Fix hard coding bug in partial vertical LGR setup;

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/release.yml

@@ -1,29 +1,47 @@
 name: Publish release
-
 on:
   push:
-    # Sequence of patterns matched against refs/tags
-    tags:
-      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+    branches:
+      - master
+      # branchname trigger if we had the ability to auto-prep release PRs
+      # (turned off for doi-usgs org)
+      #- v[0-9]+.[0-9]+.[0-9]+*
+  release:
+    types:
+      - published
 
 jobs:
+
   release:
     name: Create Release
+    # runs only when changes are merged to master
+    if: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v3
+      - name: Checkout master branch
+        uses: actions/checkout@v4
+        with:
+          ref: master
+      - name: Bump version and push tag
+        id: tag_version
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
       - name: Create Release
         id: create_release
         uses: actions/create-release@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
+          tag_name: ${{ steps.tag_version.outputs.new_tag }}
+          release_name: Modflow-setup ${{ steps.tag_version.outputs.new_tag }}
           body: |
             Changes in this Release:
-          draft: false
+            ${{ steps.tag_version.outputs.changelog }}
+          draft: true
           prerelease: false
 
   docs:
@@ -33,9 +51,11 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         persist-credentials: false
+        ref: master
+        fetch-tags: true
 
     - name: Get latest release version number
       id: get_version
@@ -49,16 +69,9 @@ jobs:
     - name: Setup Micromamba
       uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: ci/test_environment.yaml
-        cache-environment: false
-        cache-downloads: false
-        # persist on the same day.
-        # cache-environment-key: environment-${{ steps.date.outputs.date }}
-        # cache-downloads-key: downloads-${{ steps.date.outputs.date }}
-        create-args: >-
-          python=${{ matrix.python-version }}
-        init-shell: >-
-          bash
+        environment-file: ci/test_environment.yml
+        cache-environment: true
+        cache-downloads: true
 
     - name: Conda info
       shell: bash -l {0}
@@ -91,7 +104,7 @@ jobs:
     - name: Run tests
       shell: bash -l {0}
       run: |
-        pytest mfsetup/test/test_notebooks.py
+        pytest mfsetup/tests/test_notebooks.py
 
     - name: Build docs
       shell: bash -l {0}
@@ -108,23 +121,50 @@ jobs:
         CLEAN: false
         TARGET_FOLDER: ${{ steps.get_version.outputs.version }}
 
-  deploy:
-    needs: release
-    runs-on: ubuntu-latest
+  publish:
+    name: Publish package
+    # runs only after release is published (manually promoted from draft)
+    # (allows editing of release notes, etc.)
+    if: ${{ github.event_name == 'release' }}
+    runs-on: ubuntu-latest  #ubuntu-22.04
+    permissions:
+      contents: write
+      pull-requests: write
+      id-token: write  # mandatory for trusted publishing
+    environment:  # requires a 'release' environment in repo settings
+      name: release
+      url: https://pypi.org/p/modflow-setup
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.ALL_PROJECTS }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+
+      - name: Checkout master branch
+        uses: actions/checkout@v4
+        with:
+          ref: master
+          fetch-tags: true
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check package
+        run: twine check --strict dist/*
+
+      - name: Upload package
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

docs/source/input/ic.rst

@@ -1,6 +1,88 @@
 =======================================================================================
-Specifying Initial Conditions
+Initial Conditions
 =======================================================================================
 
