diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8c81ad3..12a80f4 100644 --- a/.github/workflows/main.yml +++ b/.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-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: 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 diff --git a/.github/workflows/pymake-gcc.yml b/.github/workflows/pymake-gcc.yml index f6163ce..206607f 100644 --- a/.github/workflows/pymake-gcc.yml +++ b/.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-pixi@v0.8.1 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 diff --git a/.github/workflows/pymake-linting-install.yml b/.github/workflows/pymake-linting-install.yml index ca256e9..feafe89 100644 --- a/.github/workflows/pymake-linting-install.yml +++ b/.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-pixi@v0.8.1 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 diff --git a/.gitignore b/.gitignore index 79b8dbb..f700a60 100644 --- a/.gitignore +++ b/.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. diff --git a/autotest/ci_setup.py b/autotest/ci_setup.py index 268fb28..7eac513 100644 --- a/autotest/ci_setup.py +++ b/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) diff --git a/autotest/test_build.py b/autotest/test_build.py index 67315b2..1e02c2e 100644 --- a/autotest/test_build.py +++ b/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) diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py index 661bd72..f31e0a3 100644 --- a/autotest/test_cli_cmds.py +++ b/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) diff --git a/autotest/test_gridgen.py b/autotest/test_gridgen.py index 6dbb1b3..1c69312 100644 --- a/autotest/test_gridgen.py +++ b/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 diff --git a/autotest/test_mf6_existing_meson.py b/autotest/test_mf6_existing_meson.py index a3bfd89..26cd762 100644 --- a/autotest/test_mf6_existing_meson.py +++ b/autotest/test_mf6_existing_meson.py @@ -1,24 +1,21 @@ import os import sys from pathlib import Path +from platform import system from typing import List import pytest +from modflow_devtools.ostags import get_binary_suffixes import pymake +from pymake import linker_update_environment @pytest.fixture(scope="module") def targets() -> List[Path]: target = "mf6" - ext = "" - shared_ext = ".so" + ext, shared_ext = get_binary_suffixes() executables = [target, "zbud6", "mf5to6", "libmf6"] - if sys.platform.lower() == "win32": - ext = ".exe" - shared_ext = ".dll" - elif sys.platform.lower() == "darwin": - shared_ext = ".dylib" for idx, _ in enumerate(executables[:3]): executables[idx] += ext executables[3] += shared_ext @@ -40,6 +37,7 @@ def pm(workspace, targets) -> pymake.Pymake: pm = pymake.Pymake(verbose=True) pm.target = str(targets[0]) pm.appdir = str(workspace / "bin") + pm.fc = os.environ.get("FC", "gfortran") pm.meson = True pm.makeclean = True pm.mesondir = str(workspace) @@ -83,6 +81,8 @@ def test_build_with_existing_meson(pm, module_tmpdir, workspace, targets): pm.download_target(targets[0], download_path=module_tmpdir) assert pm.download, f"could not download {targets[0]} distribution" + linker_update_environment(cc=cc, fc=fc) + # make modflow 6 with existing meson.build file returncode = pymake.meson_build( workspace, diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..692465a --- /dev/null +++ b/pixi.lock @@ -0,0 +1,10491 @@ +version: 4 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py39h3d6467e_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda + - 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__osx >=11.0 + - libzlib >=1.2.13,<2.0.0a0 + license: BSD-3-Clause + license_family: BSD + size: 405089 + timestamp: 1714723101397 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 0000000..589bea5 --- /dev/null +++ b/pixi.toml @@ -0,0 +1,51 @@ +[project] +name = "pymake" +channels = ["conda-forge"] +platforms = ["win-64", "linux-64", "linux-aarch64", "osx-arm64", "osx-64"] +version = "1.2.10.dev0" + +[dependencies] +appdirs = "*" +codespell = "*" +coverage = "*" +filelock = "*" +flaky = "*" +flopy = "*" +matplotlib = "*" +meson = "1.3.0" +modflow-devtools = "*" +networkx = "*" +ninja = "*" +numpy = "*" +pip = "*" +pydotplus = "*" +pytest = "!=8.1.0" +pytest-benchmark = "*" +pytest-cov = "*" +pytest-dotenv = "*" +pytest-order = "*" +pytest-xdist = "*" +python = "3.9.