Pytest, github-actions, and codecov. (#114)

* Create python-package-conda.yml

* delete travis.

* replace raw_input with input to support python3.

* add more python versions.

* update yaml to use multiple python versions.

* include pytest-cov.

* install.

* fix space.

* sync pytest with codecov.

* fix covfile name.

* replace test_dspec with pytest statements.

* migrate test_plot to pytest.

* migrate test_utils.

* migrate test_utils.

* remove 3.7

.github/workflows/python-package-conda.yml

@@ -0,0 +1,50 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # 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: Install
+      run: |
+        pip install .
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        conda install pytest-cov
+        pytest --cov=./ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        directory: ./coverage/reports/
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true
+        path_to_write_report: ./coverage/codecov_report.txt
+        verbose: true

scripts/plot_uv.py

@@ -27,7 +27,7 @@
     help="Dynamic range in color of image, in units matching plotting mode. Default max(data)-min(data).")
 o.add_option('-m', '--mode', dest='mode', default='log',
     help='Plot mode can be log (logrithmic), abs (absolute), phs (phase), real, or imag.')
-o.add_option('-t', '--time', dest='time', default='all', 
+o.add_option('-t', '--time', dest='time', default='all',
     help='Select which time samples to plot. Options are: "all" (default), "<time1 #>_<time2 #>" (a range of times to plot), or "<time1 #>,<time2 #>" (a list of times to plot).')
 o.add_option('-u', '--unmask', dest='unmask', action='store_true',
     help='Plot masked data, too.')
@@ -128,7 +128,7 @@ def parse_range(chanstr):
     plot_f['freq'] = meta['freqs'].flatten().take(chan)
     plot_f['chan'] = chan
     dat, flg, _ = uvf.read(bls, freq_chans=chan)
-    data.append(dat); flgs.append(flg) 
+    data.append(dat); flgs.append(flg)
 
 # Concatenate the data from all the files
 if len(data) > 1:
@@ -243,7 +243,7 @@ def sort_func(a, b):
     def click(event):
         print([event.key])
         if event.key == 'm':
-            mode = raw_input('Enter new mode: ')
+            mode = input('Enter new mode: ')
             for k in plots:
                 try:
                     d = uvtools.plot.data_mode(plt_data[k], mode)
@@ -252,10 +252,10 @@ def click(event):
                     print('Unrecognized plot mode')
             plt.draw()
         elif event.key == 'd':
-            max = raw_input('Enter new max: ')
+            max = input('Enter new max: ')
             try: max = float(max)
             except(ValueError): max = None
-            drng = raw_input('Enter new drng: ')
+            drng = input('Enter new drng: ')
             try: drng = float(drng)
             except(ValueError): drng = None
             for k in plots: