evaluate data-loading fixtures at test time, not set-up and reorganize (

#278)

- fix #206 
- speed up tests by avoiding to evaluate fixtures at test collection time
- reorganized fixtures: fixtures that load data are now global in `conftest.py`
- updated tests
- updated CHANGES

CHANGES

@@ -19,6 +19,8 @@ The rules for this file:
 
 Enhancements
   - Blackfy the codebase (PR #280).
+  - Refactor the test to make all the parsing done at conftest level
+    (issue #206, PR #278).
 
 Fixes
   - Remove most of the iloc in the tests (issue #202, PR #254).

src/alchemlyb/__init__.py

@@ -53,7 +53,13 @@ def concat(objs, *args, **kwargs):
     pandas.concat
 
 
-    .. versionadded:: 0.5.0"""
+    .. versionadded:: 0.5.0
+    .. versionchanged:: 1.0.1
+        When input is single dataframe, it will be sent out directly.
+
+    """
+    if isinstance(objs, (pd.DataFrame, pd.Series)):
+        return objs
     # Sanity check
     try:
         attrs = objs[0].attrs

src/alchemlyb/tests/conftest.py

@@ -0,0 +1,271 @@
+"""Storing the fixture to be used for the tests. Note that this file will only contain
+fixture that are made directly from parsing the files. Any additional operations like
+concat should be done at local level."""
+
+import pytest
+from alchemtest.amber import load_bace_example, load_simplesolvated
+from alchemtest.gmx import (
+    load_benzene,
+    load_expanded_ensemble_case_1,
+    load_expanded_ensemble_case_2,
+    load_expanded_ensemble_case_3,
+    load_water_particle_with_total_energy,
+    load_water_particle_with_potential_energy,
+    load_water_particle_without_energy,
+    load_ABFE,
+)
+from alchemtest.gomc import load_benzene as gomc_load_benzene
+from alchemtest.namd import (
+    load_tyr2ala,
+    load_idws,
+    load_restarted,
+    load_restarted_reversed,
+)
+
+from alchemlyb.parsing import gmx, amber, gomc, namd
+
+
+@pytest.fixture
+def gmx_benzene():
+    dataset = load_benzene()
+    return dataset["data"]
+
+
+@pytest.fixture
+def gmx_benzene_Coulomb_dHdl(gmx_benzene):
+    return [gmx.extract_dHdl(file, T=300) for file in gmx_benzene["Coulomb"]]
+
+
+@pytest.fixture
+def gmx_benzene_VDW_dHdl(gmx_benzene):
+    return [gmx.extract_dHdl(file, T=300) for file in gmx_benzene["VDW"]]
+
+
+@pytest.fixture
+def gmx_benzene_Coulomb_u_nk(gmx_benzene):
+    return [gmx.extract_u_nk(file, T=300) for file in gmx_benzene["Coulomb"]]
+
+
+@pytest.fixture
+def gmx_benzene_VDW_u_nk(gmx_benzene):
+    return [gmx.extract_u_nk(file, T=300) for file in gmx_benzene["VDW"]]
+
+
+@pytest.fixture
+def gmx_benzene_VDW_dHdl(gmx_benzene):
+    return [gmx.extract_dHdl(file, T=300) for file in gmx_benzene["VDW"]]
+
+
+@pytest.fixture
+def gmx_ABFE():
+    dataset = load_ABFE()
+    return dataset["data"]
+
+
+@pytest.fixture
+def gmx_ABFE_complex_n_uk(gmx_ABFE):
+    return [gmx.extract_u_nk(file, T=300) for file in gmx_ABFE["complex"]]
+
+
+@pytest.fixture
+def gmx_ABFE_complex_dHdl(gmx_ABFE):
+    return [gmx.extract_dHdl(file, T=300) for file in gmx_ABFE["complex"]]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_1():
+    dataset = load_expanded_ensemble_case_1()
+
+    return [
+        gmx.extract_u_nk(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_1_dHdl():
+    dataset = load_expanded_ensemble_case_1()
+
+    return [
+        gmx.extract_dHdl(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_2():
+    dataset = load_expanded_ensemble_case_2()
+
+    return [
+        gmx.extract_u_nk(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_2_dHdl():
