Add tests, and actions to run them (#22)

* Added tests, actions to run the tests

* Pip install instead of python setup.py install

.github/workflows/python_testing.yml

@@ -0,0 +1,66 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: HASP Pytest
+
+on: 
+  push:
+  pull_request:
+  schedule:
+    - cron: '00 00 * * *'  # every day at midnight
+
+jobs:
+  build:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.runs-on }}
+    env: 
+      lref: /grp/hst/cdbs/lref/
+      oref: /grp/hst/cdbs/oref/ 
+      working-directory: ./
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Python 3.11
+            runs-on: ubuntu-latest
+            python-version: '3.11'
+            toxenv: py311
+
+          - name: Python 3.10
+            runs-on: ubuntu-latest
+            python-version: '3.10'
+            toxenv: py310
+
+          - name: Python 3.9
+            runs-on: ubuntu-latest
+            python-version: '3.9'
+            toxenv: py39
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        pip install cython
+        pip install astropy
+        pip install scipy
+        pip install matplotlib
+        pip install stsci.tools==4.0.0
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+#    - 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: |
+        # run all the unit tests.
+        pip install .['test']
+        pytest tests/test_swrapper.py -v 
+      working-directory: ${{env.working-directory}}

tests/test_swrapper.py

@@ -0,0 +1,93 @@
+# Test the wrapper script
+import os
+import glob
+import shutil
+import urllib.request
+import tarfile
+
+from astropy.io.fits import FITSDiff
+
+from hasp import wrapper
+
+Program_10033 = {'name': '10033',
+                 'url': 'https://stsci.box.com/shared/static/wnmma331eixblioo5jfnmjnzz2fjt01r.gz'}
+Program_11839 = {'name': '11839',
+                 'url': 'https://stsci.box.com/shared/static/a05mixac3hreg6g07f1kkogcpphdo26a.gz'}
+HD104237E = {'name': 'hd-104237e',
+             'url': 'https://stsci.box.com/shared/static/irelgbjs7zhdiljksao4su2c6tfhyntx.gz'}
+V_HK_ORI = {'name': 'v-hk-ori',
+            'url': 'https://stsci.box.com/shared/static/az3ytnwohj0t4wnc4m8oqbw9ziozwqx1.gz'}
+
+
+class TestWrapper():
+
+    def test_10033(self):
+        program = Program_10033
+        self.setup_tree(program)
+        self.run_wrapper(program['name'])
+        report = self.compare_outputs(program['name'])
+        self.cleanup(program['name'])
+        if report is not None:
+            raise AssertionError(report)
+        return
+
+    def test_11839(self):
+        program = Program_11839
+        self.setup_tree(program)
+        self.run_wrapper(program['name'])
+        report = self.compare_outputs(program['name'])
+        self.cleanup(program['name'])
+        if report is not None:
+            raise AssertionError(report)
+        return
+
+    def setup_tree(self, program):
+        program_name = program['name']
+        url = program['url']
+        if os.path.isdir(program_name):
+            shutil.rmtree(program_name)
+        filename = program_name + '.tar.gz'
+        _ = urllib.request.urlretrieve(url, filename)
+        data_tarfile = tarfile.open(filename, mode='r|gz')
+        data_tarfile.extractall()
+        return
+
+    def run_wrapper(self, program):
+        indir = program + '/input/'
+        wrapper.main(indir, outdir=indir)
+        return
+
+    def compare_outputs(self, program):
+        report = None
+        # Outputs from current run are in ./, truth files to compare
+        # with are in ./truth
+        all_ok = True
+        fitsdiff_report = ''
+        keywords_to_ignore = ['DATE', 'FITS_SW', 'FILENAME',
+                              'HLSP_VER', 'S_REGION']
+        new_hlsps = glob.glob(program + '/input/hst_')
+        for new_product in new_hlsps:
+            truth_filename = self.get_truth_filename(program, new_product)
+            fdiff = FITSDiff(new_product, truth_filename,
+                             ignore_hdus=['provenance'],
+                             ignore_keywords=keywords_to_ignore,
+                             rtol=1.0e-7)
+            fitsdiff_report += fdiff.report()
+            if not fdiff.identical and all_ok:
+                all_ok = False
+        if not all_ok:
+            report = os.linesep + fitsdiff_report
+            return report
+        print(fitsdiff_report)
+        return None
+
+    def get_truth_filename(self, program, product):
+        # Get the truth filename.  The data release might be different
+        filename = os.path.basename(product)
+        truth_filename = program + '/truth/' + filename
+        return truth_filename
+
+    def cleanup(self, program):
+        shutil.rmtree(program)
+        os.remove(program + '.tar.gz')
+        return