Merge pull request #34 from jrenaud90/dev

v0.3.5 fixes issues introduced in v0.3.4

.github/workflows/pr_tests.yml

@@ -17,19 +17,22 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install flake8
+          python -m pip install -r requirements.txt
       - name: Lint with flake8
         run: |
-          $CONDA/bin/conda install flake8
           # stop the build if there are Python syntax errors or undefined names
-          $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
   # Run a test suite with numba on to test functionality, no coverage.
   test-numba:
     runs-on: ubuntu-latest
+    env:
+      NUMBA_DISABLE_JIT: 0
     strategy:
       matrix:
         group: [1, 2, 3, 4, 5]
@@ -41,10 +44,11 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install -r requirements.txt
       - name: Run pytest
-        run: $CONDA/bin/pytest --splits 5 --group ${{ matrix.group }}
+        run: python -m pytest --splits 5 --group ${{ matrix.group }}
 
   # Run a test suite with numba off to somewhat test functionality but more to get coverage.
   test-no-numba:
@@ -62,10 +66,11 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install -r requirements.txt
       - name: Run pytest
-        run: $CONDA/bin/pytest --cov=TidalPy --splits 5 --group ${{ matrix.group }}
+        run: python -m pytest --cov=TidalPy --splits 5 --group ${{ matrix.group }}
       - name: Upload coverage
         uses: actions/upload-artifact@v3
         with:
@@ -84,14 +89,15 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install -r requirements.txt
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
       - name: Run coverage
         run: |
-          $CONDA/bin/coverage combine coverage*/.coverage*
-          $CONDA/bin/coverage report --fail-under=50
-          $CONDA/bin/coverage xml
+          coverage combine coverage*/.coverage*
+          coverage report --fail-under=50
+          coverage xml
       - uses: codecov/codecov-action@v3.0.0

.github/workflows/push_tests.yml

@@ -17,15 +17,16 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install flake8
+          python -m pip install -r requirements.txt
       - name: Lint with flake8
         run: |
-          $CONDA/bin/conda install flake8
           # stop the build if there are Python syntax errors or undefined names
-          $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
   # Run a test suite with numba off to somewhat test functionality but more to get coverage.
   test-no-numba:
@@ -43,10 +44,11 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install -r requirements.txt
       - name: Run pytest
-        run: $CONDA/bin/pytest --cov --splits 5 --group ${{ matrix.group }}
+        run: python -m pytest --cov=TidalPy --splits 5 --group ${{ matrix.group }}
       - name: Upload coverage
         uses: actions/upload-artifact@v3
         with:
@@ -65,14 +67,15 @@ jobs:
           python-version: 3.9
       - name: Install Dependencies
         run: |
-          # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda env update --file environment.yml --name base
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov pytest-split
+          python -m pip install -r requirements.txt
       - name: Download all artifacts
         # Downloads coverage1, coverage2, etc.
         uses: actions/download-artifact@v3
       - name: Run coverage
         run: |
-          $CONDA/bin/coverage combine coverage*/.coverage*
-          $CONDA/bin/coverage report --fail-under=50
-          $CONDA/bin/coverage xml
+          coverage combine coverage*/.coverage*
+          coverage report --fail-under=50
+          coverage xml
       - uses: codecov/codecov-action@v3.0.0

CHANGES.md

@@ -1,5 +1,15 @@
 # TidalPy Major Change Log
 
+### Version 0.3.5 Alpha (Spring 2022)
+
+* Minor Changes
+  * Removed the soon-to-be deprecated np.float, np.complex, np.int references.
+  * Added a check to see if cartopy is installed before functions that depend on it are imported.
+* Bug Fixes
+  * Fixed coverage problem with github actions.
+  * Fixed issue importing nbTuple.
+  * Fixed issues with GitHub actions and coverage.
+
 ### Version 0.3.4 Alpha (Winter/Spring 2022)
 
 *Multilayer scripts based on 0.3.3 or earlier will likely break with this version!*

Documentation/Performance & Benchmarking/tides/mode_manipulation_speed.ipynb

@@ -92,7 +92,7 @@
    },
    "outputs": [],
    "source": [
-    "N_range = np.logspace(0, 6, 20, dtype=np.int)\n",
+    "N_range = np.logspace(0, 6, 20, dtype=np.int32)\n",
     "order_ls = {'-': 2, '--': 3, '-.': 4}\n",
     "eccen_truncs = {'b': 2, 'g': 6, 'orange': 10, 'r': 20}\n",
     "\n",

