From 2102c832a1f48b25e6a483e97eccff25e0b71527 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 09:42:19 +0100
Subject: [PATCH 01/28] Use request.node.name for make_dantzig scenarios

---
 ixmp/testing/data.py               | 24 ++++++++++++++++++-----
 ixmp/tests/backend/test_base.py    |  4 ++--
 ixmp/tests/backend/test_jdbc.py    | 22 ++++++++++-----------
 ixmp/tests/core/test_scenario.py   |  4 ++--
 ixmp/tests/report/test_operator.py | 12 ++++++------
 ixmp/tests/report/test_reporter.py |  8 ++++----
 ixmp/tests/test_integration.py     | 31 ++++++++++++------------------
 ixmp/tests/test_model.py           |  8 ++++----
 ixmp/tests/test_util.py            | 22 ++++++++++-----------
 9 files changed, 71 insertions(+), 64 deletions(-)

diff --git a/ixmp/testing/data.py b/ixmp/testing/data.py
index 877c64f6e..216e06925 100644
--- a/ixmp/testing/data.py
+++ b/ixmp/testing/data.py
@@ -1,12 +1,13 @@
 # Methods are in alphabetical order
 from itertools import product
 from math import ceil
-from typing import Any, List
+from typing import Any, List, Optional
 
 import genno
 import numpy as np
 import pandas as pd
 import pint
+import pytest
 
 from ixmp import Platform, Scenario, TimeSeries
 from ixmp.backend import IAMC_IDX
@@ -158,7 +159,12 @@ def add_test_data(scen: Scenario):
     return t, t_foo, t_bar, x
 
 
-def make_dantzig(mp: Platform, solve: bool = False, quiet: bool = False) -> Scenario:
+def make_dantzig(
+    mp: Platform,
+    solve: bool = False,
+    quiet: bool = False,
+    request: Optional["pytest.FixtureRequest"] = None,
+) -> Scenario:
     """Return :class:`ixmp.Scenario` of Dantzig's canning/transport problem.
 
     Parameters
@@ -169,6 +175,8 @@ def make_dantzig(mp: Platform, solve: bool = False, quiet: bool = False) -> Scen
         If :obj:`True`. then solve the scenario before returning. Default :obj:`False`.
     quiet : bool, optional
         If :obj:`True`, suppress console output when solving.
+    request : :class:`pytest.FixtureRequest`, optional
+        If present, use for a distinct scenario name for each test.
 
     Returns
     -------
@@ -189,14 +197,20 @@ def make_dantzig(mp: Platform, solve: bool = False, quiet: bool = False) -> Scen
     # Initialize a new Scenario, and use the DantzigModel class' initialize()
     # method to populate it
     annot = "Dantzig's transportation problem for illustration and testing"
-    scen = Scenario(
-        mp,
-        **models["dantzig"],  # type: ignore [arg-type]
+    args = dict(
+        **models["dantzig"],
         version="new",
         annotation=annot,
         scheme="dantzig",
         with_data=True,
     )
+    if request:
+        # Use a distinct scenario name for a particular test
+        args.update(scenario=request.node.name)
+    scen = Scenario(
+        mp,
+        **args,  # type: ignore [arg-type]
+    )
 
     # commit the scenario
     scen.commit("Import Dantzig's transport problem for testing.")
diff --git a/ixmp/tests/backend/test_base.py b/ixmp/tests/backend/test_base.py
index 4020d9066..deb83c7f0 100644
--- a/ixmp/tests/backend/test_base.py
+++ b/ixmp/tests/backend/test_base.py
@@ -135,14 +135,14 @@ def test_cache_invalidate(self, test_mp):
 
         backend.cache_invalidate(ts, "par", "baz", dict(x=["x1", "x2"], y=["y1", "y2"]))
 
-    def test_del_ts(self, test_mp):
+    def test_del_ts(self, test_mp, request):
         """Test CachingBackend.del_ts()."""
         # Since CachingBackend is an abstract class, test it via JDBCBackend
         backend = test_mp._backend
         cache_size_pre = len(backend._cache)
 
         # Load data, thereby adding to the cache
-        s = make_dantzig(test_mp)
+        s = make_dantzig(test_mp, request=request)
         s.par("d")
 
         # Cache size has increased
diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index e59d4703e..b1bc5efd1 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -273,7 +273,7 @@ def test_connect_message(capfd, caplog):
 
 
 @pytest.mark.parametrize("arg", [True, False])
-def test_cache_arg(arg):
+def test_cache_arg(arg, request):
     """Test 'cache' argument, passed to CachingBackend."""
     mp = ixmp.Platform(
         backend="jdbc",
@@ -281,7 +281,7 @@ def test_cache_arg(arg):
         url="jdbc:hsqldb:mem://test_cache_false",
         cache=arg,
     )
-    scen = make_dantzig(mp)
+    scen = make_dantzig(mp, request=request)
 
     # Maybe put something in the cache
     scen.par("a")
@@ -339,8 +339,8 @@ def test_init(tmp_env, args, kwargs, action, kind, match):
         ixmp.Platform(*args, **kwargs)
 
 
-def test_gh_216(test_mp):
-    scen = make_dantzig(test_mp)
+def test_gh_216(test_mp, request):
+    scen = make_dantzig(test_mp, request=request)
 
     filters = dict(i=["seattle", "beijing"])
 
@@ -382,7 +382,7 @@ def test_verbose_exception(test_mp, exception_verbose_true):
     # See also test_base.TestCachingBackend.test_del_ts
     reason="https://github.com/iiasa/ixmp/issues/463",
 )
-def test_del_ts():
+def test_del_ts(request):
     mp = ixmp.Platform(
         backend="jdbc",
         driver="hsqldb",
@@ -394,9 +394,9 @@ def test_del_ts():
 
     # Create a list of some Scenario objects
     N = 8
-    scenarios = [make_dantzig(mp)]
+    scenarios = [make_dantzig(mp, request=request)]
     for i in range(1, N):
-        scenarios.append(scenarios[0].clone(scenario=f"clone {i}"))
+        scenarios.append(scenarios[0].clone(scenario=f"{request.node.name} clone {i}"))
 
     # Number of referenced objects has increased by 8
     assert len(mp._backend.jindex) == N_obj + N
@@ -648,8 +648,8 @@ def test_reload_cycle(
     memory_usage("shutdown")
 
 
-def test_docs(test_mp):
-    scen = make_dantzig(test_mp)
+def test_docs(test_mp, request):
+    scen = make_dantzig(test_mp, request=request)
     # test model docs
     test_mp.set_doc("model", {scen.model: "Dantzig model"})
     assert test_mp.get_doc("model") == {"canning problem": "Dantzig model"}
@@ -672,9 +672,9 @@ def test_docs(test_mp):
     assert ex.value.args[0] == exp
 
 
-def test_cache_clear(test_mp):
+def test_cache_clear(test_mp, request):
     """Removing set elements causes the cache to be cleared entirely."""
-    scen = make_dantzig(test_mp)
+    scen = make_dantzig(test_mp, request=request)
 
     # Load an item so that it is cached
     d0 = scen.par("d")
diff --git a/ixmp/tests/core/test_scenario.py b/ixmp/tests/core/test_scenario.py
index c61460a39..6259066fb 100644
--- a/ixmp/tests/core/test_scenario.py
+++ b/ixmp/tests/core/test_scenario.py
@@ -696,7 +696,7 @@ def test_filter_str(scen_empty):
     assert_frame_equal(exp[["s", "value"]], obs[["s", "value"]])
 
 
-def test_solve_callback(test_mp):
+def test_solve_callback(test_mp, request):
     """Test the callback argument to Scenario.solve().
 
     In real usage, callback() would compute some kind of convergence criterion. This
@@ -705,7 +705,7 @@ def test_solve_callback(test_mp):
     equals an expected value, and the model has 'converged'.
     """
     # Set up the Dantzig problem
-    scen = make_dantzig(test_mp)
+    scen = make_dantzig(test_mp, request=request)
 
     # Solve the scenario as configured
     solve_args = dict(model="dantzig", quiet=True)
diff --git a/ixmp/tests/report/test_operator.py b/ixmp/tests/report/test_operator.py
index 9e653c3b8..04ddfc95f 100644
--- a/ixmp/tests/report/test_operator.py
+++ b/ixmp/tests/report/test_operator.py
@@ -27,8 +27,8 @@
 pytestmark = pytest.mark.usefixtures("parametrize_quantity_class")
 
 
-def test_from_url(test_mp) -> None:
-    ts = make_dantzig(test_mp)
+def test_from_url(test_mp, request) -> None:
+    ts = make_dantzig(test_mp, request=request)
 
     full_url = f"ixmp://{ts.platform.name}/{ts.url}"
 
@@ -45,8 +45,8 @@ def test_from_url(test_mp) -> None:
     assert ts.url == result.url
 
 
-def test_get_remove_ts(caplog, test_mp) -> None:
-    ts = make_dantzig(test_mp)
+def test_get_remove_ts(caplog, test_mp, request) -> None:
+    ts = make_dantzig(test_mp, request=request)
 
     caplog.set_level(logging.INFO, "ixmp")
 
