ci: Add isort to linting step (#1343)

Update flopy using latest version of black. Add autotest\pull_request_prepare.py to help contributors to run isort and black prior to a pull request. Clean-up unused examples/Testing directory. Modified t064_test_performance.py to guard against failures on macOS.
modflowpy · Feb 1, 2022 · 9cc6e3e · 9cc6e3e
1 parent a13f8b9
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diff --git a/.docs/conf.py b/.docs/conf.py
@@ -15,10 +15,10 @@
 
 # add flopy root directory to the python path
 sys.path.insert(0, os.path.abspath(".."))
-from flopy import __version__, __author__
+from flopy import __author__, __version__
 
 # -- determine if running on readthedocs ------------------------------------
-on_rtd = os.environ.get('READTHEDOCS') == 'True'
+on_rtd = os.environ.get("READTHEDOCS") == "True"
 
 # -- determine if this version is a release candidate
 with open("../README.md", "r") as f:

diff --git a/.docs/create_rstfiles.py b/.docs/create_rstfiles.py
@@ -19,8 +19,11 @@ def create_tutorial_rst():
     tutorial_dict = {}
     for dirpath, _, filenames in os.walk(pth):
         key = os.path.basename(os.path.normpath(dirpath))
-        files = [filename.replace(".py", "") for filename in sorted(filenames)
-                 if filename.endswith(".py")]
+        files = [
+            filename.replace(".py", "")
+            for filename in sorted(filenames)
+            if filename.endswith(".py")
+        ]
         if len(files) > 0:
             tutorial_dict[key] = files
 

diff --git a/.docs/create_tutorials.py b/.docs/create_tutorials.py
@@ -14,8 +14,11 @@ def create_notebooks():
     # get a list of python files
     py_files = []
     for dirpath, _, filenames in os.walk(pth):
-        py_files += [os.path.join(dirpath, filename) for filename in
-                     sorted(filenames) if filename.endswith(".py")]
+        py_files += [
+            os.path.join(dirpath, filename)
+            for filename in sorted(filenames)
+            if filename.endswith(".py")
+        ]
     # sort the python files
     py_files = sorted(py_files)
 
@@ -43,10 +46,12 @@ def create_notebooks():
     os.makedirs(npth)
 
     for filepath in py_files:
-        src = os.path.join(wpth,
-                           os.path.basename(filepath).replace(".py", ".ipynb"))
-        dst = os.path.join(npth,
-                           os.path.basename(filepath).replace(".py", ".ipynb"))
+        src = os.path.join(
+            wpth, os.path.basename(filepath).replace(".py", ".ipynb")
+        )
+        dst = os.path.join(
+            npth, os.path.basename(filepath).replace(".py", ".ipynb")
+        )
         shutil.copyfile(src, dst)
     shutil.rmtree(".working")
 

diff --git a/.docs/pysrc/tutorial1.py b/.docs/pysrc/tutorial1.py
@@ -1,6 +1,8 @@
 import os
 import sys
+
 import numpy as np
+
 import flopy
 
 # Assign name and create modflow model object
@@ -52,6 +54,7 @@
 mf.run_model()
 
 import matplotlib.pyplot as plt
+
 import flopy.utils.binaryfile as bf
 
 plt.subplot(1, 1, 1, aspect="equal")

diff --git a/.docs/pysrc/tutorial2.py b/.docs/pysrc/tutorial2.py
@@ -1,5 +1,7 @@
 import os
+
 import numpy as np
+
 import flopy
 
 # Model domain and grid definition
@@ -121,6 +123,7 @@
 
 # Imports
 import matplotlib.pyplot as plt
+
 import flopy.utils.binaryfile as bf
 
 # Create the headfile and budget file objects

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -76,9 +76,20 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r etc/requirements.pip.txt
 
