Refactor test for comparing output, do not show plots while testing, no default behavior modified

.pre-commit-config.yaml

@@ -15,6 +15,7 @@ repos:
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
+        exclude: \.json$
       - id: trailing-whitespace
       - id: check-case-conflict
       - id: check-merge-conflict

src/diffpy/nmf_mapping/main.py

@@ -132,8 +132,6 @@ def tup(s):
             n_iter=args1.n_iter,
         )
 
-    print(f"Number of components: {len(df_components.columns)}")
-
     fig1 = nmf.component_plot(df_components, args1.xrd, args1.x_units, args1.show)
     fig2 = nmf.component_ratio_plot(df_component_weight_timeseries, args1.show)
     fig3 = nmf.reconstruction_error_plot(df_reconstruction_error, args1.show)

tests/output/output_1/component_index_vs_RE_value.json

@@ -1 +1 @@
-{"0":{"1":297.2320764418,"2":99.3169152025,"3":0.1930209752,"4":0.1930209752,"5":0.1930209752,"6":0.1930209752,"7":0.1930209752,"8":0.1930209752,"9":0.1930209752,"10":0.1930209752}}
+{"0":{"1":297.2320764418,"2":99.3384847868,"3":24.2757958967,"4":8.3941967981,"5":2.4565516346,"6":0.0706811697,"7":0.0703110956,"8":0.0208623408,"9":0.0405341728,"10":0.0089427879}}

tests/output/output_1/component_index_vs_pratio_col.json

@@ -1 +1 @@
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tests/output/output_2/component_index_vs_RE_value.json

@@ -1 +1 @@
-{"0":{"1":477.1151575591,"2":181.8950165697,"3":0.5234417462,"4":0.5234417462,"5":0.5234417462,"6":0.5234417462,"7":0.5234417462,"8":0.5234417462,"9":0.5234417462,"10":0.5234417462}}
+{"0":{"1":477.1151575591,"2":181.9381472904,"3":3.8968296168,"4":15.4446994529,"5":0.050537146,"6":0.1378804104,"7":0.0095666506,"8":0.0625164884,"9":0.0060391372,"10":0.0309647978}}

tests/output/output_2/component_index_vs_pratio_col.json

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tests/output/output_3/component_index_vs_RE_value.json

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tests/output/output_3/component_index_vs_pratio_col.json

