fixed coverage

.github/workflows/ci.yml

@@ -1,12 +1,12 @@
-name: Python package
+name: Pytest (Linux)
 on: [push, pull_request]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - name: Checkout
@@ -24,17 +24,9 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e ".[test]"
 
-#      - name: Lint with flake8
-#        run: |
-#          # stop the build if there are Python syntax errors or undefined names
-#          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-#          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-#          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-
       - name: Test with pytest
         run: |
-          pytest tests --cov=./src/pacman --cov-report=xml
+          pytest tests --cov=./src/pacman --cov-report=xml -s 
 
       - name: Upload coverage.xml as artifact
         uses: actions/upload-artifact@v4
@@ -52,3 +44,11 @@ jobs:
           #name: codecov-umbrella # optional
           fail_ci_if_error: false # optional (default = false)
           verbose: true # optional (default = false)
+
+#      - name: Lint with flake8
+#        run: |
+#          # stop the build if there are Python syntax errors or undefined names
+#          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+#          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+#          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+

.github/workflows/ci_windows.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: Pytest (Windows)
 on: [push, pull_request]
 
 jobs:
@@ -23,7 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ".[test]"
+          pip install -e ".[test]"
 
       - name: Test with pytest
         run: |

src/pacman/s10_direct_images.py

@@ -95,6 +95,6 @@ def run10(eventlabel, workdir: Path, meta=None):
     # Save results
     print('Saving Metadata')
     me.saveevent(meta, meta.workdir / f'WFC3_{meta.eventlabel}_Meta_Save', save=[])
-    print('tmp: ', 2+1)
+
     print('Finished s10 \n')
     return meta

tests/test_all.py

@@ -321,120 +321,120 @@ def test_sim_source(capsys):
     assert source_ypos-1 <= results[3] <= source_ypos+1
 
