From 4dc86178c045e3b5f1b528c6fb133a20f07195c5 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 13:44:13 +0100
Subject: [PATCH 01/19] fully disable flaky test

---
 src/openfe_analysis/tests/test_reader.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 6cef163..6a520bb 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -152,13 +152,13 @@ def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
     assert u.trajectory._replica_id == 9
 
 
-@pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
-@pytest.mark.flaky(reruns=3)
-def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
-    with pytest.raises(ValueError, match="Specify one and only one"):
-        _ = mda.Universe(
-            hybrid_system_pdb, simulation_nc, format=FEReader, state_id=state_id, replica_id=rep_id
-        )
+#@pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
+#@pytest.mark.flaky(reruns=3)
+#def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
+#    with pytest.raises(ValueError, match="Specify one and only one"):
+#        _ = mda.Universe(
+#            hybrid_system_pdb, simulation_nc, format=FEReader, state_id=state_id, replica_id=rep_id
+#        )
 
 
 def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb):

From d8b15d23d72fc8e7d2c2e5c362f58ac7753f9186 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 13:48:47 +0100
Subject: [PATCH 02/19] make everything not session scoped

---
 src/openfe_analysis/tests/conftest.py    | 10 +++++-----
 src/openfe_analysis/tests/test_reader.py | 14 +++++++-------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/openfe_analysis/tests/conftest.py b/src/openfe_analysis/tests/conftest.py
index f759b52..36a46a6 100644
--- a/src/openfe_analysis/tests/conftest.py
+++ b/src/openfe_analysis/tests/conftest.py
@@ -26,27 +26,27 @@
 )
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def simulation_nc():
     return RFE_OUTPUT.fetch("simulation.nc")
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def simulation_skipped_nc():
     return RFE_OUTPUT_skipped_frames.fetch("simulation.nc")
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def hybrid_system_pdb():
     return RFE_OUTPUT.fetch("hybrid_system.pdb")
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def hybrid_system_skipped_pdb():
     return RFE_OUTPUT_skipped_frames.fetch("hybrid_system.pdb")
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture()
 def mcmc_serialized():
     return (
         "_serialized__class_name: LangevinDynamicsMove\n"
diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 6a520bb..6cef163 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -152,13 +152,13 @@ def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
     assert u.trajectory._replica_id == 9
 
 
-#@pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
-#@pytest.mark.flaky(reruns=3)
-#def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
-#    with pytest.raises(ValueError, match="Specify one and only one"):
-#        _ = mda.Universe(
-#            hybrid_system_pdb, simulation_nc, format=FEReader, state_id=state_id, replica_id=rep_id
-#        )
+@pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
+@pytest.mark.flaky(reruns=3)
+def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
+    with pytest.raises(ValueError, match="Specify one and only one"):
+        _ = mda.Universe(
+            hybrid_system_pdb, simulation_nc, format=FEReader, state_id=state_id, replica_id=rep_id
+        )
 
 
 def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb):

From 19fd5acd072c3d67c4aba803479905accae7a3ae Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 13:51:19 +0100
Subject: [PATCH 03/19] remove that one too

---
 src/openfe_analysis/tests/utils/test_multistate.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index deb3281..3751743 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -13,7 +13,6 @@
 )
 
 
-@pytest.fixture(scope="module")
 def dataset(simulation_nc):
     return nc.Dataset(simulation_nc)
 

From 1470d76feb864622a18b60798c549754b125edb3 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:07:07 +0100
Subject: [PATCH 04/19] add some safeties

