add tests

baredSC_dev_env.yml → .github/baredSC_dev_env.yml

@@ -18,6 +18,7 @@ dependencies:
    - ipython # For the doc
    - sphinx-argparse # For the doc
    - twine # For the upload
+   - pytest
    - pip
    - pip:
       - sphinx-autorun # For the doc

.github/workflows/test.yml

@@ -0,0 +1,78 @@
+name: Test
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  build-linux:
+    name: Test on Linux
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@main
+      with:
+        environment-file: ./baredSC_dev_env.yml
+        cache-downloads: true
+        environment-name: baredSC_dev
+    - name: pip install
+      run: |
+        micromamba activate baredSC_dev
+        pip install .
+    - name: Test baredSC
+      run: |
+        micromamba activate baredSC_dev
+        pytest -v
+    - name: make an artifact
+      run: |
+        micromamba activate baredSC_dev
+        rm -f dist/*
+        python -m build
+    - uses: actions/upload-artifact@master
+      with:
+        name: "Dist files"
+        path: "dist"
+  test-wheels:
+    name: test wheel
+    runs-on: ubuntu-latest
+    needs: build-linux
+    strategy:
+      matrix:
+        python-version: ['3.7','3.8','3.9','3.10', '3.11']
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v3
+        with:
+          name: "Dist files"
+          path: ~/dist/
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: install wheel
+        run: |
+          pip install ~/dist/*whl
+          baredSC_1d -h
+      - name: pytest
+        run: |
+          pip install pytest
+          pytest -v
+  build-osx:
+    name: Test on OSX
+    runs-on: macOS-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@main
+      with:
+        environment-file: .github/baredSC_dev.yml
+        cache-downloads: true
+        environment-name: baredSC_dev
+    - name: pip install
+      run: |
+        micromamba activate baredSC_dev
+        pip install .
+    - name: Test baredSC
+      run: |
+        micromamba activate baredSC_dev
+        pytest -v

baredSC/tests/generateAllOutput.sh

@@ -0,0 +1,48 @@
+
+# baredSC_1d
+baredSC_1d \
+    --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt \
+    --geneColName 0.5_0_0_0.5_x \
+    --output example/first_example_1d_1gauss \
+    --nnorm 1 \
+    --figure example/first_example_1d_1gauss.png \
+    --title "first gene 1 gauss" \
+    --logevidence example/first_example_1d_1gauss_logevid.txt
+baredSC_1d \
+    --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt \
+    --metadata1ColName 0_0.5_0.5_0_group \
+    --metadata1Values 1.0 \
+    --xmin -15 \
+    --xmax -7 \
+    --nx 25 \
+    --xscale log \
+    --minNeff 400 \
+    --geneColName 0.5_0_0_0.5_x \
+    --output example/first_example_1d_2gauss_log \
+    --nnorm 2 \
+    --figure example/first_example_1d_2gauss_log.pdf \
+    --title "first gene 2 gauss log scale" \
+    --logevidence example/first_example_1d_2gauss_log_logevid.txt
+
+# Combined_1d
+for nnorm in 1 2; do
+    baredSC_1d --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt --geneColName 0.5_0_0_0.5_x --nnorm ${nnorm} --output baredSC/tests/test_data/small_${nnorm}gauss --nx 10 --nsampMCMC 20000 --force
+done
+combineMultipleModels_1d --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt --geneColName 0.5_0_0_0.5_x \
+    --outputs baredSC/tests/test_data/small_1gauss baredSC/tests/test_data/small_2gauss \
+    --nx 10 --title 'first gene combine 1 and 2 gauss' --prettyBins 100 --figure baredSC/tests/test_data/combine_test1.png
+
+# baredSC 2d prep
+for nnorm in 1 2; do
+    baredSC_2d  --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt --geneXColName '0.5_0_0_0.5_x' --geneYColName '0.5_0_0_0.5_y' --nnorm ${nnorm} --output baredSC/tests/test_data/2d_small_${nnorm}gauss --nx 10 --ny 12 --nsampMCMC 20000 --force
+done
+
+# baredSC 2d plot
+nnorm=2
+baredSC_2d  --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt --geneXColName '0.5_0_0_0.5_x' --geneYColName '0.5_0_0_0.5_y' --nnorm ${nnorm} --output baredSC/tests/test_data/2d_small_${nnorm}gauss --nx 10 --ny 12 --nsampMCMC 20000 --figure baredSC/tests/test_data/2d_small_${nnorm}gauss.png --prettyBinsx 50 --prettyBinsy 50
+
+# combined_2d
+combineMultipleModels_2d --input baredSC/tests/test_data/nih3t3_generated_2d_2.txt --geneXColName '0.5_0_0_0.5_x' --geneYColName '0.5_0_0_0.5_y' \
+    --outputs baredSC/tests/test_data/2d_small_1gauss baredSC/tests/test_data/2d_small_2gauss \
+    --nx 10 --ny 12 --prettyBinsx 50 --prettyBinsy 50 \
+    --figure baredSC/tests/test_data/2d_small_combined.pdf

