V0.1.0 (#15)

* Fix typo in README (#4)
* modflowapi interface (#8)
* update package: manual variable address assembly updated to use xmipy get_variable_addr()
* update additional manual variable address assembly statements
* Refactor code and added functionality:
* add stress_period_start, stress_period_end Callbacks
* fix ApiModel __repr__
* added Exchanges, TDIS, ATS, and SLN support
* added ScalarInput and ScalarPackage support
* update autotests
* added parallel testing support through pytest-xdist
* updated markers and split the extensions tests from the mf6 examples tests
* added a test for ATS
* update setup.cfg
* update ci.yml
* update(ListInput): add auxvar to stress_period_data when auxiliary variables are used
* Allow None to be passed to stress_period_data.values to disable stresses for a package
* updates: ApiModel, ApiSimulation, run_simulation
* added a `totim` property on `ApiSimulation` and `ApiModel`
* added docstrings to ApiModel property methods
* updated termination message in run_simulation
* added a finalize callback to Callbacks and run_simulation
* add support for AUXNAME_CST
* add(Head Monitor Example): Add a head monitor example application
* ApiModel: adjust X based on nodetouser
* ApiPackage: enforce lower cased variable names in get_advanced_var
* ArrayPointer: trap for arrays that are not adjusted by reduced node numbers (ex. idomain)
* update setup.cfg
* try reformatting the xmipy installation instructions
* fix(get value): fixed error handling when modflowapi fails to get a pointer to a value from the API (#9)
Co-authored-by: scottrp <45947939+scottrp@users.noreply.github.com>
* update(rhs, hcof, AdvancedInput): bug fixes for setting variable values for advanced inputs
* update rhs and hcof to copy values to pointer instead of overwriting the pointer
* add a check for AdvancedInput variables that do not have pointer support in xmipy
* update setting routine for AdvancedInput
* refactor(EOL): change CRLF to LF line endings for source files (#12)
* Use pyproject.toml for project metadata, add citation info (#11)
* add(test_rhs_hcof_advanced): add additional test  (#13)
* added test for getting and setting rhs, hcof, and advanced variable values
* update project to use unix line separators
* use np.testing.assert_allclose() instead of AssertionError
* Add missing RIV support to modflowapi (#16)
* add(test_rhs_hcof_advanced): add additional test
* added test for getting and setting rhs, hcof, and advanced variable values
* update project to use unix line separators
* use np.testing.assert_allclose() instead of AssertionError
* Add missing riv package to modflowapi
* release: v0.1.0
---------

Co-authored-by: Hofer-Julian <30049909+Hofer-Julian@users.noreply.github.com>
Co-authored-by: Joshua Larsen <jlarsen@usgs.gov>
Co-authored-by: spaulins-usgs <spaulinski@usgs.gov>
Co-authored-by: scottrp <45947939+scottrp@users.noreply.github.com>
Co-authored-by: Mike Taves <mwtoews@gmail.com>

.flake8

@@ -8,29 +8,24 @@ exclude =
     autotest
 ignore =
     # https://flake8.pycqa.org/en/latest/user/error-codes.html
-    F401, # 'module' imported but unused
+    # 'module' imported but unused
+    F401,
     # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes
-    E121, # continuation line under-indented for hanging indent
-    E122, # continuation line missing indentation or outdented
-    E126, # continuation line over-indented for hanging indent
-    E127, # continuation line over-indented for visual indent
-    E128, # continuation line under-indented for visual indent
-    E203, # whitespace before
-    E221, # multiple spaces before operator
-    E222, # multiple spaces after operator
-    E226, # missing whitespace around arithmetic operator
-    E231, # missing whitespace after ','
-    E241, # multiple spaces after ','
-    E402, # module level import not at top of file
-    E501, # line too long (> 79 characters)
-    E502, # backslash is redundant between brackets
-    E722, # do not use bare 'except'
-    E741, # ambiguous variable name
-    W291, # trailing whitespace
-    W292, # no newline at end of file
-    W293, # blank line contains whitespace
-    W391, # blank line at end of file
-    W503, # line break before binary operator
-    W504  # line break after binary operator
+    # E1: Indentation
+    E121, E122, E126, E127, E128,
+    # E2: Whitespace
+    E203, E221, E222, E226, E231, E241,
+    # E4: Import
+    E402,
+    # E5: Line length
+    E501, E502,
+    # E7: Statement
+    E722, E741,
+    # W2: Whitespace warning
+    W291, W292, W293,
+    # W3: Blank line warning
+    W391,
+    # W5: Line break warning
+    W503, W504
 