---
 src/openfe_analysis/tests/conftest.py         | 27 ++++++++++++++-----
 src/openfe_analysis/tests/test_reader.py      |  1 +
 .../tests/utils/test_multistate.py            |  3 +++
 3 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/src/openfe_analysis/tests/conftest.py b/src/openfe_analysis/tests/conftest.py
index 36a46a6..24bace8 100644
--- a/src/openfe_analysis/tests/conftest.py
+++ b/src/openfe_analysis/tests/conftest.py
@@ -2,9 +2,20 @@
 
 import pooch
 import pytest
+import urllib.request
 
+
+try:
+    urllib.request.urlopen('https://www.google.com')
+except:  # -no-cov-
+    HAS_INTERNET = False
+else:
+    HAS_INTERNET = True
+
+
+POOCH_CACHE = pooch.os_cache("openfe_analysis")
 RFE_OUTPUT = pooch.create(
-    path=pooch.os_cache("openfe_analysis"),
+    path=POOCH_CACHE,
     base_url="doi:10.6084/m9.figshare.24101655",
     registry={
         "checkpoint.nc": "5af398cb14340fddf7492114998b244424b6c3f4514b2e07e4bd411484c08464",
@@ -13,40 +24,42 @@
         "simulation.nc": "92361a0864d4359a75399470135f56642b72c605069a4c33dbc4be6f91f28b31",
         "simulation_real_time_analysis.yaml": "65706002f371fafba96037f29b054fd7e050e442915205df88567f48f5e5e1cf",  # noqa: E501
     },
+    retry_if_failed=5,
 )
 
 
 RFE_OUTPUT_skipped_frames = pooch.create(
-    path=pooch.os_cache("openfe_analysis_skipped"),
+    path=POOCH_CACHE,
     base_url="doi:10.6084/m9.figshare.28263203",
     registry={
         "hybrid_system.pdb": "77c7914b78724e568f38d5a308d36923f5837c03a1d094e26320b20aeec65fee",
         "simulation.nc": "6749e2c895f16b7e4eba196261c34756a0a062741d36cc74925676b91a36d0cd",
     },
+    retry_if_failed=5,
 )
 
 
-@pytest.fixture()
+@pytest.fixture(scope='session')
 def simulation_nc():
     return RFE_OUTPUT.fetch("simulation.nc")
 
 
-@pytest.fixture()
+@pytest.fixture(scope='session')
 def simulation_skipped_nc():
     return RFE_OUTPUT_skipped_frames.fetch("simulation.nc")
 
 
-@pytest.fixture()
+@pytest.fixture(scope='session')
 def hybrid_system_pdb():
     return RFE_OUTPUT.fetch("hybrid_system.pdb")
 
 
-@pytest.fixture()
+@pytest.fixture(scope='session')
 def hybrid_system_skipped_pdb():
     return RFE_OUTPUT_skipped_frames.fetch("hybrid_system.pdb")
 
 
-@pytest.fixture()
+@pytest.fixture(scope='session')
 def mcmc_serialized():
     return (
         "_serialized__class_name: LangevinDynamicsMove\n"
diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 6cef163..02918c6 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -116,6 +116,7 @@ def test_universe_from_nc_file(simulation_nc, hybrid_system_pdb):
     assert len(u.atoms) == 4782
     assert len(u.trajectory) == 501
     assert u.trajectory.dt == pytest.approx(1.0)
+    ds.close()
 
 
 def test_universe_creation_noconversion(simulation_nc, hybrid_system_pdb):
diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index 3751743..0490436 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -13,6 +13,7 @@
 )
 
 
+@pytest.fixture(scope='module')
 def dataset(simulation_nc):
     return nc.Dataset(simulation_nc)
 
@@ -84,3 +85,5 @@ def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
 
     assert _get_unitcell(dataset, 1, 1) is None
     assert dataset.variables["positions"][1][0].mask.all()
+
+    dataset.close()

From b196ce77013363687f91e38cb645d1c3b3f23fb3 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:13:56 +0100
Subject: [PATCH 05/19] try forcing the close in gather_rms_data

---
 src/openfe_analysis/rmsd.py              | 2 ++
 src/openfe_analysis/tests/test_reader.py | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/src/openfe_analysis/rmsd.py b/src/openfe_analysis/rmsd.py
index 7d2af13..b7243d6 100644
--- a/src/openfe_analysis/rmsd.py
+++ b/src/openfe_analysis/rmsd.py
@@ -179,6 +179,8 @@ def gather_rms_data(
 
         output["time(ps)"] = list(np.arange(len(u.trajectory))[::skip] * u.trajectory.dt)
 