-.. note::
-   This page is a work in progress and needs some more work.
+Similar to other packages, input of initial conditions follows the structure of MODFLOW and Flopy. Setting the starting heads from the model top is often a good way to go initially. After the model has been run, starting heads can then be :ref:`updated from the initial model head output <Example script for updating starting heads from a previous run>` to improve convergence on subsequent runs.
+
+    .. Note::
+
+        With any transient model, an :ref:`initial steady-state stress period <Time Discretization>` is recommended, regardless of initial conditions. Specification of initial conditions is mostly a consideration for improving model convergence.
+
+Starting heads defaults
+--------------------------
+Omitting or leaving the ``ic:`` block blank triggers one of two default actions:
+
+* If there is no parent model, or a parent model with the ``default_source_data`` option turned off, starting heads are set to the model top.
+* If there is a parent model with the ``default_source_data`` option turned on, starting heads are set from the parent model starting heads.
+
+Specifying starting heads directly
+-----------------------------------
+For MODFLOW 6 models, the "Options" and "Griddata" input blocks are represented as sub-blocks within the ``ic:`` block. Within the ``griddata:`` block, model inputs can be specified directly, as long as they are consistent with the definition of the model grid. For example, if ``strt: [100., 100.]`` is specified, the model must be either two layers (for "LAYERED" input; see MODFLOW input instructions) or two cells. An example of specifying a uniform starting head condition for a model of any size:
+
+.. code-block:: yaml
+
+    ic:
+      griddata:
+        strt: 100.
+
+Or specifying uniform starting heads by layer:
+
+.. code-block:: yaml
+
+    ic:
+      griddata:
+        strt: [100., 99.]
+
+External files can also be supplied, following the Flopy format:
+
+.. code-block:: yaml
+
+    ic:
+      griddata:
+        strt:
+          - {'filename': 'strt_000.dat'}
+          - {'filename': 'strt_001.dat'}
+
+Specifying starting heads from grid-independent sources
+--------------------------------------------------------
+Similar to other packages, input specified via a ``source_data:`` sub-block can be mapped to the model grid from a variety of sources.
+
+Explicitly setting starting heads to the model top (for example, to override the default behavior with ``default_source_data`` from a parent model):
+
+.. code-block:: yaml
+
+    ic:
+      source_data:
+        strt: 'from_model_top'
+
+Setting starting heads from a binary head save file (pathed relative to the configuration file):
+
+.. code-block:: yaml
+
+    ic:
+      source_data:
+        strt:
+          from_parent:
+            binaryfile: '/path/to/pleasant.hds'
+            stress_period: 0
+
+Explicitly setting starting heads to the parent model starting heads (for example, to override the default behavior if ``default_source_data`` is ``False``)
+
+.. code-block:: yaml
+
+    ic:
+      source_data:
+        strt: from_parent
+
+Example script for updating starting heads from a previous run
+---------------------------------------------------------------
+The following example script opens MODFLOW binary head results using Flopy, and writes them to external files that can then be input to the IC or BAS6 Packages (for MODFLOW 6 or MODFLOW-NWT models, respectively). If you followed the Modflow-setup defaults to write external files to an ``external/`` folder, with starting head files named as shown in the script, this will overwrite your previous starting head files, requiring no additional action after running the script.
+
+    .. literalinclude:: ../../../examples/update_starting_heads_from_previous.py
+        :language: python
+        :linenos:
+
+    Download the file:
+    :download:`update_starting_heads_from_previous.py <../../../examples/update_starting_heads_from_previous.py>`
+
+**Note:** This script can be run as soon as the initial steady-state stress period is done solving. The current MODFLOW run can then be canceled and MODFLOW restarted, hopefully with improved convergence in the initial period.

docs/source/input/index.rst

@@ -7,7 +7,7 @@ Input instructions by package
    Specifying Aquifer Properties (UPW, NPF, STO) <props.rst>
    Basic stress packages (CHD, DRN, GHB, RCH, RIV, WEL) <basic-stress.rst>
    The Discretization Package (DIS, TDIS, BAS6) <dis.rst>
-   Specifying Initial Conditions (IC, BAS6) <ic.rst>
+   Initial Conditions (IC, BAS6) <ic.rst>
    The Lake Package (LAK) <lak.rst>
    The Streamflow Routing Package (SFR, GAGE) <sfr.rst>
    Head observations (OBS, HYD) <obs.rst>

examples/pleasant_lgr_parent.yml

@@ -135,12 +135,11 @@ tdis:
 
 # Initial Conditions Package
 ic:
-  # starting heads sampled from parent model
+  # override default_source_data: True setting
+  # (to set starting heads from the parent model starting heads)
+  # set starting heads to the model top
   source_data:
-    strt:
-      from_parent:
-        binaryfile: 'data/pleasant/pleasant.hds'
-        stress_period: 0
+    strt: from_model_top
 
 # Node Property Flow Package
 npf:

examples/update_starting_heads_from_previous.py

@@ -0,0 +1,20 @@
+"""Update model starting heads from previous (initial steady-state) solution
+"""
+from pathlib import Path
+
+import numpy as np
+from flopy.utils import binaryfile as bf
+
+model_ws = Path('.')
+headfile = model_ws / 'model.hds'
+starting_heads_file_fmt = str(model_ws / 'external/strt_{:03d}.dat')
+
+
+hdsobj = bf.HeadFile(headfile)
+print(f'reading {headfile}...')
+
+initial_ss_heads = hdsobj.get_data(kstpkper=(0, 0))
+for per, layer_heads in enumerate(initial_ss_heads):
+    outfile = starting_heads_file_fmt.format(per)
+    np.savetxt(starting_heads_file_fmt.format(per), layer_heads, fmt='%.2f')
+    print(f"updated {outfile}")

mfsetup/discretization.py

@@ -428,6 +428,16 @@ def make_lgr_idomain(parent_modelgrid, inset_modelgrid,
     y1 = inset_modelgrid.ycellcenters[-1, -1]
     pi1, pj1 = parent_modelgrid.intersect(x1, y1, forgive=True)
     idomain = np.ones(parent_modelgrid.shape, dtype=int)
+    if any(np.isnan([pi0, pj0])):
+        raise ValueError(f"LGR model upper left corner {pi0}, {pj0} "
+                         "is outside of the parent model domain! "
+                         "Check the grid offset and dimensions."
+                         )
+    if any(np.isnan([pi1, pj1])):
+        raise ValueError(f"LGR model lower right corner {pi0}, {pj0} "
+                         "is outside of the parent model domain! "
+                         "Check the grid offset and dimensions."
+                         )
     idomain[0:(np.array(ncppl) > 0).sum(),
             pi0:pi1+1, pj0:pj1+1] = 0
     return idomain