@@ -107,8 +107,8 @@ def test_map_as_qty() -> None:
     assert_qty_equal(exp, result)
 
 
-def test_update_scenario(caplog, test_mp) -> None:
-    scen = make_dantzig(test_mp)
+def test_update_scenario(caplog, test_mp, request) -> None:
+    scen = make_dantzig(test_mp, request=request)
     scen.check_out()
     scen.add_set("j", "toronto")
     scen.commit("Add j=toronto")
diff --git a/ixmp/tests/report/test_reporter.py b/ixmp/tests/report/test_reporter.py
index 230f9ad19..86b413df0 100644
--- a/ixmp/tests/report/test_reporter.py
+++ b/ixmp/tests/report/test_reporter.py
@@ -23,7 +23,7 @@ def scenario(test_mp):
 
 
 @pytest.mark.usefixtures("protect_rename_dims")
-def test_configure(test_mp, test_data_path) -> None:
+def test_configure(test_mp, test_data_path, request) -> None:
     # Configure globally; handles 'rename_dims' section
     configure(rename_dims={"i": "i_renamed"})
 
@@ -33,7 +33,7 @@ def test_configure(test_mp, test_data_path) -> None:
     assert "i" in RENAME_DIMS
 
     # Reporting uses the RENAME_DIMS mapping of 'i' to 'i_renamed'
-    scen = make_dantzig(test_mp)
+    scen = make_dantzig(test_mp, request=request)
     rep = Reporter.from_scenario(scen)
     assert "d:i_renamed-j" in rep, rep.graph.keys()
     assert ["seattle", "san-diego"] == rep.get("i_renamed")
@@ -142,10 +142,10 @@ def test_platform_units(test_mp, caplog, ureg) -> None:
     assert unit.dimensionality == {"[USD]": 1, "[pkm]": -1}
 
 
-def test_cli(ixmp_cli, test_mp, test_data_path) -> None:
+def test_cli(ixmp_cli, test_mp, test_data_path, request) -> None:
     # Put something in the database
     test_mp.open_db()
-    make_dantzig(test_mp)
+    make_dantzig(test_mp, request=request)
     test_mp.close_db()
 
     platform_name = test_mp.name
diff --git a/ixmp/tests/test_integration.py b/ixmp/tests/test_integration.py
index f5f3a2753..38606c3b8 100644
--- a/ixmp/tests/test_integration.py
+++ b/ixmp/tests/test_integration.py
@@ -1,6 +1,4 @@
 import logging
-import os
-import platform
 
 import numpy as np
 import pytest
@@ -14,7 +12,7 @@
 TS_DF_CLEARED.loc[0, 2005] = np.nan
 
 
-def test_run_clone(caplog, test_mp):
+def test_run_clone(caplog, test_mp, request):
     caplog.set_level(logging.WARNING)
 
     # this test is designed to cover the full functionality of the GAMS API
@@ -24,7 +22,7 @@ def test_run_clone(caplog, test_mp):
     # - reads back the solution from the output
     # - performs the test on the objective value and the timeseries data
     mp = test_mp
-    scen = make_dantzig(mp, solve=True, quiet=True)
+    scen = make_dantzig(mp, solve=True, quiet=True, request=request)
     assert np.isclose(scen.var("z")["lvl"], 153.675)
     assert_frame_equal(scen.timeseries(iamc=True), TS_DF)
 
@@ -57,10 +55,10 @@ def test_run_clone(caplog, test_mp):
     assert_frame_equal(scen4.timeseries(iamc=True), TS_DF_CLEARED)
 
 
-def test_run_remove_solution(test_mp):
+def test_run_remove_solution(test_mp, request):
     # create a new instance of the transport problem and solve it
     mp = test_mp
-    scen = make_dantzig(mp, solve=True, quiet=True)
+    scen = make_dantzig(mp, solve=True, quiet=True, request=request)
     assert np.isclose(scen.var("z")["lvl"], 153.675)
 
     # check that re-solving the model will raise an error if a solution exists
@@ -95,16 +93,10 @@ def get_distance(scen):
     return scen.par("d").set_index(["i", "j"]).loc["san-diego", "topeka"]["value"]
 
 
-@pytest.mark.flaky(
-    reruns=5,
-    rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Darwin",
-    reason="Flaky; see iiasa/ixmp#489",
-)
-def test_multi_db_run(tmpdir):
+def test_multi_db_run(tmpdir, request):
     # create a new instance of the transport problem and solve it
     mp1 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp1")
-    scen1 = make_dantzig(mp1, solve=True, quiet=True)
+    scen1 = make_dantzig(mp1, solve=True, quiet=True, request=request)
 
     mp2 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp2")
     # add other unit to make sure that the mapping is correct during clone
@@ -124,7 +116,8 @@ def test_multi_db_run(tmpdir):
     # reopen the connection to the second platform and reload scenario
     _mp2 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp2")
     assert_multi_db(mp1, _mp2)
-    scen2 = ixmp.Scenario(_mp2, **models["dantzig"])
+    args = dict(**models["dantzig"]).update(scenario=request.node.name)
+    scen2 = ixmp.Scenario(_mp2, **args)
 
     # check that sets, variables and parameter were copied correctly
     assert_array_equal(scen1.set("i"), scen2.set("i"))
@@ -138,10 +131,10 @@ def test_multi_db_run(tmpdir):
     assert_frame_equal(scen2.timeseries(iamc=True), TS_DF)
 
 
-def test_multi_db_edit_source(tmpdir):
+def test_multi_db_edit_source(tmpdir, request):
     # create a new instance of the transport problem
     mp1 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp1")
-    scen1 = make_dantzig(mp1)
+    scen1 = make_dantzig(mp1, request=request)
 
     mp2 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp2")
     scen2 = scen1.clone(platform=mp2)
@@ -163,10 +156,10 @@ def test_multi_db_edit_source(tmpdir):
     assert_multi_db(mp1, mp2)
 
 
-def test_multi_db_edit_target(tmpdir):
+def test_multi_db_edit_target(tmpdir, request):
     # create a new instance of the transport problem
     mp1 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp1")
-    scen1 = make_dantzig(mp1)
+    scen1 = make_dantzig(mp1, request=request)
 
     mp2 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp2")
     scen2 = scen1.clone(platform=mp2)
diff --git a/ixmp/tests/test_model.py b/ixmp/tests/test_model.py
index d9fd14ba2..83259563d 100644
--- a/ixmp/tests/test_model.py
+++ b/ixmp/tests/test_model.py
@@ -23,9 +23,9 @@ class M1(Model):
         M1()
 
 
-def test_model_initialize(test_mp, caplog):
+def test_model_initialize(test_mp, caplog, request):
     # Model.initialize runs on an empty Scenario
-    s = make_dantzig(test_mp)
+    s = make_dantzig(test_mp, request=request)
     b1 = s.par("b")
     assert len(b1) == 3
 
@@ -108,8 +108,8 @@ def test_gams_version():
 
 class TestGAMSModel:
     @pytest.fixture(scope="class")
-    def dantzig(self, test_mp):
-        yield make_dantzig(test_mp)
+    def dantzig(self, test_mp, request):
+        yield make_dantzig(test_mp, request=request)
 
     @pytest.mark.parametrize("char", r'<>"/\|?*')
     def test_filename_invalid_char(self, dantzig, char):
diff --git a/ixmp/tests/test_util.py b/ixmp/tests/test_util.py
index 8cf70219a..05f12e37e 100644
--- a/ixmp/tests/test_util.py
+++ b/ixmp/tests/test_util.py
@@ -56,10 +56,10 @@ def test_check_year():
     assert util.check_year(y3, s3) is True
 
 
-def test_diff_identical(test_mp):
+def test_diff_identical(test_mp, request):
     """diff() of identical Scenarios."""
-    scen_a = make_dantzig(test_mp)
-    scen_b = make_dantzig(test_mp)
+    scen_a = make_dantzig(test_mp, request=request)
+    scen_b = make_dantzig(test_mp, request=request)
 
     # Compare identical scenarios: produces data of same length
     for name, df in util.diff(scen_a, scen_b):
@@ -72,10 +72,10 @@ def test_diff_identical(test_mp):
         assert exp_name == name and len(df) == N
 
 
-def test_diff_data(test_mp):
+def test_diff_data(test_mp, request):
     """diff() when Scenarios contain the same items, but different data."""
-    scen_a = make_dantzig(test_mp)
-    scen_b = make_dantzig(test_mp)
+    scen_a = make_dantzig(test_mp, request=request)
+    scen_b = make_dantzig(test_mp, request=request)
 
     # Modify `scen_a` and `scen_b`
     scen_a.check_out()
@@ -133,10 +133,10 @@ def test_diff_data(test_mp):
             pdt.assert_frame_equal(exp_d.iloc[[0, 3], :].reset_index(drop=True), df)
 