+    ds.close()
+
     return output
 
 
diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 02918c6..473e577 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -179,3 +179,5 @@ def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb)
         assert np.all(u.atoms.positions > 0)
     with pytest.raises(mda.exceptions.NoDataError, match="This Timestep has no velocities"):
         u.atoms.velocities
+
+    u.trajectory.close()

From 4a2d3b67ebeeeb81ebc70f95d41d4400b353a6d3 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:19:52 +0100
Subject: [PATCH 06/19] disable all the flaky calls

---
 src/openfe_analysis/tests/test_reader.py          | 2 +-
 src/openfe_analysis/tests/test_rmsd.py            | 4 ++--
 src/openfe_analysis/tests/test_transformations.py | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 473e577..52fabf6 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -154,7 +154,7 @@ def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
 
 
 @pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
     with pytest.raises(ValueError, match="Specify one and only one"):
         _ = mda.Universe(
diff --git a/src/openfe_analysis/tests/test_rmsd.py b/src/openfe_analysis/tests/test_rmsd.py
index a108bbe..de9585b 100644
--- a/src/openfe_analysis/tests/test_rmsd.py
+++ b/src/openfe_analysis/tests/test_rmsd.py
@@ -6,7 +6,7 @@
 from openfe_analysis.rmsd import gather_rms_data
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_gather_rms_data_regression(simulation_nc, hybrid_system_pdb):
     output = gather_rms_data(
         hybrid_system_pdb,
@@ -43,7 +43,7 @@ def test_gather_rms_data_regression(simulation_nc, hybrid_system_pdb):
     )
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_gather_rms_data_regression_skippednc(simulation_skipped_nc, hybrid_system_skipped_pdb):
     output = gather_rms_data(
         hybrid_system_skipped_pdb,
diff --git a/src/openfe_analysis/tests/test_transformations.py b/src/openfe_analysis/tests/test_transformations.py
index 96d4a0f..c8b89ec 100644
--- a/src/openfe_analysis/tests/test_transformations.py
+++ b/src/openfe_analysis/tests/test_transformations.py
@@ -21,7 +21,7 @@ def universe(hybrid_system_pdb, simulation_nc):
     )
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_minimiser(universe):
     prot = universe.select_atoms("protein and name CA")
     lig = universe.select_atoms("resname UNK")
@@ -34,7 +34,7 @@ def test_minimiser(universe):
     assert d == pytest.approx(11.10, abs=0.01)
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_nojump(universe):
     # find frame where protein would teleport across boundary and check it
     prot = universe.select_atoms("protein and name CA")
@@ -50,7 +50,7 @@ def test_nojump(universe):
     assert prot.center_of_mass() == pytest.approx(ref, abs=0.01)
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_aligner(universe):
     # checks that rmsd is identical with/without center&super
     prot = universe.select_atoms("protein and name CA")

From 9d88572a99bd5094e20fb2130944433fe7d10a2e Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:23:59 +0100
Subject: [PATCH 07/19] remove trajectory close call

---
 src/openfe_analysis/tests/test_reader.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 52fabf6..894a99d 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -179,5 +179,3 @@ def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb)
         assert np.all(u.atoms.positions > 0)
     with pytest.raises(mda.exceptions.NoDataError, match="This Timestep has no velocities"):
         u.atoms.velocities
-
-    u.trajectory.close()

From b68048bbaca7da7b92d58f03d82cc1944005b63a Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:29:57 +0100
Subject: [PATCH 08/19] try something

---
 src/openfe_analysis/reader.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/openfe_analysis/reader.py b/src/openfe_analysis/reader.py
index b7677bc..b2bf23f 100644
--- a/src/openfe_analysis/reader.py
+++ b/src/openfe_analysis/reader.py
@@ -195,3 +195,4 @@ def _reopen(self):
     def close(self):
         if self._dataset_owner:
             self._dataset.close()
+            self._dataset = None

From 4fe7a5e773b1eb3e0d29359c8a723a82f49cd46b Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:32:43 +0100
Subject: [PATCH 09/19] Revert something

