git a/...s/data/lomap_basic/methylcyclohexane.mol2 → ...s/data/lomap_basic/methylcyclohexane.mol2 b/...s/data/lomap_basic/methylcyclohexane.mol2 → ...s/data/lomap_basic/methylcyclohexane.mol2
diff --git a/openfe/tests/data/lomap_basic/toluene.mol2 → ...penfe/tests/data/lomap_basic/toluene.mol2 b/openfe/tests/data/lomap_basic/toluene.mol2 → ...penfe/tests/data/lomap_basic/toluene.mol2
diff --git a/openfe/tests/data/multi_molecule.sdf → src/openfe/tests/data/multi_molecule.sdf b/openfe/tests/data/multi_molecule.sdf → src/openfe/tests/data/multi_molecule.sdf
diff --git a/...nmm_afe/ABFEProtocol_json_results.json.gz → ...nmm_afe/ABFEProtocol_json_results.json.gz b/...nmm_afe/ABFEProtocol_json_results.json.gz → ...nmm_afe/ABFEProtocol_json_results.json.gz
diff --git a/...a/openmm_afe/AHFEProtocol_json_results.gz → ...a/openmm_afe/AHFEProtocol_json_results.gz b/...a/openmm_afe/AHFEProtocol_json_results.gz → ...a/openmm_afe/AHFEProtocol_json_results.gz
diff --git a/...ts/data/openmm_afe/T4_abfe_system.xml.bz2 → ...ts/data/openmm_afe/T4_abfe_system.xml.bz2 b/...ts/data/openmm_afe/T4_abfe_system.xml.bz2 → ...ts/data/openmm_afe/T4_abfe_system.xml.bz2
diff --git a/openfe/tests/data/openmm_afe/__init__.py → src/openfe/tests/data/openmm_afe/__init__.py b/openfe/tests/data/openmm_afe/__init__.py → src/openfe/tests/data/openmm_afe/__init__.py
diff --git a/...data/openmm_md/MDProtocol_json_results.gz → ...data/openmm_md/MDProtocol_json_results.gz b/...data/openmm_md/MDProtocol_json_results.gz → ...data/openmm_md/MDProtocol_json_results.gz
diff --git a/openfe/tests/data/openmm_md/__init__.py → src/openfe/tests/data/openmm_md/__init__.py b/openfe/tests/data/openmm_md/__init__.py → src/openfe/tests/data/openmm_md/__init__.py
diff --git a/...a/openmm_rfe/RHFEProtocol_json_results.gz → ...a/openmm_rfe/RHFEProtocol_json_results.gz b/...a/openmm_rfe/RHFEProtocol_json_results.gz → ...a/openmm_rfe/RHFEProtocol_json_results.gz
diff --git a/openfe/tests/data/openmm_rfe/__init__.py → src/openfe/tests/data/openmm_rfe/__init__.py b/openfe/tests/data/openmm_rfe/__init__.py → src/openfe/tests/data/openmm_rfe/__init__.py
diff --git a/...uene_hybrid_top/hybrid_topology_atoms.csv → ...uene_hybrid_top/hybrid_topology_atoms.csv b/...uene_hybrid_top/hybrid_topology_atoms.csv → ...uene_hybrid_top/hybrid_topology_atoms.csv
diff --git a/...uene_hybrid_top/hybrid_topology_bonds.txt → ...uene_hybrid_top/hybrid_topology_bonds.txt b/...uene_hybrid_top/hybrid_topology_bonds.txt → ...uene_hybrid_top/hybrid_topology_bonds.txt
diff --git a/...ests/data/openmm_rfe/charged_benzenes.sdf → ...ests/data/openmm_rfe/charged_benzenes.sdf b/...ests/data/openmm_rfe/charged_benzenes.sdf → ...ests/data/openmm_rfe/charged_benzenes.sdf
diff --git a/...ata/openmm_rfe/dummy_charge_ligand_23.sdf → ...ata/openmm_rfe/dummy_charge_ligand_23.sdf b/...ata/openmm_rfe/dummy_charge_ligand_23.sdf → ...ata/openmm_rfe/dummy_charge_ligand_23.sdf
diff --git a/...ata/openmm_rfe/dummy_charge_ligand_55.sdf → ...ata/openmm_rfe/dummy_charge_ligand_55.sdf b/...ata/openmm_rfe/dummy_charge_ligand_55.sdf → ...ata/openmm_rfe/dummy_charge_ligand_55.sdf
diff --git a/openfe/tests/data/openmm_rfe/ligand_23.sdf → ...penfe/tests/data/openmm_rfe/ligand_23.sdf b/openfe/tests/data/openmm_rfe/ligand_23.sdf → ...penfe/tests/data/openmm_rfe/ligand_23.sdf
diff --git a/openfe/tests/data/openmm_rfe/ligand_55.sdf → ...penfe/tests/data/openmm_rfe/ligand_55.sdf b/openfe/tests/data/openmm_rfe/ligand_55.sdf → ...penfe/tests/data/openmm_rfe/ligand_55.sdf
diff --git a/...penmm_rfe/malt1_shapefit_1832577-09-9.sdf → ...penmm_rfe/malt1_shapefit_1832577-09-9.sdf b/...penmm_rfe/malt1_shapefit_1832577-09-9.sdf → ...penmm_rfe/malt1_shapefit_1832577-09-9.sdf
diff --git a/...penmm_rfe/malt1_shapefit_Pfizer-01-01.sdf → ...penmm_rfe/malt1_shapefit_Pfizer-01-01.sdf b/...penmm_rfe/malt1_shapefit_Pfizer-01-01.sdf → ...penmm_rfe/malt1_shapefit_Pfizer-01-01.sdf
diff --git a/openfe/tests/data/openmm_rfe/reference.xml → ...penfe/tests/data/openmm_rfe/reference.xml b/openfe/tests/data/openmm_rfe/reference.xml → ...penfe/tests/data/openmm_rfe/reference.xml
diff --git a/...e/tests/data/openmm_rfe/vacuum_nocoord.nc → ...e/tests/data/openmm_rfe/vacuum_nocoord.nc b/...e/tests/data/openmm_rfe/vacuum_nocoord.nc → ...e/tests/data/openmm_rfe/vacuum_nocoord.nc
diff --git a/...a/openmm_rfe/vacuum_nocoord_checkpoint.nc → ...a/openmm_rfe/vacuum_nocoord_checkpoint.nc b/...a/openmm_rfe/vacuum_nocoord_checkpoint.nc → ...a/openmm_rfe/vacuum_nocoord_checkpoint.nc
