ci: add pixi to CI workflow (#177)

* add pymake function to add syslibs option for Darwin + gcc toolchain + CLT > 14.*

.github/workflows/main.yml

@@ -19,10 +19,13 @@ jobs:
   pymakeCI-os-intel:
     name: pymake CI intel on different OSs
     runs-on: ${{ matrix.os }}
+    env:
+      FC: intel-classic
+      FC_V: "2021.7"
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-2019]
+        os: [ubuntu-latest, macos-13, windows-2019]
     defaults:
       run:
         shell: bash
@@ -31,53 +34,50 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Setup Intel Fortran Classic
+      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
         uses: fortran-lang/setup-fortran@v1
         with:
-          compiler: intel-classic
-          version: "2021.7"
+          compiler: ${{ env.FC }}
+          version: ${{ env.FC_V }}
 
       - name: Setup Graphviz
         if: runner.os == 'Linux'
         uses: ts-graphviz/setup-graphviz@v2
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-[email protected]
         with:
-          python-version: "3.12"
+          pixi-version: v0.19.1
+          manifest-path: "pixi.toml"
 
-      - name: Install python packages
+      - name: pixi post-install
+        working-directory: pymake
         run: |
-          python -m pip install --upgrade pip
-          pip install ".[test]"
+          pixi run postinstall
 
       - name: Download examples for pytest runs
         run: |
-          .github/common/download-examples.sh
+          pixi run download-examples 
 
       - 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
+          pixi run autotest
 
       - 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
+          pixi run autotest-base
 
       - 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 --basetemp=pytest_temp
+          pixi run autotest-Windows
 
       - name: Print coverage report before upload
-        working-directory: ./autotest
         run: |
-          coverage report
+          pixi run coverage-report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

.github/workflows/pymake-gcc.yml

@@ -24,17 +24,12 @@ jobs:
       matrix:
         include:
           # test latest gcc and python
-          - {os: ubuntu-latest, gcc: 13, python: "3.12"}
-          - {os: windows-latest, gcc: 13, python: "3.12"}
-          - {os: macos-latest, gcc: 13, python: "3.12"}
-          # test latest gcc and previous python
-          - {os: ubuntu-latest, gcc: 13, python: "3.11"}
-          - {os: ubuntu-latest, gcc: 13, python: "3.10"}
-          - {os: ubuntu-latest, gcc: 13, python: 3.9}
-          - {os: ubuntu-latest, gcc: 13, python: 3.8}
+          - {os: ubuntu-latest, gcc: 13}
+          - {os: windows-latest, gcc: 13}
+          - {os: macos-latest, gcc: 13}
           # test latest python and previous gcc
-          - {os: ubuntu-latest, gcc: 12, python: "3.12"}
-          - {os: ubuntu-latest, gcc: 11, python: "3.12"}
+          - {os: ubuntu-latest, gcc: 12}
+          - {os: ubuntu-latest, gcc: 11}
     defaults:
       run:
         shell: bash
@@ -47,15 +42,16 @@ jobs:
         if: runner.os == 'Linux'
         uses: ts-graphviz/setup-graphviz@v2
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-[email protected]
         with:
-          python-version: ${{ matrix.python }}
+          pixi-version: v0.19.1
+          manifest-path: "pixi.toml"
 
-      - name: Install python packages
+      - name: pixi post-install
+        working-directory: pymake
         run: |
-          python -m pip install --upgrade pip
-          pip install ".[test]"
+          pixi run postinstall
 
       - name: Setup GNU Fortran
         uses: fortran-lang/setup-fortran@main
@@ -64,24 +60,27 @@ jobs:
           version: ${{ matrix.gcc }}
 
       - name: Download examples for pytest runs
-        run: .github/common/download-examples.sh
+        run: |
+          pixi run download-examples 
       
       - name: Install make
         if: runner.os == 'Windows'
         run: choco install make
 
-      - name: Run pytest
-        working-directory: ./autotest
+      - name: Run pytest on Linux and MacOS
+        if: runner.os != 'Windows'
         run: |
-          markers="base"
-          if [[ ${{ matrix.gcc }} == 13 ]]; then
-            markers="base or regression"
-          fi
-          pytest -v --dist=loadfile -n=auto --durations=0 --basetemp=pytest_temp --cov=pymake --cov-report=xml --cov-append -m "$markers"
+          pixi run autotest-base
+
+      - name: test on Windows
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          pixi run autotest-Windows
 
       - name: Print coverage report before upload
-        working-directory: ./autotest
-        run: coverage report
+        run: |
+          pixi run coverage-report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

.github/workflows/pymake-linting-install.yml

@@ -20,22 +20,17 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-[email protected]
         with:
-          python-version: "3.12"
-
-      - name: Setup Graphviz
-        uses: ts-graphviz/setup-graphviz@v2
-
-      - name: Install packages
-        run: pip install ".[lint]"
+          pixi-version: v0.19.1
+          manifest-path: "pixi.toml"
 
       - name: Lint
-        run: ruff check .
+        run: pixi run check-lint
 
       - name: Check format
-        run: ruff format . --check
+        run: pixi run check-format
 
   pymake_setup:
     name: standard installation

.gitignore

@@ -24,6 +24,9 @@ var/
 .installed.cfg
 *.egg
 
+# pixi
+.pixi/
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

autotest/ci_setup.py

@@ -12,9 +12,6 @@
 mf6_exdir = temp_pth / "mf6examples"
 if mf6_exdir.is_dir():
     shutil.rmtree(mf6_exdir)
-gsflow_exdir = temp_pth / "gsflowexamples"
-if gsflow_exdir.is_dir():
-    shutil.rmtree(gsflow_exdir)
 
 
 def download_mf6_examples(verbose=False):
@@ -71,83 +68,6 @@ def examples_list(verbose=False):
     return
 
