Release 1.3.0 (#204)

* ci(release): update version to 1.2.11.dev0 * ci: fix schedule for windows (#193) * fix(requests): update available assets (#194) Add macarm.zip asset * chore: reformat Python code with line length = 88 (#198) Reformat the code with a maximum line length of 88 characters to better represent the code. See modflowpy/flopy#2362 for a related PR with rational and discussion. Also change some of Ruff's configuration: - Remove target-version, since it is automatically evaluated from pyproject.toml - Remove include so that Ruff will work globally in this repo * fix: cleanup _get_optlevel verbose param in pymake_base (#199) Co-authored-by: mjreno <mjreno@IGSAAA071L01144.gs.doi.net> * refactor: clean-up strings and Path related aspects, add a few Ruff rules (#200) Refactor a few semi-related aspects: - Revise strings and whitespace using a few methods with Ruff and manual edits - Revise a few aspects of pathlib.Path -- these changes are added here to shorten some string formatting, but remain consistent throughout the code base - Fix one more instance of removed verbose parameter in _get_optlevel(), similar to #199 - Apply Ruff pyupgrade (UP) rules - Apply Ruff section-underline-matches-section-length (D409) rule - Apply Ruff-specific rules (RUF) * build(deps): bump dawidd6/action-download-artifact from 6 to 7 (#201) * update for mf6.6.0 (#203) * fix fortran submodule evaluation * update sutra and mfusg_gsi versions. * update pixi version * ci(release): set version to 1.3.0 --------- Co-authored-by: wpbonelli <wbonelli@ucar.edu> Co-authored-by: jdhughes-usgs <jdhughes@usgs.gov> Co-authored-by: Mike Taves <mwtoews@gmail.com> Co-authored-by: mjreno <renomik@gmail.com> Co-authored-by: mjreno <mjreno@IGSAAA071L01144.gs.doi.net> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
modflowpy · Dec 20, 2024 · 9e611df · 9e611df
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -27,19 +27,19 @@ jobs:
       matrix:
         include:
           # test latest gcc and python
-          - {os: ubuntu-latest, FC: gcc, FC_V: 13}
-          - {os: macos-latest, FC: gcc, FC_V: 13}
-          - {os: windows-latest, FC: gcc, FC_V: 13}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: macos-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: windows-latest, FC: gcc, FC_V: 13, shell: pwsh}
           # test latest python and intel-classic
-          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: macos-13, FC: intel-classic, FC_V: 2021.7}
-          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7}
+          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: macos-13, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7, shell: pwsh}
           # test latest python and previous gcc
-          - {os: ubuntu-latest, FC: gcc, FC_V: 12}
-          - {os: ubuntu-latest, FC: gcc, FC_V: 11}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 12, shell: bash}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 11, shell: bash}
     defaults:
       run:
-        shell: bash
+        shell: ${{ matrix.shell }}
 
     steps:
       - name: Checkout repo
@@ -57,7 +57,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.19.1
+          pixi-version: v0.34.0
           manifest-path: "pixi.toml"
 
       - name: pixi post-install
@@ -91,7 +91,6 @@ jobs:
 
       - name: test on Windows
         if: runner.os == 'Windows'
-        shell: pwsh
         run: |
           pixi run autotest-base
 
@@ -122,16 +121,16 @@ jobs:
       matrix:
         include:
           # test latest gcc and python
-          - {os: ubuntu-latest, FC: gcc, FC_V: 13}
-          - {os: macos-latest, FC: gcc, FC_V: 13}
-          - {os: windows-latest, FC: gcc, FC_V: 13}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: macos-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: windows-latest, FC: gcc, FC_V: 13, shell: pwsh}
           # test latest python and intel
-          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: macos-13, FC: intel-classic, FC_V: 2021.7}
-          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7}
+          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: macos-13, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7, shell: pwsh}
     defaults:
       run:
-        shell: bash
+        shell: ${{ matrix.shell }}
 
     steps:
       - name: Checkout repo
@@ -149,7 +148,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.19.1
+          pixi-version: v0.34.0
           manifest-path: "pixi.toml"
 
       - name: pixi post-install
@@ -170,13 +169,13 @@ jobs:
       - name: Run scheduled tests
         run: |
           pixi run autotest-schedule
-
+  
       - name: Upload failed test output
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: failed-schedule-${{ matrix.os }}-${{ matrix.FC }}-${{ matrix.FC_V }}
-          path: ./autotest/.failed
+          path: autotest/.failed
 
       - name: Print coverage report before upload
         run: |

diff --git a/.github/workflows/pymake-linting-install.yml b/.github/workflows/pymake-linting-install.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.19.1
+          pixi-version: v0.34.0
           manifest-path: "pixi.toml"
 
       - name: Lint

diff --git a/.github/workflows/pymake-requests.yml b/.github/workflows/pymake-requests.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          pixi-version: v0.19.1
+          pixi-version: v0.34.0
           manifest-path: "pixi.toml"
 
       - name: pixi post-install

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -120,7 +120,7 @@ jobs:
           pip install ".[test]"
 
       - name: Download artifacts
-        uses: dawidd6/action-download-artifact@v6
+        uses: dawidd6/action-download-artifact@v7
 
       - name: Draft release
         env:

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 Python package for building MODFLOW-based programs from source files.
 