 
-def test_diff_items(test_mp):
+def test_diff_items(test_mp, request):
     """diff() when Scenarios contain the different items."""
-    scen_a = make_dantzig(test_mp)
-    scen_b = make_dantzig(test_mp)
+    scen_a = make_dantzig(test_mp, request=request)
+    scen_b = make_dantzig(test_mp, request=request)
 
     # Modify `scen_a` and `scen_b`
     scen_a.check_out()
@@ -156,11 +156,11 @@ def test_diff_items(test_mp):
         pass  # No check of the contents
 
 
-def test_discard_on_error(caplog, test_mp):
+def test_discard_on_error(caplog, test_mp, request):
     caplog.set_level(logging.INFO, "ixmp.util")
 
     # Create a test scenario, checked-in state
-    s = make_dantzig(test_mp)
+    s = make_dantzig(test_mp, request=request)
     url = s.url
 
     # Some actions that don't trigger exceptions

From c625e12312e273bc6806c4ddf7e0ce77882e2fb6 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:04:38 +0100
Subject: [PATCH 02/28] Fix typo in docstring

---
 ixmp/core/platform.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ixmp/core/platform.py b/ixmp/core/platform.py
index 10b770b27..ce7021858 100644
--- a/ixmp/core/platform.py
+++ b/ixmp/core/platform.py
@@ -214,6 +214,7 @@ def export_timeseries_data(
             - subannual
             - year
             - value
+
         default : bool, optional
             :obj:`True` to include only TimeSeries versions marked as default.
         model: str, optional

From 31d7a44a012dfa1ee8389d815a0f858934772488 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:05:13 +0100
Subject: [PATCH 03/28] Group tutorials that depend on each other

---
 ixmp/tests/test_tutorials.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/ixmp/tests/test_tutorials.py b/ixmp/tests/test_tutorials.py
index 08fb739cd..7bea28fa2 100644
--- a/ixmp/tests/test_tutorials.py
+++ b/ixmp/tests/test_tutorials.py
@@ -7,15 +7,10 @@
 
 from ixmp.testing import get_cell_output, run_notebook
 
-FLAKY = pytest.mark.flaky(
-    reruns=5,
-    rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Darwin",
-    reason="Flaky; see iiasa/ixmp#489",
-)
+group_base_name = platform.system() + platform.python_version()
 
 
-@FLAKY
+@pytest.mark.xdist_group(name=f"{group_base_name}-0")
 def test_py_transport(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "py_transport.ipynb"
     nb, errors = run_notebook(fname, tmp_path, tmp_env)
@@ -25,7 +20,7 @@ def test_py_transport(tutorial_path, tmp_path, tmp_env):
     assert np.isclose(get_cell_output(nb, -5)["lvl"], 153.6750030517578)
 
 
-@FLAKY
+@pytest.mark.xdist_group(name=f"{group_base_name}-0")
 def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "py_transport_scenario.ipynb"
     nb, errors = run_notebook(fname, tmp_path, tmp_env)
@@ -35,7 +30,7 @@ def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
     assert np.isclose(get_cell_output(nb, "scen-detroit-z")["lvl"], 161.324)
 
 
-@FLAKY
+@pytest.mark.xdist_group(name=f"{group_base_name}-1")
 @pytest.mark.rixmp
 # TODO investigate and resolve the cause of the time outs; remove this mark
 @pytest.mark.skipif(
@@ -47,7 +42,7 @@ def test_R_transport(tutorial_path, tmp_path, tmp_env):
     assert errors == []
 
 
-@FLAKY
+@pytest.mark.xdist_group(name=f"{group_base_name}-1")
 @pytest.mark.rixmp
 # TODO investigate and resolve the cause of the time outs; remove this mark
 @pytest.mark.skipif(

From d68f757b4177436e8cf1d1711a5d2829e2f06682 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:05:55 +0100
Subject: [PATCH 04/28] Give every platform a test-specific name

---
 ixmp/tests/test_cli.py | 42 ++++++++++++++++++++++++++++++------------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/ixmp/tests/test_cli.py b/ixmp/tests/test_cli.py
index 48dd48151..15c66db1d 100644
--- a/ixmp/tests/test_cli.py
+++ b/ixmp/tests/test_cli.py
@@ -165,8 +165,9 @@ def call(*args, exit_0=True):
     assert UsageError.exit_code == r.exit_code
 
 
-def test_platform_copy(ixmp_cli, tmp_path):
+def test_platform_copy(ixmp_cli, tmp_path, request):
     """Test 'platform' command."""
+    test_specific_name = request.node.name
 
     def call(*args, exit_0=True):
         result = ixmp_cli.invoke(["platform"] + list(map(str, args)))
@@ -174,30 +175,47 @@ def call(*args, exit_0=True):
         return result
 
     # Add some temporary platform configuration
-    call("add", "p1", "jdbc", "oracle", "HOSTNAME", "USER", "PASSWORD")
-    call("add", "p2", "jdbc", "hsqldb", tmp_path.joinpath("p2"))
+    call(
+        "add",
+        f"p1-{test_specific_name}",
+        "jdbc",
+        "oracle",
+        "HOSTNAME",
+        "USER",
+        "PASSWORD",
+    )
+    call(
+        "add",
+        f"p2-{test_specific_name}",
+        "jdbc",
+        "hsqldb",
+        tmp_path.joinpath(f"p2-{test_specific_name}"),
+    )
     # Force connection to p2 so that files are created
-    ixmp_cli.invoke(["--platform=p2", "list"])
+    ixmp_cli.invoke([f"--platform=p2-{test_specific_name}", "list"])
 
     # Dry-run produces expected output
-    r = call("copy", "p2", "p3")
-    assert re.search("Copy .*p2.script → .*p3.script", r.output)
+    r = call("copy", f"p2-{test_specific_name}", f"p3-{test_specific_name}")
+    assert re.search(
+        f"Copy .*p2-{test_specific_name}.script → .*p3-{test_specific_name}.script",
+        r.output,
+    )
     with pytest.raises(ValueError):
         # New platform configuration is not saved
-        ixmp.config.get_platform_info("p3")
+        ixmp.config.get_platform_info(f"p3-{test_specific_name}")
 
     # --go actually copies files, saves new platform config
-    r = call("copy", "--go", "p2", "p3")
-    assert tmp_path.joinpath("p3.script").exists()
-    assert ixmp.config.get_platform_info("p3")
+    r = call("copy", "--go", f"p2-{test_specific_name}", f"p3-{test_specific_name}")
+    assert tmp_path.joinpath(f"p3-{test_specific_name}.script").exists()
+    assert ixmp.config.get_platform_info(f"p3-{test_specific_name}")
 
     # Dry-run again with existing config and files
-    r = call("copy", "p2", "p3")
+    r = call("copy", f"p2-{test_specific_name}", f"p3-{test_specific_name}")
     assert "would replace existing file" in r.output
 
     # Copying a non-HyperSQL-backed platform fails
     with pytest.raises(AssertionError):
-        call("copy", "p1", "p3")
+        call("copy", f"p1-{test_specific_name}", f"p3-{test_specific_name}")
 
 
 def test_import_ts(ixmp_cli, test_mp, test_data_path):

From 6a8bd547f9b3707bdf6fb2fc5718acb5c8813893 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:06:47 +0100
Subject: [PATCH 05/28] Use test-specific name for scenarios

---
 ixmp/tests/core/test_timeseries.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ixmp/tests/core/test_timeseries.py b/ixmp/tests/core/test_timeseries.py
index 50a6a6288..f7af7263b 100644
--- a/ixmp/tests/core/test_timeseries.py
+++ b/ixmp/tests/core/test_timeseries.py
@@ -87,7 +87,7 @@ def ts(self, request, mp):
         node = hash(request.node.nodeid.replace("/", " "))
         # Class of object to yield
         cls = request.param
-        yield cls(mp, model=f"test-{node}", scenario="test", version="new")
+        yield cls(mp, model=f"test-{node}", scenario=f"test-{node}", version="new")
 
     # Initialize TimeSeries
     @pytest.mark.parametrize("cls", [TimeSeries, Scenario])

From c7d94ef8d281076a63a5190c2f68ede734532b65 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:07:22 +0100
Subject: [PATCH 06/28] Use test-specific name for platforms

* Split up test_close to receive only clean stdout
---
 ixmp/tests/backend/test_jdbc.py | 40 ++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index b1bc5efd1..a8c937900 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -47,13 +47,7 @@ def test_jvm_warn(recwarn):
         assert len(recwarn) == 0, recwarn.pop().message
 
 
-@pytest.mark.flaky(
-    reruns=5,
-    rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
-    reason="Flaky; see iiasa/ixmp#489",
-)
-def test_close(test_mp_f, capfd):
+def test_close_default_logging(test_mp_f, capfd):
     """Platform.close_db() doesn't throw needless exceptions."""
     # Use the session-scoped fixture to avoid affecting other tests in this file
     mp = test_mp_f
@@ -68,9 +62,21 @@ def test_close(test_mp_f, capfd):
     captured = capfd.readouterr()
     assert captured.out == ""
 