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+{"0":{"0":0.0168483558,"1":0.117327529,"2":0.0,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.8658241152},"1":{"0":0.0179629734,"1":0.1170146489,"2":0.0,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.8650223778},"2":{"0":0.0262724752,"1":0.1146821194,"2":0.0,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.8590454054},"3":{"0":0.0805258769,"1":0.0994528482,"2":0.0,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.820021275},"4":{"0":0.2555019877,"1":0.0441429394,"2":0.0064862269,"3":0.0073345631,"4":1.146011953e-16,"5":3.546697364e-17,"6":8.140367365e-18,"7":3.231527263e-17,"8":4.990301329e-18,"9":0.6865342829},"5":{"0":0.4061366003,"1":0.0000654218,"2":0.0132761594,"3":0.0003124753,"4":2.346387479e-18,"5":2.896192144e-17,"6":1.213711146e-18,"7":2.770338831e-17,"8":3.260488575e-19,"9":0.5802093432},"6":{"0":0.449054886,"1":0.0,"2":0.0147890624,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.5361560515},"7":{"0":0.4516724924,"1":0.0,"2":0.015230926,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.5330965816},"8":{"0":0.4465301811,"1":0.0,"2":0.0156226071,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.5378472119},"9":{"0":0.4380744452,"1":0.0,"2":0.0161455081,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.5457800467},"10":{"0":0.4264071166,"1":0.0,"2":0.0168538394,"3":0.0,"4":0.0,"5":0.0,"6":0.0,"7":0.0,"8":0.0,"9":0.556739044},"11":{"0":0.4148289826,"1":0.0043123039,"2":0.017697499,"3":0.0004905993,"4":3.474720006e-17,"5":5.777310661e-18,"6":3.34966024e-17,"7":4.447510266e-18,"8":3.152805328e-17,"9":0.5626706152},"12":{"0":0.4011490489,"1":0.0111071105,"2":0.0187456136,"3":0.0014332389,"4":3.953478394e-17,"5":1.111267914e-17,"6":3.906374586e-17,"7":9.685651253e-18,"8":3.549408614e-17,"9":0.5675649881},"13":{"0":0.3841734669,"1":0.0196221281,"2":0.0200615948,"3":0.0023327278,"4":2.522326894e-17,"5":5.313558256e-17,"6":2.131873785e-17,"7":3.610242092e-17,"8":6.274111642e-18,"9":0.5738100825},"14":{"0":0.3636549619,"1":0.0300043761,"2":0.0216688716,"3":0.0031277202,"4":3.288153694e-17,"5":3.413422277e-18,"6":3.209816748e-17,"7":2.085207332e-18,"8":2.901151457e-17,"9":0.5815440702},"15":{"0":0.3395655167,"1":0.0424597029,"2":0.0236050523,"3":0.0031976087,"4":5.746894537e-17,"5":2.678184911e-17,"6":5.355612749e-17,"7":2.380789845e-17,"8":5.143729232e-17,"9":0.5911721194},"16":{"0":0.3118806072,"1":0.0567959587,"2":0.0258342655,"3":0.0032068532,"4":2.737908101e-17,"5":5.697172716e-17,"6":2.525153279e-17,"7":5.477632262e-17,"8":2.381830614e-17,"9":0.6022823153},"17":{"0":0.2809213168,"1":0.0728278083,"2":0.0283271347,"3":0.0032171912,"4":1.063655904e-16,"5":1.39931364e-17,"6":4.466989042e-17,"7":1.387778602e-17,"8":4.396144972e-17,"9":0.6147065489},"18":{"0":0.2473168644,"1":0.0902294193,"2":0.0310329947,"3":0.0032284124,"4":5.708350806e-17,"5":2.552189034e-17,"6":5.66807739e-17,"7":2.508600621e-17,"8":5.530763378e-17,"9":0.6281923092},"19":{"0":0.2120123944,"1":0.1085113614,"2":0.0338757416,"3":0.0032402013,"4":1.261304571e-16,"5":2.910178085e-17,"6":6.081715666e-17,"7":2.73617201e-17,"8":5.492411636e-17,"9":0.6423603013},"20":{"0":0.1762369906,"1":0.1270371702,"2":0.0367564085,"3":0.0032521475,"4":5.011707666e-17,"5":1.602241291e-17,"6":4.901316229e-17,"7":1.059994125e-17,"8":4.194337415e-17,"9":0.6567172833},"21":{"0":0.1414069941,"1":0.1450734126,"2":0.0395609504,"3":0.003263778,"4":9.04426869e-17,"5":5.594916817e-17,"6":2.167730137e-17,"7":5.407301009e-17,"8":1.977703592e-17,"9":0.670694865},"22":{"0":0.1089649458,"1":0.1618748962,"2":0.0421735466,"3":0.0032687469,"4":2.025346899e-17,"5":4.78285362e-17,"6":1.124366533e-17,"7":4.275183056e-17,"8":7.725132856e-18,"9":0.6837178645},"23":{"0":0.0801810212,"1":0.1767986608,"2":0.0444946526,"3":0.0032186804,"4":6.820673466e-18,"5":3.876675101e-17,"6":1.768636834e-18,"7":3.225350444e-17,"8":6.455904412e-17,"9":0.695306985},"24":{"0":0.0559427859,"1":0.189365596,"2":0.046449199,"3":0.0031765207,"4":2.276258085e-17,"5":5.826882038e-17,"6":1.660093435e-17,"7":5.136226195e-17,"8":8.729763766e-18,"9":0.7050658984},"25":{"0":0.0366470633,"1":0.1993699587,"2":0.0480051862,"3":0.0031429579,"4":8.67235385e-17,"5":5.050123714e-17,"6":1.420989364e-17,"7":4.764800072e-17,"8":1.024884564e-17,"9":0.7128348339},"26":{"0":0.0221731668,"1":0.2068743219,"2":0.0491723463,"3":0.0031177821,"4":4.746986759e-17,"5":1.074970294e-17,"6":4.41946748e-17,"7":4.781835484e-18,"8":4.090038725e-17,"9":0.7186623829},"27":{"0":0.011978764,"1":0.2121748779,"2":0.0499971849,"3":0.0030513758,"4":2.065360703e-17,"5":5.629411166e-17,"6":1.889775622e-17,"7":4.781741198e-17,"8":1.12436204e-17,"9":0.7227977974},"28":{"0":0.0052756543,"1":0.2157441734,"2":0.0505550643,"3":0.0027351542,"4":4.207732493e-17,"5":5.097127229e-18,"6":4.08430727e-17,"7":1.590182423e-18,"8":3.610812023e-17,"9":0.7256899539},"29":{"0":0.0011851247,"1":0.2180607643,"2":0.0509210858,"3":0.0020931008,"4":6.038140987e-17,"5":2.318324433e-17,"6":5.60307935e-17,"7":1.579304212e-17,"8":5.02007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tests/test_NMF_analysis_code.py

