* update request ci to use pixi

modflowpy · Jun 16, 2024 · 133ab83 · 133ab83
1 parent 74bcb07
commit 133ab83
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,24 +19,90 @@ concurrency:
   cancel-in-progress: true
 jobs:
 
-  pymakeCI-os-compiler:
+  pymake-schedule:
     name: pymake CI gcc on different OSs
+    if: ${{ github.event_name == 'schedule' }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       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}
+          # 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}
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - uses: maxim-lobanov/setup-xcode@v1
+        if: ${{ (runner.os == 'macOS') && (matrix.FC == 'intel-classic') }}
+        with:
+          xcode-version: "14.3.1"
+
+      - name: Setup Graphviz on Linux
+        if: runner.os == 'Linux'
+        uses: ts-graphviz/setup-graphviz@v2
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          pixi-version: v0.19.1
+          manifest-path: "pixi.toml"
+
+      - name: pixi post-install
+        working-directory: pymake
+        run: |
+          pixi run postinstall
+
+      - name: Setup ${{ matrix.FC }} ${{ matrix.FC_V }} on ${{ matrix.os }}
+        uses: fortran-lang/setup-fortran@main
+        with:
+          compiler: ${{ matrix.FC }}
+          version: ${{ matrix.FC_V }}
+
+      - name: Install make
+        if: runner.os == 'Windows'
+        run: choco install make
+
+      - name: Run scheduled tests
+        run: |
+          pixi run autotest-schedule
+
+      - name: Upload failed test output
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: failed-schedule-${{ matrix.os }}-${{ matrix.FC }}-${{ matrix.FC_V }}
+          path: ./autotest/.failed
+
+
+  pymake-os-compiler:
+    name: pymake CI gcc on different OSs
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      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}
+          # 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}
           # test latest python and previous gcc
           - {os: ubuntu-latest, FC: gcc, FC_V: 12}
           - {os: ubuntu-latest, FC: gcc, FC_V: 11}
-          # test latest python and intel
-          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: windows-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: macos-13, FC: intel-classic, FC_V: 2021.7}
     defaults:
       run:
         shell: bash
@@ -65,7 +131,7 @@ jobs:
         run: |
           pixi run postinstall
 
-      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
+      - name: Setup ${{ matrix.FC }} ${{ matrix.FC_V }} on ${{ matrix.os }}
         uses: fortran-lang/setup-fortran@main
         with:
           compiler: ${{ matrix.FC }}
@@ -96,14 +162,5 @@ jobs:
         with:
           name: failed-${{ matrix.os }}-${{ matrix.FC }}-${{ matrix.FC_V }}
           path: ./autotest/.failed
-
-      - name: Print coverage report before upload
-        run: |
-          pixi run coverage-report
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-        with:
-          file: ./autotest/coverage.xml
+
diff --git a/.github/workflows/pymake-requests.yml b/.github/workflows/pymake-requests.yml
@@ -30,32 +30,32 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
         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: Run pytest
-        working-directory: ./autotest
         run: |
-          pytest -v -n=auto -m requests --durations=0 --cov=pymake --cov-report=xml
+          pixi run autotest-request
 
-      - name: Run scheduled tests
-        if: ${{ github.event_name == 'schedule' }}
-        working-directory: ./autotest
-        run: |
-          pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml
+      - name: Upload failed test output
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: failed-requests
+          path: ./autotest/.failed
 
       - 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
         env:

diff --git a/autotest/test_build.py b/autotest/test_build.py
@@ -12,11 +12,6 @@
 RERUNS = 3
 
 targets = pymake.usgs_program_data.get_keys(current=True)
-targets_make = [
-    t
-    for t in targets
-    if t not in ("libmf6", "gridgen", "mf2000", "swtv4", "mflgr")
-]
 test_ostag = get_ostag()
 test_fc_env = os.environ.get("FC")
 if "win" in test_ostag:
@@ -27,6 +22,15 @@
     meson_exclude = ("sutra",)
 targets_meson = [t for t in targets if t not in meson_exclude]
 
