release(1.2.8): update mf6 version (#132)

* Add latest version of mfusg_gsi (v2.1.1). * Update test_request.py::test_latest_assets with latest asset list * Update pymake calls in GH Actions workflows to use working-directory
modflowpy · Jul 5, 2023 · cde7860 · cde7860
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -2,7 +2,7 @@ name: pymake continuous integration
 
 on:
   schedule:
-    - cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
+    - cron: '0 7 * * *' # run at 7 AM UTC every day
   push:
     branches: [ master ]
   pull_request:
@@ -47,25 +47,29 @@ jobs:
 
       - name: test on Linux
         if: runner.os == 'Linux'
+        working-directory: ./autotest
         run: |
-          pytest -v -n=auto --dist=loadfile -m="base or regression" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v -n=auto --dist=loadfile -m="base or regression" --durations=0 --cov=pymake --cov-report=xml
 
       - name: test on MacOS
         if: runner.os == 'macOS'
+        working-directory: ./autotest
         run: |
-          pytest -v -n=auto --dist=loadfile -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v -n=auto --dist=loadfile -m="base" --durations=0 --cov=pymake --cov-report=xml
 
       - name: test on Windows
         if: runner.os == 'Windows'
+        working-directory: ./autotest
         shell: cmd
         run: |
-          pytest -v -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v -m="base" --durations=0 --cov=pymake --cov-report=xml
 
       - name: Print coverage report before upload
+        working-directory: ./autotest
         run: |
           coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/[email protected]
         with:
-          file: ./coverage.xml
+          file: ./autotest/coverage.xml
diff --git a/.github/workflows/pymake-gcc.yml b/.github/workflows/pymake-gcc.yml
@@ -2,7 +2,7 @@ name: pymake gcc build
 
 on:
   schedule:
-    - cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
+    - cron: '0 7 * * *' # run at 7 AM UTC every day
   push:
     branches: [ master ]
   pull_request:
@@ -46,17 +46,19 @@ jobs:
           .github/common/download-examples.sh
 
       - name: Run pytest
+        working-directory: ./autotest
         run: |
-          pytest -v --dist=loadfile -n=auto -m="base or regression" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v --dist=loadfile -n=auto -m="base or regression" --durations=0 --cov=pymake --cov-report=xml
 
       - name: Print coverage report before upload
+        working-directory: ./autotest
         run: |
           coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/[email protected]
         with:
-          file: ./coverage.xml
+          file: ./autotest/coverage.xml
 
   pymakeCI-gcc-prev:
     name: pymake CI GCC 9 and 8
@@ -102,17 +104,19 @@ jobs:
           .github/common/download-examples.sh
 
       - name: Run pytest
+        working-directory: ./autotest
         run: |
-          pytest -v --dist=loadfile -n=auto -m="base" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v --dist=loadfile -n=auto -m="base" --durations=0 --cov=pymake --cov-report=xml
 
       - name: Print coverage report before upload
+        working-directory: ./autotest
         run: |
           coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/[email protected]
         with:
-          file: ./coverage.xml
+          file: ./autotest/coverage.xml
 
   pymakeCI-python-prev:
     name: pymake CI with previous python versions

diff --git a/.github/workflows/pymake-requests.yml b/.github/workflows/pymake-requests.yml
@@ -2,7 +2,7 @@ name: pymake requests
 
 on:
   schedule:
-    - cron: '0 3 * * 3' # run at 3 AM UTC every Wednesday
+    - cron: '0 7 * * *' # run at 7 AM UTC every day
   push:
     branches: [ master ]
   pull_request:
@@ -31,19 +31,22 @@ jobs:
           .github/common/install-python.sh
 
       - name: Run pytest
+        working-directory: ./autotest
         run: |
-          pytest -v -n=auto -m requests --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v -n=auto -m requests --durations=0 --cov=pymake --cov-report=xml
 
       - name: Run scheduled tests
         if: ${{ github.event_name == 'schedule' }}
+        working-directory: ./autotest
         run: |
-          pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml autotest/
+          pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml
 
       - name: Print coverage report before upload
+        working-directory: ./autotest
         run: |
           coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/[email protected]
         with:
-          file: ./coverage.xml
+          file: ./autotest/coverage.xml
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 Python package for building MODFLOW-based programs from source files.
 