+    dataset = load_expanded_ensemble_case_2()
+
+    return [
+        gmx.extract_dHdl(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_3():
+    dataset = load_expanded_ensemble_case_3()
+
+    return [
+        gmx.extract_u_nk(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_expanded_ensemble_case_3_dHdl():
+    dataset = load_expanded_ensemble_case_3()
+
+    return [
+        gmx.extract_dHdl(filename, T=300, filter=False)
+        for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_with_total_energy():
+    dataset = load_water_particle_with_total_energy()
+
+    return [
+        gmx.extract_u_nk(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_with_total_energy_dHdl():
+    dataset = load_water_particle_with_total_energy()
+
+    return [
+        gmx.extract_dHdl(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_with_potential_energy():
+    dataset = load_water_particle_with_potential_energy()
+
+    return [
+        gmx.extract_u_nk(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_with_potential_energy_dHdl():
+    dataset = load_water_particle_with_potential_energy()
+
+    return [
+        gmx.extract_dHdl(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_without_energy():
+    dataset = load_water_particle_without_energy()
+
+    return [
+        gmx.extract_u_nk(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def gmx_water_particle_without_energy_dHdl():
+    dataset = load_water_particle_without_energy()
+
+    return [
+        gmx.extract_dHdl(filename, T=300) for filename in dataset["data"]["AllStates"]
+    ]
+
+
+@pytest.fixture
+def amber_simplesolvated():
+    dataset = load_simplesolvated()
+    return dataset["data"]
+
+
+@pytest.fixture
+def amber_simplesolvated_charge_dHdl(amber_simplesolvated):
+    return [
+        amber.extract_dHdl(filename, T=298.0)
+        for filename in amber_simplesolvated["charge"]
+    ]
+
+
+@pytest.fixture
+def amber_simplesolvated_vdw_dHdl(amber_simplesolvated):
+    return [
+        amber.extract_dHdl(filename, T=298.0)
+        for filename in amber_simplesolvated["vdw"]
+    ]
+
+
+@pytest.fixture
+def amber_bace_example_complex_vdw():
+    dataset = load_bace_example()
+
+    return [
+        amber.extract_u_nk(filename, T=298.0)
+        for filename in dataset["data"]["complex"]["vdw"]
+    ]
+
+
+@pytest.fixture
+def gomc_benzene():
+    dataset = gomc_load_benzene()
+    return dataset["data"]
+
+
+@pytest.fixture
+def gomc_benzene_u_nk(gomc_benzene):
+    return [gomc.extract_u_nk(filename, T=298) for filename in gomc_benzene]
+
+
+@pytest.fixture
+def gomc_benzene_dHdl(gomc_benzene):
+    return [gomc.extract_dHdl(filename, T=298) for filename in gomc_benzene]
+
+
+@pytest.fixture
+def namd_tyr2ala():
+    dataset = load_tyr2ala()
+    u_nk1 = namd.extract_u_nk(dataset["data"]["forward"][0], T=300)
+    u_nk2 = namd.extract_u_nk(dataset["data"]["backward"][0], T=300)
+
+    # combine dataframes of fwd and rev directions
+    u_nk1[u_nk1.isna()] = u_nk2
+    u_nk = u_nk1.sort_index(level=u_nk1.index.names[1:])
+
+    return u_nk
+
+
+@pytest.fixture
+def namd_idws():
+    dataset = load_idws()
+    u_nk = namd.extract_u_nk(dataset["data"]["forward"], T=300)
+
+    return u_nk
+
+
+@pytest.fixture
+def namd_idws_restarted():
+    dataset = load_restarted()
+    u_nk = namd.extract_u_nk(dataset["data"]["both"], T=300)
+
+    return u_nk
+
+
+@pytest.fixture
+def namd_idws_restarted_reversed():
+    dataset = load_restarted_reversed()
+    u_nk = namd.extract_u_nk(dataset["data"]["both"], T=300)
+
+    return u_nk