From 17638e497520c594a527e6eb5b3060bbafc37190 Mon Sep 17 00:00:00 2001 From: Joseph D Hughes Date: Mon, 17 Jun 2024 11:25:57 -0500 Subject: [PATCH] Revert "Release 1.2.10 (#186)" This reverts commit b6177e46f6f37d6a4ebdffa1fdff718832437363. --- .flake8 | 29 + .github/workflows/ci.yml | 192 - .github/workflows/main.yml | 80 + .github/workflows/pymake-gcc.yml | 80 + .github/workflows/pymake-linting-install.yml | 46 +- .github/workflows/pymake-requests.yml | 42 +- .github/workflows/pymake-rtd.yml | 4 - .github/workflows/release.yml | 174 - .gitignore | 9 +- README.md | 84 +- autotest/ci_setup.py | 103 +- autotest/pytest.ini | 1 - autotest/test_build.py | 85 +- autotest/test_cli_cmds.py | 65 +- autotest/test_gridgen.py | 17 +- autotest/test_gsflow.py | 83 + autotest/test_mf2005.py | 11 +- autotest/test_mf6.py | 78 +- autotest/test_mf6_existing_meson.py | 118 +- autotest/test_mflgr.py | 34 + autotest/test_mfnwt.py | 91 + autotest/test_mfusg.py | 9 +- autotest/test_misc_programs.py | 24 + autotest/test_mp6.py | 11 +- autotest/test_mp7.py | 12 +- autotest/{test_mt3dusgs.py => test_mt3d.py} | 34 +- autotest/test_seawat.py | 12 +- autotest/test_triangle_makefile.py | 69 + docs/build_apps.md | 46 +- docs/index.rst | 2 +- docs/installation.md | 6 +- pixi.lock | 10491 ----------------- pixi.toml | 54 - pymake/__init__.py | 1 - pymake/cmds/build.py | 34 +- pymake/cmds/createjson.py | 32 +- pymake/cmds/mfpymakecli.py | 1 - pymake/config.py | 10 +- pymake/pymake.py | 57 +- pymake/pymake_base.py | 3 +- pymake/pymake_build_apps.py | 34 +- pymake/pymake_parser.py | 2 +- pymake/utils/_Popen_wrapper.py | 4 +- pymake/utils/_compiler_language_files.py | 3 +- pymake/utils/_compiler_switches.py | 111 +- pymake/utils/_usgs_src_update.py | 124 +- pymake/utils/download.py | 50 +- pymake/utils/usgsprograms.py | 91 +- pymake/utils/usgsprograms.txt | 17 +- pyproject.toml | 45 +- scripts/update_version.py | 149 - version.txt | 1 - 52 files changed, 1235 insertions(+), 11730 deletions(-) create mode 100644 .flake8 delete mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/main.yml create mode 100644 .github/workflows/pymake-gcc.yml delete mode 100644 .github/workflows/release.yml create mode 100644 autotest/test_gsflow.py create mode 100644 autotest/test_mflgr.py create mode 100644 autotest/test_mfnwt.py create mode 100644 autotest/test_misc_programs.py rename autotest/{test_mt3dusgs.py => test_mt3d.py} (84%) create mode 100644 autotest/test_triangle_makefile.py delete mode 100644 pixi.lock delete mode 100644 pixi.toml delete mode 100644 scripts/update_version.py delete mode 100644 version.txt diff --git a/.flake8 b/.flake8 new file mode 100644 index 00000000..fdfc7cc5 --- /dev/null +++ b/.flake8 @@ -0,0 +1,29 @@ +[flake8] +exclude = + .git + __pycache__ + build + dist + examples + autotest +ignore = + # https://flake8.pycqa.org/en/latest/user/error-codes.html + F401, + # https://pycodestyle.readthedocs.io/en/latest/intro.html#error-codes + # Indentation + E121, E122, E126, E127, E128, + # Whitespace + E203, E221, E222, E226, E231, E241, + # Import + E402, + # Line length + E501, E502, + # Statement + E722, E741, + # Whitespace warning + W291, W292, W293, + # Blank line warning + W391, + # Line break warning + W503, W504 +statistics = True \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index f9935c63..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,192 +0,0 @@ -name: pymake continuous integration - -on: - schedule: - - cron: '0 7 * * *' # run at 7 AM UTC every day - push: - paths-ignore: - - 'README.md' - - 'docs/*.md' - pull_request: - branches: - - master - - develop - paths-ignore: - - 'README.md' - - 'docs/*.md' -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true -jobs: - - pymake-os-compiler: - name: pymake CI on different OSs with gcc and intel-classic - 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} - 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: ${{ matrix.FC_V }} - - - name: Download examples for pytest runs - run: | - pixi run download-examples - - - name: Install make - if: runner.os == 'Windows' - run: choco install make - - - name: test on Linux - if: runner.os == 'Linux' - run: | - pixi run autotest - - - name: test on MacOS - if: runner.os == 'macOS' - run: | - pixi run autotest-base - - - name: test on Windows - if: runner.os == 'Windows' - shell: pwsh - run: | - pixi run autotest-base - - - name: Upload failed test output - if: failure() - uses: actions/upload-artifact@v4 - with: - name: failed-${{ 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 - - pymake-schedule: - name: pymake scheduled CI different OSs with gcc and intel-classic - 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 - - - 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/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..20d107ad --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,80 @@ +name: pymake continuous integration + +on: + schedule: + - cron: '0 7 * * *' # run at 7 AM UTC every day + push: + pull_request: + branches: + - master +jobs: + + pymakeCI-os-intel: + name: pymake CI intel on different OSs + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, macos-latest, windows-2019] + defaults: + run: + shell: bash + + steps: + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Setup Intel Fortran Classic + uses: fortran-lang/setup-fortran@v1 + with: + compiler: intel-classic + version: "2021.7" + + - name: Setup Graphviz + if: runner.os == 'Linux' + uses: ts-graphviz/setup-graphviz@v2 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + + - name: Install python packages + run: | + python -m pip install --upgrade pip + pip install ".[test]" + + - name: Download examples for pytest runs + run: | + .github/common/download-examples.sh + + - 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 + + - 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 + + - 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 + + - name: Print coverage report before upload + working-directory: ./autotest + 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-gcc.yml b/.github/workflows/pymake-gcc.yml new file mode 100644 index 00000000..68af5269 --- /dev/null +++ b/.github/workflows/pymake-gcc.yml @@ -0,0 +1,80 @@ +name: pymake gcc build + +on: + schedule: + - cron: '0 7 * * *' # run at 7 AM UTC every day + push: + pull_request: + branches: + - master +jobs: + + pymakeCI-os-gcc: + 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, 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} + # test latest python and previous gcc + - {os: ubuntu-latest, gcc: 12, python: "3.12"} + - {os: ubuntu-latest, gcc: 11, python: "3.12"} + defaults: + run: + shell: bash + + steps: + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Setup Graphviz on Linux + if: runner.os == 'Linux' + uses: ts-graphviz/setup-graphviz@v2 + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Install python packages + run: | + python -m pip install --upgrade pip + pip install ".[test]" + + - name: Setup GNU Fortran + uses: fortran-lang/setup-fortran@v1 + with: + compiler: gcc + version: ${{ matrix.gcc }} + + - name: Download examples for pytest runs + run: .github/common/download-examples.sh + + - name: Run pytest + working-directory: ./autotest + 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" + + - name: Print coverage report before upload + working-directory: ./autotest + 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-linting-install.yml b/.github/workflows/pymake-linting-install.yml index 589551c5..2c79b7b0 100644 --- a/.github/workflows/pymake-linting-install.yml +++ b/.github/workflows/pymake-linting-install.yml @@ -7,10 +7,6 @@ on: pull_request: branches: - master - - develop -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true jobs: @@ -23,17 +19,43 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.8.1 + - name: Set up Python + uses: actions/setup-python@v5 with: - pixi-version: v0.19.1 - manifest-path: "pixi.toml" + python-version: "3.12" + + - name: Setup Graphviz + uses: ts-graphviz/setup-graphviz@v2 - - name: Lint - run: pixi run check-lint + - name: Install packages + run: | + pip install requests pydotplus appdirs numpy matplotlib + pip install https://github.com/modflowpy/flopy/zipball/develop + pip install pylint flake8 black - - name: Check format - run: pixi run check-format + - name: Run isort + run: | + echo "if isort check fails update isort using" + echo " pip install isort --upgrade" + echo "and run" + echo " isort ./flopy" + echo "and then commit the changes." + isort --verbose --check --diff ./pymake + + - name: Run black + run: | + echo "if black check fails update black using" + echo " pip install black --upgrade" + echo "and run" + echo " black ./flopy" + echo "and then commit the changes." + black --check --diff ./pymake + + - name: Run flake8 + run: flake8 --count --show-source --exit-zero ./pymake + + - name: Run pylint + run: pylint --jobs=2 --errors-only --exit-zero ./pymake