improvements to tests remove cache clearing (no longer needed) and cl…

…ose all test data files after reading to avoid warnings

TODO.md

@@ -25,3 +25,4 @@ lines marked with '!x' are current priorities
 * Fasta export - done
 * xEasy shifts - done
 release - done
+test_filter not committed

src/nef_pipelines/tests/chains/test_clone.py

@@ -4,7 +4,7 @@
 from nef_pipelines.lib.test_lib import (
     assert_lines_match,
     isolate_frame,
-    path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.tools.chains.clone import clone
@@ -13,13 +13,13 @@
 app = typer.Typer()
 app.command()(clone)
 
+INPUT_3AA_NEF = read_test_data("3aa.nef", __file__)
 
-# noinspection PyUnusedLocal
-def test_clone_basic(clear_cache):
 
-    INPUT = open(path_in_test_data(__file__, "3aa.nef")).read()
+# noinspection PyUnusedLocal
+def test_clone_basic():
 
-    result = run_and_report(app, ["A", "2"], input=INPUT)
+    result = run_and_report(app, ["A", "2"], input=INPUT_3AA_NEF)
 
     EXPECTED = """\
             save_nef_molecular_system
@@ -54,33 +54,27 @@ def test_clone_basic(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_bad_count(clear_cache):
+def test_bad_count():
 
-    INPUT = open(path_in_test_data(__file__, "3aa.nef")).read()
-
-    result = run_and_report(app, ["A", "0"], input=INPUT, expected_exit_code=1)
+    result = run_and_report(app, ["A", "0"], input=INPUT_3AA_NEF, expected_exit_code=1)
 
     assert result.exit_code == 1
 
     assert "clone count must be > 0" in result.stdout
 
 
 # noinspection PyUnusedLocal
-def test_bad_target(clear_cache):
-
-    INPUT = open(path_in_test_data(__file__, "3aa.nef")).read()
+def test_bad_target():
 
-    result = run_and_report(app, ["B", "1"], input=INPUT, expected_exit_code=1)
+    result = run_and_report(app, ["B", "1"], input=INPUT_3AA_NEF, expected_exit_code=1)
 
     assert "couldn't find target chain B" in result.stdout
 
 
 # noinspection PyUnusedLocal
-def test_custom_chains(clear_cache):
-
-    INPUT = open(path_in_test_data(__file__, "3aa.nef")).read()
+def test_custom_chains():
 
-    result = run_and_report(app, ["A", "2", "--chains", "D,E"], input=INPUT)
+    result = run_and_report(app, ["A", "2", "--chains", "D,E"], input=INPUT_3AA_NEF)
 
     EXPECTED = """\
             save_nef_molecular_system
@@ -115,9 +109,9 @@ def test_custom_chains(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_clone_chain_clash(clear_cache):
+def test_clone_chain_clash():
 
-    INPUT = open(path_in_test_data(__file__, "3aa_x3.nef")).read()
+    INPUT = read_test_data("3aa_x3.nef", __file__)
 
     result = run_and_report(app, ["A", "2"], input=INPUT)
 

src/nef_pipelines/tests/chains/test_list.py

@@ -2,7 +2,7 @@
 
 from nef_pipelines.lib.test_lib import (
     assert_lines_match,
-    path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.tools.chains.list import list as list_app
@@ -12,11 +12,11 @@
 
 
 # noinspection PyUnusedLocal
-def test_frame_basic(clear_cache):
+def test_frame_basic():
 
-    path = path_in_test_data(__file__, "multi_chain.nef")
+    input_data = read_test_data("multi_chain.nef", __file__)
 
-    result = run_and_report(app, [], input=open(path).read())
+    result = run_and_report(app, [], input=input_data)
 