 statistics = True

.gitattributes

@@ -15,4 +15,3 @@
 
 # Do not modify the model data in various directories
 examples/data/** binary
-examples/groundwater_paper/uspb/** binary

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ on:
       - develop
       - 'release*'
   pull_request:
-    branches: [master, develop]
+    branches: [main, develop]
 
 jobs:
 
@@ -26,28 +26,28 @@ jobs:
 
     # check out repo
     - name: Checkout repo
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3
 
-    - name: Setup Python 3.8
-      uses: actions/setup-python@v2
+    - name: Setup Python
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.x
 
     - name: Upgrade pip
       run: |
         python -m pip install --upgrade pip
 
     - name: Base installation
       run: |
-        pip install . --use-feature=in-tree-build
-
+        pip install -e .
+        
     - name: Print version
       run: |
         python -c "import modflowapi; print(modflowapi.__version__)"
 
 
   lint:
-    name: linting
+    name: lint
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -59,31 +59,31 @@ jobs:
     steps:
     # check out repo
     - name: Checkout repo
-      uses: actions/checkout@v2.3.4
+      uses: actions/checkout@v3
 
-    # Standard python fails on windows without GDAL installation. Using
+    # Standard python fails on Windows without GDAL installation. Using
     # standard python here since only linting on linux.
     # Use standard bash shell with standard python
-    - name: Setup Python 3.8
-      uses: actions/setup-python@v2
+    - name: Setup Python
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.x
 
     - name: Print python version
       run: |
         python --version
 
-    - name: Install Python 3.8 packages
+    - name: Install Python packages
       run: |
         python -m pip install --upgrade pip
-        pip install -r etc/requirements.pip.txt
+        pip install -e .[lint]
 
     - name: Run black
       run: |
         echo "if black check fails run"
-        echo "  black --line-length 79 ./modflowapi"
+        echo "  black ./modflowapi"
         echo "and then commit the changes."
-        black --check --line-length 79 ./modflowapi
+        black --check ./modflowapi
 
     - name: Run flake8
       run: |
@@ -93,3 +93,92 @@ jobs:
       run: |
         pylint --jobs=2 --errors-only --exit-zero ./modflowapi
 
+  autotest_extensions:
+    name: modflowapi extensions autotests
+    needs: lint
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      # check out repo
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://git@github.com/Deltares/xmipy@develop
+          pip install git+https://git@github.com/MODFLOW-USGS/modflow-devtools@develop
+          pip install .[test]
+
+      - name: Install modflow executables
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ~/work/modflowapi/modflowapi/autotest
+          repo: modflow6-nightly-build
+
+      - name: Run autotests
+        working-directory: ./autotest
+        shell: bash -l {0}
+        run: |
+          # chmod a+x libmf6*
+          pytest -n auto -m "not mf6"
+          
+  autotest_mf6_examples:
+    name: modflowapi mf6 examples autotests
+    needs: lint
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      # check out repo
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://git@github.com/Deltares/xmipy@develop
+          pip install git+https://git@github.com/MODFLOW-USGS/modflow-devtools@develop
+          pip install .[test]
+
+      - name: Install modflow executables
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ~/work/modflowapi/modflowapi/autotest
+          repo: modflow6-nightly-build
+
+      - name: Run autotests
+        working-directory: ./autotest
+        shell: bash -l {0}
+        run: |
+          # chmod a+x libmf6*
+          pytest -n auto -m "mf6 and not extensions"