-    # With log level INFO, a message is printed
+
+def test_close_increased_logging(test_mp_f, capfd):
+    """Platform.close_db() doesn't throw needless exceptions."""
+    # Use the session-scoped fixture to avoid affecting other tests in this file
+    mp = test_mp_f
+
+    # Close once
+    mp.close_db()
+
+    # Set higher log level INFO
     level = mp.get_log_level()
     mp.set_log_level(logging.INFO)
+
+    # Close again, once already closed
+    # With logging.INFO, a message is printed
     mp.close_db()
     captured = capfd.readouterr()
     msg = "Database connection could not be closed or was already closed"
@@ -237,19 +243,16 @@ def test_invalid_properties_file(test_data_path):
         ixmp.Platform(dbprops=test_data_path / "hsqldb.properties")
 
 
-@pytest.mark.flaky(
-    reruns=5,
-    rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
-    reason="Flaky; see iiasa/ixmp#489",
-)
-def test_connect_message(capfd, caplog):
-    msg = "connected to database 'jdbc:hsqldb:mem://ixmptest' (user: ixmp)..."
+def test_connect_message(capfd, caplog, request):
+    msg = (
+        f"connected to database 'jdbc:hsqldb:mem://{request.node.name}' (user: ixmp)..."
+    )
 
     ixmp.Platform(
+        name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
-        url="jdbc:hsqldb:mem://ixmptest",
+        url=f"jdbc:hsqldb:mem://{request.node.name}",
         log_level="INFO",
     )
 
@@ -262,9 +265,10 @@ def test_connect_message(capfd, caplog):
     #    in the above call. Try again now that the level is INFO:
 
     ixmp.Platform(
+        name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
-        url="jdbc:hsqldb:mem://ixmptest",
+        url=f"jdbc:hsqldb:mem://{request.node.name}",
     )
 
     # Instead, log messages are printed to stdout

From 38ac1745d1e09d556e5941ca53225a2c10649598 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:10:27 +0100
Subject: [PATCH 07/28] Revert temporary fix from #510

---
 .github/workflows/pytest.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index 8df2bee22..2f0fa21d2 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -135,13 +135,12 @@ jobs:
       shell: Rscript {0}
 
     - name: Run test suite using pytest
-    # FIXME: Use --numprocesses=auto once flaky tests are fixed
       run: |
         pytest ixmp \
           -m "not performance" \
           --color=yes -rA --verbose \
           --cov-report=xml \
-          --numprocesses=1
+          --numprocesses=auto --dist=loadgroup
       shell: bash
 
     - name: Upload test coverage to Codecov.io

From b955aab23123d7aad73a5d451f23d2ad5a7ff6b7 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Tue, 12 Mar 2024 13:48:13 +0100
Subject: [PATCH 08/28] Copy model["dantzig"] properly

* Adapt expected values to new scenario names
---
 ixmp/tests/test_integration.py | 36 ++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/ixmp/tests/test_integration.py b/ixmp/tests/test_integration.py
index 38606c3b8..caf5d6b88 100644
--- a/ixmp/tests/test_integration.py
+++ b/ixmp/tests/test_integration.py
@@ -24,12 +24,18 @@ def test_run_clone(caplog, test_mp, request):
     mp = test_mp
     scen = make_dantzig(mp, solve=True, quiet=True, request=request)
     assert np.isclose(scen.var("z")["lvl"], 153.675)
-    assert_frame_equal(scen.timeseries(iamc=True), TS_DF)
+    assert_frame_equal(
+        scen.timeseries(iamc=True),
+        TS_DF.assign(scenario=[scen.scenario, scen.scenario]),
+    )
 
     # cloning with `keep_solution=True` keeps all timeseries and the solution
     scen2 = scen.clone(keep_solution=True)
     assert np.isclose(scen2.var("z")["lvl"], 153.675)
-    assert_frame_equal(scen2.timeseries(iamc=True), TS_DF)
+    assert_frame_equal(
+        scen2.timeseries(iamc=True),
+        TS_DF.assign(scenario=[scen.scenario, scen.scenario]),
+    )
 
     # version attribute of the clone increments the original (GitHub #211)
     assert scen2.version == scen.version + 1
@@ -45,14 +51,19 @@ def test_run_clone(caplog, test_mp, request):
     # timeseries set as `meta=True`
     scen3 = scen.clone(keep_solution=False)
     assert np.isnan(scen3.var("z")["lvl"])
-    assert_frame_equal(scen3.timeseries(iamc=True), HIST_DF)
+    assert_frame_equal(
+        scen3.timeseries(iamc=True), HIST_DF.assign(scenario=scen.scenario)
+    )
 
     # cloning with `keep_solution=False` and `first_model_year`
     # drops the solution and removes all timeseries not marked `meta=True`
     # in the model horizon (i.e, `year >= first_model_year`)
     scen4 = scen.clone(keep_solution=False, shift_first_model_year=2005)
     assert np.isnan(scen4.var("z")["lvl"])
-    assert_frame_equal(scen4.timeseries(iamc=True), TS_DF_CLEARED)
+    assert_frame_equal(
+        scen4.timeseries(iamc=True),
+        TS_DF_CLEARED.assign(scenario=[scen.scenario, scen.scenario]),
+    )
 
 
 def test_run_remove_solution(test_mp, request):
@@ -70,7 +81,9 @@ def test_run_remove_solution(test_mp, request):
     scen2.remove_solution()
     assert not scen2.has_solution()
     assert np.isnan(scen2.var("z")["lvl"])
-    assert_frame_equal(scen2.timeseries(iamc=True), HIST_DF)
+    assert_frame_equal(
+        scen2.timeseries(iamc=True), HIST_DF.assign(scenario=scen.scenario)
+    )
 
     # remove the solution with a specific year as first model year, check that
     # variables are empty and timeseries not marked `meta=True` are removed
@@ -78,7 +91,10 @@ def test_run_remove_solution(test_mp, request):
     scen3.remove_solution(first_model_year=2005)
     assert not scen3.has_solution()
     assert np.isnan(scen3.var("z")["lvl"])
-    assert_frame_equal(scen3.timeseries(iamc=True), TS_DF_CLEARED)
+    assert_frame_equal(
+        scen3.timeseries(iamc=True),
+        TS_DF_CLEARED.assign(scenario=[scen.scenario, scen.scenario]),
+    )
 
 
 def scenario_list(mp):
@@ -116,7 +132,8 @@ def test_multi_db_run(tmpdir, request):
     # reopen the connection to the second platform and reload scenario
     _mp2 = ixmp.Platform(backend="jdbc", driver="hsqldb", path=tmpdir / "mp2")
     assert_multi_db(mp1, _mp2)
-    args = dict(**models["dantzig"]).update(scenario=request.node.name)
+    args = models["dantzig"].copy()
+    args.update(scenario=request.node.name)
     scen2 = ixmp.Scenario(_mp2, **args)
 
     # check that sets, variables and parameter were copied correctly
@@ -128,7 +145,10 @@ def test_multi_db_run(tmpdir, request):
     # check that custom unit, region and timeseries are migrated correctly
     assert scen2.par("f")["value"] == 90.0
     assert scen2.par("f")["unit"] == "USD/km"
-    assert_frame_equal(scen2.timeseries(iamc=True), TS_DF)
+    assert_frame_equal(
+        scen2.timeseries(iamc=True),
+        TS_DF.assign(scenario=[scen2.scenario, scen2.scenario]),
+    )
 
 
 def test_multi_db_edit_source(tmpdir, request):

From 3b629328a0e5ea3fa5ab482a585e4cdc98aa536d Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 09:07:03 +0100
Subject: [PATCH 09/28] Avoid searching for to-be-created test-specific
 platforms

---
 ixmp/tests/backend/test_jdbc.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index a8c937900..b736c524a 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -248,8 +248,10 @@ def test_connect_message(capfd, caplog, request):
         f"connected to database 'jdbc:hsqldb:mem://{request.node.name}' (user: ixmp)..."
     )
 
+    # TODO Specifying a name will fail because the test is looking for a platform with
+    # that name which doesn't exist yet.
     ixmp.Platform(
-        name=request.node.name,
+        # name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
         url=f"jdbc:hsqldb:mem://{request.node.name}",
@@ -265,7 +267,7 @@ def test_connect_message(capfd, caplog, request):
     #    in the above call. Try again now that the level is INFO:
 
     ixmp.Platform(
-        name=request.node.name,
+        # name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
         url=f"jdbc:hsqldb:mem://{request.node.name}",

From 540d6134c962ee79a0d72a993152ba63796484e6 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 09:27:27 +0100
Subject: [PATCH 10/28] Search for correct new scenario name

---
 ixmp/tests/report/test_reporter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ixmp/tests/report/test_reporter.py b/ixmp/tests/report/test_reporter.py
index 86b413df0..22e9cdf35 100644
--- a/ixmp/tests/report/test_reporter.py
+++ b/ixmp/tests/report/test_reporter.py
@@ -159,7 +159,7 @@ def test_cli(ixmp_cli, test_mp, test_data_path, request) -> None:
         "--model",
         "canning problem",
         "--scenario",
-        "standard",
+        f"{request.node.name}",
         "report",
         "--config",
         str(test_data_path / "report-config-0.yaml"),