     EXPECTED = "A B C"
 

src/nef_pipelines/tests/chains/test_rename.py

@@ -1,9 +1,10 @@
 import typer
+from pytest import fixture
 from typer.testing import CliRunner
 
 from nef_pipelines.lib.test_lib import (
     assert_lines_match,
-    path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.tools.chains.rename import rename
@@ -17,12 +18,17 @@
 RENAME_CHAINS_A_E = ["A", "E"]
 
 
+@fixture
+def INPUT_MULTI_CHAIN_SHIFTS_NEF():
+    return read_test_data("multi_chain_shifts.nef", __file__)
+
+
 # noinspection PyUnusedLocal
-def test_rename_basic(clear_cache):
+def test_rename_basic():
 
-    path = path_in_test_data(__file__, "multi_chain.nef")
+    INPUT = read_test_data("multi_chain.nef", __file__)
 
-    result = run_and_report(app, [*RENAME_CHAINS_B_D], input=open(path))
+    result = run_and_report(app, [*RENAME_CHAINS_B_D], input=INPUT)
 
     if result.exit_code != 0:
         print("INFO: stdout from failed read:\n", result.stdout)
@@ -65,11 +71,11 @@ def test_rename_basic(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_rename_multi_frame(clear_cache):
+def test_rename_multi_frame(INPUT_MULTI_CHAIN_SHIFTS_NEF):
 
-    path = path_in_test_data(__file__, "multi_chain_shifts.nef")
-
-    result = run_and_report(app, [*RENAME_CHAINS_A_E], input=open(path))
+    result = run_and_report(
+        app, [*RENAME_CHAINS_A_E], input=INPUT_MULTI_CHAIN_SHIFTS_NEF
+    )
 
     if result.exit_code != 0:
         print("INFO: stdout from failed read:\n", result.stdout)
@@ -140,12 +146,10 @@ def test_rename_multi_frame(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_rename_select_frame_by_name(clear_cache):
-
-    path = path_in_test_data(__file__, "multi_chain_shifts.nef")
+def test_rename_select_frame_by_name(INPUT_MULTI_CHAIN_SHIFTS_NEF):
 
     result = run_and_report(
-        app, ["--frame", "test", *RENAME_CHAINS_A_E], input=open(path)
+        app, ["--frame", "test", *RENAME_CHAINS_A_E], input=INPUT_MULTI_CHAIN_SHIFTS_NEF
     )
 
     if result.exit_code != 0:
@@ -213,14 +217,11 @@ def test_rename_select_frame_by_name(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_rename_select_frame_by_category(clear_cache):
-
-    path = path_in_test_data(__file__, "multi_chain_shifts.nef")
-    input = open(path).read()
+def test_rename_select_frame_by_category(INPUT_MULTI_CHAIN_SHIFTS_NEF):
 
     command = [*RENAME_CHAINS_A_E, "--frame", "mol", "--selector-type", "category"]
 
-    result = run_and_report(app, command, input=input)
+    result = run_and_report(app, command, input=INPUT_MULTI_CHAIN_SHIFTS_NEF)
 
     if result.exit_code != 0:
         print("INFO: stdout from failed read:\n", result.stdout)

src/nef_pipelines/tests/conftest.py

@@ -8,28 +8,6 @@ def fixed_seed():
     seed(42)
 
 
-@pytest.fixture
-def clear_cache():
-    """
-    clear the lru cache used by lib.util cached_stdin
-    see https://stackoverflow.com/questions/40273767/clear-all-lru-cache-in-python
-    """
-    import functools
-    import gc
-
-    gc.collect()
-    wrappers = []
-    for elem in gc.get_objects():
-        try:
-            if isinstance(elem, functools._lru_cache_wrapper):
-                wrappers.append(elem)
-        except ReferenceError:
-            pass
-
-    for wrapper in wrappers:
-        wrapper.cache_clear()
-
-
 def pytest_configure(config):
     from nef_pipelines.main import create_nef_app
 

src/nef_pipelines/tests/csv/test_import_rdcs.py

@@ -1,9 +1,11 @@
 import typer
+from pytest import fixture
 
 from nef_pipelines.lib.test_lib import (
     assert_lines_match,
     isolate_frame,
     path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.transcoders.csv.importers.rdcs import rdcs
@@ -12,15 +14,17 @@
 app.command()(rdcs)
 