*" +requests = "*" +ruff = "*" + +[tasks] +postinstall = "pip install --no-build-isolation --no-deps --disable-pip-version-check -e ." + +# format +check-lint = "ruff check ." +fix-lint = "ruff check . --fix" +check-format = "ruff format . --check" +fix-format = "ruff format ." + +# build +test = "meson test --verbose --no-rebuild -C" + +# test +download-examples = {cmd = "python ci_setup.py", cwd = "autotest"} +autotest = { cmd = "pytest -v -n auto --dist=loadfile -m='base or regression' --durations 0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } +autotest-base = { cmd = "pytest -v -n auto --dist=loadfile -m='base' --durations 0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } +autotest-Windows = { cmd = "pytest -v -m='base' --durations 0 --cov=pymake --cov-report=xml --basetemp=$RUNNER_TEMP/pytest_temp --keep-failed .failed", cwd = "autotest" } + +# coverage report +coverage-report = { cmd = "coverage report", cwd = "autotest"} diff --git a/pymake/__init__.py b/pymake/__init__.py index 969ad52..d9926a6 100644 --- a/pymake/__init__.py +++ b/pymake/__init__.py @@ -21,6 +21,7 @@ from .pymake_base import get_temporary_directories, main from .pymake_build_apps import build_apps from .pymake_parser import parser +from .utils._compiler_switches import linker_update_environment from .utils._meson_build import meson_build, meson_install, meson_setup from .utils.download import ( download_and_unzip, diff --git a/pymake/utils/_compiler_switches.py b/pymake/utils/_compiler_switches.py index 0b1dfa6..d19eff4 100644 --- a/pymake/utils/_compiler_switches.py +++ b/pymake/utils/_compiler_switches.py @@ -1,9 +1,10 @@ -"""Private functions for setting c/c++ and fortran compiler flags and -appropriate linker flags for defined targets. +"""Public and private functions for setting c/c++ and fortran compiler +flags and appropriate linker flags for defined targets. """ import os import sys +from subprocess import check_output from ._compiler_language_files import ( _get_c_files, @@ -17,6 +18,28 @@ ) +def linker_update_environment(cc="gcc", fc="gfortran", verbose=False): + """Add additional LDFLAGS to the environment based on OS and compilers. + + Parameters + ---------- + fc : str + fortran compiler + cc : str + c or cpp compiler + verbose : bool + boolean for verbose output to terminal + + Returns + ------- + None + """ + syslibs = _darwin_syslibs(cc, fc, verbose=verbose) + if syslibs is not None: + environ = os.environ + environ.update({"LDFLAGS": syslibs}) + + def _check_gnu_switch_available(switch, compiler="gfortran", verbose=False): """Determine if a specified GNU compiler switch exists. Not all switches will be detected, for example '-O2' adn '-fbounds-check=on'. @@ -971,6 +994,10 @@ def _set_syslibs( if default_syslibs: syslibs.append("-lc") + darwin_options = _darwin_syslibs(cc, fc, verbose) + if darwin_options is not None: + syslibs.append(darwin_options) + # add additional syslibs for select programs if target == "triangle": if osname in ("linux", "darwin"): @@ -1033,3 +1060,46 @@ def _get_os_macro(osname=None): else: os_macro = None return os_macro + + +def _darwin_syslibs(cc, fc, verbose=False): + """Get additional syslibs for Darwin systems using gcc + tool chain and command line tools greater than 14 + + Parameters + ---------- + cc : str + c compiler + fc : str + fortran compiler + verbose : bool + boolean for verbose output to terminal + + Returns + ------- + linker_str : str + additiona; linker flags for darwin systems. Default is None + """ + linker_str = None + if _get_osname() == "darwin": + if cc in ( + "gcc", + "g++", + ) or fc in ("gfortran",): + cmd = ["pkgutil", "--pkg-info=com.apple.pkg.CLTools_Executables"] + out_lines = check_output(cmd).decode("utf-8").splitlines() + version = None + tag = "version: " + for line in out_lines: + if line.startswith(tag): + version = line.replace(tag, "") + break + if version is not None: + major = int(version.split(".")[0]) + if major > 14: + linker_str = "-Wl,-ld_classic" + if verbose: + print(f"C/C++ compiler: {cc} \nFortran compiler: {fc}") + print(f"Command line tools version: {version}") + print(f"Command line tools major version number: {major}") + return linker_str diff --git a/pyproject.toml b/pyproject.toml index a83c756..db98945 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ requires-python = ">=3.8" dependencies = [ "numpy", "requests", - "networkx >= 2.6.3", + "networkx", "meson", "ninja", "pydotplus",