diff --git a/...nmm_septop/SepTopProtocol_json_results.gz → ...nmm_septop/SepTopProtocol_json_results.gz b/...nmm_septop/SepTopProtocol_json_results.gz → ...nmm_septop/SepTopProtocol_json_results.gz
diff --git a/openfe/tests/data/openmm_septop/__init__.py → ...enfe/tests/data/openmm_septop/__init__.py b/openfe/tests/data/openmm_septop/__init__.py → ...enfe/tests/data/openmm_septop/__init__.py
diff --git a/...e/tests/data/openmm_septop/system.xml.bz2 → ...e/tests/data/openmm_septop/system.xml.bz2 b/...e/tests/data/openmm_septop/system.xml.bz2 → ...e/tests/data/openmm_septop/system.xml.bz2
diff --git a/openfe/tests/data/serialization/__init__.py → ...enfe/tests/data/serialization/__init__.py b/openfe/tests/data/serialization/__init__.py → ...enfe/tests/data/serialization/__init__.py
diff --git a/...ts/data/serialization/ethane_template.sdf → ...ts/data/serialization/ethane_template.sdf b/...ts/data/serialization/ethane_template.sdf → ...ts/data/serialization/ethane_template.sdf
diff --git a/...ta/serialization/network_template.graphml → ...ta/serialization/network_template.graphml b/...ta/serialization/network_template.graphml → ...ta/serialization/network_template.graphml
diff --git a/openfe/tests/dev/__init__.py → src/openfe/tests/dev/__init__.py b/openfe/tests/dev/__init__.py → src/openfe/tests/dev/__init__.py
diff --git a/...tests/dev/serialization_test_templates.py → ...tests/dev/serialization_test_templates.py b/...tests/dev/serialization_test_templates.py → ...tests/dev/serialization_test_templates.py
diff --git a/openfe/tests/protocols/__init__.py → src/openfe/tests/protocols/__init__.py b/openfe/tests/protocols/__init__.py → src/openfe/tests/protocols/__init__.py
diff --git a/openfe/tests/protocols/conftest.py → src/openfe/tests/protocols/conftest.py b/openfe/tests/protocols/conftest.py → src/openfe/tests/protocols/conftest.py
diff --git a/...e/tests/protocols/openmm_abfe/__init__.py → ...e/tests/protocols/openmm_abfe/__init__.py b/...e/tests/protocols/openmm_abfe/__init__.py → ...e/tests/protocols/openmm_abfe/__init__.py
diff --git a/...e/tests/protocols/openmm_abfe/conftest.py → ...e/tests/protocols/openmm_abfe/conftest.py b/...e/tests/protocols/openmm_abfe/conftest.py → ...e/tests/protocols/openmm_abfe/conftest.py
diff --git a/...otocols/openmm_abfe/test_abfe_energies.py → ...otocols/openmm_abfe/test_abfe_energies.py b/...otocols/openmm_abfe/test_abfe_energies.py → ...otocols/openmm_abfe/test_abfe_energies.py
diff --git a/...otocols/openmm_abfe/test_abfe_protocol.py → ...otocols/openmm_abfe/test_abfe_protocol.py b/...otocols/openmm_abfe/test_abfe_protocol.py → ...otocols/openmm_abfe/test_abfe_protocol.py
diff --git a/...openmm_abfe/test_abfe_protocol_results.py → ...openmm_abfe/test_abfe_protocol_results.py b/...openmm_abfe/test_abfe_protocol_results.py → ...openmm_abfe/test_abfe_protocol_results.py
diff --git a/...otocols/openmm_abfe/test_abfe_settings.py → ...otocols/openmm_abfe/test_abfe_settings.py b/...otocols/openmm_abfe/test_abfe_settings.py → ...otocols/openmm_abfe/test_abfe_settings.py
diff --git a/...s/protocols/openmm_abfe/test_abfe_slow.py → ...s/protocols/openmm_abfe/test_abfe_slow.py b/...s/protocols/openmm_abfe/test_abfe_slow.py → ...s/protocols/openmm_abfe/test_abfe_slow.py
diff --git a/...ols/openmm_abfe/test_abfe_tokenization.py → ...ols/openmm_abfe/test_abfe_tokenization.py b/...ols/openmm_abfe/test_abfe_tokenization.py → ...ols/openmm_abfe/test_abfe_tokenization.py
diff --git a/...ocols/openmm_abfe/test_abfe_validation.py → ...ocols/openmm_abfe/test_abfe_validation.py b/...ocols/openmm_abfe/test_abfe_validation.py → ...ocols/openmm_abfe/test_abfe_validation.py
diff --git a/...e/tests/protocols/openmm_ahfe/__init__.py → ...e/tests/protocols/openmm_ahfe/__init__.py b/...e/tests/protocols/openmm_ahfe/__init__.py → ...e/tests/protocols/openmm_ahfe/__init__.py
diff --git a/...otocols/openmm_ahfe/test_ahfe_protocol.py → ...otocols/openmm_ahfe/test_ahfe_protocol.py b/...otocols/openmm_ahfe/test_ahfe_protocol.py → ...otocols/openmm_ahfe/test_ahfe_protocol.py
diff --git a/...otocols/openmm_ahfe/test_ahfe_settings.py → ...otocols/openmm_ahfe/test_ahfe_settings.py b/...otocols/openmm_ahfe/test_ahfe_settings.py → ...otocols/openmm_ahfe/test_ahfe_settings.py
diff --git a/...s/protocols/openmm_ahfe/test_ahfe_slow.py → ...s/protocols/openmm_ahfe/test_ahfe_slow.py b/...s/protocols/openmm_ahfe/test_ahfe_slow.py → ...s/protocols/openmm_ahfe/test_ahfe_slow.py
diff --git a/...ols/openmm_ahfe/test_ahfe_tokenization.py → ...ols/openmm_ahfe/test_ahfe_tokenization.py b/...ols/openmm_ahfe/test_ahfe_tokenization.py → ...ols/openmm_ahfe/test_ahfe_tokenization.py
