TST: Organise test files

tests/test_cli_graphbin.py

@@ -0,0 +1,40 @@
+import pathlib
+import pytest
+
+from click.testing import CliRunner
+
+from gbintk.cli import graphbin
+
+
+__author__ = "Vijini Mallawaarachchi"
+__credits__ = ["Vijini Mallawaarachchi"]
+
+
+DATADIR = pathlib.Path(__file__).parent / "data"
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("tmp")
+
+
+@pytest.fixture(autouse=True)
+def workingdir(tmp_dir, monkeypatch):
+    """set the working directory for all tests"""
+    monkeypatch.chdir(tmp_dir)
+
+
+@pytest.fixture(scope="session")
+def runner():
+    """exportrc works correctly."""
+    return CliRunner()
+
+
+def test_graphbin_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "ESC_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "ESC_metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "ESC_metaSPAdes" / "contigs.paths"
+    binned = DATADIR / "ESC_metaSPAdes" / "initial_binning_res.csv"
+    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --output {outpath}".split()
+    r = runner.invoke(graphbin, args, catch_exceptions=False)
+    assert r.exit_code == 0, r.output

tests/test_cli_graphbin2.py

@@ -0,0 +1,42 @@
+import pathlib
+import pytest
+
+from click.testing import CliRunner
+
+from gbintk.cli import graphbin2
+
+
+__author__ = "Vijini Mallawaarachchi"
+__credits__ = ["Vijini Mallawaarachchi"]
+
+
+DATADIR = pathlib.Path(__file__).parent / "data"
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("tmp")
+
+
+@pytest.fixture(autouse=True)
+def workingdir(tmp_dir, monkeypatch):
+    """set the working directory for all tests"""
+    monkeypatch.chdir(tmp_dir)
+
+
+@pytest.fixture(scope="session")
+def runner():
+    """exportrc works correctly."""
+    return CliRunner()
+
+
+def test_graphbin2_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    binned = DATADIR / "Sim-5G+metaSPAdes" / "initial_contig_bins.csv"
+    abundance = DATADIR / "Sim-5G+metaSPAdes" / "abundance.abund"
+    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --abundance {abundance} --output {outpath}".split()
+    r = runner.invoke(graphbin2, args, catch_exceptions=False)
+    assert r.exit_code == 0, r.output
+

tests/test_cli_metacoag.py

@@ -0,0 +1,40 @@
+import pathlib
+import pytest
+
+from click.testing import CliRunner
+
+from gbintk.cli import metacoag
+
+
+__author__ = "Vijini Mallawaarachchi"
+__credits__ = ["Vijini Mallawaarachchi"]
+
+
+DATADIR = pathlib.Path(__file__).parent / "data"
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("tmp")
+
+
+@pytest.fixture(autouse=True)
+def workingdir(tmp_dir, monkeypatch):
+    """set the working directory for all tests"""
+    monkeypatch.chdir(tmp_dir)
+
+
+@pytest.fixture(scope="session")
+def runner():
+    """exportrc works correctly."""
+    return CliRunner()
+
+
+def test_metacoag_run(runner, tmp_dir):
+    outpath = tmp_dir
+    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
+    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
+    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
+    abundance = DATADIR / "Sim-5G+metaSPAdes" / "coverm_mean_coverage.tsv"
+    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --abundance {abundance} --output {outpath}".split()
+    r = runner.invoke(metacoag, args, catch_exceptions=False)
+    assert r.exit_code == 0, r.output

tests/test_cli.py → tests/test_visualise.py

@@ -3,7 +3,7 @@
 
 from click.testing import CliRunner
 
-from gbintk.cli import graphbin, graphbin2, metacoag, visualise
+from gbintk.cli import visualise
 
 
 __author__ = "Vijini Mallawaarachchi"
@@ -29,37 +29,6 @@ def runner():
     return CliRunner()
 
 
-def test_graphbin_run(runner, tmp_dir):
-    outpath = tmp_dir
-    graph = DATADIR / "ESC_metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "ESC_metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "ESC_metaSPAdes" / "contigs.paths"
-    binned = DATADIR / "ESC_metaSPAdes" / "initial_binning_res.csv"
-    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --output {outpath}".split()
-    r = runner.invoke(graphbin, args, catch_exceptions=False)
-    assert r.exit_code == 0, r.output
-
-def test_graphbin2_run(runner, tmp_dir):
-    outpath = tmp_dir
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
-    binned = DATADIR / "Sim-5G+metaSPAdes" / "initial_contig_bins.csv"
-    abundance = DATADIR / "Sim-5G+metaSPAdes" / "abundance.abund"
-    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --binned {binned} --abundance {abundance} --output {outpath}".split()
-    r = runner.invoke(graphbin2, args, catch_exceptions=False)
-    assert r.exit_code == 0, r.output
-
-def test_metacoag_run(runner, tmp_dir):
-    outpath = tmp_dir
-    graph = DATADIR / "Sim-5G+metaSPAdes" / "assembly_graph_with_scaffolds.gfa"
-    contigs = DATADIR / "Sim-5G+metaSPAdes" / "contigs.fasta"
-    paths = DATADIR / "Sim-5G+metaSPAdes" / "contigs.paths"
-    abundance = DATADIR / "Sim-5G+metaSPAdes" / "coverm_mean_coverage.tsv"
-    args = f"--assembler spades --graph {graph} --contigs {contigs} --paths {paths} --abundance {abundance} --output {outpath}".split()
-    r = runner.invoke(metacoag, args, catch_exceptions=False)
-    assert r.exit_code == 0, r.output
-
 def test_visualise_run(runner, tmp_dir):
     outpath = tmp_dir
     initial = DATADIR / "Sim-5G+metaSPAdes" / "metacoag_res.csv"