+if "win" in test_ostag and test_fc_env in ("ifort",):
+    targets_make = []
+else:
+    targets_make = [
+        t
+        for t in targets
+        if t not in ("libmf6", "gridgen", "mf2000", "swtv4", "mflgr")
+    ]
+
 
 def build_with_makefile(target, path, fc):
     success = True
@@ -103,7 +107,6 @@ def test_meson_build(function_tmpdir, target: str) -> None:
 
 @pytest.mark.base
 @flaky(max_runs=RERUNS)
-@pytest.mark.skipif(sys.platform == "win32", reason="do not run on Windows")
 @pytest.mark.parametrize("target", targets_make)
 def test_makefile_build(function_tmpdir, target: str) -> None:
     pm = pymake.Pymake(verbose=True)

diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py
@@ -46,43 +46,46 @@ def run_cli_cmd(cmd: list) -> None:
 @pytest.mark.base
 @pytest.mark.parametrize("target", targets)
 def test_make_program(function_tmpdir, target: str) -> None:
-    cmd = [
-        "make-program",
-        target,
-        "--appdir",
-        str(function_tmpdir),
-        "--verbose",
-    ]
-    run_cli_cmd(cmd)
+    with set_dir(function_tmpdir):
+        cmd = [
+            "make-program",
+            target,
+            "--appdir",
+            str(function_tmpdir),
+            "--verbose",
+        ]
+        run_cli_cmd(cmd)
 
 
 @flaky(max_runs=RERUNS)
 @pytest.mark.dependency(name="make_program")
 @pytest.mark.base
 def test_make_program_double(function_tmpdir) -> None:
-    cmd = [
-        "make-program",
-        "mf2005",
-        "--double",
-        "--verbose",
-        "--appdir",
-        str(function_tmpdir),
-    ]
-    run_cli_cmd(cmd)
+    with set_dir(function_tmpdir):
+        cmd = [
+            "make-program",
+            "mf2005",
+            "--double",
+            "--verbose",
+            "--appdir",
+            str(function_tmpdir),
+        ]
+        run_cli_cmd(cmd)
 
 
 @pytest.mark.dependency(name="make_program_all")
 @pytest.mark.schedule
 def test_make_program_all(module_tmpdir) -> None:
-    cmd = [
-        "make-program",
-        ":",
-        "--appdir",
-        str(module_tmpdir / "all"),
-        "--verbose",
-        "--dryrun",
-    ]
-    run_cli_cmd(cmd)
+    with set_dir(module_tmpdir):
+        cmd = [
+            "make-program",
+            ":",
+            "--appdir",
+            str(module_tmpdir / "all"),
+            "--verbose",
+            "--dryrun",
+        ]
+        run_cli_cmd(cmd)
 
 
 @flaky(max_runs=RERUNS)

diff --git a/autotest/test_gridgen.py b/autotest/test_gridgen.py
@@ -59,14 +59,14 @@ def run_gridgen(cmd, ws, exe):
 
 
 @pytest.mark.dependency(name="download")
-@pytest.mark.base
+@pytest.mark.regression
 def test_download(pm, module_tmpdir, target):
     pm.download_target(target, download_path=module_tmpdir)
     assert pm.download, f"could not download {target} distribution"
 
 
 @pytest.mark.dependency(name="build", depends=["download"])
-@pytest.mark.base
+@pytest.mark.regression
 def test_compile(pm, target):
     assert pm.build() == 0, f"could not compile {target}"
 

diff --git a/autotest/test_mf2005.py b/autotest/test_mf2005.py
@@ -43,14 +43,14 @@ def run_mf2005(namefile, ws, exe):
 