pymake_setup: name: standard installation diff --git a/.github/workflows/pymake-requests.yml b/.github/workflows/pymake-requests.yml index 472efb90..e889fbc6 100644 --- a/.github/workflows/pymake-requests.yml +++ b/.github/workflows/pymake-requests.yml @@ -4,19 +4,9 @@ on: schedule: - cron: '0 7 * * *' # run at 7 AM UTC every day push: - paths-ignore: - - 'README.md' - - 'docs/*.md' pull_request: branches: - master - - develop - paths-ignore: - - 'README.md' - - 'docs/*.md' -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true jobs: pymakeCI-requests: @@ -30,32 +20,32 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.8.1 + - name: Set up Python + uses: actions/setup-python@v5 with: - pixi-version: v0.19.1 - manifest-path: "pixi.toml" + python-version: "3.12" - - name: pixi post-install - working-directory: pymake + - name: Install python packages run: | - pixi run postinstall + python -m pip install --upgrade pip + pip install ".[test]" - name: Run pytest + working-directory: ./autotest run: | - pixi run autotest-request + pytest -v -n=auto -m requests --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: Run scheduled tests + if: ${{ github.event_name == 'schedule' }} + working-directory: ./autotest + run: | + pytest -v -m="schedule" --durations=0 --cov=pymake --cov-report=xml - name: Print coverage report before upload + working-directory: ./autotest run: | - pixi run coverage-report - + coverage report + - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 env: diff --git a/.github/workflows/pymake-rtd.yml b/.github/workflows/pymake-rtd.yml index 8d8e1a97..49e6f8d0 100644 --- a/.github/workflows/pymake-rtd.yml +++ b/.github/workflows/pymake-rtd.yml @@ -7,10 +7,6 @@ on: pull_request: branches: - master - - develop -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true jobs: pymake_rtd: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml deleted file mode 100644 index 0884e479..00000000 --- a/.github/workflows/release.yml +++ /dev/null @@ -1,174 +0,0 @@ -name: Release -on: - push: - branches: - - master - - v[0-9]+.[0-9]+.[0-9]+* - release: - types: - - published -jobs: - prep: - name: Prepare release - runs-on: ubuntu-latest - if: ${{ github.event_name == 'push' && github.ref_name != 'master' }} - permissions: - contents: write - pull-requests: write - defaults: - run: - shell: bash - steps: - - - name: Checkout release branch - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Setup Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml - - - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install build twine - pip install . - pip install ".[lint, test]" - - - name: Make code.md - run: make-code-json - - - name: Upload code.md - uses: actions/upload-artifact@v3 - with: - name: code.md - path: code.md - - - name: Update version - id: version - run: | - ref="${{ github.ref_name }}" - version="${ref#"v"}" - python scripts/update_version.py -v "$version" - python -c "import pymake; print('Version: ', pymake.__version__)" - echo "version=$version" >> $GITHUB_OUTPUT - - - name: Lint - run: ruff check . - - - name: Format - run: ruff format . - - - name: Push release branch - env: - GITHUB_TOKEN: ${{ github.token }} - run: | - ver="${{ steps.version.outputs.version }}" - - # commit and push changes - git config core.sharedRepository true - git config user.name "github-actions[bot]" - git config user.email "41898282+github-actions[bot]@users.noreply.github.com" - git add pymake - git commit -m "ci(release): set version to ${{ steps.version.outputs.version }}" - git push origin "${{ github.ref_name }}" - - title="Release $ver" - body=' - # Release '$ver' - - The release can be approved by merging this pull request into `master`. This will trigger a job to publish the release to PyPI. - ' - gh pr create -B "master" -H "${{ github.ref_name }}" --title "$title" --draft --body "$body" - - release: - name: Draft release - # runs only when changes are merged to master - if: ${{ github.event_name == 'push' && github.ref_name == 'master' }} - runs-on: ubuntu-latest - permissions: - contents: write - pull-requests: write - steps: - - - name: Checkout repo - uses: actions/checkout@v4 - with: - ref: master - - - name: Setup Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - - - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install . - pip install ".