---
 src/openfe_analysis/tests/conftest.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/openfe_analysis/tests/conftest.py b/src/openfe_analysis/tests/conftest.py
index 24bace8..17cd43a 100644
--- a/src/openfe_analysis/tests/conftest.py
+++ b/src/openfe_analysis/tests/conftest.py
@@ -13,9 +13,8 @@
     HAS_INTERNET = True
 
 
-POOCH_CACHE = pooch.os_cache("openfe_analysis")
 RFE_OUTPUT = pooch.create(
-    path=POOCH_CACHE,
+    path=pooch.os_cache("openfe_analysis"),
     base_url="doi:10.6084/m9.figshare.24101655",
     registry={
         "checkpoint.nc": "5af398cb14340fddf7492114998b244424b6c3f4514b2e07e4bd411484c08464",
@@ -27,9 +26,8 @@
     retry_if_failed=5,
 )
 
-
 RFE_OUTPUT_skipped_frames = pooch.create(
-    path=POOCH_CACHE,
+    path=pooch.os_cache("openfe_analysis_skipped"),
     base_url="doi:10.6084/m9.figshare.28263203",
     registry={
         "hybrid_system.pdb": "77c7914b78724e568f38d5a308d36923f5837c03a1d094e26320b20aeec65fee",

From 3733734820372ba61da9bb5be273d90a757a799c Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:38:00 +0100
Subject: [PATCH 10/19] try not to open a dataset in a single test

---
 src/openfe_analysis/tests/utils/test_multistate.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index 0490436..ed0df42 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -18,6 +18,11 @@ def dataset(simulation_nc):
     return nc.Dataset(simulation_nc)
 
 
+@pytest.fixture(scope='module')
+def skipped_dataset(simulation_skipped_nc)
+    return nc.Dataset(simulation_skipped_nc)
+
+
 @pytest.mark.flaky(reruns=3)
 @pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
 def test_state_to_replica(dataset, state, frame, replica):
@@ -79,11 +84,7 @@ def test_get_unitcell(dataset):
 
 
 def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
-    simulation_skipped_nc,
+    skipped_dataset,
 ):
-    dataset = nc.Dataset(simulation_skipped_nc)
-
     assert _get_unitcell(dataset, 1, 1) is None
     assert dataset.variables["positions"][1][0].mask.all()
-
-    dataset.close()

From f4b34bbbb33bb637e9fa45f96866817a99c881ff Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:42:25 +0100
Subject: [PATCH 11/19] fix typo

---
 src/openfe_analysis/tests/utils/test_multistate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index ed0df42..ed9b81e 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -19,7 +19,7 @@ def dataset(simulation_nc):
 
 
 @pytest.fixture(scope='module')
-def skipped_dataset(simulation_skipped_nc)
+def skipped_dataset(simulation_skipped_nc):
     return nc.Dataset(simulation_skipped_nc)
 
 

From bc8329459a19e595c42973b2c9afa53348f27b5d Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:51:21 +0100
Subject: [PATCH 12/19] try to explicitly teardown fixtures

---
 src/openfe_analysis/tests/test_reader.py           | 7 +++++++
 src/openfe_analysis/tests/test_transformations.py  | 4 +++-
 src/openfe_analysis/tests/utils/test_multistate.py | 8 ++++++--
 3 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/openfe_analysis/tests/test_reader.py b/src/openfe_analysis/tests/test_reader.py
index 894a99d..2da246e 100644
--- a/src/openfe_analysis/tests/test_reader.py
+++ b/src/openfe_analysis/tests/test_reader.py
@@ -105,6 +105,8 @@ def test_universe_creation(simulation_nc, hybrid_system_pdb):
     )
     assert_allclose(u.dimensions, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
 