CITATION.cff

@@ -0,0 +1,61 @@
+cff-version: 1.2.0
+message: If you use this software, please cite both the article from preferred-citation
+  and the software itself.
+type: software
+title: MODFLOW API
+version: 0.1.0
+date-released: '2023-04-19'
+abstract: An extension to xmipy for the MODFLOW API.
+repository-artifact: https://pypi.org/project/modflowapi
+repository-code: https://github.com/MODFLOW-USGS/modflowapi
+license: CC0-1.0
+authors:
+- family-names: Hughes
+  given-names: Joseph D.
+  alias: jdhughes-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0003-1311-2354
+- family-names: Russcher
+  given-names: Martijn
+  alias: mjr-deltares
+  affiliation: Deltares
+  orcid: https://orcid.org/0000-0001-8799-6514
+- family-names: Langevin
+  given-names: Christian D.
+  alias: langevin-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0001-5610-9759
+- family-names: Hofer
+  given-names: Julian
+  alias: Hofer-Julian
+  affiliation: Deltares
+- family-names: Larsen
+  given-names: Joshua D.
+  alias: jlarsen-usgs
+  affiliation: U.S. Geological Survey
+  orcid: https://orcid.org/0000-0002-1218-800X
+preferred-citation:
+  type: article
+  authors:
+  - family-names: Hughes
+    given-names: Joseph D.
+    orcid: https://orcid.org/0000-0003-1311-2354
+  - family-names: Russcher
+    given-names: Martijn J.
+    orcid: https://orcid.org/0000-0001-8799-6514
+  - family-names: Langevin
+    given-names: Christian D.
+    orcid: https://orcid.org/0000-0001-5610-9759
+  - family-names: Morway
+    given-names: Eric D.
+    orcid: https://orcid.org/0000-0002-8553-6140
+  - family-names: McDonald
+    given-names: Richard R.
+    orcid: https://orcid.org/0000-0002-0703-0638
+  title: The MODFLOW Application Programming Interface for simulation control and software interoperability
+  doi: 10.1016/j.envsoft.2021.105257
+  journal: Environmental Modelling & Software
+  volume: 138
+  start: 105257
+  year: 2022
+  month: 2

README.md

@@ -1,10 +1,25 @@
 # modflowapi
 
-`modflowapi` is an extension to [xmiipy](https://pypi.org/project/xmipy/) for the MODFLOW API.
+`modflowapi` is an extension to [xmipy](https://pypi.org/project/xmipy/) for the MODFLOW API.
+
+The `modflowapi` can be used to access functionality in the eXtended Model Interface (XMI) wrapper (XmiWrapper) 
+and additional functionality specific to the MODFLOW API. Currently it is a joint development of the USGS and Deltares.
+
+Use of modflowapi and modflowapi extensions can be found in the [Quickstart](examples/notebooks/Quickstart.ipynb) and the [Extensions](examples/notebooks/MODFLOW-API_extensions_objects.ipynb) Notebooks. An example of using the MODFLOW API to monitor heads during a simulation can be found in the [Head Monitor Example](examples/notebooks/Head_Monitor_Example.ipynb) Notebook. 
 
-The `modflowapi` can be used to access functionality in the eXtended Model Interface (XMI) wrapper (XmiWrapper) and additional functionality specific to the MODFLOW API. Currently it is a joint development of the USGS and Deltares.
 
 `modflowapi` can be installed by running
+
 ```
 pip install modflowapi
-```
+```
+
+or
+
+```
+conda install -c conda-forge modflowapi
+```
+
+### Citation
+
+Hughes, Joseph D., Russcher, M. J., Langevin, C. D., Morway, E. D. and McDonald, R. R., 2022, The MODFLOW Application Programming Interface for simulationcontrol and software interoperability: Environmental Modelling & Software, v. 148, p. 105257, [doi:10.1016/j.envsoft.2021.105257](https://doi.org/10.1016/j.envsoft.2021.105257).

autotest/__init__.py

@@ -0,0 +1 @@
+# init file for pytest