-### Version 1.2.7
+### Version 1.2.8
 
 ![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)
 [![codecov](https://codecov.io/gh/modflowpy/pymake/branch/master/graph/badge.svg)](https://codecov.io/gh/modflowpy/pymake)

diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py
@@ -2,7 +2,6 @@
 import pathlib as pl
 import shutil
 import subprocess
-import sys
 
 import pytest
 

diff --git a/autotest/test_mf6_existing_meson.py b/autotest/test_mf6_existing_meson.py
@@ -1,8 +1,6 @@
-import contextlib
 import os
 import shutil
 import sys
-import time
 
 import flopy
 import pytest

diff --git a/autotest/test_requests.py b/autotest/test_requests.py
@@ -107,9 +107,9 @@ def test_latest_assets():
     keys = assets.keys()
     test_keys = [
         "code.json",
+        "code.md",
         "mac.zip",
         "linux.zip",
-        "win32.zip",
         "win64.zip",
     ]
     for key in keys:

diff --git a/pymake/config.py b/pymake/config.py
@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "December 8, 2022"
-__version__ = "1.2.7"
+__date__ = "July 5, 2023"
+__version__ = "1.2.8"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "[email protected]"
 __status__ = "Production"

diff --git a/pymake/utils/_usgs_src_update.py b/pymake/utils/_usgs_src_update.py
@@ -7,6 +7,7 @@
 import shutil
 import sys
 import types
+from typing import Union
 
 from .usgsprograms import usgs_program_data
 
@@ -65,8 +66,7 @@ def _build_replace(targets):
 
     # remove exe extension from targets
     for idx, target in enumerate(targets):
-        if ".exe" in target.lower():
-            targets[idx] = target[:-4]
+        targets[idx] = pl.Path(target).with_suffix("").name
 
     # get a dictionary of update functions
     funcs = _get_function_names(sys.modules[__name__], select_name="_update_")
@@ -432,6 +432,11 @@ def _update_mfusg_gsi_files(srcdir, fc, cc, arch, double):
         "FMTARG = 'BINARY'": "FMTARG = 'UNFORMATTED'\n        ACCARG = 'STREAM'",
         ",SHARED,ACCESS='SEQUENTIAL'": ",ACCESS='SEQUENTIAL'",
         "FORM=FMTARG,SHARED,": "FORM=FMTARG,",
+        ",BUFFERED='YES',": ",",
+        ", BUFFERED='NO')": ")",
+        ",SHARE = 'DENYNONE'": ",",
+        ", SHARE = 'DENYNONE',": ",",
+        "FORM='FORMATTED',ACCESS='SEQUENTIAL',": "FORM='FORMATTED',ACCESS='SEQUENTIAL'",
     }
 
     fpth = pl.Path(srcdir) / "glo2basu1.f"
@@ -446,6 +451,20 @@ def _update_mfusg_gsi_files(srcdir, fc, cc, arch, double):
             f.write(line)
         f.close()
 
+    tags = {",share='DENYNONE',": ","}
+
+    fpth = pl.Path(srcdir) / "UpdtSt.for"
+    if fpth.exists():
+        with open(fpth) as f:
+            lines = f.readlines()
+        f = open(fpth, "w")
+        for idx, line in enumerate(lines):
+            for key, value in tags.items():
+                if key in line:
+                    line = line.replace(key, value)
+            f.write(line)
+        f.close()
+
     tag = "DEALLOCATE(ITHFLG)"
     tag2 = "DEALLOCATE(LAYTYP)"
     fpth = pl.Path(srcdir) / "gwf2bcf-lpf-u1.f"
@@ -829,7 +848,116 @@ def _update_vs2dt_files(srcdir, fc, cc, arch, double):
     return
 
 
+def _update_mf6_files(
+    srcdir: Union[str, os.PathLike],
+    fc: str,
+    cc: str,
+    arch: str,
+    double: bool,
+) -> None:
+    """
+    Update MODFLOW 6 source files to remove files with external dependencies.
+    This was required for releases >= 6.4.2
+
+    Parameters
+    ----------
+    srcdir : str
+        path to directory with source files
+    fc : str
+        fortran compiler
+    cc : str
+        c/c++ compiler
+    arch : str
+        architecture
+    double : bool
+        boolean indicating if compiler switches are used to build a
+        double precision target
+
+    Returns
+    -------
+
+    """
+    _update_mf6_external_dependencies(srcdir)
+    return
+
+
+def _update_libmf6_files(
+    srcdir: Union[str, os.PathLike],
+    fc: str,
+    cc: str,
+    arch: str,
+    double: bool,
+) -> None:
+    """
+    Update MODFLOW 6 shared object source files to remove files with external
+    dependencies. This was required for releases >= 6.4.2
+
+    Parameters
+    ----------
+    srcdir : str
+        path to directory with source files
+    fc : str
+        fortran compiler
+    cc : str
+        c/c++ compiler
+    arch : str
+        architecture
+    double : bool
+        boolean indicating if compiler switches are used to build a
+        double precision target
+
+    Returns
+    -------
+
+    """
+    _update_mf6_external_dependencies(srcdir, target="libmf6")
+    return
+
+
 # common source file replacement functions
+def _update_mf6_external_dependencies(
+    srcdir: Union[str, os.PathLike],
+    target: str = "mf6",
+) -> None:
+    """
+    Remove MODFLOW 6 files with external library dependencies (PETSc, MPI).
+
+
+    Parameters
+    ----------
+    srcdir : os.PathLike
+        path to directory with source files
+    target: str
+        target to create (Default is mf6)
+
+    Returns
+    -------
+    None
+
+    """
+    if not isinstance(srcdir, pl.Path):
+        srcdir = pl.Path(srcdir)
+    if target == "libmf6":
+        srcdir = srcdir.parent / "src"
+    parallel_files = (
+        "Utilities/Vector/PetscVector.F90",
+        "Utilities/Matrix/PetscMatrix.F90",
+        "Solution/PETSc/PetscSolver.F90",
+        "Solution/PETSc/PetscConvergence.F90",
+        "Distributed/MpiMessageBuilder.f90",
+        "Distributed/MpiRouter.f90",
+        "Distributed/MpiRunControl.F90",
+        "Distributed/MpiWorld.f90",
+        "Solution/ParallelSolution.f90",
+    )
+    for file in parallel_files:
+        path = srcdir / file
+        if path.is_file():
+            print(f'Removing..."{path}"')
+            os.remove(path)
+    return
+
+
 def _update_utl7(srcdir):
     """Update utl7.f source file
 