 
-def download_gsflow_examples(verbose=False):
-    """Download gsflow examples and return location of folder"""
-
-    examples_dirs = (
-        "sagehen",
-        "acfb_dyn_params",
-        "acfb_water_use",
-    )
-
-    target = "gsflow"
-    pm = pymake.Pymake(verbose=True)
-    pm.target = target
-
-    # download the gsflow release
-    pm.download_target(target, download_path=temp_pth)
-    assert pm.download, f"could not download {target} distribution"
-
-    # get program dictionary
-    prog_dict = pymake.usgs_program_data.get_target(target)
-
-    # set path to example
-    temp_download_dir = temp_pth / prog_dict.dirname
-    temp_dir = temp_download_dir / "data"
-
-    print(f"copying files to...{gsflow_exdir}")
-    shutil.copytree(temp_dir, gsflow_exdir)
-
-    # create list of examples to test and edit files if necessary
-    src_folders = []
-    for ex_dir in examples_dirs:
-        out_path = gsflow_exdir / ex_dir
-
-        if "sagehen" in ex_dir:
-            out_path = out_path / "linux"
-            modify_gsflow_sagehen(out_path)
-        elif "acfb" in ex_dir:
-            shutil.copy(
-                out_path / "control/control", out_path / "gsflow.control"
-            )
-
-        # add final example path to src_folders list
-        src_folders.append(out_path)
-
-    print(f"removing...{temp_download_dir} directory")
-    shutil.rmtree(temp_download_dir)
-
-    # create a  list of gsflow examples
-    fpth = gsflow_exdir / "gsflowexamples.txt"
-    f = open(fpth, "w")
-    for idx, folder in enumerate(src_folders):
-        if verbose:
-            if idx == 0:
-                print(f"\n\nGSFLOW examples:\n{78 * '-'}")
-            print(f"{idx + 1:>3d}: {folder}")
-        f.write(f"{os.path.abspath(folder)}\n")
-    f.close()
-
-    return gsflow_exdir.resolve()
-
-
-def modify_gsflow_sagehen(temp_pth):
-    fpth = temp_pth / "gsflow.control"
-    with open(fpth) as f:
-        lines = f.readlines()
-    with open(fpth, "w") as f:
-        idx = 0
-        while idx < len(lines):
-            line = lines[idx]
-            if "end_time" in line:
-                line += "6\n1\n1981\n"
-                idx += 3
-            f.write(line)
-            idx += 1
-    return
-
-
 if __name__ == "__main__":
     mf6pth = download_mf6_examples(verbose=True)
     examples_list(verbose=True)
-    gsflowpth = download_gsflow_examples(verbose=True)

autotest/test_build.py

@@ -69,8 +69,7 @@ def test_build(function_tmpdir, target: str) -> None:
         pm = pymake.Pymake(verbose=True)
         pm.target = target
         pm.inplace = True
-        if system() == "Darwin":
-            pm.syslibs = "-Wl,-ld_classic"
+        fc = os.environ.get("FC", "gfortran")
         assert (
             pymake.build_apps(
                 target,
@@ -87,8 +86,9 @@ def test_build(function_tmpdir, target: str) -> None:
 @pytest.mark.parametrize("target", targets_meson)
 def test_meson_build(function_tmpdir, target: str) -> None:
     kwargs = {}
-    if system() == "Darwin":
-        kwargs["LDFLAGS"] = "-Wl,-ld_classic"
+    cc = os.environ.get("CC", "gcc")
+    fc = os.environ.get("FC", "gfortran")
+    pymake.linker_update_environment(cc=cc, fc=fc)
     with set_dir(function_tmpdir), set_env(**kwargs):
         assert (
             pymake.build_apps(
@@ -113,8 +113,6 @@ def test_makefile_build(function_tmpdir, target: str) -> None:
     pm.inplace = True
     pm.dryrun = True
     pm.makeclean = False
-    if system() == "Darwin":
-        pm.syslibs = "-Wl,-ld_classic"
 
     with set_dir(function_tmpdir):
         pm.download_target(target)

autotest/test_cli_cmds.py

@@ -1,10 +1,13 @@
 import os
 import pathlib as pl
 import subprocess
+from platform import system
 
 import pytest
 from flaky import flaky
-from modflow_devtools.misc import set_dir
+from modflow_devtools.misc import set_dir, set_env
+
+from pymake import linker_update_environment
 
 RERUNS = 3
 
@@ -106,10 +109,15 @@ def test_mfpymake(function_tmpdir, meson: bool) -> None:
             "--verbose",
             "-fc",
         ]
+        fc = "gfortran"
         if os.environ.get("FC") is None:
-            cmd.append("gfortran")
+            cmd.append(fc)
         else:
-            cmd.append(os.environ.get("FC"))
+            fc = os.environ.get("FC")
+            cmd.append(fc)
+
+        linker_update_environment(fc=fc)
+
         if meson:
             cmd.append("--meson")
         run_cli_cmd(cmd)

autotest/test_gridgen.py

@@ -31,9 +31,7 @@ def pm(module_tmpdir, target) -> pymake.Pymake:
     pm.target = str(target)
     pm.appdir = str(module_tmpdir)
     pm.cc = environ.get("CXX", "g++")
-    pm.fc = environ.get("FC", "gfortran")
-    if system() == "Darwin":
-        pm.syslibs = "-Wl,-ld_classic"
+    pm.fc = None
     pm.inplace = True
     pm.makeclean = True
     yield pm