+    u.trajectory.close()
+
 
 def test_universe_from_nc_file(simulation_nc, hybrid_system_pdb):
     ds = nc.Dataset(simulation_nc)
@@ -135,6 +137,7 @@ def test_universe_creation_noconversion(simulation_nc, hybrid_system_pdb):
             ]
         ),
     )
+    u.trajectory.close()
 
 
 def test_fereader_negative_state(simulation_nc, hybrid_system_pdb):
@@ -143,6 +146,7 @@ def test_fereader_negative_state(simulation_nc, hybrid_system_pdb):
 
     assert u.trajectory._state_id == 10
     assert u.trajectory._replica_id is None
+    u.trajectory.close()
 
 
 def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
@@ -151,6 +155,7 @@ def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
 
     assert u.trajectory._state_id is None
     assert u.trajectory._replica_id == 9
+    u.trajectory.close()
 
 
 @pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
@@ -179,3 +184,5 @@ def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb)
         assert np.all(u.atoms.positions > 0)
     with pytest.raises(mda.exceptions.NoDataError, match="This Timestep has no velocities"):
         u.atoms.velocities
+
+    u.trajectory.close()
diff --git a/src/openfe_analysis/tests/test_transformations.py b/src/openfe_analysis/tests/test_transformations.py
index c8b89ec..3244137 100644
--- a/src/openfe_analysis/tests/test_transformations.py
+++ b/src/openfe_analysis/tests/test_transformations.py
@@ -13,12 +13,14 @@
 
 @pytest.fixture
 def universe(hybrid_system_pdb, simulation_nc):
-    return mda.Universe(
+    u = mda.Universe(
         hybrid_system_pdb,
         simulation_nc,
         format="MultiStateReporter",
         state_id=0,
     )
+    yield u
+    u.trajectory.close()
 
 
 #@pytest.mark.flaky(reruns=3)
diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index ed9b81e..bc21dde 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -15,12 +15,16 @@
 
 @pytest.fixture(scope='module')
 def dataset(simulation_nc):
-    return nc.Dataset(simulation_nc)
+    ds =  nc.Dataset(simulation_nc)
+    yield ds
+    ds.close()
 
 
 @pytest.fixture(scope='module')
 def skipped_dataset(simulation_skipped_nc):
-    return nc.Dataset(simulation_skipped_nc)
+    ds = nc.Dataset(simulation_skipped_nc)
+    yield ds
+    ds.close()
 
 
 @pytest.mark.flaky(reruns=3)

From 5dd31dd5f5ff0a5d61f5add555faeeac91900e64 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:54:20 +0100
Subject: [PATCH 13/19] None safety

---
 src/openfe_analysis/reader.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/openfe_analysis/reader.py b/src/openfe_analysis/reader.py
index b2bf23f..884550b 100644
--- a/src/openfe_analysis/reader.py
+++ b/src/openfe_analysis/reader.py
@@ -193,6 +193,7 @@ def _reopen(self):
         self._frame_index = -1
 
     def close(self):
-        if self._dataset_owner:
-            self._dataset.close()
-            self._dataset = None
+        if self._dataset is not None:
+            if self._dataset_owner:
+                self._dataset.close()
+                self._dataset = None

From 9439efdba8d3ed23440ba65dba85b0b2ba2d867f Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 14:57:22 +0100
Subject: [PATCH 14/19] disable some tests

---
 .../tests/utils/test_multistate.py            | 82 ++++++++++---------
 1 file changed, 42 insertions(+), 40 deletions(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index bc21dde..0eab99b 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -13,32 +13,32 @@
 )
 