baredSC/tests/test_baredSC_1d.py

@@ -0,0 +1,108 @@
+# -*- coding: utf-8 -*-
+""" Test for baredSC_1d
+"""
+from tempfile import NamedTemporaryFile
+import os.path
+import matplotlib as mpl
+from matplotlib.testing.compare import compare_images
+import baredSC.baredSC_1d
+
+mpl.use('agg')
+
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "test_data")
+
+EXAMPLE = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "..",  "..", "example")
+
+BARED_1D_IMAGES_SUFFIX = ['', '_convergence', '_p', '_corner', '_individuals',
+                          '_with_posterior', '_posterior_individuals',
+                          '_posterior_andco']
+
+BARED_1D_TEXT_SUFFIX = ['_neff.txt', '_p.txt', '_pdf.txt', '_posterior_per_cell.txt']
+
+TOLERENCE = 13  # default matplotlib pixed difference tolerance
+
+
+def test_baredSC_1d_1gauss_default():
+    """First test matching example
+    """
+    extension = 'png'
+    expected = os.path.join(EXAMPLE, 'first_example_1d_1gauss')
+    outfile = NamedTemporaryFile(prefix='baredSC_test_',  # pylint: disable=R1732
+                                 delete=False)
+    outfig = NamedTemporaryFile(suffix= f'.{extension}', prefix='baredSC_test_',  # pylint: disable=R1732
+                                delete=False)
+    outfig_base = outfig.name[:-(len(extension) + 1)]
+    outfile_evid = NamedTemporaryFile(suffix='.txt', prefix='baredSC_test_',  # pylint: disable=R1732
+                                      delete=False)
+    args = f"--input {ROOT}/nih3t3_generated_2d_2.txt " \
+           "--geneColName 0.5_0_0_0.5_x " \
+           f"--output {outfile.name}.npz " \
+           "--nnorm 1 " \
+           f"--figure {outfig.name} " \
+           f"--logevidence {outfile_evid.name}".split()
+    args += ['--title', 'first gene 1 gauss']
+    baredSC.baredSC_1d.main(args)
+    for suffix in BARED_1D_IMAGES_SUFFIX:
+        expected_file = f'{expected}{suffix}.{extension}'
+        obtained_file = f'{outfig_base}{suffix}.{extension}'
+        res = compare_images(expected_file,
+                             obtained_file, TOLERENCE)
+        assert res is None, res
+
+        os.remove(obtained_file)
+    # for suffix in BARED_1D_TEXT_SUFFIX:
+    #     expected_file = f'{expected}{suffix}'
+    #     obtained_file = f'{outfig_base}{suffix}'
+    #     expected_mat = np.loadtxt(expected_file, skiprows=1)
+    #     obtained_mat = np.loadtxt(obtained_file, skiprows=1)
+    #     assert np.all(np.isclose(obtained_mat, expected_mat))
+
+    #     os.remove(obtained_file)
+
+
+def test_baredSC_1d_2gauss_log_pdf():
+    """Second test with pdf cells subset prettyBins...
+    """
+
+    extension = 'pdf'
+    expected = os.path.join(EXAMPLE, 'first_example_1d_2gauss_log')
+    outfile = NamedTemporaryFile(prefix='baredSC_test_',  # pylint: disable=R1732
+                                 delete=False)
+    outfig = NamedTemporaryFile(suffix= f'.{extension}', prefix='baredSC_test_',  # pylint: disable=R1732
+                                delete=False)
+    outfig_base = outfig.name[:-(len(extension) + 1)]
+    outfile_evid = NamedTemporaryFile(suffix='.txt', prefix='baredSC_test_',  # pylint: disable=R1732
+                                      delete=False)
+    args = f"--input {ROOT}/nih3t3_generated_2d_2.txt " \
+           "--metadata1ColName 0_0.5_0.5_0_group " \
+           "--metadata1Values 1.0 " \
+           "--xmin -15 " \
+           "--xmax -7 " \
+           "--nx 25 " \
+           "--xscale log " \
+           "--minNeff 400 " \
+           "--geneColName 0.5_0_0_0.5_x " \
+           f"--output {outfile.name}.npz " \
+           "--nnorm 2 " \
+           f"--figure {outfig.name} " \
+           f"--logevidence {outfile_evid.name}".split()
+    args += ['--title', 'first gene 2 gauss log scale']
+    baredSC.baredSC_1d.main(args)
+    for suffix in BARED_1D_IMAGES_SUFFIX:
+        expected_file = f'{expected}{suffix}.{extension}'
+        obtained_file = f'{outfig_base}{suffix}.{extension}'
+        res = compare_images(expected_file,
+                             obtained_file, TOLERENCE)
+        assert res is None, res
+
+        os.remove(obtained_file)
+    # for suffix in BARED_1D_TEXT_SUFFIX:
+    #     expected_file = f'{expected}{suffix}'
+    #     obtained_file = f'{outfig_base}{suffix}'
+    #     expected_mat = np.loadtxt(expected_file, skiprows=1)
+    #     obtained_mat = np.loadtxt(obtained_file, skiprows=1)
+    #     assert np.all(np.isclose(obtained_mat, expected_mat))
+
+    #     os.remove(obtained_file)