diff --git a/pymake/utils/usgsprograms.txt b/pymake/utils/usgsprograms.txt
@@ -1,7 +1,7 @@
 target     ,  version,  current, url                                                                                            , dirname             , srcdir              ,    standard_switch, double_switch, shared_object
-mf6        ,  6.4.1  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip             , mf6.4.1_linux       , src                 ,    True           , False        , False
-zbud6      ,  6.4.1  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip             , mf6.4.1_linux       , utils/zonebudget/src,    True           , False        , False
-libmf6     ,  6.4.1  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.1/mf6.4.1_linux.zip             , mf6.4.1_linux       , srcbmi              ,    True           , False        , True
+mf6        ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , src                 ,    True           , False        , False
+zbud6      ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , utils/zonebudget/src,    True           , False        , False
+libmf6     ,  6.4.2  ,  True   , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.2/mf6.4.2_linux.zip             , mf6.4.2_linux       , srcbmi              ,    True           , False        , True
 mp7        ,  7.2.001,  True   , https://water.usgs.gov/water-resources/software/MODPATH/modpath_7_2_001.zip                    , modpath_7_2_001     , source              ,    True           , False        , False
 mt3dms     ,  5.3.0  ,  True   , https://hydro.geo.ua.edu/mt3d/mt3dms_530.exe                                                   , mt3dms5.3.0         , src/true-binary     ,    True           , False        , False
 mt3dusgs   ,  1.1.0  ,  True   , https://water.usgs.gov/water-resources/software/MT3D-USGS/mt3dusgs1.1.0.zip                    , mt3dusgs1.1.0       , src                 ,    True           , False        , False
@@ -18,6 +18,6 @@ swtv4      ,  4.00.05,  True   , https://water.usgs.gov/water-resources/software
 mp6        ,  6.0.1  ,  True   , https://water.usgs.gov/water-resources/software/MODPATH/modpath.6_0_01.zip                     , modpath.6_0         , src                 ,    True           , False        , False
 mflgr      ,  2.0.0  ,  True   , https://water.usgs.gov/ogw/modflow-lgr/modflow-lgr-v2.0.0/mflgrv2_0_00.zip                     , mflgr.2_0           , src                 ,    True           , True         , False
 zonbud3    ,  3.01   ,  True   , https://water.usgs.gov/water-resources/software/ZONEBUDGET/zonbud3_01.exe                      , Zonbud.3_01         , Src                 ,    True           , False        , False
-mfnwt1.1.4 ,  1.1.4  ,  False  , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.1.4.zip              , MODFLOW-NWT_1.1.4      , src                 ,    True           , False        , False
-mfnwt      ,  1.3.0  ,  True   , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip              , MODFLOW-NWT            , src                 ,    True           , True         , False
-mfusg_gsi  ,  2.01.0 ,  True   , https://www.gsienv.com/wp-content/uploads/2023/01/USG-Transport-V_2.1.0-1.zip                  , .                     , Source              ,    True           , True         , False
+mfnwt1.1.4 ,  1.1.4  ,  False  , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.1.4.zip              , MODFLOW-NWT_1.1.4   , src                 ,    True           , False        , False
+mfnwt      ,  1.3.0  ,  True   , https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.3.0.zip              , MODFLOW-NWT         , src                 ,    True           , True         , False
+mfusg_gsi  ,  2.1.1  ,  True   , https://www.gsienv.com/wp-content/uploads/2023/04/USG-Transport-V_2.1.1.zip                    , USGT-v2-1-1-source  , .                   ,    True           , False        , False