fix packaging (#323)

* Add init files + recursive-includes

* Add init to storage

* Add CI test for package build

* add verbosity to pytest calls

Co-authored-by: Mike Henry <[email protected]>

* update manifest

* try something out

* override defined benzene_modifications

* limit gufe imports

* fix gufe imports

* more imports

* how about this?

* minimum fix

* how about pulling all the fixtures directly into openfe?

* make package test a cron job

* separate out the yaml files

---------

Co-authored-by: Mike Henry <[email protected]>

Author: IAlibay

.github/workflows/ci.yaml

@@ -8,7 +8,7 @@ on:
       - main
   schedule:
     # At 07:00 UTC on Monday and Thursday.
-    - cron: "0 7 * * 1,4"
+    - cron: "0 7 * * *"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.ref }}"

.github/workflows/package-tests.yaml

@@ -0,0 +1,45 @@
+name: "CI"
+on:
+  schedule:
+    # At 07:00 UTC on Monday and Thursday.
+    - cron: "0 7 * * *"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  package-tests:
+    runs-on: ubuntu-latest
+    name: "package install tests"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: environment.yml
+          environment-name: openfe
+          extra-specs: python==3.10
+
+      - name: "install extra deps"
+        run: pip install pipx wheel twine readme-renderer
+
+      - name: "build sdist"
+        run: pipx run build --sdist --outdir dist
+
+      - name: "check package build"
+        run: |
+          dist=$(ls -t1 dist/openfe-*tar.gz | head -n1)
+          test -n "${dist}" || { echo "no distribution found"; exit 1; }
+          twine check $dist
+
+      - name: "install from source dist"
+        working-directory: ./dist
+        run: python -m pip install openfe-*tar.gz
+
+      - name: "run tests"
+        working-directory: ./dist
+        run: |
+          pytest -n auto -v --pyargs openfe.tests
+          pytest -n auto -v --pyargs openfecli.tests

MANIFEST.in

@@ -0,0 +1,7 @@
+recursive-include openfe/tests/data/ *.sdf
+recursive-include openfe/tests/data/ *.pdb
+recursive-include openfe/tests/data/ *.mol2
+recursive-include openfe/tests/data/ *.xml
+recursive-include openfe/tests/data/ *.graphml
+include openfecli/tests/data/*.json
+include openfecli/tests/data/*.tar.gz

openfe/storage/__init__.py

@@ -1 +1,102 @@
-from gufe.tests.conftest import *
+import pytest
+from openff.units import unit
+import gufe
+from gufe import SolventComponent, ChemicalSystem
+from gufe.tests.test_protocol import DummyProtocol
+
+
+@pytest.fixture
+def solv_comp():
+    yield SolventComponent(positive_ion="K", negative_ion="Cl",
+                           ion_concentration=0.0 * unit.molar)
+
+@pytest.fixture
+def solvated_complex(T4_protein_component, benzene_transforms, solv_comp):
+    return ChemicalSystem(
+        {"ligand": benzene_transforms['toluene'],
+         "protein": T4_protein_component, "solvent": solv_comp,}
+    )
+
+
+@pytest.fixture
+def solvated_ligand(benzene_transforms, solv_comp):
+    return ChemicalSystem(
+        {"ligand": benzene_transforms['toluene'],
+         "solvent": solv_comp,}
+    )
+
+
+@pytest.fixture
+def absolute_transformation(solvated_ligand, solvated_complex):
+    return gufe.Transformation(
+        solvated_ligand,
+        solvated_complex,
+        protocol=DummyProtocol(settings=None),
+        mapping=None,
+    )
+
+
+@pytest.fixture
+def complex_equilibrium(solvated_complex):
+    return gufe.NonTransformation(
+        solvated_complex,
+        protocol=DummyProtocol(settings=None),
+    )
+
+
+@pytest.fixture
+def benzene_variants_star_map(benzene_transforms, solv_comp,
+                              T4_protein_component):
+    variants = ['toluene', 'phenol', 'benzonitrile', 'anisole',
+                'benzaldehyde', 'styrene']
+
+    # define the solvent chemical systems and transformations between
+    # benzene and the others
+    solvated_ligands = {}
+    solvated_ligand_transformations = {}
+
+    solvated_ligands['benzene'] = ChemicalSystem(
+        {"solvent": solv_comp, "ligand": benzene_transforms['benzene'],},
+        name="benzene-solvent",
+    )
+
+    for ligand in variants:
+        solvated_ligands[ligand] = ChemicalSystem(
+            {"solvent": solv_comp, "ligand": benzene_transforms[ligand],},
+            name=f"{ligand}-solvent"
+        )
+
+        solvated_ligand_transformations[("benzene", ligand)] = gufe.Transformation(
+            solvated_ligands['benzene'], solvated_ligands[ligand],
+            protocol=DummyProtocol(settings=None),
+            mapping=None,
+        )
+
+    # define the complex chemical systems and transformations between
+    # benzene and the others
+    solvated_complexes = {}
+    solvated_complex_transformations = {}
+
+    solvated_complexes["benzene"] = gufe.ChemicalSystem(
+        {"protein": T4_protein_component, "solvent": solv_comp,
+         "ligand": benzene_transforms['benzene']},
+        name="benzene-complex",
+    )
+
+    for ligand in variants:
+        solvated_complexes[ligand] = gufe.ChemicalSystem(
+            {"protein": T4_protein_component, "solvent": solv_comp,
+             "ligand": benzene_transforms[ligand]},
+            name=f"{ligand}-complex",
+        )
+        solvated_complex_transformations[("benzene", ligand)] = gufe.Transformation(
+            solvated_complexes["benzene"],
+            solvated_complexes[ligand],
+            protocol=DummyProtocol(settings=None),
+            mapping=None,
+        )
+
+    return gufe.AlchemicalNetwork(
+        list(solvated_ligand_transformations.values())
+        + list(solvated_complex_transformations.values())
+    )