refactor(createpackages): use jinja for mf6 module code generation

.github/workflows/benchmark.yml

@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: etc/environment.yml
           cache-environment: true

.github/workflows/commit.yml

@@ -144,7 +144,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: etc/environment.yml
           cache-environment: true
@@ -181,10 +181,13 @@ jobs:
         working-directory: autotest
         run: |
           pytest -v -m="not example" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
-          coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Report coverage
+        working-directory: autotest
+        run: coverage report
+
       - name: Upload failed test outputs
         uses: actions/upload-artifact@v4
         if: failure()

.github/workflows/examples.yml

@@ -22,7 +22,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: etc/environment.yml
           cache-environment: true

.github/workflows/rtd.yml

@@ -80,7 +80,7 @@ jobs:
           echo $GITHUB_EVENT_NAME
 
       - name: Setup Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: etc/environment.yml
           cache-environment: true

autotest/test_codegen.py

@@ -0,0 +1,73 @@
+import pytest
+
+from autotest.conftest import get_project_root_path
+from flopy.mf6.utils.codegen.context import get_context_names
+from flopy.mf6.utils.codegen.dfn import Dfn
+from flopy.mf6.utils.codegen.make import (
+    DfnName,
+    make_all,
+    make_context,
+    make_targets,
+)
+
+PROJ_ROOT = get_project_root_path()
+MF6_PATH = PROJ_ROOT / "flopy" / "mf6"
+TGT_PATH = MF6_PATH / "modflow"
+DFN_PATH = MF6_PATH / "data" / "dfn"
+DFN_NAMES = [
+    dfn.stem
+    for dfn in DFN_PATH.glob("*.dfn")
+    if dfn.stem not in ["common", "flopy"]
+]
+
+
+@pytest.mark.parametrize("dfn_name", DFN_NAMES)
+def test_dfn_load(dfn_name):
+    dfn_path = DFN_PATH / f"{dfn_name}.dfn"
+    with open(dfn_path, "r") as f:
+        dfn = Dfn.load(f, name=DfnName(*dfn_name.split("-")))
+        if dfn_name in ["sln-ems", "exg-gwfprt", "exg-gwfgwe", "exg-gwfgwt"]:
+            assert not any(dfn)
+        else:
+            assert any(dfn)
+
+
+@pytest.mark.parametrize(
+    "dfn, n_vars, n_flat, n_meta",
+    [("gwf-ic", 2, 2, 0), ("prt-prp", 18, 40, 1)],
+)
+def test_make_context(dfn, n_vars, n_flat, n_meta):
+    with open(DFN_PATH / "common.dfn") as f:
+        commonvars = Dfn.load(f)
+
+    with open(DFN_PATH / f"{dfn}.dfn") as f:
+        dfn = DfnName(*dfn.split("-"))
+        definition = Dfn.load(f, name=dfn)
+
+    context_names = get_context_names(dfn)
+    context_name = context_names[0]
+    context = make_context(context_name, definition, commonvars)
+    assert len(context_names) == 1
+    assert len(context.variables) == n_vars
+    assert len(context.definition) == n_flat
+    assert len(context.definition.metadata) == n_meta
+
+
+@pytest.mark.parametrize("dfn_name", DFN_NAMES)
+def test_make_targets(dfn_name, function_tmpdir):
+    with open(DFN_PATH / "common.dfn") as f:
+        common = Dfn.load(f)
+
+    with open(DFN_PATH / f"{dfn_name}.dfn", "r") as f:
+        dfn_name = DfnName(*dfn_name.split("-"))
+        dfn = Dfn.load(f, name=dfn_name)
+
+    make_targets(dfn, function_tmpdir, commonvars=common)
+    for ctx_name in get_context_names(dfn_name):
+        source_path = function_tmpdir / ctx_name.target
+        assert source_path.is_file()
+
+
+def test_make_all(function_tmpdir):
+    make_all(DFN_PATH, function_tmpdir, verbose=True)
+    assert any(function_tmpdir.glob("*.py"))

docs/mf6_dev_guide.md

@@ -10,38 +10,44 @@ FPMF6 uses meta-data files located in flopy/mf6/data/dfn to define the model and
 
 All meta-data can be accessed from the flopy.mf6.data.mfstructure.MFStructure class.  This is a singleton class, meaning only one instance of this class can be created.  The class contains a sim_struct attribute (which is a flopy.mf6.data.mfstructure.MFSimulationStructure object) which contains all of the meta-data for all package files.  Meta-data is stored in a structured format. MFSimulationStructure contains MFModelStructure and MFInputFileStructure objects, which contain the meta-data for each model type and each "simulation-level" package (tdis, ims, ...).  MFModelStructure contains model specific meta-data and a MFInputFileStructure object for each package in that model.  MFInputFileStructure contains package specific meta-data and a MFBlockStructure object for each block contained in the package file.  MFBlockStructure contains block specific meta-data and a MFDataStructure object for each data structure defined in the block, and MFDataStructure contains data structure specific meta-data and a MFDataItemStructure object for each data item contained in the data structure.  Data structures define the structure of data that is naturally grouped together, for example, the data in a numpy recarray.  Data item structures define the structure of specific pieces of data, for example, a single column of a numpy recarray.  The meta-data defined in these classes provides all the information FloPy needs to read and write MODFLOW 6 package and name files, create the Flopy interface, and check the data for various constraints.
 
