Merge branch '6-fixing-tests-for-the-export-function' into 'main'

Fixed the export_test bug. The tests used to fail when the test_graph was not...

Closes #6

See merge request pydisk/examples/vizitig!6

vizitig/generate_graph.py

 import argparse
 from itertools import groupby
 from pathlib import Path
-from typing import Iterator, Mapping, MutableMapping, Tuple, Any
+from typing import Any, Iterator, Mapping, MutableMapping, Tuple
 
 import networkdisk as nd
 from tqdm import tqdm
@@ -22,7 +22,7 @@ def chunk(g, n):
 def nodes_iter_from_desc(
     it: Iterator[NodeHeader],
     k: int,
-    gene_annotation: None | MutableMapping[str, set[str]] = None
+    gene_annotation: None | MutableMapping[str, set[str]] = None,
 ) -> Iterator[Tuple[int, Mapping]]:
     for node in it:
         d: MutableMapping[str, Any] = dict(seq=node.sequence)
@@ -81,7 +81,7 @@ def generate_graph(
             G.add_nodes_from(list(u))
         else:
             list(u)
-    
+
     G.graph["genes"] = {k: tuple(v) for k,v in genes_metas_data.items() }
 
     log(timed=True)
@@ -110,7 +110,7 @@ def generate_graph(
     if not parse_only:
         G.reindex()
         log(timed=True)
-    
+
 
 
 def build_cli(args):

vizitig/genes/__init__.py

 from pathlib import Path
+from typing import Iterator
 
 from vizitig.cli import subparsers
 from vizitig.info import get_graph, reload_graph
 from vizitig.parsing import parse_gtf, parse_reference_sequences
 from vizitig.update.bulk_update import tag_graph_from_kmer_gene
-from typing import Iterator
+
 
 def main(args):
     Graph = get_graph(args.graph_name)

vizitig/metadata.py

 import re
-from typing import Any, Iterable, Literal, Optional, Mapping
+from typing import Any, Iterable, Literal, Optional
 
 from networkdisk.sqlite import DiGraph
 from pydantic import BaseModel

vizitig/tests/test_export.py

 import random
+from pathlib import Path
 
-from pytest import raises
+from pytest import fixture, mark, raises
 
-from vizitig.errors import *
+from vizitig.errors import EmptyExportError
 from vizitig.export import export_graph
+from vizitig.tests.utils import create_dummy_graph, delete_dummy_graph, test_graph_name
 
 
-def test_export_graph_bcalm_in_normal_conditions(tmp_path):
+@fixture(scope="function")
+def Setup_and_cleaning_fixture_for_vizitig_graph_testing():
+    """This fixture is used to setup and clean before and after a test.
+    First it calls create_dummy_grah that creates a dummy graph and will be 
+    used for testing, then it deletes all the files that contain the 
+    test_graph_name wth delete_dummy_graph, to remove the .db and .fa
+    files that were created for the test. 
+    In between, it runs the test. 
+    """
+    create_dummy_graph()
+    yield
+    delete_dummy_graph()
+
+
+@mark.usefixtures("Setup_and_cleaning_fixture_for_vizitig_graph_testing")
+def test_export_graph_bcalm_in_normal_conditions(tmp_path: Path):
     test_file = tmp_path / "file"
-    export_graph("test", list(range(32)), "bcalm", test_file)
+    export_graph(test_graph_name, list(range(32)), "bcalm", test_file)
     assert test_file.exists()
     test_file.unlink()
 
 
-def test_export_graph_bcalm_subgraph(tmp_path):
+@mark.usefixtures("Setup_and_cleaning_fixture_for_vizitig_graph_testing")
+def test_export_graph_bcalm_subgraph(tmp_path: Path):
     test_file = tmp_path / "file"
-    export_graph("test", random.sample(list(range(32)), 16), "bcalm", test_file)
+    sample_nodes = random.sample(list(range(32)), 16) + [1] #We want to extract at least the first node.
+    #With small example graphs, it can happen that no nodes are picked in the sample so we add
+    #at least the first node to avoid the EmptyExportError
+    export_graph(test_graph_name, sample_nodes, "bcalm", test_file)
     assert test_file.exists()
     test_file.unlink()
 
 
-def test_export_graph_bcalm_crashes_with_bad_nodes_id(tmp_path):
+@mark.usefixtures("Setup_and_cleaning_fixture_for_vizitig_graph_testing")
+def test_export_graph_bcalm_crashes_with_bad_nodes_id(tmp_path: Path):
     test_file = tmp_path / "file"
     with raises(EmptyExportError):
-        export_graph("test", list([-1]), "bcalm", test_file)
+        export_graph(test_graph_name, list([-1]), "bcalm", test_file)
     assert not test_file.exists()
 
-
-"""
-def test_deux():
-    assert True
-    assert True
-
-def test_trois():
-    with raises(ValueError):
-        raise ValueError()
-
-def test_quatres():
-    with raises(ValueError):
-        raise TypeError()
-"""