[test]" - - - name: Download artifacts - uses: dawidd6/action-download-artifact@v6 - - - name: Draft release - env: - GITHUB_TOKEN: ${{ github.token }} - run: | - version=$(python scripts/update_version.py -g) - title="pymake $version" - notes=$(cat code.md) - gh release create "$version" \ - --target master \ - --title "$title" \ - --notes "$notes" \ - --draft \ - --latest - - publish: - name: Publish package - # runs only after release is published (manually promoted from draft) - if: github.event_name == 'release' && github.repository_owner == 'modflowpy' - runs-on: ubuntu-22.04 - permissions: - contents: write - pull-requests: write - id-token: write - environment: # requires a 'release' environment in repo settings - name: release - url: https://pypi.org/p/mfpymake - steps: - - - name: Checkout master branch - uses: actions/checkout@v4 - with: - ref: master - - - name: Setup Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - - - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install build twine - pip install . - - - name: Build package - run: python -m build - - - name: Check package - run: twine check --strict dist/* - - - name: Upload package - uses: actions/upload-artifact@v4 - with: - name: dist - path: dist - - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.gitignore b/.gitignore index 66ff0ef3..437620cd 100644 --- a/.gitignore +++ b/.gitignore @@ -24,9 +24,6 @@ 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. @@ -66,7 +63,6 @@ target/ # files in the autotest directory autotest/temp*/ -autotest/.failed/ autotest/*.json autotest/code.md mod_temp/ @@ -82,7 +78,4 @@ docs/source/ venv/ # mac files -**/.DS_Store - -# environment files -**.env \ No newline at end of file +**/.DS_Store \ No newline at end of file diff --git a/README.md b/README.md index 14dda821..e0daf377 100644 --- 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 1.2.9.dev0 [![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) @@ -55,8 +55,13 @@ The help message identifies required positional arguments and optional arguments default values. ``` -usage: mfpymake [-h] [-fc {ifort,mpiifort,gfortran,none}] [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}] [-ar {ia32,ia32_intel64,intel64}] [-mc] [-dbl] [-dbg] [-e] [-dr] [-sd] [-ff FFLAGS] - [-cf CFLAGS] [-sl {-lc,-lm}] [-mf] [-md] [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES] [-so] [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace] [--networkx] [--meson] [--mesondir] +usage: mfpymake [-h] [-fc {ifort,mpiifort,gfortran,none}] + [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}] + [-ar {ia32,ia32_intel64,intel64}] [-mc] [-dbl] [-dbg] [-e] + [-dr] [-sd] [-ff FFLAGS] [-cf CFLAGS] [-sl {-lc,-lm}] [-mf] + [-md] [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES] + [-so] [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace] + [--networkx] [--meson] [--mesondir] srcdir target This is the pymake program for compiling fortran, c, and c++ source @@ -68,45 +73,70 @@ positional arguments: srcdir Path source directory. target Name of target to create. (can include path) -options: +optional arguments: -h, --help show this help message and exit -fc {ifort,mpiifort,gfortran,none} Fortran compiler to use. (default is gfortran) -cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none} C/C++ compiler to use. (default is gcc) -ar {ia32,ia32_intel64,intel64}, --arch {ia32,ia32_intel64,intel64} - Architecture to use for Intel and Microsoft compilers on Windows. (default is intel64) - -mc, --makeclean Clean temporary object, module, and source files when done. (default is False) + Architecture to use for Intel and Microsoft compilers + on Windows. (default is intel64) + -mc, --makeclean Clean temporary object, module, and source files when + done. (default is False) -dbl, --double Force double precision. (default is False) -dbg, --debug Create debug version. (default is False) - -e, --expedite Only compile out of date source files. Clean must not have been used on previous build. (default is False) - -dr, --dryrun Do not actually compile. Files will be deleted, if --makeclean is used. Does not work yet for ifort. (default is False) - -sd, --subdirs Include source files in srcdir subdirectories. (default is None) + -e, --expedite Only compile out of date source files. Clean must not + have been used on previous build. (default is False) + -dr, --dryrun Do not actually compile. Files will be deleted, if + --makeclean is used. Does not work yet for ifort. + (default is False) + -sd, --subdirs Include source files in srcdir subdirectories. + (default is None) -ff FFLAGS, --fflags FFLAGS - Additional Fortran compiler flags. Fortran compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-ff or --fflags) with a equal sign - (-ff='-O3'). (default is None) + Additional Fortran compiler flags. Fortran compiler + flags should be enclosed in quotes and start with a + blank space or separated from the name (-ff or + --fflags) with a equal sign (-ff='-O3'). (default is + None) -cf CFLAGS, --cflags CFLAGS - Additional C/C++ compiler flags. C/C++ compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-cf or --cflags) with a equal sign - (-cf='-O3'). (default is None) + Additional C/C++ compiler flags. C/C++ compiler flags + should be enclosed in quotes and start with a blank + space or separated from the name (-cf or --cflags) + with a equal sign (-cf='-O3'). (default is None) -sl {-lc,-lm}, --syslibs {-lc,-lm} - Linker system libraries. Linker libraries should be enclosed in quotes and start with a blank space or separated from the name (-sl or --syslibs) with a equal sign (-sl='-libgcc'). - (default is None) + Linker system libraries. Linker libraries should be + enclosed in quotes and start with a blank space or + separated from the name (-sl or --syslibs) with a + equal sign (-sl='-libgcc'). (default is None) -mf, --makefile Create a GNU make makefile. (default is False) -md, --makefiledir GNU make makefile directory. (default is '.') -cs COMMONSRC, --commonsrc COMMONSRC - Additional directory with common source files. (default is None) + Additional directory with common source files. + (default is None) -ef EXTRAFILES, --extrafiles EXTRAFILES - List of extra source files to include in the compilation. extrafiles can be either a list of files or the name of a text file that contains a list of files. (default is None) + List of extra source files to include in the + compilation. extrafiles can be either a list of files + or the name of a text file that contains a list of + files. (default is None) -exf EXCLUDEFILES, --excludefiles EXCLUDEFILES - List of extra source files to exclude from the compilation. excludefiles can be either a list of files or the name of a text file that contains a list of files. (default is None) - -so, --sharedobject Create shared object or dll on Windows. (default is False) + List of extra source files to exclude from the + compilation. excludefiles can be either a list of + files or the name of a text file that contains a list + of files. (default is None) + -so, --sharedobject Create shared object or dll on Windows. (default is + False) -ad APPDIR, --appdir APPDIR - Target path that overides path defined target path (default is None) + Target path that overides path defined target path + (default is None) -v, --verbose Verbose output to terminal. (default is False) --keep Keep existing executable. (default is False) - --zip ZIP Zip built executable. (default is None) - --inplace Source files in srcdir are used directly. (default is False) - --networkx Use networkx package to build Directed Acyclic Graph use to determine the order source files are compiled in. (default is False) + --zip ZIP Zip built executable. (default is False) + --inplace Source files in srcdir are used directly. (default is + False) + --networkx Use networkx package to build Directed Acyclic Graph + use to determine the order source files are compiled + in. (default is False) --meson Use meson to build executable. (default is False) --mesondir meson directory. (default is '.') @@ -173,7 +203,7 @@ python mymf6script.py -fc ifort -cc icc When pymake is installed, a `make-program` (or `make-program.exe` for Windows) program is installed. `make-program` can be used to build MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, MODFLOW-LGR, MODFLOW-2000, MODPATH 6, MODPATH 7, -GSFLOW, VS2DT, MT3DMS, MT3D-USGS, SEAWAT, and SUTRA. Utility programs CRT, Triangle, and GRIDGEN can also +GSFLOW, VS2DT, MT3DMS, MT3D-USGS, SEAWAT, GSFLOW, PRMS, and SUTRA. Utility programs CRT, Triangle, and GRIDGEN can also be built. `make-program` downloads the distribution file (requires an internet connection), unzips the file, sets the pymake settings required to build the program, and compiles the program from the source files. Optional pymake command line arguments can be used to customize the build (`-fc`, `-cc`, `--fflags`, etc.). For example, MODFLOW 6 could be @@ -200,14 +230,14 @@ To install pymake using conda type: conda install -c conda-forge mfpymake ``` -To install the latest pymake release directly from the git