-
-***
-MFStructure --+ MFSimulationStructure --+ MFModelStructure --+ MFInputFileStructure --+ MFBlockStructure --+ MFDataStructure --+ MFDataItemStructure
-
-Figure 1: FPMF6 generic data structure classes.  Lines connecting classes show a relationship defined between the two connected classes.  A "*" next to the class means that the  class is a sub-class of the connected class.  A "+" next to the class means that the class is contained within the connected class.
-***
+```mermaid
+classDiagram
+    MFStructure --* "1" MFSimulationStructure : has
+    MFSimulationStructure --* "1+" MFModelStructure : has
+    MFModelStructure --* "1" MFInputFileStructure : has
+    MFInputFileStructure --* "1+" MFBlockStructure : has
+    MFBlockStructure --* "1+" MFDataStructure : has
+    MFDataStructure --* "1+" MFDataItemStructure : has
+```
+
+Figure 1: Generic data structure hierarchy.  Connections show composition relationships.
 
 Package and Data Base Classes
 -----------------------------------------------
 
 The package and data classes are related as shown below in figure 2.  On the top of the figure 2 is the MFPackage class, which is the base class for all packages.  MFPackage contains generic methods for building data objects and reading and writing the package to a file.  MFPackage contains a MFInputFileStructure object that defines how the data is structured in the package file.  MFPackage also contains a dictionary of blocks (MFBlock).  The MFBlock class is a generic class used to represent a block within a package.  MFBlock contains a MFBlockStructure object that defines how the data in the block is structured.  MFBlock also contains a dictionary of data objects (subclasses of MFData) contained in the block and a list of block headers (MFBlockHeader) for that block.  Block headers contain the block's name and optionally data items (eg. iprn).
 
 
-***
-MFPackage --+ MFBlock --+ MFData
-
-MFPackage --+ MFInputFileStructure
-
-MFBlock --+ MFBlockStructure
-
-MFData --+ MFDataStructure
-
-MFData --* MFArray --* MFTransientArray
-
-MFData --* MFList --* MFTransientList
-
-MFData --* MFScalar --* MFTransientScalar
-
-MFTransientData --* MFTransientArray, MFTransientList, MFTransientScalar
+```mermaid
+classDiagram
+
+MFPackage --* "1+" MFBlock : has
+MFBlock --* "1+" MFData : has
+MFPackage --* "1" MFInputFileStructure : has
+MFBlock --* "1" MFBlockStructure : has
+MFData --* "1" MFDataStructure : has
+MFData --|> MFArray
+MFArray --|> MFTransientArray
+MFData --|> MFList
+MFList --|> MFTransientList
+MFData --|> MFScalar
+MFScalar --|> MFTransientScalar
+MFTransientData --|> MFTransientArray
+MFTransientData --|> MFTransientList
+MFTransientData --|> MFTransientScalar
+```
 							 
 Figure 2:  FPMF6 package and data classes.  Lines connecting classes show a relationship defined between the two connected classes.  A "*" next to the class means that the  class is a sub-class of the connected class.  A "+" next to the class means that the class is contained within the connected class.
-***
 
 There are three main types of data, MFList, MFArray, and MFScalar data.  All three of these data types are derived from the MFData abstract base class.  MFList data is the type of data stored in a spreadsheet with different column headings.  For example, the data describing a flow barrier are of type MFList.  MFList data is stored in numpy recarrays.  MFArray data is data of a single type (eg. all integer values).  For example, the model's HK values are of type MFArray.  MFArrays are stored in numpy ndarrays.  MFScalar data is a single data item.  Most MFScalar data are options.  All MFData subclasses contain an MFDataStructure object that defines the expected structure and types of the data.
 

flopy/mf6/data/dfn/utl-tas.dfn

@@ -19,6 +19,7 @@ type keyword
 shape
 reader urword
 optional false
+in_record true
 longname
 description xxx
 
@@ -29,6 +30,7 @@ shape any1d
 tagged false
 reader urword
 optional false
+in_record true
 longname
 description Name by which a package references a particular time-array series. The name must be unique among all time-array series used in a package.
 
@@ -48,6 +50,7 @@ type keyword
 shape
 reader urword
 optional false
+in_record true
 longname
 description  xxx
 
@@ -59,6 +62,7 @@ shape
 tagged false
 reader urword
 optional false
+in_record true
 longname
 description Interpolation method, which is either STEPWISE or LINEAR.
 
@@ -78,6 +82,7 @@ type keyword
 shape
 reader urword
 optional false
+in_record true
 longname
 description  xxx
 
@@ -88,6 +93,7 @@ shape time_series_name
 tagged false
 reader urword
 optional false
+in_record true
 longname
 description Scale factor, which will multiply all array values in time series. SFAC is an optional attribute; if omitted, SFAC = 1.0.