release: version 3.3.5

.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:
@@ -37,9 +37,9 @@
 with open(rst_name, "w") as f:
     for line in lines:
         if line.startswith("**Documentation for version"):
-            line = "**Documentation for version {}".format(__version__)
+            line = f"**Documentation for version {__version__}"
             if rc_text != "":
-                line += " --- {}".format(rc_text)
+                line += f" --- {rc_text}"
             line += "**\n"
         f.write(line)
 
@@ -64,7 +64,7 @@
             )
             authors = __author__.split(sep=",")
             for author in authors:
-                line += " * {}\n".format(author.strip())
+                line += f" * {author.strip()}\n"
             line += " * and others\n\n"
             f.write(line)
         elif line.startswith(tag_end):
@@ -91,7 +91,7 @@
 
 # -- Project information -----------------------------------------------------
 project = "flopy Documentation"
-copyright = "2021, {}".format(__author__)
+copyright = f"2021, {__author__}"
 author = __author__
 
 # The version.

.docs/create_rstfiles.py

@@ -4,11 +4,11 @@
 def create_section(f, title, filenames, upper_case=False):
     if upper_case:
         title = title.upper()
-    title = "{} Tutorials".format(title)
-    line = "{}\n".format(title) + len(title) * "-" + "\n\n"
+    title = f"{title} Tutorials"
+    line = f"{title}\n" + len(title) * "-" + "\n\n"
     line += "Contents:\n\n.. toctree::\n   :maxdepth: 2\n\n"
     for filename in filenames:
-        line += "   _notebooks/{}\n".format(filename)
+        line += f"   _notebooks/{filename}\n"
     line += "\n\n"
     f.write(line)
 
@@ -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
 

.docs/create_tutorials.py

@@ -14,15 +14,18 @@ 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)
 
     # copy the python files
     for src in py_files:
         dst = os.path.join(wpth, os.path.basename(src))
-        print("{} -> {}".format(src, dst))
+        print(f"{src} -> {dst}")
         shutil.copyfile(src, dst)
 
     # create and run notebooks
@@ -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")
 

.docs/main.rst

@@ -6,7 +6,7 @@
 FloPy Documentation
 ===================
 
-**Documentation for version 3.3.4 --- release candidate**
+**Documentation for version 3.3.5 --- release candidate**
 
 Return to the Github `FloPy <https://github.com/modflowpy/flopy>`_ website where the code resides.
 

.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
@@ -52,10 +54,11 @@
 mf.run_model()
 
 import matplotlib.pyplot as plt
+
 import flopy.utils.binaryfile as bf
 
 plt.subplot(1, 1, 1, aspect="equal")
-hds = bf.HeadFile(modelname + ".hds")
+hds = bf.HeadFile(f"{modelname}.hds")
 head = hds.get_data(totim=1.0)
 levels = np.arange(1, 10, 1)
 extent = (delr / 2.0, Lx - delc / 2.0, Ly - delc / 2.0, delc / 2.0)
@@ -66,12 +69,12 @@
 fig = plt.figure(figsize=(10, 10))
 ax = fig.add_subplot(1, 1, 1, aspect="equal")
 
-hds = bf.HeadFile(modelname + ".hds")
+hds = bf.HeadFile(f"{modelname}.hds")
 times = hds.get_times()
 head = hds.get_data(totim=times[-1])
 levels = np.linspace(0, 10, 11)
 
-cbb = bf.CellBudgetFile(modelname + ".cbc")
+cbb = bf.CellBudgetFile(f"{modelname}.cbc")
 kstpkper_list = cbb.get_kstpkper()
 frf = cbb.get_data(text="FLOW RIGHT FACE", totim=times[-1])[0]
 fff = cbb.get_data(text="FLOW FRONT FACE", totim=times[-1])[0]

.docs/pysrc/tutorial2.py

@@ -1,5 +1,7 @@
 import os
+
 import numpy as np
+
 import flopy
 
 # Model domain and grid definition
@@ -121,12 +123,13 @@
 
 # Imports
 import matplotlib.pyplot as plt
+
 import flopy.utils.binaryfile as bf
 
 # Create the headfile and budget file objects
-headobj = bf.HeadFile(modelname + ".hds")
+headobj = bf.HeadFile(f"{modelname}.hds")
 times = headobj.get_times()
-cbb = bf.CellBudgetFile(modelname + ".cbc")
+cbb = bf.CellBudgetFile(f"{modelname}.cbc")
 