README.md

@@ -1,10 +1,11 @@
-<h1 align="center">TidalPy</h1>
-<h3 align="center">v0.3 Alpha</h3>
-
-<p align="center">
-    <a href="https://github.com/jrenaud90/TidalPy/actions/workflows/push_tests.yml?query=branch%3Amaster" /><img src="https://github.com/jrenaud90/TidalPy/actions/workflows/push_tests.yml/badge.svg?branch=master" /></a> <a href="https://codecov.io/gh/jrenaud90/TidalPy"><img src="https://codecov.io/gh/jrenaud90/TidalPy/branch/master/graph/badge.svg?token=35OY4ZLOA5"/></a><br />
-    <a href="https://mybinder.org/v2/gh/jrenaud90/TidalPy/master?filepath=%2FCookbooks%2F"><img src="https://mybinder.org/badge_logo.svg" /></a>
-    <a href="https://gitter.im/TidalPy/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge"><img src="https://badges.gitter.im/TidalPy/community.svg" /></a>
+<h1 style="text-align: center">TidalPy</h1>
+<h3 style="text-align: center">v0.3.5 Beta</h3>
+
+<p style="text-align: center">
+    <a href="https://github.com/jrenaud90/TidalPy/actions/workflows/push_tests.yml?query=branch%3Amaster"><img src="https://github.com/jrenaud90/TidalPy/actions/workflows/push_tests.yml/badge.svg?branch=master" alt="Push Test Pass/Fail" /></a>
+    <a href="https://codecov.io/gh/jrenaud90/TidalPy"><img src="https://codecov.io/gh/jrenaud90/TidalPy/branch/master/graph/badge.svg?token=35OY4ZLOA5" alt="Code Coverage"/></a><br />
+    <a href="https://mybinder.org/v2/gh/jrenaud90/TidalPy/master?filepath=%2FCookbooks%2F"><img src="https://mybinder.org/badge_logo.svg" alt="Binder" /></a>
+    <a href="https://gitter.im/TidalPy/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge"><img src="https://badges.gitter.im/TidalPy/community.svg" alt="Gitter" /></a>
 </p>
 
 ## Purpose
@@ -78,6 +79,11 @@ following in a terminal:
 However, there can be several gotchas that come with this simple installation process. It is recommended to use the
 advanced installation described in the next section.
 
+_Note: As of TidalPy v0.3.4, if you do not install via anaconda then you will need to manually install 
+[proj v8.0.0+](https://proj.org/install.html) and [geos 3.7.2+](https://anaconda.org/conda-forge/geos) 
+(before installing TidalPy. Otherwise, the project map graphic utility may not work. 
+[Read more here](https://scitools.org.uk/cartopy/docs/latest/installing.html)_ 
+
 ### Advanced Installation
 
 It is highly recommended that you use the [Anaconda](https://www.anaconda.com/distribution/) distribution of Python.

Tests/Test_SetB_Package/test_c_tools_conversions.py

@@ -16,9 +16,9 @@
 
 def test_sec2myr():
     # Build arrays for testing
-    zero_array = np.zeros(10, dtype=np.float)
-    one_array = np.ones(10, dtype=np.float)
-    sec_array = 3.154e13 * np.ones(10, dtype=np.float)
+    zero_array = np.zeros(10, dtype=np.float64)
+    one_array = np.ones(10, dtype=np.float64)
+    sec_array = 3.154e13 * np.ones(10, dtype=np.float64)
 
     # Test sec2myr - Floats
     assert sec2myr(0.) == 0.
@@ -43,9 +43,9 @@ def test_sec2myr():
 
 def test_Au2m():
     # Build arrays for testing
-    zero_array = np.zeros(10, dtype=np.float)
-    one_array = np.ones(10, dtype=np.float)
-    meter_array = 1.496e11 * np.ones(10, dtype=np.float)
+    zero_array = np.zeros(10, dtype=np.float64)
+    one_array = np.ones(10, dtype=np.float64)
+    meter_array = 1.496e11 * np.ones(10, dtype=np.float64)
 
     # Test m2Au - Floats
     assert m2Au(0.) == 0.
@@ -71,10 +71,10 @@ def test_Au2m():
 def test_rads2days():
     # Build arrays for testing
     day_to_radians = 2. * np.pi / 86400.
-    zero_array = np.zeros(10, dtype=np.float)
-    inf_array = np.inf * np.ones(10, dtype=np.float)
-    one_array = np.ones(10, dtype=np.float)
-    radian_array = day_to_radians * np.ones(10, dtype=np.float)
+    zero_array = np.zeros(10, dtype=np.float64)
+    inf_array = np.inf * np.ones(10, dtype=np.float64)
+    one_array = np.ones(10, dtype=np.float64)
+    radian_array = day_to_radians * np.ones(10, dtype=np.float64)
 