@@ -1,62 +1,61 @@
-import os
-import tempfile
+import shutil
+from os.path import exists, join
 from pathlib import Path
-from shutil import rmtree
 
 import pytest
 
 from diffpy.nmf_mapping.main import main
 
 dir = Path(__file__).parent.resolve()
-
-data_dir = os.path.join(dir, "data/synthetic_r_vs_gr")
-
-test_map = [
-    ([data_dir, "--xrange", "5,10"], "output_1", "Number of components: 3\n"),
-    ([data_dir], "output_2", "Number of components: 3\n"),
-    ([data_dir, "--xrange", "5,10", "12,15"], "output_3", "Number of components: 3\n"),
-]
-
-
-@pytest.fixture(scope="session")
-def temp_dir():
-    """A test fixture that creates and destroys tes outputs in a temporary
-    directory.
-    This will yield the path to the directory.
-    """
-    cwd = os.getcwd()
-    name = "outputs"
-    temp_dir = Path(tempfile.gettempdir())
-    repo = os.path.join(temp_dir, name)
-    if os.path.exists(repo):
-        rmtree(repo)
-    os.chdir(temp_dir)
-    os.mkdir(name)
-    os.chdir(cwd)
-    yield repo
-    os.chdir(cwd)
-    rmtree(repo)
-
-
-@pytest.mark.parametrize("tm", test_map)
-def test_nmf_mapping_code(tm, temp_dir, capsys):
-    data_dir = tm[0]
-    working_dir = Path(temp_dir)
-    os.chdir(working_dir)
-    main(args=data_dir)
-    out, err = capsys.readouterr()
-    assert out == tm[2]
-    results_dir = os.path.join(working_dir, "nmf_result")
-    os.chdir(results_dir)
-    expected_base = os.path.join(os.path.dirname(__file__), "output")
-    test_specific_dir = os.path.join(expected_base, tm[1])
-    for root, dirs, files in os.walk("."):
-        for file in files:
-            if file in os.listdir(test_specific_dir):
-                fn1 = os.path.join(results_dir, file)
-                with open(fn1, "r") as f:
-                    actual = f.read()
-                fn2 = os.path.join(test_specific_dir, file)
-                with open(fn2, "r") as f:
-                    expected = f.read()
-                assert expected == actual
+data_dir = join(dir, "data/synthetic_r_vs_gr")
+
+
+@pytest.mark.parametrize(
+    "args, output_dir",
+    [
+        (["tests/data/synthetic_r_vs_gr", "--xrange", "5,10", "--show", "false"], "output_1"),
+        (["tests/data/synthetic_r_vs_gr", "--show", "false"], "output_2"),
+        (["tests/data/synthetic_r_vs_gr", "--xrange", "5,10", "12,15", "--show", "false"], "output_3"),
+    ],
+)
+def test_nmf_mapping_code(args, output_dir, tmpdir):
+
+    # Save the result in ("nmf_result") at the top project level (default behavior)
+    main(args=args)
+
+    # Define the copied results directory in tmpdir
+    tmp_results_dir = join(tmpdir, "nmf_result")
+    expected_output_dir = join("tests/output", output_dir)
+
+    # Copy the output to tmpdir
+    shutil.copytree("nmf_result", tmp_results_dir)
+
+    # Remove the nmf_result folder from the top project level
+    shutil.rmtree("nmf_result")
+
+    # Define the specific JSON files to check
+    json_files_to_check = [
+        "component_index_vs_pratio_col.json",
+        "component_index_vs_RE_value.json",
+        "x_index_vs_y_col_components.json",
+    ]
+
+    # Compare each specified .json file
+    for json_file in json_files_to_check:
+        # Define paths for actual and expected .json files
+        actual_file_path = join(tmp_results_dir, json_file)
+        expected_file_path = join(expected_output_dir, json_file)
+
+        # Ensure the file exists in both locations
+        assert exists(actual_file_path)
+        assert exists(expected_file_path)
+
+        # Read and compare file contents
+        with open(actual_file_path, "r") as actual_file:
+            actual = actual_file.read()
+
+        with open(expected_file_path, "r") as expected_file:
+            expected = expected_file.read()
+
+        # Assert that the contents match
+        assert actual == expected