diff --git a/...ocols/openmm_ahfe/test_ahfe_validation.py → ...ocols/openmm_ahfe/test_ahfe_validation.py b/...ocols/openmm_ahfe/test_ahfe_validation.py → ...ocols/openmm_ahfe/test_ahfe_validation.py
diff --git a/openfe/tests/protocols/openmm_md/__init__.py → ...nfe/tests/protocols/openmm_md/__init__.py b/openfe/tests/protocols/openmm_md/__init__.py → ...nfe/tests/protocols/openmm_md/__init__.py
diff --git a/...ocols/openmm_md/test_plain_md_protocol.py → ...ocols/openmm_md/test_plain_md_protocol.py b/...ocols/openmm_md/test_plain_md_protocol.py → ...ocols/openmm_md/test_plain_md_protocol.py
diff --git a/...protocols/openmm_md/test_plain_md_slow.py → ...protocols/openmm_md/test_plain_md_slow.py b/...protocols/openmm_md/test_plain_md_slow.py → ...protocols/openmm_md/test_plain_md_slow.py
diff --git a/...s/openmm_md/test_plain_md_tokenization.py → ...s/openmm_md/test_plain_md_tokenization.py b/...s/openmm_md/test_plain_md_tokenization.py → ...s/openmm_md/test_plain_md_tokenization.py
diff --git a/...fe/tests/protocols/openmm_rfe/__init__.py → ...fe/tests/protocols/openmm_rfe/__init__.py b/...fe/tests/protocols/openmm_rfe/__init__.py → ...fe/tests/protocols/openmm_rfe/__init__.py
diff --git a/openfe/tests/protocols/openmm_rfe/helpers.py → ...nfe/tests/protocols/openmm_rfe/helpers.py b/openfe/tests/protocols/openmm_rfe/helpers.py → ...nfe/tests/protocols/openmm_rfe/helpers.py
diff --git a/...otocols/openmm_rfe/test_hybrid_factory.py → ...otocols/openmm_rfe/test_hybrid_factory.py b/...otocols/openmm_rfe/test_hybrid_factory.py → ...otocols/openmm_rfe/test_hybrid_factory.py
diff --git a/...ls/openmm_rfe/test_hybrid_top_protocol.py → ...ls/openmm_rfe/test_hybrid_top_protocol.py b/...ls/openmm_rfe/test_hybrid_top_protocol.py → ...ls/openmm_rfe/test_hybrid_top_protocol.py
diff --git a/...tocols/openmm_rfe/test_hybrid_top_slow.py → ...tocols/openmm_rfe/test_hybrid_top_slow.py b/...tocols/openmm_rfe/test_hybrid_top_slow.py → ...tocols/openmm_rfe/test_hybrid_top_slow.py
diff --git a/...penmm_rfe/test_hybrid_top_tokenization.py → ...penmm_rfe/test_hybrid_top_tokenization.py b/...penmm_rfe/test_hybrid_top_tokenization.py → ...penmm_rfe/test_hybrid_top_tokenization.py
diff --git a/...tests/protocols/openmm_septop/__init__.py → ...tests/protocols/openmm_septop/__init__.py b/...tests/protocols/openmm_septop/__init__.py → ...tests/protocols/openmm_septop/__init__.py
diff --git a/...ols/openmm_septop/test_septop_protocol.py → ...ols/openmm_septop/test_septop_protocol.py b/...ols/openmm_septop/test_septop_protocol.py → ...ols/openmm_septop/test_septop_protocol.py
diff --git a/...otocols/openmm_septop/test_septop_slow.py → ...otocols/openmm_septop/test_septop_slow.py b/...otocols/openmm_septop/test_septop_slow.py → ...otocols/openmm_septop/test_septop_slow.py
diff --git a/...openmm_septop/test_septop_tokenization.py → ...openmm_septop/test_septop_tokenization.py b/...openmm_septop/test_septop_tokenization.py → ...openmm_septop/test_septop_tokenization.py
diff --git a/...tocols/openmm_septop/test_septop_utils.py → ...tocols/openmm_septop/test_septop_utils.py b/...tocols/openmm_septop/test_septop_utils.py → ...tocols/openmm_septop/test_septop_utils.py
diff --git a/...fe/tests/protocols/restraints/__init__.py → ...fe/tests/protocols/restraints/__init__.py b/...fe/tests/protocols/restraints/__init__.py → ...fe/tests/protocols/restraints/__init__.py
diff --git a/...rotocols/restraints/test_geometry_base.py → ...rotocols/restraints/test_geometry_base.py b/...rotocols/restraints/test_geometry_base.py → ...rotocols/restraints/test_geometry_base.py
diff --git a/...ocols/restraints/test_geometry_boresch.py → ...ocols/restraints/test_geometry_boresch.py b/...ocols/restraints/test_geometry_boresch.py → ...ocols/restraints/test_geometry_boresch.py
diff --git a/...restraints/test_geometry_boresch_guest.py → ...restraints/test_geometry_boresch_guest.py b/...restraints/test_geometry_boresch_guest.py → ...restraints/test_geometry_boresch_guest.py
diff --git a/.../restraints/test_geometry_boresch_host.py → .../restraints/test_geometry_boresch_host.py b/.../restraints/test_geometry_boresch_host.py → .../restraints/test_geometry_boresch_host.py
diff --git a/...ls/restraints/test_geometry_flatbottom.py → ...ls/restraints/test_geometry_flatbottom.py b/...ls/restraints/test_geometry_flatbottom.py → ...ls/restraints/test_geometry_flatbottom.py
diff --git a/...cols/restraints/test_geometry_harmonic.py → ...cols/restraints/test_geometry_harmonic.py b/...cols/restraints/test_geometry_harmonic.py → ...cols/restraints/test_geometry_harmonic.py