 
-@pytest.fixture(scope='module')
-def dataset(simulation_nc):
-    ds =  nc.Dataset(simulation_nc)
-    yield ds
-    ds.close()
-
-
-@pytest.fixture(scope='module')
-def skipped_dataset(simulation_skipped_nc):
-    ds = nc.Dataset(simulation_skipped_nc)
-    yield ds
-    ds.close()
-
-
-@pytest.mark.flaky(reruns=3)
-@pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
-def test_state_to_replica(dataset, state, frame, replica):
-    assert _state_to_replica(dataset, state, frame) == replica
-
-
-@pytest.mark.flaky(reruns=3)
-def test_replica_positions_at_frame(dataset):
-    pos = _replica_positions_at_frame(dataset, 1, -1)
-    assert_allclose(
-        pos[-3] * unit("nanometer"), np.array([0.6037003, 7.2835016, 5.804355]) * unit("nanometer")
-    )
+#@pytest.fixture(scope='module')
+#def dataset(simulation_nc):
+#    ds =  nc.Dataset(simulation_nc)
+#    yield ds
+#    ds.close()
+#
+#
+#@pytest.fixture(scope='module')
+#def skipped_dataset(simulation_skipped_nc):
+#    ds = nc.Dataset(simulation_skipped_nc)
+#    yield ds
+#    ds.close()
+#
+#
+#@pytest.mark.flaky(reruns=3)
+#@pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
+#def test_state_to_replica(dataset, state, frame, replica):
+#    assert _state_to_replica(dataset, state, frame) == replica
+#
+#
+#@pytest.mark.flaky(reruns=3)
+#def test_replica_positions_at_frame(dataset):
+#    pos = _replica_positions_at_frame(dataset, 1, -1)
+#    assert_allclose(
+#        pos[-3] * unit("nanometer"), np.array([0.6037003, 7.2835016, 5.804355]) * unit("nanometer")
+#    )
 
 
 def test_create_new_dataset(tmpdir):
@@ -78,17 +78,19 @@ def test_create_new_dataset(tmpdir):
         assert ds.variables["cell_angles"].get_dims()[1].name == "cell_angular"
         assert ds.variables["cell_angles"].dtype.name == "float64"
 
-
-def test_get_unitcell(dataset):
-    dims = _get_unitcell(dataset, 7, -1)
-    assert_allclose(dims, [82.12723, 82.12723, 82.12723, 90.0, 90.0, 90.0])
-
-    dims = _get_unitcell(dataset, 3, 1)
-    assert_allclose(dims, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
-
-
-def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
-    skipped_dataset,
-):
-    assert _get_unitcell(dataset, 1, 1) is None
-    assert dataset.variables["positions"][1][0].mask.all()
+        ds.close()
+
+
+#def test_get_unitcell(dataset):
+#    dims = _get_unitcell(dataset, 7, -1)
+#    assert_allclose(dims, [82.12723, 82.12723, 82.12723, 90.0, 90.0, 90.0])
+#
+#    dims = _get_unitcell(dataset, 3, 1)
+#    assert_allclose(dims, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
+#
+#
+#def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
+#    skipped_dataset,
+#):
+#    assert _get_unitcell(dataset, 1, 1) is None
+#    assert dataset.variables["positions"][1][0].mask.all()

From 0c95db8f05962d8a3ac7ff2deb7546bb7321e94d Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 15:45:56 +0100
Subject: [PATCH 15/19] try something

---
 .../tests/utils/test_multistate.py            | 76 +++++++++----------
 1 file changed, 37 insertions(+), 39 deletions(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index 0eab99b..78d67a3 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -13,32 +13,30 @@
 )
 
 
-#@pytest.fixture(scope='module')
-#def dataset(simulation_nc):
-#    ds =  nc.Dataset(simulation_nc)
-#    yield ds
-#    ds.close()
-#
-#
-#@pytest.fixture(scope='module')
-#def skipped_dataset(simulation_skipped_nc):
-#    ds = nc.Dataset(simulation_skipped_nc)
-#    yield ds
-#    ds.close()
-#
-#
-#@pytest.mark.flaky(reruns=3)
-#@pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
-#def test_state_to_replica(dataset, state, frame, replica):
-#    assert _state_to_replica(dataset, state, frame) == replica
-#
-#
-#@pytest.mark.flaky(reruns=3)
-#def test_replica_positions_at_frame(dataset):
-#    pos = _replica_positions_at_frame(dataset, 1, -1)
-#    assert_allclose(
-#        pos[-3] * unit("nanometer"), np.array([0.6037003, 7.2835016, 5.804355]) * unit("nanometer")
-#    )
+@pytest.fixture(scope='module')
+def dataset(simulation_nc):
+    ds = nc.Dataset(simulation_nc)
+    yield ds
+    ds.close()
+
+
+@pytest.fixture(scope='module')
+def skipped_dataset(simulation_skipped_nc):
+    ds = nc.Dataset(simulation_skipped_nc)
+    yield ds
+    ds.close()
+
+
+@pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
+def test_state_to_replica(dataset, state, frame, replica):
+    assert _state_to_replica(dataset, state, frame) == replica
+
+
+def test_replica_positions_at_frame(dataset):
+    pos = _replica_positions_at_frame(dataset, 1, -1)
+    assert_allclose(
+        pos[-3] * unit("nanometer"), np.array([0.6037003, 7.2835016, 5.804355]) * unit("nanometer")
+    )
 
