OpenFreeEnergy · hannahbaumann · Sep 30, 2024 · Sep 30, 2024 · Sep 30, 2024 · Oct 1, 2024
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -76,7 +76,7 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest -n logical -v --cov=openfe_gromacs --cov-report=xml --color=yes openfe_gromacs/tests/
+          pytest -n logical -v --cov=src/openfe_gromacs --cov-report=xml --color=yes src/openfe_gromacs/tests/
 
       - name: CodeCov
         uses: codecov/codecov-action@v3

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,17 +15,17 @@ repos:
   rev: 22.12.0
   hooks:
   - id: black
-    files: ^openfe_gromacs
+    files: ^src/openfe_gromacs
 - repo: https://github.com/PyCQA/isort
   rev: 5.12.0
   hooks:
   - id: isort
-    files: ^openfe_gromacs
+    files: ^src/openfe_gromacs
 - repo: https://github.com/PyCQA/flake8
   rev: 6.0.0
   hooks:
   - id: flake8
-    files: ^openfe_gromacs
+    files: ^src/openfe_gromacs
     additional_dependencies: [Flake8-pyproject]
 - repo: https://github.com/asottile/pyupgrade
   rev: 'v3.3.1'

diff --git a/docs/conf.py b/docs/conf.py
@@ -16,9 +16,7 @@
 from pathlib import Path
 import shutil
 import sys
-sys.path.insert(0, os.path.abspath('..'))
-
-import openfe_gromacs
+sys.path.insert(0, os.path.abspath('../src'))
 
 
 # -- Project information -----------------------------------------------------
@@ -53,7 +51,6 @@
     "sphinx_design",
     "sphinx.ext.intersphinx",
     "sphinx.ext.autosummary",
-    "docs._ext.sass",
     "myst_parser",
     "nbsphinx",
     "nbsphinx_link",

diff --git a/pyproject.toml b/pyproject.toml
@@ -82,7 +82,7 @@ match = ["*"]
 default-tag = "0.0.0"
 
 [tool.versioningit.write]
-file = "openfe_gromacs/_version.py"
+file = "src/openfe_gromacs/_version.py"
 
 
 [tool.coverage.run]
@@ -91,7 +91,7 @@ omit = [
     # Omit the tests
     "*/tests/*",
     # Omit generated versioneer
-    "openfe_gromacs/_version.py"
+    "src/openfe_gromacs/_version.py"
 ]
 
 [tool.flake8]