+    - name: Run isort
+      run: |
+        echo "if isort check fails update isort using"
+        echo "  pip install isort --upgrade"
+        echo "and run"
+        echo "  isort ./flopy"
+        echo "and then commit the changes."
+        isort --check --diff ./flopy
+
     - name: Run black
       run: |
-        echo "if black check fails run"
+        echo "if black check fails update black using"
+        echo "  pip install black --upgrade"
+        echo "and run"
         echo "  black ./flopy"
         echo "and then commit the changes."
         black --check --diff ./flopy
@@ -93,7 +104,6 @@ jobs:
 
   flopyCI:
     name: autotests
-    needs: [flopy_setup, flopy_lint]
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

diff --git a/.gitignore b/.gitignore
@@ -62,8 +62,6 @@ flopy/.idea
 examples/Notebooks/data
 examples/Notebooks/temp
 examples/FAQ/temp
-examples/Testing/.idea
-examples/Testing/data
 examples/scripts/data
 examples/groundwater_paper/Notebooks/temp
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -55,15 +55,14 @@ Before you submit your Pull Request (PR) consider the following guidelines:
      ```
 
 4. Create your patch, **including appropriate test cases**. See [Autotesting,md](autotest/Autotesting.md) for guidelines for constructing autotests. 
-5. 
-6. Run the [black formatter](https://github.com/psf/black) on Flopy source files from the git repository root directory using:
+5. Run the [isort import sorter](https://github.com/PyCQA/isort) and [black formatter](https://github.com/psf/black) on Flopy source files from the git repository `autotest` directory using:
 
    ```shell
-   black ./flopy
+   python pull_request_prepare.py
    ```
-   Note: Pull Requests must pass black format checks run on the [GitHub actions](https://github.com/modflowpy/flopy/actions) (*linting*) before they will be accepted. The black formatter can be installed using [`pip`](https://pypi.org/project/black/) and [`conda`](https://anaconda.org/conda-forge/black). 
+   Note: Pull Requests must pass isort import and black format checks run on the [GitHub actions](https://github.com/modflowpy/flopy/actions) (*linting*) before they will be accepted. isort can be installed using [`pip`](https://pypi.org/project/isort/) and [`conda`](https://anaconda.org/conda-forge/isort). The black formatter can also be installed using [`pip`](https://pypi.org/project/black/) and [`conda`](https://anaconda.org/conda-forge/black). If the Pull Request fails the *linting* job in the [flopy continuous integration](https://github.com/modflowpy/flopy/actions/workflows/ci.yml) workflow, make sure the latest versions of isort and black are installed.
 
-7. Run the full FloPy test suite and ensure that all tests pass:
+6. Run the full FloPy test suite and ensure that all tests pass:
 
     ```shell
     cd autotest
@@ -72,7 +71,7 @@ Before you submit your Pull Request (PR) consider the following guidelines:
     ```
    Note: the FloPy test suite requires the [pytest](https://pypi.org/project/pytest/) and [pymake](https://github.com/modflowpy/pymake) python packages. All the FloPy dependencies must also be installed for the tests to pass.
 
-8. Commit your changes using a descriptive commit message that follows our
+7. Commit your changes using a descriptive commit message that follows our
   [commit message conventions](#commit). Adherence to these conventions
   is necessary because release notes are automatically generated from these messages.
 
@@ -81,13 +80,13 @@ Before you submit your Pull Request (PR) consider the following guidelines:
      ```
    Note: the optional commit `-a` command line option will automatically "add" and "rm" edited files.
 
-9. Push your branch to GitHub:
+8. Push your branch to GitHub:
 
     ```shell
     git push origin my-fix-branch
     ```
 
-10. In GitHub, send a pull request to `flopy:develop`.
+9. In GitHub, send a pull request to `flopy:develop`.
 * If we suggest changes then:
   * Make the required updates.
   * Re-run the FloPy test suites, in the autotest directory, to ensure tests are still passing.

diff --git a/autotest/ci_framework.py b/autotest/ci_framework.py
@@ -212,6 +212,7 @@ def save_as_artifact(self):
             shutil.copytree(test_dir, dst)
         return
 
