Merge pull request #76 from HeloiseS/dev1.6

Merging Dev1.6 for the upcoming hoki v1.6 release

.github/workflows/testing.yml

@@ -1,6 +1,5 @@
 # This is a basic workflow to help you get started with Actions
-
-name: CI
+name: Dependency Testing
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 # events but only for the master branch
@@ -16,28 +15,29 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
 
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        python3 -m pip install tox
-        
-    - name: Run Tox
-      run: tox
-
-   # - name: Upload coverage to codecov
-   #   uses: codecov/codecov-action@v1
-   #   with:
-   #     token: ${{ secrets.CODECOV_TOKEN }}
-   #     file: ./coverage.xml
-   #     fail_ci_if_error: False
+    # The matrix of python versions to run
+    strategy:
+        matrix:
+            python-version: ['3.6','3.7']   #If adjusted here, make sure to also adjust the bindings in tox.ini
+    name: Python ${{ matrix.python-version }}
 
+    # The steps to run for each python version
+    steps:
+        # Checks out the repository
+        - uses: actions/checkout@v2
+          name: Checkout package
+        # Setups the required python version
+        - name: Setup python ${{  matrix.python-version }}
+          uses: actions/setup-python@v2
+          with:
+            python-version: ${{ matrix.python-version }}
+            architecture: x64
+        # Installs tox and tox-gh-actions to run tox testing
+        - name: Install dependencies
+          run:  |
+            python -m pip install --upgrade pip
+            python -m pip install tox tox-gh-actions
+        # Run tests with tox (tests multiple subpackages)
+        - name: Run tests with tox
+          run: tox

.gitignore

@@ -63,3 +63,5 @@ hoki/version.py
 
 # Mac OSX
 .DS_Store
+
+corner_plot.png

README.rst

@@ -58,8 +58,8 @@ This way it'll show you each test as they pass or FAIL. In the pip and github ve
 
 .. code-block:: none
 
+   `astropy`, `numpy`, `pandas`, `matplotlib`, `pyyaml`, `wheel`, `emcee`, `corner`, `numba`
 
-   `numpy`, `pandas`, `matplotlib`, `pyyaml`, `wheel`, `emcee`, `corner`
 
 **Note:** Python 2 is not supported
 

hoki/__init__.py

@@ -33,4 +33,3 @@ class UnsupportedPythonError(Exception):
     #__all__ += ['module_input', 'module_output']
     # or you can keep everything from the subpackage with the following instead
     # __all__ += example_mod.__all__
-

hoki/_astropy_init.py

@@ -2,7 +2,7 @@
 
 __all__ = ['__version__']
 
-# this indicates whether or not we are in the package's setup.py
+# this indicates whether or not we are in the package'dc setup.py
 try:
     _ASTROPY_SETUP_
 except NameError:
@@ -45,7 +45,7 @@
                 except ConfigurationDefaultMissingError as e:
                     wmsg = (e.args[0] +
                             " Cannot install default profile. If you are "
-                            "importing from source, this is expected.")
+                            "importing from models_path, this is expected.")
                     warn(ConfigurationDefaultMissingWarning(wmsg))
                     del e
                 except Exception:

hoki/age/tests/test_utils.py

@@ -0,0 +1,182 @@
+import hoki.age.utils as au
+from hoki.age.wizard import AgeWizard
+import hoki.load as load
+import pkg_resources
+import numpy as np
+import pandas as pd
+import pytest
+from hoki.utils.exceptions import HokiFatalError, HokiUserWarning, HokiFormatError
+
+# Loading Data
+
+data_path = pkg_resources.resource_filename('hoki', 'data')
+hr_file = data_path + '/hrs-sin-imf_chab100.zem4.dat'
+cmd_file = data_path + '/cmd_bv_z002_bin_imf135_300'
+myhrd = load.model_output(hr_file, hr_type='TL')
+mycmd = load.unpickle(cmd_file)
+
+#### Creating Test Inputs
+
+# Version 1 AgeWizard
+fake_hrd_input = pd.DataFrame.from_dict({'name': ['star1', 'star2', 'star3'],
+                                         'logT': np.array([4.58, 4.48, 4.14]),
+                                         'logL': np.array([4.83, 5.07, 5.40])})
+
+bad_hrd_input = pd.DataFrame.from_dict({'logT': np.array(['bla']),
+                                        'logL': np.array([4.83])})
+
+no_name_input = pd.DataFrame.from_dict({'logT': np.array([4.58, 4.48, 4.14]),
+                                        'logL': np.array([4.83, 5.07, 5.40])})
+
+bad_hrd_input2 = pd.DataFrame.from_dict({'logT': np.array([4.58, 'bla']),
+                                         'logL': np.array([4.83, 2.0])})
+
+fake_cmd_input = pd.DataFrame.from_dict({'name': ['star1', 'star2', 'STAR3'],
+                                         'col': np.array([-0.3, 0.5, -0.25]),
+                                         'mag': np.array([-5, -10, -1])})
+
+bad_cmd_input = pd.DataFrame.from_dict({'col': np.array(['bla']),
+                                        'mag': np.array([-5])})
+
+# Version 2 AgeWizard
+stars_none = pd.DataFrame.from_dict({'name': np.array(['118-1', '118-2', '118-3', '118-4']),
+                                     'logL': np.array([5.0, 5.1, 4.9, 5.9]),
+                                     'logT': np.array([4.48, 4.45, 4.46, 4.47]),
+                                     })
+
+stars_SYM = pd.DataFrame.from_dict({'name': np.array(['118-1', '118-2', '118-3', '118-4']),
+                                    'logL': np.array([5.0, 5.1, 4.9, 5.9]),
+                                    'logL_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    'logT': np.array([4.48, 4.45, 4.46, 4.47]),
+                                    'logT_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    })
+
+stars_SYM_T_err_missing = pd.DataFrame.from_dict({'name': np.array(['118-1', '118-2', '118-3', '118-4']),
+                                    'logL': np.array([5.0, 5.1, 4.9, 5.9]),
+                                    'logL_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    'logT': np.array([4.48, 4.45, 4.46, 4.47]),
+                                    'logT_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    })
+
+#########
+# MISC  #
+#########
+
+class TestNormalise1D(object):
+    def test_it_runs(self):
+        au.normalise_1d(np.array([0, 1, 4, 5, 0, 1, 7, 8]))
+
+    def test_basic(self):
+        norm = au.normalise_1d(np.array([0, 0, 1, 0, 0, 0, 0]))
+        assert norm[2] == 1, 'Normalisation done wrong'
+        assert sum(norm) == 1, "Normalisaton done wrong"
+
+class TestErrorFlag(object):
+    def test_no_err(self):
+        assert au._error_flag(stars_none) is None, "Error Flag should be None"
+
+    def test_ERR(self):
+        assert au._error_flag(stars_SYM) == 'ERR', "Error Flag should be ERR"
+
+
+#######################
+# FINDING COORDINATES #
+#######################
+
+
+class TestFindCoordinates(object):
+    def test_hrd_input(self):
+        T_coord, L_coord = au.find_coordinates(obs_df=fake_hrd_input, model=myhrd)
+        assert np.sum(
+            np.isclose([T_coord[0], T_coord[1], T_coord[2]], [45, 44, 40])) == 3, "Temperature coordinates wrong"
+        assert np.sum(
+            np.isclose([L_coord[0], L_coord[1], L_coord[2]], [77, 80, 83])) == 3, "Luminosity coordinates wrong"
+
+    def test_cmd_input(self):