diff --git a/...otocols/restraints/test_geometry_utils.py → ...otocols/restraints/test_geometry_utils.py b/...otocols/restraints/test_geometry_utils.py → ...otocols/restraints/test_geometry_utils.py
diff --git a/...otocols/restraints/test_omm_restraints.py → ...otocols/restraints/test_omm_restraints.py b/...otocols/restraints/test_omm_restraints.py → ...otocols/restraints/test_omm_restraints.py
diff --git a/...rotocols/restraints/test_openmm_forces.py → ...rotocols/restraints/test_openmm_forces.py b/...rotocols/restraints/test_openmm_forces.py → ...rotocols/restraints/test_openmm_forces.py
diff --git a/...sts/protocols/restraints/test_settings.py → ...sts/protocols/restraints/test_settings.py b/...sts/protocols/restraints/test_settings.py → ...sts/protocols/restraints/test_settings.py
diff --git a/...e/tests/protocols/test_openmm_settings.py → ...e/tests/protocols/test_openmm_settings.py b/...e/tests/protocols/test_openmm_settings.py → ...e/tests/protocols/test_openmm_settings.py
diff --git a/openfe/tests/protocols/test_openmmutils.py → ...penfe/tests/protocols/test_openmmutils.py b/openfe/tests/protocols/test_openmmutils.py → ...penfe/tests/protocols/test_openmmutils.py
diff --git a/openfe/tests/setup/__init__.py → src/openfe/tests/setup/__init__.py b/openfe/tests/setup/__init__.py → src/openfe/tests/setup/__init__.py
diff --git a/...up/alchemical_network_planner/__init__.py → ...up/alchemical_network_planner/__init__.py b/...up/alchemical_network_planner/__init__.py → ...up/alchemical_network_planner/__init__.py
diff --git a/.../alchemical_network_planner/edge_types.py → .../alchemical_network_planner/edge_types.py b/.../alchemical_network_planner/edge_types.py → .../alchemical_network_planner/edge_types.py
diff --git a/...st_relative_alchemical_network_planner.py → ...st_relative_alchemical_network_planner.py b/...st_relative_alchemical_network_planner.py → ...st_relative_alchemical_network_planner.py
diff --git a/openfe/tests/setup/atom_mapping/__init__.py → ...enfe/tests/setup/atom_mapping/__init__.py b/openfe/tests/setup/atom_mapping/__init__.py → ...enfe/tests/setup/atom_mapping/__init__.py
diff --git a/openfe/tests/setup/atom_mapping/conftest.py → ...enfe/tests/setup/atom_mapping/conftest.py b/openfe/tests/setup/atom_mapping/conftest.py → ...enfe/tests/setup/atom_mapping/conftest.py
diff --git a/...sts/setup/atom_mapping/test_atommapper.py → ...sts/setup/atom_mapping/test_atommapper.py b/...sts/setup/atom_mapping/test_atommapper.py → ...sts/setup/atom_mapping/test_atommapper.py
diff --git a/...tup/atom_mapping/test_lomap_atommapper.py → ...tup/atom_mapping/test_lomap_atommapper.py b/...tup/atom_mapping/test_lomap_atommapper.py → ...tup/atom_mapping/test_lomap_atommapper.py
diff --git a/.../setup/atom_mapping/test_lomap_scorers.py → .../setup/atom_mapping/test_lomap_scorers.py b/.../setup/atom_mapping/test_lomap_scorers.py → .../setup/atom_mapping/test_lomap_scorers.py
diff --git a/...up/atom_mapping/test_perses_atommapper.py → ...up/atom_mapping/test_perses_atommapper.py b/...up/atom_mapping/test_perses_atommapper.py → ...up/atom_mapping/test_perses_atommapper.py
diff --git a/...setup/atom_mapping/test_perses_scorers.py → ...setup/atom_mapping/test_perses_scorers.py b/...setup/atom_mapping/test_perses_scorers.py → ...setup/atom_mapping/test_perses_scorers.py
diff --git a/...etup/chemicalsystem_generator/__init__.py → ...etup/chemicalsystem_generator/__init__.py b/...etup/chemicalsystem_generator/__init__.py → ...etup/chemicalsystem_generator/__init__.py
diff --git a/...micalsystem_generator/component_checks.py → ...micalsystem_generator/component_checks.py b/...micalsystem_generator/component_checks.py → ...micalsystem_generator/component_checks.py
diff --git a/...tor/test_easy_chemicalsystem_generator.py → ...tor/test_easy_chemicalsystem_generator.py b/...tor/test_easy_chemicalsystem_generator.py → ...tor/test_easy_chemicalsystem_generator.py
diff --git a/openfe/tests/setup/test_network_planning.py → ...enfe/tests/setup/test_network_planning.py b/openfe/tests/setup/test_network_planning.py → ...enfe/tests/setup/test_network_planning.py
diff --git a/openfe/tests/storage/__init__.py → src/openfe/tests/storage/__init__.py b/openfe/tests/storage/__init__.py → src/openfe/tests/storage/__init__.py
diff --git a/openfe/tests/storage/conftest.py → src/openfe/tests/storage/conftest.py b/openfe/tests/storage/conftest.py → src/openfe/tests/storage/conftest.py