+
 def _get_mf6path():
     """
     Get the path for the MODFLOW 6 example problems

diff --git a/autotest/pull_request_prepare.py b/autotest/pull_request_prepare.py
@@ -0,0 +1,21 @@
+import os
+
+try:
+    import isort
+
+    print(f"isort version: {isort.__version__}")
+except ModuleNotFoundError:
+    print("isort not installed\n\tInstall using pip install isort")
+
+try:
+    import black
+
+    print(f"black version: {black.__version__}")
+except ModuleNotFoundError:
+    print("black not installed\n\tInstall using pip install black")
+
+print("running isort...")
+os.system("isort -v ../flopy")
+
+print("running black...")
+os.system("black -v ../flopy")
diff --git a/autotest/t020_test.py b/autotest/t020_test.py
@@ -16,7 +16,7 @@ def analyticalWaterTableSolution(h1, h2, z, R, K, L, x):
     b2 = h2 - z
     h = (
         np.sqrt(
-            b1 ** 2 - (x / L) * (b1 ** 2 - b2 ** 2) + (R * x / K) * (L - x)
+            b1**2 - (x / L) * (b1**2 - b2**2) + (R * x / K) * (L - x)
         )
         + z
     )

diff --git a/autotest/t029_test.py b/autotest/t029_test.py
@@ -328,22 +328,29 @@ def test_flowja_residuals():
 def test_structured_faceflows_3d():
     model_ws = f"{base_dir}_test_faceflows_3d"
     test_setup = FlopyTestSetup(verbose=True, test_dirs=model_ws)
-    name = 'mymodel'
-    sim = flopy.mf6.MFSimulation(sim_name=name, sim_ws=model_ws, exe_name='mf6')
+    name = "mymodel"
+    sim = flopy.mf6.MFSimulation(
+        sim_name=name, sim_ws=model_ws, exe_name="mf6"
+    )
     tdis = flopy.mf6.ModflowTdis(sim)
     ims = flopy.mf6.ModflowIms(sim)
     gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
-    dis = flopy.mf6.ModflowGwfdis(gwf, nlay=3, nrow=10, ncol=10, top=0, botm=[-1, -2, -3])
+    dis = flopy.mf6.ModflowGwfdis(
+        gwf, nlay=3, nrow=10, ncol=10, top=0, botm=[-1, -2, -3]
+    )
     ic = flopy.mf6.ModflowGwfic(gwf)
     npf = flopy.mf6.ModflowGwfnpf(gwf, save_specific_discharge=True)
-    chd = flopy.mf6.ModflowGwfchd(gwf, stress_period_data=[[(0, 0, 0), 1.],
-                                                           [(0, 9, 9), 0.]])
-    budget_file = name + '.bud'
-    head_file = name + '.hds'
-    oc = flopy.mf6.ModflowGwfoc(gwf,
-                                budget_filerecord=budget_file,
-                                head_filerecord=head_file,
-                                saverecord=[('HEAD', 'ALL'), ('BUDGET', 'ALL')])
+    chd = flopy.mf6.ModflowGwfchd(
+        gwf, stress_period_data=[[(0, 0, 0), 1.0], [(0, 9, 9), 0.0]]
+    )
+    budget_file = name + ".bud"
+    head_file = name + ".hds"
+    oc = flopy.mf6.ModflowGwfoc(
+        gwf,
+        budget_filerecord=budget_file,
+        head_filerecord=head_file,
+        saverecord=[("HEAD", "ALL"), ("BUDGET", "ALL")],
+    )
     sim.write_simulation()
     sim.run_simulation()
 
@@ -354,9 +361,15 @@ def test_structured_faceflows_3d():
         flowja,
         grb_file=os.path.join(model_ws, "mymodel.dis.grb"),
     )
-    assert frf.shape == head.shape, f"frf.shape {frf.shape} != head.shape {head.shape}"
-    assert fff.shape == head.shape, f"frf.shape {frf.shape} != head.shape {head.shape}"
-    assert flf.shape == head.shape, f"frf.shape {frf.shape} != head.shape {head.shape}"
+    assert (
+        frf.shape == head.shape
+    ), f"frf.shape {frf.shape} != head.shape {head.shape}"
+    assert (
+        fff.shape == head.shape
+    ), f"frf.shape {frf.shape} != head.shape {head.shape}"
+    assert (
+        flf.shape == head.shape
+    ), f"frf.shape {frf.shape} != head.shape {head.shape}"
     return
 
