move to src layout (#1805)

* Move openfe project layout to `src`.

.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

.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

.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

.github/workflows/test-feedstock-pkg-build.yaml

@@ -46,7 +46,7 @@ jobs:
 
       # TODO just checkout the repo where we need it?
       - name: Copy source code to recipe folder
-        run: cp -r openfe openfe-feedstock/recipe/openfe_source
+        run: cp -r src/openfe openfe-feedstock/recipe/openfe_source
       
       - name: Modify feedstock to use local path
         run: |

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
   rev: v6.0.0
   hooks:
   - id: check-added-large-files
+    args: ["--maxkb=900"]
   - id: check-case-conflict
   - id: check-executables-have-shebangs
   - id: check-symlinks

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

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