 # Setup contour parameters
 levels = np.linspace(0, 10, 11)
@@ -156,7 +159,7 @@
     # Create the plot
     f = plt.figure()
     plt.subplot(1, 1, 1, aspect="equal")
-    plt.title("stress period " + str(iplot + 1))
+    plt.title(f"stress period {iplot + 1}")
 
     modelmap = flopy.plot.PlotMapView(model=mf, layer=0)
     qm = modelmap.plot_ibound()
@@ -181,13 +184,13 @@
         zorder=9,
     )
     plt.text(wpt[0] + 25, wpt[1] - 25, "well", size=12, zorder=12)
-    plt.savefig("tutorial2-{}.png".format(iplot))
+    plt.savefig(f"tutorial2-{iplot}.png")
 
 # Plot the head versus time
 idx = (0, int(nrow / 2) - 1, int(ncol / 2) - 1)
 ts = headobj.get_ts(idx)
 plt.subplot(1, 1, 1)
-ttl = "Head at cell ({0},{1},{2})".format(idx[0] + 1, idx[1] + 1, idx[2] + 1)
+ttl = f"Head at cell ({idx[0] + 1},{idx[1] + 1},{idx[2] + 1})"
 plt.title(ttl)
 plt.xlabel("time")
 plt.ylabel("head")

.docs/tutorials.rst

@@ -53,6 +53,18 @@ Contents:
    _notebooks/tutorial02_mf
 
 
+.IPYNB_CHECKPOINTS Tutorials
+----------------------------
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   _notebooks/tutorial01_mf-checkpoint
+   _notebooks/tutorial02_mf-checkpoint
+
+
 SEAWAT Tutorials
 ----------------
 

.github/workflows/ci-mf6.yml

@@ -0,0 +1,111 @@
+name: flopy mf6 CI
+
+on:
+  schedule:
+    - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
+  push:
+    branches:
+      - master
+      - develop
+      - 'release*'
+  pull_request:
+    branches: [master, develop]
+
+jobs:
+
+  flopymf6CI:
+    name: mf6 flopy autotests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    # check out repo
+    - name: Checkout flopy repo
+      uses:  actions/checkout@v2.3.4
+
+    - name: Get branch name
+      uses: nelonoel/branch-name@v1.0.1
+
+    - name: Setup Python 3.9
+      uses: actions/setup-python@v2.2.2
+      with:
+        python-version: 3.9
+
+    - name: Install Python 3.9 packages
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r etc/requirements.pip.txt
+
+    - name: Install pymake, xmipy, modflowapi, and flopy
+      run: |
+        python -m pip install --upgrade pip
+        pip install https://github.com/modflowpy/flopy/zipball/develop
+        pip install https://github.com/modflowpy/pymake/zipball/master
+        pip install https://github.com/Deltares/xmipy/zipball/develop
+        pip install https://github.com/MODFLOW-USGS/modflowapi/zipball/develop
+        pip install . --use-feature=in-tree-build
+
+    - name: Setup symbolic links on Linux
+      run: |
+        sudo ln -fs /usr/bin/gfortran-10 /usr/local/bin/gfortran
+        sudo ln -fs /usr/bin/gcc-10 /usr/local/bin/gcc
+        sudo ln -fs /usr/bin/g++-10 /usr/local/bin/g++
+
+    - name: Print GNU compiler versions
+      run: |
+        gfortran --version
+        gcc --version
+        g++ --version
+
+    - name: Clone MODFLOW 6 repo
+      run: |
+        git clone https://github.com/MODFLOW-USGS/modflow6.git modflow6
+
+    - name: Update flopy MODFLOW 6 classes
+      working-directory: ./modflow6/autotest
+      run: |
+        python update_flopy.py
+
+    - name: Install meson
+      run: |
+        pip install meson ninja
+
+    - name: Setup modflow
+      working-directory: ./modflow6
+      run: |
+        meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin
+
+    - name: Build modflow
+      working-directory: ./modflow6
+      run: |
+        meson compile -C builddir
+
+    - name: Install modflow
+      working-directory: ./modflow6
+      run: |
+        meson install -C builddir
+
+    - name: Get executables
+      working-directory: ./modflow6/autotest
+      run: |
+        pytest -v --durations=0 get_exes.py
+
+    - name: Run pytest
+      working-directory: ./modflow6/autotest
+      run: |
+        pytest -v -n auto -k "test_gw" --durations=0 --cov=flopy --cov-report=xml
+
+    - name: Print coverage report before upload
+      working-directory: ./modflow6/autotest
+      run: |
+        coverage report
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2.1.0
+      with:
+        directory: ./modflow6/autotest
+        file: coverage.xml