baredSC/tests/test_baredSC_2d.py

@@ -0,0 +1,63 @@
+# -*- coding: utf-8 -*-
+""" Test for baredSC_2d
+"""
+from tempfile import NamedTemporaryFile
+import os.path
+import matplotlib as mpl
+from matplotlib.testing.compare import compare_images
+import baredSC.baredSC_2d
+
+mpl.use('agg')
+
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "test_data")
+
+EXAMPLE = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "..",  "..", "example")
+
+BARED_2D_IMAGES_SUFFIX = ['', '_convergence', '_p', '_corner', '_individuals',
+                          '_median']
+
+BARED_2D_TEXT_SUFFIX = ['_neff.txt', '_p.txt', '_corr.txt', '_pdf2d.txt', '_pdf2d_flat.txt']
+
+TOLERENCE = 13  # default matplotlib pixed difference tolerance
+
+
+def test_baredSC_2d_1gauss_small():
+    """First test with small
+    """
+    extension = 'png'
+    expected = os.path.join(ROOT, '2d_small_2gauss')
+    outfile = NamedTemporaryFile(prefix='baredSC_test_',  # pylint: disable=R1732
+                                 delete=False)
+    outfig = NamedTemporaryFile(suffix= f'.{extension}', prefix='baredSC_test_',  # pylint: disable=R1732
+                                delete=False)
+    outfig_base = outfig.name[:-(len(extension) + 1)]
+    outfile_evid = NamedTemporaryFile(suffix='.txt', prefix='baredSC_test_',  # pylint: disable=R1732
+                                      delete=False)
+    args = f"--input {ROOT}/nih3t3_generated_2d_2.txt " \
+           "--geneXColName 0.5_0_0_0.5_x " \
+           "--geneYColName 0.5_0_0_0.5_y " \
+           "--nx 10 --ny 12 --nsampMCMC 20000 " \
+           "--prettyBinsx 50 --prettyBinsy 50 " \
+           f"--output {outfile.name}.npz " \
+           "--nnorm 2 " \
+           f"--figure {outfig.name} " \
+           f"--logevidence {outfile_evid.name}".split()
+    baredSC.baredSC_2d.main(args)
+    for suffix in BARED_2D_IMAGES_SUFFIX:
+        expected_file = f'{expected}{suffix}.{extension}'
+        obtained_file = f'{outfig_base}{suffix}.{extension}'
+        res = compare_images(expected_file,
+                             obtained_file, TOLERENCE)
+        assert res is None, res
+
+        os.remove(obtained_file)
+    # for suffix in BARED_2D_TEXT_SUFFIX:
+    #     expected_file = f'{expected}{suffix}'
+    #     obtained_file = f'{outfig_base}{suffix}'
+    #     expected_mat = np.loadtxt(expected_file, skiprows=1)