From 4127f57e5ab6f7b50263563de27c1921fd0b0a82 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 10:02:16 +0100
Subject: [PATCH 11/28] Increase default cell runtime on GHA

---
 ixmp/tests/test_tutorials.py | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/ixmp/tests/test_tutorials.py b/ixmp/tests/test_tutorials.py
index 7bea28fa2..79da28f57 100644
--- a/ixmp/tests/test_tutorials.py
+++ b/ixmp/tests/test_tutorials.py
@@ -9,11 +9,23 @@
 
 group_base_name = platform.system() + platform.python_version()
 
+GHA = "GITHUB_ACTIONS" in os.environ
+
+
+def default_args():
+    """Default arguments for :func:`.run_notebook."""
+    if GHA:
+        # Use a longer timeout
+        return dict(timeout=30)
+    else:
+        return dict()
+
 
 @pytest.mark.xdist_group(name=f"{group_base_name}-0")
 def test_py_transport(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "py_transport.ipynb"
-    nb, errors = run_notebook(fname, tmp_path, tmp_env)
+    args = default_args()
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, **args)
     assert errors == []
 
     # FIXME use get_cell_by_name instead of assuming cell count/order is fixed
@@ -23,7 +35,8 @@ def test_py_transport(tutorial_path, tmp_path, tmp_env):
 @pytest.mark.xdist_group(name=f"{group_base_name}-0")
 def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "py_transport_scenario.ipynb"
-    nb, errors = run_notebook(fname, tmp_path, tmp_env)
+    args = default_args()
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, **args)
     assert errors == []
 
     assert np.isclose(get_cell_output(nb, "scen-z")["lvl"], 153.675)
@@ -38,7 +51,8 @@ def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
 )
 def test_R_transport(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "R_transport.ipynb"
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR")
+    args = default_args()
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR", **args)
     assert errors == []
 
 
@@ -50,5 +64,6 @@ def test_R_transport(tutorial_path, tmp_path, tmp_env):
 )
 def test_R_transport_scenario(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "R_transport_scenario.ipynb"
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR")
+    args = default_args()
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR", **args)
     assert errors == []

From 6c111d8fc32f243791eab13f4d548b0fd9cd6ba2 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 10:49:01 +0100
Subject: [PATCH 12/28] Use more test-specific platforms

---
 ixmp/tests/test_access.py | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/ixmp/tests/test_access.py b/ixmp/tests/test_access.py
index ddf3330e6..fe7d5b8ce 100644
--- a/ixmp/tests/test_access.py
+++ b/ixmp/tests/test_access.py
@@ -1,6 +1,4 @@
 import logging
-import os
-import platform
 import sys
 from subprocess import Popen
 from time import sleep
@@ -52,13 +50,7 @@ def mock(server):
     yield httpmock
 
 
-@pytest.mark.flaky(
-    reruns=5,
-    rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Darwin",
-    reason="Flaky; see iiasa/ixmp#489",
-)
-def test_check_single_model_access(mock, tmp_path, test_data_path):
+def test_check_single_model_access(mock, tmp_path, test_data_path, request):
     mock.when(
         "POST /access/list",
         body='.+"test_user".+',
@@ -71,7 +63,10 @@ def test_check_single_model_access(mock, tmp_path, test_data_path):
     ).reply("[false]", headers={"Content-Type": "application/json"}, times=FOREVER)
 
     test_props = create_test_platform(
-        tmp_path, test_data_path, "access", auth_url=mock.pretend_url
+        tmp_path,
+        test_data_path,
+        f"{request.node.name}_access",
+        auth_url=mock.pretend_url,
     )
 
     mp = ixmp.Platform(backend="jdbc", dbprops=test_props)

From 9f6afa39b8b630136a42c8079de5df8610ef4ff4 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 12:30:23 +0100
Subject: [PATCH 13/28] Make call to to-be-tested function explicit

---
 ixmp/tests/backend/test_base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ixmp/tests/backend/test_base.py b/ixmp/tests/backend/test_base.py
index deb83c7f0..b84920bea 100644
--- a/ixmp/tests/backend/test_base.py
+++ b/ixmp/tests/backend/test_base.py
@@ -138,7 +138,7 @@ def test_cache_invalidate(self, test_mp):
     def test_del_ts(self, test_mp, request):
         """Test CachingBackend.del_ts()."""
         # Since CachingBackend is an abstract class, test it via JDBCBackend
-        backend = test_mp._backend
+        backend: CachingBackend = test_mp._backend  # type: ignore
         cache_size_pre = len(backend._cache)
 
         # Load data, thereby adding to the cache
@@ -155,7 +155,7 @@ def test_del_ts(self, test_mp, request):
             s.__del__()  # Force deletion of cached objects associated with `s`
 
         # Delete the object; associated cache is freed
-        del s
+        backend.del_ts(s)
 
         # Objects were invalidated/removed from cache
         assert cache_size_pre == len(backend._cache)

From 4a6776961d9a361b0923f544d47139c788d32a6c Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Mon, 18 Mar 2024 12:55:34 +0100
Subject: [PATCH 14/28] Rename expected data files for individual tests

---
 ... => test_check_multi_model_access.properties} |  0
 .../test_check_single_model_access.properties    | 16 ++++++++++++++++
 ixmp/tests/test_access.py                        |  6 +++---
 3 files changed, 19 insertions(+), 3 deletions(-)
 rename ixmp/tests/data/{access.properties => test_check_multi_model_access.properties} (100%)
 create mode 100644 ixmp/tests/data/test_check_single_model_access.properties

diff --git a/ixmp/tests/data/access.properties b/ixmp/tests/data/test_check_multi_model_access.properties
similarity index 100%
rename from ixmp/tests/data/access.properties
rename to ixmp/tests/data/test_check_multi_model_access.properties
diff --git a/ixmp/tests/data/test_check_single_model_access.properties b/ixmp/tests/data/test_check_single_model_access.properties
new file mode 100644
index 000000000..24a595ba8
--- /dev/null
+++ b/ixmp/tests/data/test_check_single_model_access.properties
@@ -0,0 +1,16 @@
+# Used by test_access.py
+
+config.name = unit_test_db@local
+
+jdbc.driver = org.hsqldb.jdbcDriver
+jdbc.url = jdbc:hsqldb:mem:test_access
+jdbc.user = ixmp
+jdbc.pwd = ixmp
+
+application.tag = IXSE_SR15
+application.serverURL = http://localhost:8888
+
+config.server.url = {auth_url}
+config.server.config = DemoDB
+config.server.username = service_user_dev
+config.server.password = service_user_dev
diff --git a/ixmp/tests/test_access.py b/ixmp/tests/test_access.py
index fe7d5b8ce..42d6df993 100644
--- a/ixmp/tests/test_access.py
+++ b/ixmp/tests/test_access.py
@@ -65,7 +65,7 @@ def test_check_single_model_access(mock, tmp_path, test_data_path, request):
     test_props = create_test_platform(
         tmp_path,
         test_data_path,
-        f"{request.node.name}_access",
+        f"{request.node.name}",
         auth_url=mock.pretend_url,
     )
 
@@ -81,7 +81,7 @@ def test_check_single_model_access(mock, tmp_path, test_data_path, request):
     assert not granted
 
 
-def test_check_multi_model_access(mock, tmp_path, test_data_path):
+def test_check_multi_model_access(mock, tmp_path, test_data_path, request):
     mock.when(
         "POST /access/list",
         body='.+"test_user".+',
@@ -98,7 +98,7 @@ def test_check_multi_model_access(mock, tmp_path, test_data_path):
     )
 
     test_props = create_test_platform(
-        tmp_path, test_data_path, "access", auth_url=mock.pretend_url
+        tmp_path, test_data_path, f"{request.node.name}", auth_url=mock.pretend_url
     )
 
     mp = ixmp.Platform(backend="jdbc", dbprops=test_props)

From f3615ce13ad00806f84b997095ddc61c3152557e Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Fri, 22 Mar 2024 10:15:07 +0100
Subject: [PATCH 15/28] Call Scenario deletion function explicitly

---
 ixmp/tests/backend/test_jdbc.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index b736c524a..46dfa601c 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -423,7 +423,8 @@ def test_del_ts(request):
         s_jobj = mp._backend.jindex[s]
 
         # Now delete the Scenario object
-        del s
+        # del s # should work, but doesn't always resolve to s.__del__()
+        s.__del__()
 
         # Number of referenced objects decreases by 1
         assert len(mp._backend.jindex) == N_obj + N - (i + 1)

From 6216c02af09bae84e01b32d7dfc04ac01eeabbc3 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Fri, 22 Mar 2024 10:41:21 +0100
Subject: [PATCH 16/28] Call TimeSeries deletion function explicitly

---
 ixmp/tests/backend/test_jdbc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index 46dfa601c..ee68729fd 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -424,7 +424,7 @@ def test_del_ts(request):
 