diff --git a/openfe/tests/storage/test_metadatastore.py → ...penfe/tests/storage/test_metadatastore.py b/openfe/tests/storage/test_metadatastore.py → ...penfe/tests/storage/test_metadatastore.py
diff --git a/openfe/tests/storage/test_resultclient.py → ...openfe/tests/storage/test_resultclient.py b/openfe/tests/storage/test_resultclient.py → ...openfe/tests/storage/test_resultclient.py
diff --git a/openfe/tests/storage/test_resultserver.py → ...openfe/tests/storage/test_resultserver.py b/openfe/tests/storage/test_resultserver.py → ...openfe/tests/storage/test_resultserver.py
diff --git a/openfe/tests/utils/__init__.py → src/openfe/tests/utils/__init__.py b/openfe/tests/utils/__init__.py → src/openfe/tests/utils/__init__.py
diff --git a/openfe/tests/utils/conftest.py → src/openfe/tests/utils/conftest.py b/openfe/tests/utils/conftest.py → src/openfe/tests/utils/conftest.py
diff --git a/...tils/test_atommapping_network_plotting.py → ...tils/test_atommapping_network_plotting.py b/...tils/test_atommapping_network_plotting.py → ...tils/test_atommapping_network_plotting.py
diff --git a/openfe/tests/utils/test_duecredit.py → src/openfe/tests/utils/test_duecredit.py b/openfe/tests/utils/test_duecredit.py → src/openfe/tests/utils/test_duecredit.py
diff --git a/openfe/tests/utils/test_log_control.py → src/openfe/tests/utils/test_log_control.py b/openfe/tests/utils/test_log_control.py → src/openfe/tests/utils/test_log_control.py
diff --git a/openfe/tests/utils/test_network_plotting.py → ...enfe/tests/utils/test_network_plotting.py b/openfe/tests/utils/test_network_plotting.py → ...enfe/tests/utils/test_network_plotting.py
diff --git a/openfe/tests/utils/test_optional_imports.py → ...enfe/tests/utils/test_optional_imports.py b/openfe/tests/utils/test_optional_imports.py → ...enfe/tests/utils/test_optional_imports.py
diff --git a/openfe/tests/utils/test_remove_oechem.py → src/openfe/tests/utils/test_remove_oechem.py b/openfe/tests/utils/test_remove_oechem.py → src/openfe/tests/utils/test_remove_oechem.py
diff --git a/openfe/tests/utils/test_system_probe.py → src/openfe/tests/utils/test_system_probe.py b/openfe/tests/utils/test_system_probe.py → src/openfe/tests/utils/test_system_probe.py
diff --git a/openfe/tests/utils/test_visualization_3D.py → ...enfe/tests/utils/test_visualization_3D.py b/openfe/tests/utils/test_visualization_3D.py → ...enfe/tests/utils/test_visualization_3D.py
diff --git a/openfe/utils/__init__.py → src/openfe/utils/__init__.py b/openfe/utils/__init__.py → src/openfe/utils/__init__.py
diff --git a/openfe/utils/atommapping_network_plotting.py → ...nfe/utils/atommapping_network_plotting.py b/openfe/utils/atommapping_network_plotting.py → ...nfe/utils/atommapping_network_plotting.py
diff --git a/openfe/utils/custom_typing.py → src/openfe/utils/custom_typing.py b/openfe/utils/custom_typing.py → src/openfe/utils/custom_typing.py
diff --git a/openfe/utils/ligand_utils.py → src/openfe/utils/ligand_utils.py b/openfe/utils/ligand_utils.py → src/openfe/utils/ligand_utils.py
diff --git a/openfe/utils/logging_control.py → src/openfe/utils/logging_control.py b/openfe/utils/logging_control.py → src/openfe/utils/logging_control.py
diff --git a/openfe/utils/network_plotting.py → src/openfe/utils/network_plotting.py b/openfe/utils/network_plotting.py → src/openfe/utils/network_plotting.py
diff --git a/openfe/utils/optional_imports.py → src/openfe/utils/optional_imports.py b/openfe/utils/optional_imports.py → src/openfe/utils/optional_imports.py
diff --git a/openfe/utils/remove_oechem.py → src/openfe/utils/remove_oechem.py b/openfe/utils/remove_oechem.py → src/openfe/utils/remove_oechem.py
diff --git a/openfe/utils/silence_root_logging.py → src/openfe/utils/silence_root_logging.py b/openfe/utils/silence_root_logging.py → src/openfe/utils/silence_root_logging.py
diff --git a/openfe/utils/system_probe.py → src/openfe/utils/system_probe.py b/openfe/utils/system_probe.py → src/openfe/utils/system_probe.py
diff --git a/openfe/utils/visualization_3D.py → src/openfe/utils/visualization_3D.py b/openfe/utils/visualization_3D.py → src/openfe/utils/visualization_3D.py
diff --git a/openfecli/README.md → src/openfecli/README.md b/openfecli/README.md → src/openfecli/README.md
diff --git a/openfecli/__init__.py → src/openfecli/__init__.py b/openfecli/__init__.py → src/openfecli/__init__.py
diff --git a/openfecli/cli.py → src/openfecli/cli.py b/openfecli/cli.py → src/openfecli/cli.py
diff --git a/openfecli/clicktypes/__init__.py → src/openfecli/clicktypes/__init__.py b/openfecli/clicktypes/__init__.py → src/openfecli/clicktypes/__init__.py