 
 def test_create_new_dataset(tmpdir):
@@ -81,16 +79,16 @@ def test_create_new_dataset(tmpdir):
         ds.close()
 
 
-#def test_get_unitcell(dataset):
-#    dims = _get_unitcell(dataset, 7, -1)
-#    assert_allclose(dims, [82.12723, 82.12723, 82.12723, 90.0, 90.0, 90.0])
-#
-#    dims = _get_unitcell(dataset, 3, 1)
-#    assert_allclose(dims, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
-#
-#
-#def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
-#    skipped_dataset,
-#):
-#    assert _get_unitcell(dataset, 1, 1) is None
-#    assert dataset.variables["positions"][1][0].mask.all()
+def test_get_unitcell(dataset):
+    dims = _get_unitcell(dataset, 7, -1)
+    assert_allclose(dims, [82.12723, 82.12723, 82.12723, 90.0, 90.0, 90.0])
+
+    dims = _get_unitcell(dataset, 3, 1)
+    assert_allclose(dims, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
+
+
+def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
+    skipped_dataset,
+):
+    assert _get_unitcell(dataset, 1, 1) is None
+    assert dataset.variables["positions"][1][0].mask.all()

From c762775a4ab03fd2663d9e644d470742b1a8b993 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 15:47:33 +0100
Subject: [PATCH 16/19] reduce scope

---
 src/openfe_analysis/tests/utils/test_multistate.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index 78d67a3..ac79661 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -13,14 +13,14 @@
 )
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture()
 def dataset(simulation_nc):
     ds = nc.Dataset(simulation_nc)
     yield ds
     ds.close()
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture()
 def skipped_dataset(simulation_skipped_nc):
     ds = nc.Dataset(simulation_skipped_nc)
     yield ds

From 784df07909384d3d84e6a8be4143220e987299d8 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 15:50:44 +0100
Subject: [PATCH 17/19] try pinning

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 2a15530..2815e04 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
 dependencies:
   - click
   - MDAnalysis
-  - netCDF4
+  - netCDF4 <1.7.1
   - openff-units
   - pip
   - tqdm

From 3f71be642575fd7010c46b66bc9730d72946b54f Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 15:52:14 +0100
Subject: [PATCH 18/19] remove -n call

---
 .github/workflows/ci.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 0160393..36a735f 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -67,7 +67,7 @@ jobs:
 
       - name: "Run tests"
         run: |
-          pytest -n auto -v --cov=openfe_analysis --cov-report=xml --durations=10
+          pytest -v --cov=openfe_analysis --cov-report=xml --durations=10
 
       - name: "Save pooch test data cache"
         id: cache-testdata-save

From 269acdaf43ac41eb676fc4214eab4ac2639f8fff Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Mon, 1 Sep 2025 15:54:27 +0100
Subject: [PATCH 19/19] fix typo

---
 src/openfe_analysis/tests/utils/test_multistate.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/openfe_analysis/tests/utils/test_multistate.py b/src/openfe_analysis/tests/utils/test_multistate.py
index ac79661..69c5cb6 100644
--- a/src/openfe_analysis/tests/utils/test_multistate.py
+++ b/src/openfe_analysis/tests/utils/test_multistate.py
@@ -90,5 +90,5 @@ def test_get_unitcell(dataset):
 def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
     skipped_dataset,
 ):
-    assert _get_unitcell(dataset, 1, 1) is None
-    assert dataset.variables["positions"][1][0].mask.all()
+    assert _get_unitcell(skipped_dataset, 1, 1) is None
+    assert skipped_dataset.variables["positions"][1][0].mask.all()