 
+@fixture
+def INPUT_3A_AB_NEF():
+    return read_test_data("3a_ab.neff", __file__)
+
+
 # noinspection PyUnusedLocal
-def test_short_csv():
-    sequence_path = path_in_test_data(__file__, "3a_ab.neff")
+def test_short_csv(INPUT_3A_AB_NEF):
     csv_path = path_in_test_data(__file__, "short.csv")
 
-    nef_sequence = open(sequence_path, "r").read()
-
     args = [csv_path, "--chain-code", "AAAA"]
-    result = run_and_report(app, args, input=nef_sequence)
+    result = run_and_report(app, args, input=INPUT_3A_AB_NEF)
 
     EXPECTED = """\
         save_nef_rdc_restraint_list_rdcs
@@ -71,14 +75,11 @@ def test_short_csv():
     assert_lines_match(EXPECTED, result)
 
 
-def test_short_complete_csv():
-    sequence_path = path_in_test_data(__file__, "3a_ab.neff")
+def test_short_complete_csv(INPUT_3A_AB_NEF):
     csv_path = path_in_test_data(__file__, "short_complete.csv")
 
-    nef_sequence = open(sequence_path, "r").read()
-
     args = [csv_path]
-    result = run_and_report(app, args, input=nef_sequence)
+    result = run_and_report(app, args, input=INPUT_3A_AB_NEF)
 
     EXPECTED = """\
         save_nef_rdc_restraint_list_rdcs

src/nef_pipelines/tests/echidna/test_import_peaks.py

@@ -5,6 +5,7 @@
     isolate_frame,
     isolate_loop,
     path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.transcoders.echidna.importers.peaks import peaks
@@ -78,7 +79,7 @@ def test_basic():
 
     path = path_in_test_data(__file__, "echidna_peaks.txt")
 
-    data_sequence = open(path_in_test_data(__file__, "echidna_sequence.nef")).read()
+    data_sequence = read_test_data("echidna_sequence.nef", __file__)
 
     result = run_and_report(app, [path], input=data_sequence)
 

src/nef_pipelines/tests/frames/test_delete.py

@@ -3,7 +3,7 @@
 
 from nef_pipelines.lib.test_lib import (
     assert_lines_match,
-    path_in_test_data,
+    read_test_data,
     run_and_report,
 )
 from nef_pipelines.tools.frames.delete import delete
@@ -44,15 +44,13 @@
         save_
     """
 
+INPUT_PALES_TEST_1_NEF = read_test_data("pales_test_1.nef", __file__)
 
-# noinspection PyUnusedLocal
-def test_delete_type(clear_cache):
-
-    path = path_in_test_data(__file__, "pales_test_1.nef")
 
-    input_stream = open(path).read()
+# noinspection PyUnusedLocal
+def test_delete_type():
 
-    result = run_and_report(app, ["-c", "mol"], input=input_stream)
+    result = run_and_report(app, ["-c", "mol"], input=INPUT_PALES_TEST_1_NEF)
 
     assert_lines_match(EXPECTED_DELETE_CATEGORY, result.stdout)
 
@@ -85,12 +83,8 @@ def test_delete_type(clear_cache):
 
 
 # noinspection PyUnusedLocal
-def test_delete_name(clear_cache):
-
-    path = path_in_test_data(__file__, "pales_test_1.nef")
-
-    input_stream = open(path).read()
+def test_delete_name():
 
-    result = run_and_report(app, ["test_1"], input=input_stream)
+    result = run_and_report(app, ["test_1"], input=INPUT_PALES_TEST_1_NEF)
 
     assert_lines_match(EXPECTED_DELETE_NAME, result.stdout)