 
-# @pytest.mark.run(order=27)
-# def test_s20(capsys):
-#     """The extraction step. Extracts flux as a function
-#     of wavelength and time.
-#     """
-#     reload(s20)
-#     time.sleep(1)
-#
-#     workdir, eventlabel = workdir_finder()
-#
-#     # Run s20
-#     meta = s20.run20(eventlabel, workdir)
-#
-#     extracted_lc_dir_path = workdir / 'extracted_lc'
-#
-#     s20_dir = np.array([path for path in extracted_lc_dir_path.iterdir() if path.is_dir()])[0]
-#     s20_lc_spec_file = s20_dir / 'lc_spec.txt'
-#     s20_lc_white_file = s20_dir / 'lc_white.txt'
-#
-#     # Check if the files were created
-#     assert s20_lc_spec_file.exists()
-#     assert s20_lc_white_file.exists()
-#
-#     s20_lc_spec = ascii.read(s20_lc_spec_file)
-#     s20_lc_white = ascii.read(s20_lc_white_file)
-#
-#     # Check the amount of columns
-#     assert len(s20_lc_spec.colnames) == 10
-#     assert len(s20_lc_white.colnames) == 11
-#
-#     # test_optextr
-#     spectrum = np.ones((20, 9))
-#
-#     for i in range(len(spectrum)):
-#         for j in range(len(spectrum[0])):
-#             if 4 < i < 8:
-#                 if 1 < j < 7:
-#                     spectrum[i, j] = 10
-#
-#     err = np.ones((20, 9))*0.01
-#     Mnew = np.ones((20, 9))
-#     spec_box_0 = 15 * 10
-#     var_box_0 = 1
-#
-#     [f_opt_0, _, numoutliers] = optextr.optextr(
-#             spectrum, err, spec_box_0, var_box_0, Mnew,
-#             meta.nsmooth, meta.sig_cut, meta.save_optextr_plot, 0, 0, meta)
-#
-#     assert np.round(np.sum(f_opt_0), 0) == np.round(np.sum(spectrum), 0) #optimal extraction flux should be the same as the total flux in the array
-#     assert numoutliers == 0  # We didnt introduce any outliers
-#
-#
-# @pytest.mark.run(order=29)
-# def test_s21(capsys):
-#     """Creates spectroscopic light curves."""
-#     reload(s21)
-#     time.sleep(1)
-#
-#     workdir, eventlabel = workdir_finder()
-#
-#     # Run s21
-#     meta = s21.run21(eventlabel, workdir)
-#
-#     extracted_sp_dir_path = workdir / 'extracted_sp'
-#
-#     s21_dir = np.array([path for path in extracted_sp_dir_path.iterdir()
-#                         if path.is_dir()])[0]
-#     s21_wvl_table_file = s21_dir / 'wvl_table.dat'
-#     assert s21_wvl_table_file.exists()
-#     s21_wvl_table = ascii.read(s21_wvl_table_file)
-#
-#     wvl_s21 = s21_wvl_table['wavelengths']
-#
-#     # Check if the number of bins defined in the pcf is the same as
-#     # the number of wavelength bins saved into the wvl_table.dat file.
-#     assert meta.wvl_bins == len(wvl_s21)
-#
-#     # Number of light curves should be the same as meta.wvl_bins
-#     extracted_sp_lcs_files = list(s21_dir.glob("*.txt"))
-#     assert meta.wvl_bins == len(extracted_sp_lcs_files)
-#
-#     # There should be 10 columns as for the /lc_spec.txt file which was generated after running s20.
-#     extracted_sp_lc_file_0 = sn.sort_nicely(extracted_sp_lcs_files)[0]
-#     extracted_sp_lc_0 = ascii.read(extracted_sp_lc_file_0)
-#     assert len(extracted_sp_lc_0.colnames) == 10
-#
-#
-# @pytest.mark.run(order=30)
-# def test_s30(capsys):
-#     """Fits spectroscopic light curves."""
-#     reload(s30)
-#     time.sleep(1)
-#
-#     workdir, eventlabel = workdir_finder()
-#
-#     # Run s30
-#     meta = s30.run30(eventlabel, workdir)
-#
-#     dirs = np.array([path for path in workdir.iterdir() if path.is_dir()])
-#     dirs_bool = np.array(['fit_' in dir.name for dir in dirs])
-#     fit_dirs = dirs[dirs_bool]
-#     fit_dir = fit_dirs[0]
-#     assert fit_dir.exists()
-#
-#     meta.s30_fit_white = True
-#     meta.s30_most_recent_s20 = True
-#
-#     s30.run30(eventlabel, workdir, meta=meta)
-#
-#     dirs = np.array([path for path in workdir.iterdir() if path.is_dir()])
-#     dirs_bool = np.array(['fit_' in dir.name for dir in dirs])
-#
-#     print('dirs_bool: ', dirs_bool)
-#     assert True
+@pytest.mark.run(order=27)
+def test_s20(capsys):
+    """The extraction step. Extracts flux as a function
+    of wavelength and time.
+    """
+    reload(s20)
+    time.sleep(1)
+
+    workdir, eventlabel = workdir_finder()
+
+    # Run s20
+    meta = s20.run20(eventlabel, workdir)
+
+    extracted_lc_dir_path = workdir / 'extracted_lc'
+
+    s20_dir = np.array([path for path in extracted_lc_dir_path.iterdir() if path.is_dir()])[0]
+    s20_lc_spec_file = s20_dir / 'lc_spec.txt'
+    s20_lc_white_file = s20_dir / 'lc_white.txt'
+
+    # Check if the files were created
+    assert s20_lc_spec_file.exists()
+    assert s20_lc_white_file.exists()
+
+    s20_lc_spec = ascii.read(s20_lc_spec_file)
+    s20_lc_white = ascii.read(s20_lc_white_file)
+
+    # Check the amount of columns
+    assert len(s20_lc_spec.colnames) == 10
+    assert len(s20_lc_white.colnames) == 11
+
+    # test_optextr
+    spectrum = np.ones((20, 9))
+
+    for i in range(len(spectrum)):
+        for j in range(len(spectrum[0])):
+            if 4 < i < 8:
+                if 1 < j < 7:
+                    spectrum[i, j] = 10
+
+    err = np.ones((20, 9))*0.01
+    Mnew = np.ones((20, 9))
+    spec_box_0 = 15 * 10
+    var_box_0 = 1
+
+    [f_opt_0, _, numoutliers] = optextr.optextr(
+            spectrum, err, spec_box_0, var_box_0, Mnew,
+            meta.nsmooth, meta.sig_cut, meta.save_optextr_plot, 0, 0, meta)
+
+    assert np.round(np.sum(f_opt_0), 0) == np.round(np.sum(spectrum), 0) #optimal extraction flux should be the same as the total flux in the array
+    assert numoutliers == 0  # We didnt introduce any outliers
+
+
+@pytest.mark.run(order=29)
+def test_s21(capsys):
+    """Creates spectroscopic light curves."""
+    reload(s21)
+    time.sleep(1)
+
+    workdir, eventlabel = workdir_finder()
+
+    # Run s21
+    meta = s21.run21(eventlabel, workdir)
+
+    extracted_sp_dir_path = workdir / 'extracted_sp'
+
+    s21_dir = np.array([path for path in extracted_sp_dir_path.iterdir()
+                        if path.is_dir()])[0]
+    s21_wvl_table_file = s21_dir / 'wvl_table.dat'
+    assert s21_wvl_table_file.exists()
+    s21_wvl_table = ascii.read(s21_wvl_table_file)
+
+    wvl_s21 = s21_wvl_table['wavelengths']
+
+    # Check if the number of bins defined in the pcf is the same as
+    # the number of wavelength bins saved into the wvl_table.dat file.
+    assert meta.wvl_bins == len(wvl_s21)
+
+    # Number of light curves should be the same as meta.wvl_bins
+    extracted_sp_lcs_files = list(s21_dir.glob("*.txt"))
+    assert meta.wvl_bins == len(extracted_sp_lcs_files)
+
+    # There should be 10 columns as for the /lc_spec.txt file which was generated after running s20.
+    extracted_sp_lc_file_0 = sn.sort_nicely(extracted_sp_lcs_files)[0]
+    extracted_sp_lc_0 = ascii.read(extracted_sp_lc_file_0)
+    assert len(extracted_sp_lc_0.colnames) == 10
+
+
+@pytest.mark.run(order=30)
+def test_s30(capsys):
+    """Fits spectroscopic light curves."""
+    reload(s30)
+    time.sleep(1)
+
+    workdir, eventlabel = workdir_finder()
+
+    # Run s30
+    meta = s30.run30(eventlabel, workdir)
+
+    dirs = np.array([path for path in workdir.iterdir() if path.is_dir()])
+    dirs_bool = np.array(['fit_' in dir.name for dir in dirs])
+    fit_dirs = dirs[dirs_bool]
+    fit_dir = fit_dirs[0]
+    assert fit_dir.exists()
+
+    meta.s30_fit_white = True
+    meta.s30_most_recent_s20 = True
+
+    s30.run30(eventlabel, workdir, meta=meta)
+
+    dirs = np.array([path for path in workdir.iterdir() if path.is_dir()])
+    dirs_bool = np.array(['fit_' in dir.name for dir in dirs])
+
+    print('dirs_bool: ', dirs_bool)
+    assert True
 
 
 @pytest.mark.run(order=40)