         # Now delete the Scenario object
         # del s # should work, but doesn't always resolve to s.__del__()
-        s.__del__()
+        mp._backend.del_ts(s)
 
         # Number of referenced objects decreases by 1
         assert len(mp._backend.jindex) == N_obj + N - (i + 1)

From 12bfcc34a1a4e266eba4d8d8a44c4dea44db6277 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Fri, 22 Mar 2024 11:33:24 +0100
Subject: [PATCH 17/28] Add type hint for correct specific backend type

---
 ixmp/tests/backend/test_jdbc.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index ee68729fd..35c275cba 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -395,8 +395,10 @@ def test_del_ts(request):
         url="jdbc:hsqldb:mem:test_del_ts",
     )
 
+    backend: ixmp.backend.jdbc.JDBCBackend = mp._backend  # type: ignore
+
     # Number of Java objects referenced by the JDBCBackend
-    N_obj = len(mp._backend.jindex)
+    N_obj = len(backend.jindex)
 
     # Create a list of some Scenario objects
     N = 8
@@ -405,7 +407,7 @@ def test_del_ts(request):
         scenarios.append(scenarios[0].clone(scenario=f"{request.node.name} clone {i}"))
 
     # Number of referenced objects has increased by 8
-    assert len(mp._backend.jindex) == N_obj + N
+    assert len(backend.jindex) == N_obj + N
 
     # Pop and free the objects
     for i in range(N):
@@ -420,23 +422,23 @@ def test_del_ts(request):
         s_id = id(s)
 
         # Underlying Java object
-        s_jobj = mp._backend.jindex[s]
+        s_jobj = backend.jindex[s]
 
         # Now delete the Scenario object
         # del s # should work, but doesn't always resolve to s.__del__()
-        mp._backend.del_ts(s)
+        backend.del_ts(s)
 
         # Number of referenced objects decreases by 1
-        assert len(mp._backend.jindex) == N_obj + N - (i + 1)
+        assert len(backend.jindex) == N_obj + N - (i + 1)
         # ID is no longer in JDBCBackend.jindex
-        assert s_id not in mp._backend.jindex
+        assert s_id not in backend.jindex
 
         # s_jobj is the only remaining reference to the Java object
         assert getrefcount(s_jobj) - 1 == 1
         del s_jobj
 
     # Backend is again empty
-    assert len(mp._backend.jindex) == N_obj
+    assert len(backend.jindex) == N_obj
 
 
 # NB coverage is omitted because this test is not included in the standard suite

From 12464ed6bee796d0dc2137a014c65fa73cbbf2cb Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Fri, 22 Mar 2024 11:34:02 +0100
Subject: [PATCH 18/28] Remove timeseries from jindex explicitly

---
 ixmp/backend/jdbc.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ixmp/backend/jdbc.py b/ixmp/backend/jdbc.py
index 35d471385..805b9054b 100644
--- a/ixmp/backend/jdbc.py
+++ b/ixmp/backend/jdbc.py
@@ -728,6 +728,7 @@ def del_ts(self, ts):
 
         # Aggressively free memory
         self.gc()
+        self.jindex.pop(ts, None)
 
     def check_out(self, ts, timeseries_only):
         with _handle_jexception():

From d469fd3e9a13c5913ad5e93d93eb41a298926359 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Wed, 11 Sep 2024 13:21:03 +0200
Subject: [PATCH 19/28] Discard tmp_path directories after each test

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 421a53896..54e1b867e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,6 +105,7 @@ markers = [
   "rixmp: test of the ixmp R interface.",
   "performance: ixmp performance test.",
 ]
+tmp_path_retention_policy = "none"
 
 [tool.ruff.lint]
 select = ["C9", "E", "F", "I", "W"]

From bb48e78fd87998a3fd695c1f45c64a0f533e7ed9 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Wed, 11 Sep 2024 16:28:19 +0200
Subject: [PATCH 20/28] Drop workaround for jupyter/nbclient#85

---
 ixmp/testing/jupyter.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/ixmp/testing/jupyter.py b/ixmp/testing/jupyter.py
index 3c3cdbf9e..7850dc50b 100644
--- a/ixmp/testing/jupyter.py
+++ b/ixmp/testing/jupyter.py
@@ -48,16 +48,6 @@ def run_notebook(nb_path, tmp_path, env=None, **kwargs):
     import nbformat
     from nbclient import NotebookClient
 
-    # Workaround for https://github.com/jupyter/nbclient/issues/85
-    if (
-        sys.version_info[0] == 3
-        and sys.version_info[1] >= 8
-        and sys.platform.startswith("win")
-    ):
-        import asyncio
-
-        asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
-
     # Read the notebook
     nb = nbformat.read(nb_path, as_version=4)
 

From 918298f7708fa07d5e7485b713346820f3f5fba5 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Wed, 11 Sep 2024 16:47:30 +0200
Subject: [PATCH 21/28] Make second R tutorial independent with helper function

---
 tutorial/transport/R_transport_scenario.ipynb | 219 +++++++++++++-----
 1 file changed, 163 insertions(+), 56 deletions(-)

diff --git a/tutorial/transport/R_transport_scenario.ipynb b/tutorial/transport/R_transport_scenario.ipynb
index 44885e83f..76ff034a2 100644
--- a/tutorial/transport/R_transport_scenario.ipynb
+++ b/tutorial/transport/R_transport_scenario.ipynb
@@ -35,63 +35,109 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# Load reticulate, used to access the Python API from R\n",
     "library(reticulate)\n",
     "\n",
     "# Import ixmp and message_ix, just as in Python\n",
-    "ixmp <- import(\"ixmp\")"
+    "ixmp <- import(\"ixmp\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# launch the ix modeling platform using the local default database\n",
-    "mp <- ixmp$Platform()"
+    "mp <- ixmp$Platform()\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "scen_list <- mp$scenario_list()\n",
     "scen_list\n",
     "\n",
-    "# TODO: the conversion of the Java output of the `scenario_list()` function to a clean R dataframe is not yet implemented"
+    "# TODO: the conversion of the Java output of the `scenario_list()` function to a clean R dataframe is not yet implemented\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# details for loading an existing datastructure from the IX modeling platform\n",
     "model <- \"transport problem\"\n",
-    "scenario <- \"standard\""
+    "scenario <- \"standard\"\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you have just run the first, ``R_transport`` tutorial, the existing scenario should appear, and we can load it.\n",
+    "Uncomment and run the following line."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# load the default version scenario from the first tutorial\n",
-    "scen <- ixmp$Scenario(mp, model, scenario)"
+    "# scen <- ixmp$Scenario(mp, model, scenario)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If not (e.g. starting with this tutorial), we can use a function that creates the scenario from scratch in one step:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "ixmp_testing <- import(\"ixmp.testing\")\n",
+    "scen <- ixmp_testing$make_dantzig(mp, solve = \".\")\n"
    ]
   },
   {
@@ -106,38 +152,50 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# load the distance parameter\n",
-    "d = scen$par(\"d\")\n",
-    "d"
+    "d <- scen$par(\"d\")\n",
+    "d\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# show only the distances for connections from Seattle\n",
-    "d[d['i'] == \"seattle\",]"
+    "d[d[\"i\"] == \"seattle\", ]\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# for faster access or more complex filtering,\n",
     "# it may be easier to only load specific parameter elements using a dictionary\n",
-    "ele_filter = {}\n",
-    "ele_filter$i = c('seattle')\n",
-    "ele_filter$j = c('chicago', 'topeka')\n",
+    "ele_filter <- {}\n",
+    "ele_filter$i <- c(\"seattle\")\n",
+    "ele_filter$j <- c(\"chicago\", \"topeka\")\n",
     "\n",
-    "d_filtered = scen$par(\"d\", ele_filter)\n",
-    "d_filtered"
+    "d_filtered <- scen$par(\"d\", ele_filter)\n",
+    "d_filtered\n"
    ]
   },
   {
@@ -154,67 +212,83 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# create a new scenario by cloning the datastructure (without keeping the solution)\n",
-    "scen_detroit <- scen$clone(model, 'detroit', annotation='extend the Transport problem by a new city', keep_solution=FALSE)"
+    "scen_detroit <- scen$clone(model, \"detroit\", annotation = \"extend the Transport problem by a new city\", keep_solution = FALSE)\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# check out the datastructure to make changes\n",
-    "scen_detroit$check_out()"
+    "scen_detroit$check_out()\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
-    "# reduce demand \n",
-    "scen_detroit$add_par('b', 'chicago', 200, 'cases')\n",
+    "# reduce demand\n",
+    "scen_detroit$add_par(\"b\", \"chicago\", 200, \"cases\")\n",
     "\n",
     "# add a new city with demand and distances\n",
-    "scen_detroit$add_set('j', 'detroit')\n",
-    "scen_detroit$add_par('b', 'detroit', 150, 'cases')\n",
+    "scen_detroit$add_set(\"j\", \"detroit\")\n",
+    "scen_detroit$add_par(\"b\", \"detroit\", 150, \"cases\")\n",
     "\n",
-    "d_add = data.frame(i = c('seattle','san-diego'), j = c('detroit','detroit'), value = c(1.7,1.9) , unit = 'cases')\n",
-    "scen_detroit$add_par('d', d_add)"
+    "d_add <- data.frame(i = c(\"seattle\", \"san-diego\"), j = c(\"detroit\", \"detroit\"), value = c(1.7, 1.9), unit = \"cases\")\n",
+    "scen_detroit$add_par(\"d\", d_add)\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
-    "d_add = data.frame(i = c('seattle','san-diego'), j = c('detroit','detroit'), value = c(1.7,1.9) , unit = 'cases')\n",
-    "scen_detroit$add_par('d', d_add)"
+    "d_add <- data.frame(i = c(\"seattle\", \"san-diego\"), j = c(\"detroit\", \"detroit\"), value = c(1.7, 1.9), unit = \"cases\")\n",
+    "scen_detroit$add_par(\"d\", d_add)\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# save changes to database\n",
-    "comment = \"add new city 'detroit' with demand, reduce demand in 'chicago'\"\n",
-    "scen_detroit$commit(comment)                                                                                                       \n",
-    "scen_detroit$set_as_default()"
+    "comment <- \"add new city 'detroit' with demand, reduce demand in 'chicago'\"\n",
+    "scen_detroit$commit(comment)\n",
+    "scen_detroit$set_as_default()\n"
    ]
   },
   {
@@ -228,11 +302,14 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
-    "scen_detroit$solve(model='dantzig')"
+    "scen_detroit$solve(model = \"dantzig\")\n"
    ]
   },
   {
@@ -247,61 +324,85 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the objective value of the solution in the baseline scenario\n",
-    "scen$var(\"z\")"
+    "scen$var(\"z\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the objective value of the solution in the \"detroit\" scenario\n",
-    "scen_detroit$var(\"z\")"
+    "scen_detroit$var(\"z\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the quantities transported from canning plants to demand locations in the baseline scenario\n",
-    "scen$var(\"x\")"
+    "scen$var(\"x\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the quantities transported from canning plants to demand locations in the \"detroit\" scenario\n",
-    "scen_detroit$var(\"x\")"
+    "scen_detroit$var(\"x\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the quantities and marginals (=shadow prices) of the demand balance constraints in the baseline scenario\n",
-    "scen$equ(\"demand\")"
+    "scen$equ(\"demand\")\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
    "outputs": [],
    "source": [
     "# display the quantities and marginals (=shadow prices) of the demand balance constraints in the \"detroit\" scenario\n",
-    "scen_detroit$equ(\"demand\")"
+    "scen_detroit$equ(\"demand\")\n"
    ]
   },
   {
@@ -315,19 +416,25 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": [
     "# close the connection of the platform instance to the local ixmp database files\n",
-    "mp$close_db()"
+    "mp$close_db()\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "vscode": {
+     "languageId": "r"
+    }
    },
    "outputs": [],
    "source": []