 

diff --git a/autotest/t062_test_intersect.py b/autotest/t062_test_intersect.py
@@ -99,14 +99,15 @@ def get_vlist(i, j, nrow, ncol):
 
 # simple functions to load vertices and index lists for unstructured grid
 def load_verts(fname):
-    verts = np.genfromtxt(fname, dtype=[int, float, float],
-                          names=['iv', 'x', 'y'])
-    verts['iv'] -= 1  # zero based
+    verts = np.genfromtxt(
+        fname, dtype=[int, float, float], names=["iv", "x", "y"]
+    )
+    verts["iv"] -= 1  # zero based
     return verts
 
 
 def load_iverts(fname):
-    f = open(fname, 'r')
+    f = open(fname, "r")
     iverts = []
     xc = []
     yc = []
@@ -244,8 +245,12 @@ def test_unstructured_xyz_intersect():
     ncpl = np.array(3 * [len(iverts)])
     nnodes = np.sum(ncpl)
 
-    top = np.ones((nnodes), )
-    botm = np.ones((nnodes), )
+    top = np.ones(
+        (nnodes),
+    )
+    botm = np.ones(
+        (nnodes),
+    )
 
     # set top and botm elevations
     i0 = 0
@@ -258,11 +263,15 @@ def test_unstructured_xyz_intersect():
         i1 += cpl
 
     # create the modelgrid
-    mg = flopy.discretization.UnstructuredGrid(vertices=verts,
-                                               iverts=iverts,
-                                               xcenters=xc,
-                                               ycenters=yc, top=top,
-                                               botm=botm, ncpl=ncpl)
+    mg = flopy.discretization.UnstructuredGrid(
+        vertices=verts,
+        iverts=iverts,
+        xcenters=xc,
+        ycenters=yc,
+        top=top,
+        botm=botm,
+        ncpl=ncpl,
+    )
 
     xc, yc, zc = mg.xyzcellcenters
     zc = zc[0].reshape(mg.nlay, mg.ncpl[0])

diff --git a/autotest/t064_test_performance.py b/autotest/t064_test_performance.py
@@ -29,7 +29,7 @@ def setup_class(cls):
         size = 100
         nlay = 10
         nper = 10
-        nsfr = int((size ** 2) / 5)
+        nsfr = int((size**2) / 5)
 
         letters = string.ascii_lowercase
         prepend = "".join(random.choice(letters) for i in range(10))
@@ -63,7 +63,7 @@ def setup_class(cls):
             m, rech={k: 0.001 - np.cos(k) * 0.001 for k in range(nper)}
         )
 
-        ra = fm.ModflowWel.get_empty(size ** 2)
+        ra = fm.ModflowWel.get_empty(size**2)
         well_spd = {}
         for kper in range(nper):
             ra_per = ra.copy()
@@ -120,15 +120,18 @@ def test_9_load_time(self):
         print("loading model...")
         mfp = TestModflowPerformance()
         mfp.m.write_input()
-        target = 3
+        if sys.platform == "darwin":
+            target = 4.0
+        else:
+            target = 3.0
         t0 = time.time()
         m = fm.Modflow.load(
             f"{mfp.modelname}.nam", model_ws=mfp.model_ws, check=False
         )
         t1 = time.time() - t0
         assert (
             t1 < target
-        ), f"model load took {t1:.2f}s, should take {target:.1f}s"
+        ), f"model load took {t1:.2f}s, should take {target:.2f}s"
         print(f"loading the model took {t1:.2f}s")
 
     @classmethod
-Original file line number
+Diff line change
@@ Expand Up / @@ -212,6 +212,7 @@ def save_as_artifact(self): @@
                 shutil.copytree(test_dir, dst)
             return
     def _get_mf6path():
         """
         Get the path for the MODFLOW 6 example problems
@@ Expand Down @@