diff --git a/openfecli/clicktypes/hyphenchoice.py → src/openfecli/clicktypes/hyphenchoice.py b/openfecli/clicktypes/hyphenchoice.py → src/openfecli/clicktypes/hyphenchoice.py
diff --git a/openfecli/commands/__init__.py → src/openfecli/commands/__init__.py b/openfecli/commands/__init__.py → src/openfecli/commands/__init__.py
diff --git a/openfecli/commands/atommapping.py → src/openfecli/commands/atommapping.py b/openfecli/commands/atommapping.py → src/openfecli/commands/atommapping.py
diff --git a/openfecli/commands/fetch.py → src/openfecli/commands/fetch.py b/openfecli/commands/fetch.py → src/openfecli/commands/fetch.py
diff --git a/openfecli/commands/gather.py → src/openfecli/commands/gather.py b/openfecli/commands/gather.py → src/openfecli/commands/gather.py
diff --git a/openfecli/commands/gather_abfe.py → src/openfecli/commands/gather_abfe.py b/openfecli/commands/gather_abfe.py → src/openfecli/commands/gather_abfe.py
diff --git a/openfecli/commands/gather_septop.py → src/openfecli/commands/gather_septop.py b/openfecli/commands/gather_septop.py → src/openfecli/commands/gather_septop.py
diff --git a/...ecli/commands/generate_partial_charges.py → ...ecli/commands/generate_partial_charges.py b/...ecli/commands/generate_partial_charges.py → ...ecli/commands/generate_partial_charges.py
diff --git a/openfecli/commands/plan_rbfe_network.py → src/openfecli/commands/plan_rbfe_network.py b/openfecli/commands/plan_rbfe_network.py → src/openfecli/commands/plan_rbfe_network.py
diff --git a/openfecli/commands/plan_rhfe_network.py → src/openfecli/commands/plan_rhfe_network.py b/openfecli/commands/plan_rhfe_network.py → src/openfecli/commands/plan_rhfe_network.py
diff --git a/openfecli/commands/quickrun.py → src/openfecli/commands/quickrun.py b/openfecli/commands/quickrun.py → src/openfecli/commands/quickrun.py
diff --git a/openfecli/commands/test.py → src/openfecli/commands/test.py b/openfecli/commands/test.py → src/openfecli/commands/test.py
diff --git a/openfecli/commands/view_ligand_network.py → ...openfecli/commands/view_ligand_network.py b/openfecli/commands/view_ligand_network.py → ...openfecli/commands/view_ligand_network.py
diff --git a/openfecli/fetchables.py → src/openfecli/fetchables.py b/openfecli/fetchables.py → src/openfecli/fetchables.py
diff --git a/openfecli/fetching.py → src/openfecli/fetching.py b/openfecli/fetching.py → src/openfecli/fetching.py
diff --git a/openfecli/parameters/__init__.py → src/openfecli/parameters/__init__.py b/openfecli/parameters/__init__.py → src/openfecli/parameters/__init__.py
diff --git a/openfecli/parameters/mapper.py → src/openfecli/parameters/mapper.py b/openfecli/parameters/mapper.py → src/openfecli/parameters/mapper.py
diff --git a/openfecli/parameters/misc.py → src/openfecli/parameters/misc.py b/openfecli/parameters/misc.py → src/openfecli/parameters/misc.py
diff --git a/openfecli/parameters/mol.py → src/openfecli/parameters/mol.py b/openfecli/parameters/mol.py → src/openfecli/parameters/mol.py
diff --git a/openfecli/parameters/molecules.py → src/openfecli/parameters/molecules.py b/openfecli/parameters/molecules.py → src/openfecli/parameters/molecules.py
diff --git a/openfecli/parameters/output.py → src/openfecli/parameters/output.py b/openfecli/parameters/output.py → src/openfecli/parameters/output.py
diff --git a/openfecli/parameters/output_dir.py → src/openfecli/parameters/output_dir.py b/openfecli/parameters/output_dir.py → src/openfecli/parameters/output_dir.py
diff --git a/openfecli/parameters/plan_network_options.py → ...nfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py → ...nfecli/parameters/plan_network_options.py
diff --git a/openfecli/parameters/protein.py → src/openfecli/parameters/protein.py b/openfecli/parameters/protein.py → src/openfecli/parameters/protein.py
diff --git a/openfecli/parameters/utils.py → src/openfecli/parameters/utils.py b/openfecli/parameters/utils.py → src/openfecli/parameters/utils.py
diff --git a/openfecli/plan_alchemical_networks_utils.py → ...enfecli/plan_alchemical_networks_utils.py b/openfecli/plan_alchemical_networks_utils.py → ...enfecli/plan_alchemical_networks_utils.py
diff --git a/openfecli/plugins.py → src/openfecli/plugins.py b/openfecli/plugins.py → src/openfecli/plugins.py
diff --git a/openfecli/tests/__init__.py → src/openfecli/tests/__init__.py b/openfecli/tests/__init__.py → src/openfecli/tests/__init__.py
diff --git a/...cli/tests/clicktypes/test_hyphenchoice.py → ...cli/tests/clicktypes/test_hyphenchoice.py b/...cli/tests/clicktypes/test_hyphenchoice.py → ...cli/tests/clicktypes/test_hyphenchoice.py