+    #     obtained_mat = np.loadtxt(obtained_file, skiprows=1)
+    #     assert np.all(np.isclose(obtained_mat, expected_mat))
+
+    #     os.remove(obtained_file)

baredSC/tests/test_combine_1d.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+""" Test for combineMultipleModels_1d
+"""
+from tempfile import NamedTemporaryFile
+import os.path
+import matplotlib as mpl
+from matplotlib.testing.compare import compare_images
+import baredSC.combineMultipleModels_1d
+
+mpl.use('agg')
+
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "test_data")
+
+EXAMPLE = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                    "..",  "..", "example")
+
+BARED_1D_IMAGES_SUFFIX = ['', '_individuals',
+                          '_with_posterior', '_posterior_individuals',
+                          '_posterior_andco']
+
+BARED_1D_TEXT_SUFFIX = ['_pdf.txt', '_posterior_per_cell.txt']
+
+TOLERENCE = 13  # default matplotlib pixed difference tolerance
+
+
+def test_combine_1d_test1():
+    """Simple test from small npz
+    """
+
+    extension = 'png'
+    expected = os.path.join(ROOT, 'combine_test1')
+    with NamedTemporaryFile(suffix= f'.{extension}', prefix='baredSC_test_',
+                            delete=False) as outfig:
+        outfig_base = outfig.name[:-(len(extension) + 1)]
+        args = f"--input {ROOT}/nih3t3_generated_2d_2.txt " \
+            "--geneColName 0.5_0_0_0.5_x " \
+            f"--outputs {ROOT}/small_1gauss {ROOT}/small_2gauss " \
+            "--nx 10 --prettyBins 100 " \
+            f"--figure {outfig.name}".split()
+        args += ['--title', 'first gene combine 1 and 2 gauss']
+        baredSC.combineMultipleModels_1d.main(args)
+        for suffix in BARED_1D_IMAGES_SUFFIX:
+            expected_file = f'{expected}{suffix}.{extension}'
+            obtained_file = f'{outfig_base}{suffix}.{extension}'
+            res = compare_images(expected_file,
+                                obtained_file, TOLERENCE)
+            assert res is None, res
+
+            os.remove(obtained_file)
+    # for suffix in BARED_1D_TEXT_SUFFIX:
+    #     expected_file = f'{expected}{suffix}'
+    #     obtained_file = f'{outfig_base}{suffix}'
+    #     expected_mat = np.loadtxt(expected_file, skiprows=1)
+    #     obtained_mat = np.loadtxt(obtained_file, skiprows=1)
+    #     assert np.all(np.isclose(obtained_mat, expected_mat))
+
+    #     os.remove(obtained_file)