 
 @pytest.mark.dependency(name="download")
-@pytest.mark.base
+@pytest.mark.regression
 def test_download(pm, module_tmpdir, target):
     pm.download_target(target, download_path=module_tmpdir)
     assert pm.download, f"could not download {target}"
 
 
 @pytest.mark.dependency(name="build", depends=["download"])
-@pytest.mark.base
+@pytest.mark.regression
 def test_compile(pm, target):
     assert pm.build() == 0, f"could not compile {target}"
 

diff --git a/autotest/test_mf6.py b/autotest/test_mf6.py
@@ -100,14 +100,14 @@ def build_with_makefile(pm, workspace, exe):
 
 
 @pytest.mark.dependency(name="download")
-@pytest.mark.base
+@pytest.mark.regression
 def test_download(pm, module_tmpdir, target):
     pm.download_target(target, download_path=module_tmpdir)
     assert pm.download, f"could not download {target} distribution"
 
 
 @pytest.mark.dependency(name="build", depends=["download"])
-@pytest.mark.base
+@pytest.mark.regression
 def test_compile(pm, target):
     assert pm.build() == 0, f"could not compile {target}"
 
@@ -118,39 +118,3 @@ def test_compile(pm, target):
 def test_mf6(ws, target):
     success, _ = flopy.run_model(target, None, model_ws=ws, silent=False)
     assert success, f"could not run {ws}"
-
-
-@pytest.mark.dependency(name="makefile", depends=["build"])
-@pytest.mark.base
-def test_makefile(pm, module_tmpdir, target):
-    assert build_with_makefile(
-        pm, module_tmpdir, target
-    ), f"could not compile {target} with makefile"
-
-
-@pytest.mark.dependency(name="shared", depends=["makefile"])
-@pytest.mark.base
-def test_sharedobject(pm, module_tmpdir, workspace, target_so, prog_data):
-    # reconfigure pymake object
-    pm.target = str(target_so)
-    pm.appdir = module_tmpdir
-    pm.srcdir = workspace / prog_data.srcdir
-    pm.srcdir2 = workspace / "src"
-    pm.excludefiles = [os.path.join(pm.srcdir2, "mf6.f90")]
-    pm.makefile = True
-    pm.makeclean = True
-    pm.sharedobject = True
-    pm.inplace = True
-    pm.dryrun = False
-
-    # build the target
-    assert pm.build() == 0, f"could not compile {pm.target}"
-    assert target_so.is_file()
-
-
-@pytest.mark.dependency(name="shared_makefile", depends=["shared", "makefile"])
-@pytest.mark.base
-def test_sharedobject_makefile(pm, module_tmpdir, target_so):
-    assert build_with_makefile(
-        pm, module_tmpdir, target_so
-    ), f"could not compile {target_so} with makefile"
diff --git a/autotest/test_mfusg.py b/autotest/test_mfusg.py
@@ -68,7 +68,7 @@ def run_mfusg(fn, exe):
 
 
 @pytest.mark.dependency(name="download")
-@pytest.mark.base
+@pytest.mark.regrression
 def test_download(pm, pm_gsi, module_tmpdir, targets):
     pm.download_target(targets[0], download_path=module_tmpdir)
     assert pm.download, f"could not download {targets[0]}"
@@ -78,7 +78,7 @@ def test_download(pm, pm_gsi, module_tmpdir, targets):
 
 
 @pytest.mark.dependency(name="build", depends=["download"])
-@pytest.mark.base
+@pytest.mark.regression
 def test_compile(pm, pm_gsi, targets):
     assert pm.build() == 0, f"could not compile {targets[0]}"
     assert (targets[0]).is_file()
@@ -87,7 +87,7 @@ def test_compile(pm, pm_gsi, targets):
     assert targets[1].is_file()
 
 
-@pytest.mark.dependency(name="test", depends=["build"])
+@pytest.mark.dependency(name="test", depends=["download", "build"])
 @pytest.mark.regression
 @pytest.mark.parametrize(
     "namefile",