diff --git a/openfe_gromacs/__init__.py → src/openfe_gromacs/__init__.py b/openfe_gromacs/__init__.py → src/openfe_gromacs/__init__.py
diff --git a/openfe_gromacs/protocols/__init__.py → src/openfe_gromacs/protocols/__init__.py b/openfe_gromacs/protocols/__init__.py → src/openfe_gromacs/protocols/__init__.py
diff --git a/..._gromacs/protocols/gromacs_md/__init__.py → ..._gromacs/protocols/gromacs_md/__init__.py b/..._gromacs/protocols/gromacs_md/__init__.py → ..._gromacs/protocols/gromacs_md/__init__.py
diff --git a/...romacs/protocols/gromacs_md/md_methods.py → ...romacs/protocols/gromacs_md/md_methods.py b/...romacs/protocols/gromacs_md/md_methods.py → ...romacs/protocols/gromacs_md/md_methods.py
diff --git a/...omacs/protocols/gromacs_md/md_settings.py → ...omacs/protocols/gromacs_md/md_settings.py b/...omacs/protocols/gromacs_md/md_settings.py → ...omacs/protocols/gromacs_md/md_settings.py
diff --git a/openfe_gromacs/py.typed → src/openfe_gromacs/py.typed b/openfe_gromacs/py.typed → src/openfe_gromacs/py.typed
diff --git a/openfe_gromacs/tests/__init__.py → src/openfe_gromacs/tests/__init__.py b/openfe_gromacs/tests/__init__.py → src/openfe_gromacs/tests/__init__.py
diff --git a/openfe_gromacs/tests/conftest.py → src/openfe_gromacs/tests/conftest.py b/openfe_gromacs/tests/conftest.py → src/openfe_gromacs/tests/conftest.py
diff --git a/openfe_gromacs/tests/data/181l_only.pdb → src/openfe_gromacs/tests/data/181l_only.pdb b/openfe_gromacs/tests/data/181l_only.pdb → src/openfe_gromacs/tests/data/181l_only.pdb
diff --git a/openfe_gromacs/tests/data/CN.sdf → src/openfe_gromacs/tests/data/CN.sdf b/openfe_gromacs/tests/data/CN.sdf → src/openfe_gromacs/tests/data/CN.sdf
diff --git a/...acs/tests/data/MDProtocol_json_results.gz → ...acs/tests/data/MDProtocol_json_results.gz b/...acs/tests/data/MDProtocol_json_results.gz → ...acs/tests/data/MDProtocol_json_results.gz
diff --git a/...sts/data/MDProtocol_json_results_no_EM.gz → ...sts/data/MDProtocol_json_results_no_EM.gz b/...sts/data/MDProtocol_json_results_no_EM.gz → ...sts/data/MDProtocol_json_results_no_EM.gz
diff --git a/...macs/tests/data/benzene_modifications.sdf → ...macs/tests/data/benzene_modifications.sdf b/...macs/tests/data/benzene_modifications.sdf → ...macs/tests/data/benzene_modifications.sdf
diff --git a/openfe_gromacs/tests/data/eg5/__init__.py → ...openfe_gromacs/tests/data/eg5/__init__.py b/openfe_gromacs/tests/data/eg5/__init__.py → ...openfe_gromacs/tests/data/eg5/__init__.py
diff --git a/...e_gromacs/tests/data/eg5/eg5_cofactor.sdf → ...e_gromacs/tests/data/eg5/eg5_cofactor.sdf b/...e_gromacs/tests/data/eg5/eg5_cofactor.sdf → ...e_gromacs/tests/data/eg5/eg5_cofactor.sdf
diff --git a/...fe_gromacs/tests/data/eg5/eg5_ligands.sdf → ...fe_gromacs/tests/data/eg5/eg5_ligands.sdf b/...fe_gromacs/tests/data/eg5/eg5_ligands.sdf → ...fe_gromacs/tests/data/eg5/eg5_ligands.sdf
diff --git a/...fe_gromacs/tests/data/eg5/eg5_protein.pdb → ...fe_gromacs/tests/data/eg5/eg5_protein.pdb b/...fe_gromacs/tests/data/eg5/eg5_protein.pdb → ...fe_gromacs/tests/data/eg5/eg5_protein.pdb
diff --git a/openfe_gromacs/tests/protocols/__init__.py → ...penfe_gromacs/tests/protocols/__init__.py b/openfe_gromacs/tests/protocols/__init__.py → ...penfe_gromacs/tests/protocols/__init__.py
diff --git a/openfe_gromacs/tests/protocols/conftest.py → ...penfe_gromacs/tests/protocols/conftest.py b/openfe_gromacs/tests/protocols/conftest.py → ...penfe_gromacs/tests/protocols/conftest.py
diff --git a/...romacs/tests/protocols/test_gromacs_md.py → ...romacs/tests/protocols/test_gromacs_md.py b/...romacs/tests/protocols/test_gromacs_md.py → ...romacs/tests/protocols/test_gromacs_md.py
diff --git a/...omacs/tests/protocols/test_md_settings.py → ...omacs/tests/protocols/test_md_settings.py b/...omacs/tests/protocols/test_md_settings.py → ...omacs/tests/protocols/test_md_settings.py
diff --git a/...s/tests/protocols/test_md_tokenization.py → ...s/tests/protocols/test_md_tokenization.py b/...s/tests/protocols/test_md_tokenization.py → ...s/tests/protocols/test_md_tokenization.py