     # Test rads2days - Floats
     with pytest.raises(ZeroDivisionError) as e_info:
@@ -106,9 +106,9 @@ def test_semi_a2orbital_motion():
     sun_mass = 1.988435e30  # kg
     earth_orb_motion = (G * (earth_mass + sun_mass) / earth_distance**3)**(1 / 2)  # radians second-1
 
-    zero_array = np.zeros(10, dtype=np.float)
-    distance_array = earth_distance * np.ones(10, dtype=np.float)
-    frequency_array = earth_orb_motion * np.ones(10, dtype=np.float)
+    zero_array = np.zeros(10, dtype=np.float64)
+    distance_array = earth_distance * np.ones(10, dtype=np.float64)
+    frequency_array = earth_orb_motion * np.ones(10, dtype=np.float64)
 
     # Test semi_a2orbital_motion - Floats
     with pytest.raises(ZeroDivisionError) as e_info:

Tests/Test_SetB_Package/test_c_tools_timing.py

@@ -15,9 +15,9 @@ def test_convert_hms():
     assert type(result) == tuple
 
     day, hour, minute, second = result
-    assert type(day) in [int, np.int, np.int32]
-    assert type(hour) in [int, np.int, np.int32]
-    assert type(minute) in [int, np.int, np.int32]
+    assert type(day) in [int, np.int32]
+    assert type(hour) in [int, np.int32]
+    assert type(minute) in [int, np.int32]
     assert type(second) in [float, np.float64]
 
     assert day == 0

Tests/Test_SetB_Package/test_h_voxel_volume.py

@@ -37,9 +37,9 @@ def test_voxel_volume_numpy():
     """ Test the voxel volume calculation using the numpy version of the func.
     Check that the results match expectations. """
 
-    radius_array = np.linspace(0., planet_radius, 50)
+    radius_array = np.linspace(0., planet_radius, 20)
     longitude_array_deg = np.linspace(0., 360., 20)
-    colatitude_array_deg = np.linspace(0., 180., 25)
+    colatitude_array_deg = np.linspace(0., 180., 20)
     longitude_array = np.radians(longitude_array_deg)
     colatitude_array = np.radians(colatitude_array_deg)
 
@@ -63,8 +63,8 @@ def test_voxel_volume_numba_higherN():
     """ See if using a higher N will result in better results. """
 
     radius_array = np.linspace(0., planet_radius, 400)
-    longitude_array_deg = np.linspace(0., 360., 400)
-    colatitude_array_deg = np.linspace(0., 180., 400)
+    longitude_array_deg = np.linspace(0., 360., 100)
+    colatitude_array_deg = np.linspace(0., 180., 100)
     longitude_array = np.radians(longitude_array_deg)
     colatitude_array = np.radians(colatitude_array_deg)
 

Tests/Test_SetF_Functional/Test_Dynamics/test_single_dissipation.py

@@ -101,5 +101,5 @@ def test_single_disp_arrays():
     assert result[0].dtype in [float, np.float64]
     assert result[0].shape == (10,)
     assert type(result[1]) == np.ndarray
-    assert result[1].dtype in [float, np.float, np.float64]
+    assert result[1].dtype in [float, np.float64]
     assert result[1].shape == (10,)

Tests/Test_SetF_Functional/Test_Integrate/test_RK_integrator.py

@@ -224,7 +224,7 @@ def diffeq(t, y):
     assert success
     assert type(message) == str
     assert type(ts) == np.ndarray
-    assert ts.dtype in (float, np.float, np.float64)
+    assert ts.dtype in (float, np.float64)
     assert type(ys) == np.ndarray
     assert ys.dtype in (complex, np.complex128)
     np.testing.assert_almost_equal(ts[0], t_span[0])
@@ -264,9 +264,9 @@ def diffeq(t, z):
     assert success
     assert type(message) == str
     assert type(ts) == np.ndarray
-    assert ts.dtype in (float, np.float, np.float64)
+    assert ts.dtype in (float, np.float64)
     assert type(ys) == np.ndarray
-    assert ys.dtype in (float, np.float, np.float64)
+    assert ys.dtype in (float, np.float64)
     np.testing.assert_almost_equal(ts[0], t_span[0])
     np.testing.assert_almost_equal(ts[-1], t_span[-1])
     assert ys.shape[0] == 2
@@ -303,9 +303,9 @@ def diffeq(t, z):
     assert success
     assert type(message) == str
     assert type(ts) == np.ndarray
-    assert ts.dtype in (float, np.float, np.float64)
+    assert ts.dtype in (float, np.float64)
     assert type(ys) == np.ndarray
-    assert ys.dtype in (float, np.float, np.float64)
+    assert ys.dtype in (float, np.float64)
     np.testing.assert_almost_equal(ts[0], t_span[0])
     np.testing.assert_almost_equal(ts[-1], t_span[-1])
     assert ys.shape[0] == 2