+        col_coord, mag_range = au.find_coordinates(obs_df=fake_cmd_input, model=mycmd)
+        assert np.sum(
+            np.isclose([col_coord[0], col_coord[1], col_coord[2]], [27, 35, 27])) == 3, "color coordinates wrong"
+        assert np.sum(
+            np.isclose([mag_range[0], mag_range[1], mag_range[2]], [90, 40, 130])) == 3, "magnitude coordinates wrong"
+
+
+class TestFindCMDCoordinates(object):
+    def test_fake_input(self):
+        col_coord, mag_range = au._find_cmd_coordinates(obs_df=fake_cmd_input, mycmd=mycmd)
+        assert np.sum(
+            np.isclose([col_coord[0], col_coord[1], col_coord[2]], [27, 35, 27])) == 3, "color coordinates wrong"
+        assert np.sum(
+            np.isclose([mag_range[0], mag_range[1], mag_range[2]], [90, 40, 130])) == 3, "magnitude coordinates wrong"
+
+    def test_bad_input(self):
+        with pytest.raises(HokiFormatError):
+            col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_hrd_input, mycmd=mycmd)
+
+    def test_bad_input_2(self):
+        col_coord, mag_range = au._find_cmd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)
+        assert np.isclose(mag_range[0], 90), "This L coordinate is wrong - test_bad_input."
+
+
+class TestFindHRDCoordinates(object):
+    def test_fake_input(self):
+        T_coord, L_coord = au._find_hrd_coordinates(obs_df=fake_hrd_input, myhrd=myhrd)
+        assert np.sum(
+            np.isclose([T_coord[0], T_coord[1], T_coord[2]], [45, 44, 40])) == 3, "Temperature coordinates wrong"
+        assert np.sum(
+            np.isclose([L_coord[0], L_coord[1], L_coord[2]], [77, 80, 83])) == 3, "Luminosity coordinates wrong"
+
+    def test_bad_input(self):
+        with pytest.raises(HokiFormatError):
+            __, __ = au._find_hrd_coordinates(obs_df=bad_cmd_input, mycmd=mycmd)
+
+    def test_bad_input(self):
+        T_coord, L_coord = au._find_hrd_coordinates(obs_df=bad_hrd_input, myhrd=myhrd)
+        #assert np.isnan(T_coord[0]), "This should be a nan"
+        assert np.isclose(L_coord[0], 77), "This L coordinate is wrong - test_bad_input."
+
+
+###############################
+# CALCULATING INDIVIDUAL PDFS #
+###############################
+
+
+class TestCalculatePDFs(object):
+    def test_fake_input(self):
+        pdf_df = au.calculate_individual_pdfs(fake_hrd_input, myhrd)
+        assert 'star1' in pdf_df.columns, "Column name issue"
+        assert int(sum(pdf_df.star1)) == 1, "PDF not calculated correctly"
+
+    def test_input_without_name(self):
+        pdf_df = au.calculate_individual_pdfs(no_name_input, myhrd)
+
+        assert 's1' in pdf_df.columns, "Column names not created right"
+
+    def test_bad_input(self):
+        pdf_df = au.calculate_individual_pdfs(bad_hrd_input2, myhrd)
+        assert not np.isnan(sum(pdf_df.s0)), "something went wrong"
+
+    def test_symmetric_errors(self):
+        pdf_df = au.calculate_individual_pdfs(stars_SYM, myhrd)
+        assert not np.isnan(sum(pdf_df['118-4'])), "something went wrong with symmetric errors"
+
+#####################################
+# PUTTING PDFS TOGETHER IN SOME WAY #
+#####################################
+
+
+class TestCalculateSamplePDF(object):
+    def test_basic(self):
+        distributions = au.calculate_distributions(fake_hrd_input, myhrd)
+        combined = au.calculate_sample_pdf(distributions)
+        assert np.isclose(combined.pdf[9], 0.2715379752638662), "combined PDF not right"
+
+    def test_drop_bad(self):
+        distributions = au.calculate_distributions(fake_hrd_input, myhrd)
+        combined = au.calculate_sample_pdf(distributions, not_you=[3])
+        assert np.isclose(combined.pdf[9], 0.2715379752638662), "combined PDF not right"
+
+    def test_drop_good(self):
+        distributions = au.calculate_distributions(fake_hrd_input, myhrd)
+        combined = au.calculate_sample_pdf(distributions, not_you=['star1'])
+        assert np.isclose(combined.pdf[9], 0.774602971512809), "combined PDF not right"
+

hoki/age/tests/test_wizard.py

@@ -0,0 +1,95 @@
+import hoki.age.utils as au
+from hoki.age.wizard import AgeWizard
+import hoki.load as load
+import pkg_resources
+import numpy as np
+import pandas as pd
+import pytest
+from hoki.utils.exceptions import HokiFatalError, HokiUserWarning, HokiFormatError
+
+
+# Loading Data
+
+data_path = pkg_resources.resource_filename('hoki', 'data')
+hr_file = data_path + '/hrs-sin-imf_chab100.zem4.dat'
+cmd_file = data_path + '/cmd_bv_z002_bin_imf135_300'
+myhrd = load.model_output(hr_file, hr_type='TL')
+mycmd = load.unpickle(cmd_file)
+# Creating Test Inputs
+
+fake_hrd_input = pd.DataFrame.from_dict({'name': ['star1', 'star2', 'star3'],
+                                         'logT': np.array([4.58, 4.48, 4.14]),
+                                         'logL': np.array([4.83, 5.07, 5.40])})
+
+bad_hrd_input = pd.DataFrame.from_dict({'logT': np.array(['bla']),
+                                        'logL': np.array([4.83])})
+
+no_name_input = pd.DataFrame.from_dict({'logT': np.array([4.58, 4.48, 4.14]),
+                                        'logL': np.array([4.83, 5.07, 5.40])})
+
+bad_hrd_input2 = pd.DataFrame.from_dict({'logT': np.array([4.58, 'bla']),
+                                         'logL': np.array([4.83, 2.0])})
+
+fake_cmd_input = pd.DataFrame.from_dict({'name': ['star1', 'star2', 'STAR3'],
+                                         'col': np.array([-0.3, 0.5, -0.25]),
+                                         'mag': np.array([-5, -10, -1])})
+
+bad_cmd_input = pd.DataFrame.from_dict({'col': np.array(['bla']),
+                                        'mag': np.array([-5])})
+
+
+stars_SYM = pd.DataFrame.from_dict({'name': np.array(['118-1', '118-2', '118-3', '118-4']),
+                                    'logL': np.array([5.0, 5.1, 4.9, 5.9]),
+                                    'logL_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    'logT': np.array([4.48, 4.45, 4.46, 4.47]),
+                                    'logT_err': np.array([0.1, 0.2, 0.1, 0.1]),
+                                    })
+
+class TestAgeWizardBasic(object):
+    def test_init_basic(self):
+        assert AgeWizard(obs_df=fake_hrd_input, model=hr_file), "Loading HRD file path failed"
+        assert AgeWizard(obs_df=fake_hrd_input, model=myhrd), "Loading with hoki.hrdiagrams.HRDiagram failed"
+        assert AgeWizard(obs_df=fake_cmd_input, model=mycmd), 'Loading with hoki.cmd.CMD'
+        assert AgeWizard(obs_df=fake_cmd_input, model=cmd_file), 'Loading CMD from frile failed'
+
+    def test_bad_init(self):
+        with pytest.raises(HokiFatalError):
+            __, __ = AgeWizard(obs_df=fake_cmd_input, model='sdfghj'), 'HokiFatalError should be raised'
+
+        with pytest.raises(HokiFormatError):
+            __, __ = AgeWizard(obs_df='edrftgyhu', model=cmd_file), 'HokiFormatError should be raised'
+
+    def test_combine_pdfs_not_you(self):
+        wiz = AgeWizard(fake_hrd_input, myhrd)
+        wiz.calculate_sample_pdf(not_you=['star1'])
+        cpdf = wiz.sample_pdf.pdf
+        assert np.sum(np.isclose([cpdf[0], cpdf[9]], [0.0,  0.7231526323765232])) == 2, "combined pdf is not right"
+
+    def test_most_likely_age(self):
+        wiz = AgeWizard(obs_df=fake_hrd_input, model=hr_file)
+        assert np.isclose(wiz.most_likely_age[0], 6.9), "Most likely age wrong"
+
+    def test_most_likely_ages(self):
+        wiz = AgeWizard(obs_df=fake_hrd_input, model=hr_file)
+        a = wiz.most_likely_ages
+        assert np.sum(np.isclose([a[0], a[1], a[2]], [6.9, 6.9, 6.9])) == 3, "Most likely ages not right"
+
+    def test_combine_pdfs(self):
+        wiz = AgeWizard(fake_hrd_input, myhrd)
+        wiz.calculate_sample_pdf()
+        assert np.isclose(wiz.sample_pdf.pdf[9],0.551756734145878), "Something is wrong with the combined_Age PDF"
+
+    def test_calculate_p_given_age_range(self):
+        wiz = AgeWizard(fake_hrd_input, myhrd)
+        probas = wiz.calculate_p_given_age_range([6.7, 6.9])
+        assert np.sum(np.isclose([probas[0], probas[1], probas[2]],
+                                 [0.515233714952414, 0.7920611550946726, 0.6542441096583737])) == 3, \
+            "probability given age range is messed up"
+
+
+class TestAgeWizardErrors(object):
+    def test_agewizard_with_errors_runs(self):
+        wiz = AgeWizard(stars_SYM, myhrd, nsamples=200)
+        wiz.calculate_sample_pdf()
+
+