diff --git a/openfecli/tests/commands/__init__.py → src/openfecli/tests/commands/__init__.py b/openfecli/tests/commands/__init__.py → src/openfecli/tests/commands/__init__.py
diff --git a/openfecli/tests/commands/conftest.py → src/openfecli/tests/commands/conftest.py b/openfecli/tests/commands/conftest.py → src/openfecli/tests/commands/conftest.py
diff --git a/openfecli/tests/commands/test_atommapping.py → ...nfecli/tests/commands/test_atommapping.py b/openfecli/tests/commands/test_atommapping.py → ...nfecli/tests/commands/test_atommapping.py
diff --git a/.../tests/commands/test_charge_generation.py → .../tests/commands/test_charge_generation.py b/.../tests/commands/test_charge_generation.py → .../tests/commands/test_charge_generation.py
diff --git a/openfecli/tests/commands/test_gather.py → src/openfecli/tests/commands/test_gather.py b/openfecli/tests/commands/test_gather.py → src/openfecli/tests/commands/test_gather.py
diff --git a/...est_gather/test_abfe_full_results_dg_.tsv → ...est_gather/test_abfe_full_results_dg_.tsv b/...est_gather/test_abfe_full_results_dg_.tsv → ...est_gather/test_abfe_full_results_dg_.tsv
diff --git a/...st_gather/test_abfe_full_results_raw_.tsv → ...st_gather/test_abfe_full_results_raw_.tsv b/...st_gather/test_abfe_full_results_raw_.tsv → ...st_gather/test_abfe_full_results_raw_.tsv
diff --git a/...st_gather/test_abfe_single_repeat_dg_.tsv → ...st_gather/test_abfe_single_repeat_dg_.tsv b/...st_gather/test_abfe_single_repeat_dg_.tsv → ...st_gather/test_abfe_single_repeat_dg_.tsv
diff --git a/...t_gather/test_abfe_single_repeat_raw_.tsv → ...t_gather/test_abfe_single_repeat_raw_.tsv b/...t_gather/test_abfe_single_repeat_raw_.tsv → ...t_gather/test_abfe_single_repeat_raw_.tsv
diff --git a/...est_gather/test_cmet_failed_edge_ddg_.tsv → ...est_gather/test_cmet_failed_edge_ddg_.tsv b/...est_gather/test_cmet_failed_edge_ddg_.tsv → ...est_gather/test_cmet_failed_edge_ddg_.tsv
diff --git a/...est_gather/test_cmet_failed_edge_raw_.tsv → ...est_gather/test_cmet_failed_edge_raw_.tsv b/...est_gather/test_cmet_failed_edge_raw_.tsv → ...est_gather/test_cmet_failed_edge_raw_.tsv
diff --git a/...st_gather/test_cmet_full_results_ddg_.tsv → ...st_gather/test_cmet_full_results_ddg_.tsv b/...st_gather/test_cmet_full_results_ddg_.tsv → ...st_gather/test_cmet_full_results_ddg_.tsv
diff --git a/...est_gather/test_cmet_full_results_dg_.tsv → ...est_gather/test_cmet_full_results_dg_.tsv b/...est_gather/test_cmet_full_results_dg_.tsv → ...est_gather/test_cmet_full_results_dg_.tsv
diff --git a/...st_gather/test_cmet_full_results_raw_.tsv → ...st_gather/test_cmet_full_results_raw_.tsv b/...st_gather/test_cmet_full_results_raw_.tsv → ...st_gather/test_cmet_full_results_raw_.tsv
diff --git a/...g_all_complex_legs_allow_partial_ddg_.tsv → ...g_all_complex_legs_allow_partial_ddg_.tsv b/...g_all_complex_legs_allow_partial_ddg_.tsv → ...g_all_complex_legs_allow_partial_ddg_.tsv
diff --git a/...et_missing_all_complex_legs_fail_ddg_.tsv → ...et_missing_all_complex_legs_fail_ddg_.tsv b/...et_missing_all_complex_legs_fail_ddg_.tsv → ...et_missing_all_complex_legs_fail_ddg_.tsv
diff --git a/...met_missing_all_complex_legs_fail_dg_.tsv → ...met_missing_all_complex_legs_fail_dg_.tsv b/...met_missing_all_complex_legs_fail_dg_.tsv → ...met_missing_all_complex_legs_fail_dg_.tsv
diff --git a/...er/test_cmet_missing_complex_leg_ddg_.tsv → ...er/test_cmet_missing_complex_leg_ddg_.tsv b/...er/test_cmet_missing_complex_leg_ddg_.tsv → ...er/test_cmet_missing_complex_leg_ddg_.tsv
diff --git a/...her/test_cmet_missing_complex_leg_dg_.tsv → ...her/test_cmet_missing_complex_leg_dg_.tsv b/...her/test_cmet_missing_complex_leg_dg_.tsv → ...her/test_cmet_missing_complex_leg_dg_.tsv
diff --git a/...er/test_cmet_missing_complex_leg_raw_.tsv → ...er/test_cmet_missing_complex_leg_raw_.tsv b/...er/test_cmet_missing_complex_leg_raw_.tsv → ...er/test_cmet_missing_complex_leg_raw_.tsv
diff --git a/...st_gather/test_cmet_missing_edge_ddg_.tsv → ...st_gather/test_cmet_missing_edge_ddg_.tsv b/...st_gather/test_cmet_missing_edge_ddg_.tsv → ...st_gather/test_cmet_missing_edge_ddg_.tsv
diff --git a/...est_gather/test_cmet_missing_edge_dg_.tsv → ...est_gather/test_cmet_missing_edge_dg_.tsv b/...est_gather/test_cmet_missing_edge_dg_.tsv → ...est_gather/test_cmet_missing_edge_dg_.tsv
diff --git a/...st_gather/test_cmet_missing_edge_raw_.tsv → ...st_gather/test_cmet_missing_edge_raw_.tsv b/...st_gather/test_cmet_missing_edge_raw_.tsv → ...st_gather/test_cmet_missing_edge_raw_.tsv
