Fix tests, add cli tests and fix some broken cli elements

Fix tests, add cli tests and fix some broken cli elements

.gitignore

@@ -140,4 +140,10 @@ ENV/
 
 # docs 
 docs/_build/
-docs/API/_autosummary/
+docs/API/_autosummary/
+
+# pyc files
+*.pyc
+
+# pycache files 
+__pycache__/

choppa/cli/cli.py

@@ -6,7 +6,7 @@
 from choppa.align import AlignFactory
 from choppa.render import PublicationView, InteractiveView
 from choppa.cli.utils import SpecialHelpOrder
-
+from pathlib import Path
 
 @click.group(
     cls=SpecialHelpOrder,
@@ -111,9 +111,11 @@ def render(
     confidence_column: Optional[str] = None,
 ):
 
-    if not outfile_publication[-4:] == ".pse":
+    # check extensions
+    if not Path(outfile_publication).suffix == ".pse":
         raise ValueError("--op/--outfile-publication should end in '.pse'.")
-    elif not outfile_interactive[-5:] == ".html":
+
+    if not Path(outfile_interactive).suffix == ".html":
         raise ValueError("--oi/--outfile-interactive should end in '.html'.")
 
     fitness_dict = FitnessFactory(

choppa/tests/test_choppa.py

@@ -28,7 +28,7 @@ def test_choppa_imported():
 from choppa import render
 
 
-def test_choppa_render_toy_mac1_sectioned():
+def test_choppa_render_toy_mac1_sectioned(tmp_path):
     """Tests that `choppa` is able to render views on a fitness dataset that
     has poor (fractioned) overlap with a toy PDB file."""
 
@@ -50,18 +50,22 @@ def test_choppa_render_toy_mac1_sectioned():
     assert "".join([val["aa"] for val in alignment[6:25]]) == "KLTDNVYIKNADIVEEAKK"
 
     render.PublicationView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
     ).render()
 
     render.InteractiveView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
     ).render()
 
     # we know the intended output, test on this.
     assert len(filled_aligned_fitness_dict) == 164
     assert 4 not in filled_aligned_fitness_dict
     assert 5 in filled_aligned_fitness_dict
 
+    # check files exist
+    assert (tmp_path / "test.pse").exists()
+    assert (tmp_path / "test.html").exists()
+
 
 def test_choppa_correct_custom_columns():
     """Tests that `choppa` is able to read in correct columns in input fitness data."""
@@ -89,7 +93,7 @@ def test_choppa_incorrect_custom_columns():
         ).get_fitness_basedict()
 
 
-def test_choppa_render_toy_mac1_sectioned_noconf():
+def test_choppa_render_toy_mac1_sectioned_noconf(tmp_path):
     """Tests that `choppa` is able to render views on a fitness dataset that
     has poor (fractioned) overlap with a toy PDB file, while not adding confidence."""
 
@@ -100,17 +104,21 @@ def test_choppa_render_toy_mac1_sectioned_noconf():
     filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
 
     render.PublicationView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
     ).render()
 
     render.InteractiveView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
     ).render()
 
     assert len(filled_aligned_fitness_dict) == 164
 
+    # check files exist
+    assert (tmp_path / "test.pse").exists()
+    assert (tmp_path / "test.html").exists()
+
 
-def test_choppa_render_toy_mac1_full():
+def test_choppa_render_toy_mac1_full(tmp_path):
     """Tests that `choppa` is able to render views on a fitness dataset that
     has complete overlap with a toy PDB file."""
 
@@ -123,17 +131,20 @@ def test_choppa_render_toy_mac1_full():
     filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
 
     render.PublicationView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
     ).render()
 
     render.InteractiveView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
     ).render()
 
     assert len(filled_aligned_fitness_dict) == 164
 
+    # check files exist
+    assert (tmp_path / "test.pse").exists()
+    assert (tmp_path / "test.html").exists()
 
-def test_choppa_render_toy_mac1_truncated():
+def test_choppa_render_toy_mac1_truncated(tmp_path):
     """Tests that `choppa` is able to render views on a fitness dataset that
     has decenr (trunacted at either end) overlap with a toy PDB file."""
 
@@ -146,11 +157,15 @@ def test_choppa_render_toy_mac1_truncated():
     filled_aligned_fitness_dict = AlignFactory(fitness_dict, complex).align_fitness()
 
     render.PublicationView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.pse"
     ).render()
 
     render.InteractiveView(
-        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7
+        filled_aligned_fitness_dict, complex, complex_rdkit, fitness_threshold=0.7, output_session_file=tmp_path/"test.html"
     ).render()
 
     assert len(filled_aligned_fitness_dict) == 164
+
+    # check files exist
+    assert (tmp_path / "test.pse").exists()
+    assert (tmp_path / "test.html").exists()

choppa/tests/test_cli.py

@@ -0,0 +1,47 @@
+from click.testing import CliRunner
+import traceback
+import pytest
+
+
+def click_success(result):
+    if result.exit_code != 0:  # -no-cov-  (only occurs on test error)
+        print(result.output)
+        traceback.print_tb(result.exc_info[2])
+        print(result.exc_info[0], result.exc_info[1])
+    return result.exit_code == 0
+
+
+from choppa.cli.cli import cli
+from choppa.data.toy_data.resources import (
+    TOY_COMPLEX,
+    TOY_FITNESS_DATA_COMPLETE,
+    TOY_FITNESS_DATA_TRUNCATED,
+)
+from choppa.data.toy_data.resources import (
+    TOY_FITNESS_DATA_SECTIONED,
+    TOY_FITNESS_DATA_COMPLETE_NOCONF,
+)
+
+def test_choppa_cli_help():
+    runner = CliRunner()
+    result = runner.invoke(cli, ["--help"])
+    assert click_success(result)
+
+
+def test_choppa_cli_render(tmp_path):
+    runner = CliRunner()
+    result = runner.invoke(cli, ["render",
+                                "--pdb-file", TOY_COMPLEX,
+                                "--fitness-file", TOY_FITNESS_DATA_SECTIONED,
+                                "--fitness-threshold", 0.7,
+                                "--outfile-publication", tmp_path / "out.pse",
+                                "--outfile-interactive", tmp_path / "out.html",
+                                  ])
+    assert click_success(result)
+    # check the files exist
+    assert (tmp_path / "out.pse").exists()
+    assert (tmp_path / "out.html").exists()
+
+
+
+