-### Version 1.2.10
+### Version 1.3.0
 
 [![PyPI Version](https://img.shields.io/pypi/v/mfpymake.png)](https://pypi.python.org/pypi/mfpymake)
 [![Anaconda Version](https://anaconda.org/conda-forge/mfpymake/badges/version.svg)](https://anaconda.org/conda-forge/mfpymake)  

diff --git a/autotest/ci_setup.py b/autotest/ci_setup.py
@@ -1,14 +1,13 @@
 import os
-import pathlib as pl
 import shutil
+from pathlib import Path
 
 from modflow_devtools.misc import get_model_paths
 
 import pymake
 
-temp_pth = pl.Path("temp")
-if not temp_pth.exists():
-    temp_pth.mkdir()
+temp_pth = Path("temp")
+temp_pth.mkdir(exist_ok=True)
 mf6_exdir = temp_pth / "mf6examples"
 if mf6_exdir.is_dir():
     shutil.rmtree(mf6_exdir)

diff --git a/autotest/test_build.py b/autotest/test_build.py
@@ -61,13 +61,7 @@ def test_build(function_tmpdir, target: str) -> None:
         pm.inplace = True
         fc = os.environ.get("FC", "gfortran")
         assert (
-            pymake.build_apps(
-                target,
-                pm,
-                verbose=True,
-                clean=False,
-            )
-            == 0
+            pymake.build_apps(target, pm, verbose=True, clean=False) == 0
         ), f"could not compile {target}"
 
 
@@ -80,13 +74,7 @@ def test_meson_build(function_tmpdir, target: str) -> None:
     pymake.linker_update_environment(cc=cc, fc=fc)
     with set_dir(function_tmpdir):
         assert (
-            pymake.build_apps(
-                target,
-                verbose=True,
-                clean=False,
-                meson=True,
-            )
-            == 0
+            pymake.build_apps(target, verbose=True, clean=False, meson=True) == 0
         ), f"could not compile {target}"
 
 

diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py
@@ -1,7 +1,8 @@
 import os
-import pathlib as pl
 import subprocess
+from pathlib import Path
 from platform import system
+from textwrap import dedent
 
 import pytest
 from flaky import flaky
@@ -47,13 +48,7 @@ def run_cli_cmd(cmd: list) -> None:
 @pytest.mark.parametrize("target", targets)
 def test_make_program(function_tmpdir, target: str) -> None:
     with set_dir(function_tmpdir):
-        cmd = [
-            "make-program",
-            target,
-            "--appdir",
-            str(function_tmpdir),
-            "--verbose",
-        ]
+        cmd = ["make-program", target, "--appdir", ".", "--verbose"]
         run_cli_cmd(cmd)
 
 
@@ -62,28 +57,15 @@ def test_make_program(function_tmpdir, target: str) -> None:
 @pytest.mark.base
 def test_make_program_double(function_tmpdir) -> None:
     with set_dir(function_tmpdir):
-        cmd = [
-            "make-program",
-            "mf2005",
-            "--double",
-            "--verbose",
-            "--appdir",
-            str(function_tmpdir),
-        ]
+        cmd = ["make-program", "mf2005", "--double", "--verbose", "--appdir", "."]
         run_cli_cmd(cmd)
 
 
 @pytest.mark.dependency(name="make_program_all")
 @pytest.mark.schedule
 def test_make_program_all(module_tmpdir) -> None:
     with set_dir(module_tmpdir):
-        cmd = [
-            "make-program",
-            ":",
-            "--appdir",
-            str(module_tmpdir / "all"),
-            "--verbose",
-        ]
+        cmd = ["make-program", ":", "--appdir", ".", "--verbose"]
         run_cli_cmd(cmd)
 