diff --git a/..._gather/test_septop_full_results_ddg_.tsv → ..._gather/test_septop_full_results_ddg_.tsv b/..._gather/test_septop_full_results_ddg_.tsv → ..._gather/test_septop_full_results_ddg_.tsv
diff --git a/...t_gather/test_septop_full_results_dg_.tsv → ...t_gather/test_septop_full_results_dg_.tsv b/...t_gather/test_septop_full_results_dg_.tsv → ...t_gather/test_septop_full_results_dg_.tsv
diff --git a/..._gather/test_septop_full_results_raw_.tsv → ..._gather/test_septop_full_results_raw_.tsv b/..._gather/test_septop_full_results_raw_.tsv → ..._gather/test_septop_full_results_raw_.tsv
diff --git a/...gather/test_septop_single_repeat_ddg_.tsv → ...gather/test_septop_single_repeat_ddg_.tsv b/...gather/test_septop_single_repeat_ddg_.tsv → ...gather/test_septop_single_repeat_ddg_.tsv
diff --git a/..._gather/test_septop_single_repeat_dg_.tsv → ..._gather/test_septop_single_repeat_dg_.tsv b/..._gather/test_septop_single_repeat_dg_.tsv → ..._gather/test_septop_single_repeat_dg_.tsv
diff --git a/...gather/test_septop_single_repeat_raw_.tsv → ...gather/test_septop_single_repeat_raw_.tsv b/...gather/test_septop_single_repeat_raw_.tsv → ...gather/test_septop_single_repeat_raw_.tsv
diff --git a/...ts/commands/test_ligand_network_viewer.py → ...ts/commands/test_ligand_network_viewer.py b/...ts/commands/test_ligand_network_viewer.py → ...ts/commands/test_ligand_network_viewer.py
diff --git a/.../tests/commands/test_plan_rbfe_network.py → .../tests/commands/test_plan_rbfe_network.py b/.../tests/commands/test_plan_rbfe_network.py → .../tests/commands/test_plan_rbfe_network.py
diff --git a/.../tests/commands/test_plan_rhfe_network.py → .../tests/commands/test_plan_rhfe_network.py b/.../tests/commands/test_plan_rhfe_network.py → .../tests/commands/test_plan_rhfe_network.py
diff --git a/openfecli/tests/commands/test_quickrun.py → ...openfecli/tests/commands/test_quickrun.py b/openfecli/tests/commands/test_quickrun.py → ...openfecli/tests/commands/test_quickrun.py
diff --git a/openfecli/tests/commands/test_test.py → src/openfecli/tests/commands/test_test.py b/openfecli/tests/commands/test_test.py → src/openfecli/tests/commands/test_test.py
diff --git a/openfecli/tests/conftest.py → src/openfecli/tests/conftest.py b/openfecli/tests/conftest.py → src/openfecli/tests/conftest.py
diff --git a/openfecli/tests/data/__init__.py → src/openfecli/tests/data/__init__.py b/openfecli/tests/data/__init__.py → src/openfecli/tests/data/__init__.py
diff --git a/openfecli/tests/data/bad_transformation.json → ...nfecli/tests/data/bad_transformation.json b/openfecli/tests/data/bad_transformation.json → ...nfecli/tests/data/bad_transformation.json
diff --git a/openfecli/tests/data/rbfe_results.tar.gz → src/openfecli/tests/data/rbfe_results.tar.gz b/openfecli/tests/data/rbfe_results.tar.gz → src/openfecli/tests/data/rbfe_results.tar.gz
diff --git a/...ecli/tests/data/rbfe_tutorial/__init__.py → ...ecli/tests/data/rbfe_tutorial/__init__.py b/...ecli/tests/data/rbfe_tutorial/__init__.py → ...ecli/tests/data/rbfe_tutorial/__init__.py
diff --git a/...tests/data/rbfe_tutorial/tyk2_ligands.sdf → ...tests/data/rbfe_tutorial/tyk2_ligands.sdf b/...tests/data/rbfe_tutorial/tyk2_ligands.sdf → ...tests/data/rbfe_tutorial/tyk2_ligands.sdf
diff --git a/...tests/data/rbfe_tutorial/tyk2_protein.pdb → ...tests/data/rbfe_tutorial/tyk2_protein.pdb b/...tests/data/rbfe_tutorial/tyk2_protein.pdb → ...tests/data/rbfe_tutorial/tyk2_protein.pdb
diff --git a/openfecli/tests/data/transformation.json → src/openfecli/tests/data/transformation.json b/openfecli/tests/data/transformation.json → src/openfecli/tests/data/transformation.json
diff --git a/openfecli/tests/dev/__init__.py → src/openfecli/tests/dev/__init__.py b/openfecli/tests/dev/__init__.py → src/openfecli/tests/dev/__init__.py
diff --git a/...li/tests/dev/write_transformation_json.py → ...li/tests/dev/write_transformation_json.py b/...li/tests/dev/write_transformation_json.py → ...li/tests/dev/write_transformation_json.py
diff --git a/openfecli/tests/parameters/__init__.py → src/openfecli/tests/parameters/__init__.py b/openfecli/tests/parameters/__init__.py → src/openfecli/tests/parameters/__init__.py
diff --git a/openfecli/tests/parameters/test_mapper.py → ...openfecli/tests/parameters/test_mapper.py b/openfecli/tests/parameters/test_mapper.py → ...openfecli/tests/parameters/test_mapper.py
diff --git a/openfecli/tests/parameters/test_mol.py → src/openfecli/tests/parameters/test_mol.py b/openfecli/tests/parameters/test_mol.py → src/openfecli/tests/parameters/test_mol.py