From 34f059593f7c338470371f83055c57cf2261253f Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 08:46:37 +0200
Subject: [PATCH 22/28] Mark first tutorial tests as flaky on Windows

---
 ixmp/tests/test_tutorials.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/ixmp/tests/test_tutorials.py b/ixmp/tests/test_tutorials.py
index 79da28f57..dc7cee6fb 100644
--- a/ixmp/tests/test_tutorials.py
+++ b/ixmp/tests/test_tutorials.py
@@ -12,6 +12,14 @@
 GHA = "GITHUB_ACTIONS" in os.environ
 
 
+FLAKY = pytest.mark.flaky(
+    reruns=5,
+    rerun_delay=2,
+    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
+    reason="Flaky; see iiasa/ixmp#543",
+)
+
+
 def default_args():
     """Default arguments for :func:`.run_notebook."""
     if GHA:
@@ -21,6 +29,7 @@ def default_args():
         return dict()
 
 
+@FLAKY
 @pytest.mark.xdist_group(name=f"{group_base_name}-0")
 def test_py_transport(tutorial_path, tmp_path, tmp_env):
     fname = tutorial_path / "transport" / "py_transport.ipynb"
@@ -43,6 +52,7 @@ def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
     assert np.isclose(get_cell_output(nb, "scen-detroit-z")["lvl"], 161.324)
 
 
+@FLAKY
 @pytest.mark.xdist_group(name=f"{group_base_name}-1")
 @pytest.mark.rixmp
 # TODO investigate and resolve the cause of the time outs; remove this mark

From 6a50d322e8238c3121214e7154c7d3c6d63a4947 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 08:46:58 +0200
Subject: [PATCH 23/28] Mark test_del_ts as flaky on Windows

---
 ixmp/tests/backend/test_jdbc.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index 35c275cba..1b61b44a3 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -382,6 +382,12 @@ def test_verbose_exception(test_mp, exception_verbose_true):
     assert "at.ac.iiasa.ixmp.Platform.getScenario" in exc_msg
 
 
+@pytest.mark.flaky(
+    reruns=5,
+    rerun_delay=2,
+    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
+    reason="Flaky; see iiasa/ixmp#543",
+)
 @pytest.mark.xfail(
     condition=sys.version_info.minor <= 10,
     raises=AssertionError,

From 5b30a639afd3edf165a5ab64d92e0d85b2fc3b4d Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 10:14:28 +0200
Subject: [PATCH 24/28] Remove xfail marker for consistently xpassing test

---
 ixmp/tests/backend/test_jdbc.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index 1b61b44a3..22b92d418 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -2,7 +2,6 @@
 import logging
 import os
 import platform
-import sys
 from sys import getrefcount
 from typing import Tuple
 
@@ -388,12 +387,6 @@ def test_verbose_exception(test_mp, exception_verbose_true):
     condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
     reason="Flaky; see iiasa/ixmp#543",
 )
-@pytest.mark.xfail(
-    condition=sys.version_info.minor <= 10,
-    raises=AssertionError,
-    # See also test_base.TestCachingBackend.test_del_ts
-    reason="https://github.com/iiasa/ixmp/issues/463",
-)
 def test_del_ts(request):
     mp = ixmp.Platform(
         backend="jdbc",

From fc76fab72d679cb85c3d49afdac90c1465a5734c Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 10:43:28 +0200
Subject: [PATCH 25/28] Distinguish platforms for more stability

---
 ixmp/tests/backend/test_jdbc.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/ixmp/tests/backend/test_jdbc.py b/ixmp/tests/backend/test_jdbc.py
index 22b92d418..aebfc56bb 100644
--- a/ixmp/tests/backend/test_jdbc.py
+++ b/ixmp/tests/backend/test_jdbc.py
@@ -244,16 +244,14 @@ def test_invalid_properties_file(test_data_path):
 
 def test_connect_message(capfd, caplog, request):
     msg = (
-        f"connected to database 'jdbc:hsqldb:mem://{request.node.name}' (user: ixmp)..."
+        f"connected to database 'jdbc:hsqldb:mem://{request.node.name}_0' "
+        "(user: ixmp)..."
     )
 
-    # TODO Specifying a name will fail because the test is looking for a platform with
-    # that name which doesn't exist yet.
     ixmp.Platform(
-        # name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
-        url=f"jdbc:hsqldb:mem://{request.node.name}",
+        url=f"jdbc:hsqldb:mem://{request.node.name}_0",
         log_level="INFO",
     )
 
@@ -264,12 +262,14 @@ def test_connect_message(capfd, caplog, request):
     #    a previous run may have left the Java log level higher than INFO, in which
     #    case the Java Platform object would not write to stderr before set_log_level()
     #    in the above call. Try again now that the level is INFO:
-
+    msg = (
+        f"connected to database 'jdbc:hsqldb:mem://{request.node.name}_1' "
+        "(user: ixmp)..."
+    )
     ixmp.Platform(
-        # name=request.node.name,
         backend="jdbc",
         driver="hsqldb",
-        url=f"jdbc:hsqldb:mem://{request.node.name}",
+        url=f"jdbc:hsqldb:mem://{request.node.name}_1",
     )
 
     # Instead, log messages are printed to stdout

From 61b40cbf2e9485c098e23a2f05233e955469295c Mon Sep 17 00:00:00 2001
From: Paul Natsuo Kishimoto <mail@paul.kishimoto.name>
Date: Thu, 12 Sep 2024 11:41:33 +0200
Subject: [PATCH 26/28] Expand typing in .testing.data

---
 ixmp/testing/data.py | 56 +++++++++++++++++++++++++++++---------------
 1 file changed, 37 insertions(+), 19 deletions(-)

diff --git a/ixmp/testing/data.py b/ixmp/testing/data.py
index 216e06925..9de18009c 100644
--- a/ixmp/testing/data.py
+++ b/ixmp/testing/data.py
@@ -1,7 +1,7 @@
 # Methods are in alphabetical order
 from itertools import product
 from math import ceil
-from typing import Any, List, Optional
+from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
 import genno
 import numpy as np
@@ -12,8 +12,31 @@
 from ixmp import Platform, Scenario, TimeSeries
 from ixmp.backend import IAMC_IDX
 