 
@@ -93,13 +75,13 @@ def test_make_program_all(module_tmpdir) -> None:
 @pytest.mark.parametrize("meson", meson_parm)
 def test_mfpymake(function_tmpdir, meson: bool) -> None:
     with set_dir(function_tmpdir):
-        src = (
-            "program hello\n"
-            + "  ! This is a comment line; it is ignored by the compiler\n"
-            + "  print *, 'Hello, World!'\n"
-            + "end program hello\n"
-        )
-        src_file = pl.Path("src/hello.f90")
+        src = dedent("""\
+            program hello
+              ! This is a comment line; it is ignored by the compiler
+              print *, 'Hello, World!'
+            end program hello
+        """)
+        src_file = Path("src/hello.f90")
         src_file.parent.mkdir(parents=True, exist_ok=True)
         with open(src_file, "w") as f:
             f.write(src)

diff --git a/autotest/test_gridgen.py b/autotest/test_gridgen.py
@@ -1,6 +1,6 @@
-import pathlib as pl
 import subprocess
 from os import environ
+from pathlib import Path
 from platform import system
 
 import pytest
@@ -11,7 +11,7 @@
 
 
 @pytest.fixture(scope="module")
-def target(module_tmpdir) -> pl.Path:
+def target(module_tmpdir) -> Path:
     name = TARGET_NAME
     ext = ".exe" if system() == "Windows" else ""
     return module_tmpdir / f"{name}{ext}"
@@ -23,7 +23,7 @@ def prog_data(target) -> dict:
 
 
 @pytest.fixture(scope="module")
-def workspace(module_tmpdir, prog_data) -> pl.Path:
+def workspace(module_tmpdir, prog_data) -> Path:
     return module_tmpdir / prog_data.dirname
 
 
@@ -42,11 +42,7 @@ def pm(module_tmpdir, target) -> pymake.Pymake:
 
 def run_command(args, cwd):
     p = subprocess.Popen(
-        args,
-        shell=False,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        cwd=cwd,
+        args, shell=False, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=cwd
     )
     for line in p.stdout.readlines():
         print(line.decode().strip())

diff --git a/autotest/test_mf2005.py b/autotest/test_mf2005.py
@@ -91,7 +91,5 @@ def test_mf2005(namefile, workspace, target):
     if not (example_ws / namefile).is_file():
         pytest.skip(f"{namefile} does not exist")
 
-    success, _ = flopy.run_model(
-        target, namefile, model_ws=example_ws, silent=False
-    )
+    success, _ = flopy.run_model(target, namefile, model_ws=example_ws, silent=False)
     assert success, f"could not run {namefile} with {target}"
diff --git a/autotest/test_mf6_existing_meson.py b/autotest/test_mf6_existing_meson.py
@@ -89,16 +89,10 @@ def test_build_with_existing_meson(pm, module_tmpdir, workspace, targets):
         linker_update_environment(cc=cc, fc=fc)
 
         # make modflow 6 with existing meson.build file
-        returncode = pymake.meson_build(
-            workspace,
-            fc,
-            cc,
-            appdir=pm.appdir,
-        )
-        assert returncode == 0, (
-            "could not build modflow 6 applications "
-            + "using existing meson.build file"
-        )
+        returncode = pymake.meson_build(workspace, fc, cc, appdir=pm.appdir)
+        assert (
+            returncode == 0
+        ), "could not build modflow 6 applications using existing meson.build file"
 
         # check that all of the executables exist
         for executable in targets:

diff --git a/autotest/test_mp6.py b/autotest/test_mp6.py
@@ -44,20 +44,12 @@ def update_files(fn, workspace):
         if rf in fn.lower():
             fname1 = workspace / f"{rf}.locations"
             fname2 = workspace / f"{rf}_mod.locations"
-            print(
-                "copy {} to {}".format(
-                    os.path.basename(fname1), os.path.basename(fname2)
-                )
-            )
+            print(f"copy {os.path.basename(fname1)} to {os.path.basename(fname2)}")
             shutil.copy(fname1, fname2)
             print(f"deleting {os.path.basename(fname1)}")
             os.remove(fname1)
             fname1 = workspace / f"{rf.upper()}.locations"
-            print(
-                "renmae {} to {}".format(
-                    os.path.basename(fname2), os.path.basename(fname1)
-                )
-            )
+            print(f"renmae {os.path.basename(fname2)} to {os.path.basename(fname1)}")
             os.rename(fname2, fname1)
 
 
@@ -79,16 +71,12 @@ def test_compile(pm, target):
 @pytest.mark.dependency(name="test", depends=["build"])
 @pytest.mark.xdist_group(TARGET_NAME)
 @pytest.mark.regression
-@pytest.mark.parametrize(
-    "namefile", [f"EXAMPLE-{n}.mpsim" for n in range(1, 10)]
-)
+@pytest.mark.parametrize("namefile", [f"EXAMPLE-{n}.mpsim" for n in range(1, 10)])
 def test_mp6(namefile, workspace, target):
     example_ws = workspace / "example-run"
     if not (example_ws / namefile).is_file():
         pytest.skip(f"Namefile {namefile} does not exist")
 
     update_files(namefile, example_ws)
-    success, _ = flopy.run_model(
-        target, namefile, model_ws=example_ws, silent=False
-    )
+    success, _ = flopy.run_model(target, namefile, model_ws=example_ws, silent=False)
     assert success, f"could not run {namefile}"