+if TYPE_CHECKING:
+    from typing import TypedDict
+
+    class ScenarioIdentifiers(TypedDict):
+        """Identifiers of a Scenario.
+
+        Used only for type checking in this file, so version is omitted.
+        """
+
+        model: str
+        scenario: str
+
+    class ScenarioKwargs(TypedDict, total=False):
+        """Keyword arguments to Scenario.__init__()."""
+
+        model: str
+        scenario: str
+        version: str
+        scheme: str
+        annotation: str
+        with_data: Optional[bool]
+
+
 #: Common (model name, scenario name) pairs for testing.
-SCEN = {
+SCEN: Dict[str, "ScenarioIdentifiers"] = {
     "dantzig": dict(model="canning problem", scenario="standard"),
     "h2g2": dict(model="Douglas Adams", scenario="Hitchhiker"),
 }
@@ -186,7 +209,7 @@ def make_dantzig(
     --------
     .DantzigModel
     """
-    # add custom units and region for timeseries data
+    # Add custom units and region for time series data
     try:
         mp.add_unit("USD/km")
     except Exception:
@@ -194,36 +217,31 @@ def make_dantzig(
         pass
     mp.add_region("DantzigLand", "country")
 
-    # Initialize a new Scenario, and use the DantzigModel class' initialize()
-    # method to populate it
-    annot = "Dantzig's transportation problem for illustration and testing"
-    args = dict(
+    # Initialize a new Scenario, and use the DantzigModel class' initialize() method to
+    # populate it
+    args: "ScenarioKwargs" = dict(
         **models["dantzig"],
         version="new",
-        annotation=annot,
+        annotation="Dantzig's transportation problem for illustration and testing",
         scheme="dantzig",
         with_data=True,
     )
-    if request:
-        # Use a distinct scenario name for a particular test
-        args.update(scenario=request.node.name)
-    scen = Scenario(
-        mp,
-        **args,  # type: ignore [arg-type]
-    )
+    # Use a distinct scenario name for a particular test
+    args.update({"scenario": request.node.name} if request else {})
+
+    scen = Scenario(mp, **args)
 
-    # commit the scenario
+    # Commit the scenario
     scen.commit("Import Dantzig's transport problem for testing.")
 
-    # set this new scenario as the default version for the model/scenario name
+    # Set this new scenario as the default version for the model/scenario name
     scen.set_as_default()
 
     if solve:
         # Solve the model using the GAMS code provided in the `tests` folder
         scen.solve(model="dantzig", case="transport_standard", quiet=quiet)
 
-    # add timeseries data for testing `clone(keep_solution=False)`
-    # and `remove_solution()`
+    # Add time series data for testing clone(keep_solution=False) and remove_solution()
     scen.check_out(timeseries_only=True)
     scen.add_timeseries(HIST_DF, meta=True)
     scen.add_timeseries(INP_DF)

From 97f1121555a417caa2de5d3a3d83d9240790c976 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 12:09:43 +0200
Subject: [PATCH 27/28] Remove editor-specific notebook metadata

---
 tutorial/transport/R_transport_scenario.ipynb | 128 ++++--------------
 1 file changed, 23 insertions(+), 105 deletions(-)

diff --git a/tutorial/transport/R_transport_scenario.ipynb b/tutorial/transport/R_transport_scenario.ipynb
index 76ff034a2..3346c89ec 100644
--- a/tutorial/transport/R_transport_scenario.ipynb
+++ b/tutorial/transport/R_transport_scenario.ipynb
@@ -35,11 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# Load reticulate, used to access the Python API from R\n",
@@ -53,10 +49,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -67,11 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "scen_list <- mp$scenario_list()\n",
@@ -84,10 +73,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -108,10 +94,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -129,11 +112,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "ixmp_testing <- import(\"ixmp.testing\")\n",
@@ -152,11 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# load the distance parameter\n",
@@ -167,11 +142,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# show only the distances for connections from Seattle\n",
@@ -181,11 +152,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# for faster access or more complex filtering,\n",
@@ -212,10 +179,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -227,10 +191,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -241,11 +202,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# reduce demand\n",
@@ -263,10 +220,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -278,10 +232,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -302,10 +253,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -324,11 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the objective value of the solution in the baseline scenario\n",
@@ -338,11 +282,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the objective value of the solution in the \"detroit\" scenario\n",
@@ -352,11 +292,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the quantities transported from canning plants to demand locations in the baseline scenario\n",
@@ -366,11 +302,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the quantities transported from canning plants to demand locations in the \"detroit\" scenario\n",
@@ -380,11 +312,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the quantities and marginals (=shadow prices) of the demand balance constraints in the baseline scenario\n",
@@ -394,11 +322,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "# display the quantities and marginals (=shadow prices) of the demand balance constraints in the \"detroit\" scenario\n",
@@ -416,10 +340,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -431,10 +352,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true,
-    "vscode": {
-     "languageId": "r"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": []

From 749709e131c983e86137c56b545d64c7910e5824 Mon Sep 17 00:00:00 2001
From: Fridolin Glatter <glatter@iiasa.ac.at>
Date: Thu, 12 Sep 2024 12:09:59 +0200
Subject: [PATCH 28/28] Address review comments

---
 ixmp/tests/test_tutorials.py | 42 ++++++++++++++++--------------------
 1 file changed, 18 insertions(+), 24 deletions(-)

diff --git a/ixmp/tests/test_tutorials.py b/ixmp/tests/test_tutorials.py
index dc7cee6fb..6d82dc395 100644
--- a/ixmp/tests/test_tutorials.py
+++ b/ixmp/tests/test_tutorials.py
@@ -15,26 +15,23 @@
 FLAKY = pytest.mark.flaky(
     reruns=5,
     rerun_delay=2,
-    condition="GITHUB_ACTIONS" in os.environ and platform.system() == "Windows",
+    condition=GHA and platform.system() == "Windows",
     reason="Flaky; see iiasa/ixmp#543",
 )
 
 
+@pytest.fixture(scope="session")
 def default_args():
     """Default arguments for :func:`.run_notebook."""
-    if GHA:
-        # Use a longer timeout
-        return dict(timeout=30)
-    else:
-        return dict()
+    # Use a longer timeout for GHA
+    return dict(timeout=30) if GHA else dict()
 
 
 @FLAKY
 @pytest.mark.xdist_group(name=f"{group_base_name}-0")
-def test_py_transport(tutorial_path, tmp_path, tmp_env):
+def test_py_transport(tutorial_path, tmp_path, tmp_env, default_args):
     fname = tutorial_path / "transport" / "py_transport.ipynb"
-    args = default_args()
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, **args)
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, **default_args)
     assert errors == []
 
     # FIXME use get_cell_by_name instead of assuming cell count/order is fixed
@@ -42,10 +39,9 @@ def test_py_transport(tutorial_path, tmp_path, tmp_env):
 
 
 @pytest.mark.xdist_group(name=f"{group_base_name}-0")
-def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
+def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env, default_args):
     fname = tutorial_path / "transport" / "py_transport_scenario.ipynb"
-    args = default_args()
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, **args)
+    nb, errors = run_notebook(fname, tmp_path, tmp_env, **default_args)
     assert errors == []
 
     assert np.isclose(get_cell_output(nb, "scen-z")["lvl"], 153.675)
@@ -56,24 +52,22 @@ def test_py_transport_scenario(tutorial_path, tmp_path, tmp_env):
 @pytest.mark.xdist_group(name=f"{group_base_name}-1")
 @pytest.mark.rixmp
 # TODO investigate and resolve the cause of the time outs; remove this mark
-@pytest.mark.skipif(
-    "GITHUB_ACTIONS" in os.environ and sys.platform == "linux", reason="Times out"
-)
-def test_R_transport(tutorial_path, tmp_path, tmp_env):
+@pytest.mark.skipif(GHA and sys.platform == "linux", reason="Times out")
+def test_R_transport(tutorial_path, tmp_path, tmp_env, default_args):
     fname = tutorial_path / "transport" / "R_transport.ipynb"
-    args = default_args()
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR", **args)
+    nb, errors = run_notebook(
+        fname, tmp_path, tmp_env, kernel_name="IR", **default_args
+    )
     assert errors == []
 
 
 @pytest.mark.xdist_group(name=f"{group_base_name}-1")
 @pytest.mark.rixmp
 # TODO investigate and resolve the cause of the time outs; remove this mark
-@pytest.mark.skipif(
-    "GITHUB_ACTIONS" in os.environ and sys.platform == "linux", reason="Times out"
-)
-def test_R_transport_scenario(tutorial_path, tmp_path, tmp_env):
+@pytest.mark.skipif(GHA and sys.platform == "linux", reason="Times out")
+def test_R_transport_scenario(tutorial_path, tmp_path, tmp_env, default_args):
     fname = tutorial_path / "transport" / "R_transport_scenario.ipynb"
-    args = default_args()
-    nb, errors = run_notebook(fname, tmp_path, tmp_env, kernel_name="IR", **args)
+    nb, errors = run_notebook(
+        fname, tmp_path, tmp_env, kernel_name="IR", **default_args
+    )
     assert errors == []