repository type: +To install pymake directly from the git repository type: ``` pip install https://github.com/modflowpy/pymake/zipball/master ``` -To update your version of pymake with the latest development version from the git repository type: +To update your version of pymake with the latest from the git repository type: ``` -pip install https://github.com/modflowpy/pymake/zipball/develop --upgrade +pip install https://github.com/modflowpy/pymake/zipball/master --upgrade ``` diff --git a/autotest/ci_setup.py b/autotest/ci_setup.py index 7eac5134..e77b66db 100644 --- a/autotest/ci_setup.py +++ b/autotest/ci_setup.py @@ -2,8 +2,6 @@ import pathlib as pl import shutil -from modflow_devtools.misc import get_model_paths - import pymake temp_pth = pl.Path("temp") @@ -12,6 +10,9 @@ 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): @@ -53,8 +54,27 @@ def examples_list(verbose=False): "sagehen", "ex-gwt-keating", ) + src_folders = [] + + for dirName, subdirList, fileList in os.walk(mf6_exdir): + useModel = True + for exclude in exclude_models: + if exclude in dirName: + useModel = False + break + if useModel: + for exclude in exclude_examples: + if exclude in dirName: + useModel = False + break + if useModel: + for file_name in fileList: + if file_name.lower() == "mfsim.nam": + if verbose: + print(f"Found directory: {dirName}") + src_folders.append(dirName) + src_folders = sorted(src_folders) - src_folders = get_model_paths(mf6_exdir) fpth = os.path.join(mf6_exdir, "mf6examples.txt") f = open(fpth, "w") for idx, folder in enumerate(src_folders): @@ -68,6 +88,83 @@ 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/pytest.ini b/autotest/pytest.ini index 950aeb61..00fcab6d 100644 --- a/autotest/pytest.ini +++ b/autotest/pytest.ini @@ -1,5 +1,4 @@ [pytest] -addopts = --color=yes markers = base: base tests dependency: tests that depend on other tests (via pytest-dependency) diff --git a/autotest/test_build.py b/autotest/test_build.py index 11a4e454..75e602e8 100644 --- a/autotest/test_build.py +++ b/autotest/test_build.py @@ -1,7 +1,6 @@ import os import sys import time -from platform import system import pytest from flaky import flaky @@ -9,9 +8,14 @@ import pymake -RERUNS = 1 +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: @@ -22,31 +26,36 @@ meson_exclude = ("sutra",) targets_meson = [t for t in targets if t not in meson_exclude] -make_exclude = ("libmf6", "gridgen", "mf2000", "swtv4", "mflgr") -targets_make = [t for t in targets if t not in make_exclude] - -def build_with_makefile(target): +def build_with_makefile(target, path, fc): success = True - if os.path.isfile("makefile"): - # wait to delete on windows - if sys.platform.lower() == "win32": - time.sleep(6) - - # clean prior to make - print(f"clean {target} with makefile") - os.system("make clean") - - print(f"build {target} with makefile") - return_code = os.system("make") - - success = os.path.isfile(target) - if success: - errmsg = "" - else: + with set_dir(path): + if os.path.isfile("makefile"): + # wait to delete on windows + if sys.platform.lower() == "win32": + time.sleep(6) + + # clean prior to make + print(f"clean {target} with makefile") + os.system("make clean") + + # build MODFLOW-NWT with makefile + print(f"build {target} with makefile") + return_code = os.system("make") + + # test if running on Windows with ifort, if True the makefile + # should fail errmsg = f"{target} created by makefile does not exist." - else: - errmsg = "makefile does not exist" + if sys.platform.lower() == "win32" and fc == "ifort": + if return_code != 0: + success = True + else: + success = False + # verify that MODFLOW-NWT was made + else: + success = os.path.isfile(target) + else: + errmsg = "makefile does not exist" return success, errmsg @@ -56,14 +65,9 @@ def build_with_makefile(target): @pytest.mark.parametrize("target", targets) def test_build(function_tmpdir, target: str) -> None: with set_dir(function_tmpdir): - pm = pymake.Pymake(verbose=True) - pm.target = target - pm.inplace = True - fc = os.environ.get("FC", "gfortran") assert ( pymake.build_apps( target, - pm, verbose=True, clean=False, ) @@ -75,9 +79,6 @@ def test_build(function_tmpdir, target: str) -> None: @flaky(max_runs=RERUNS) @pytest.mark.parametrize("target", targets_meson) def test_meson_build(function_tmpdir, target: str) -> None: - fc = os.environ.get("FC", "gfortran") - cc = os.environ.get("CC", "gcc") - pymake.linker_update_environment(cc=cc, fc=fc) with set_dir(function_tmpdir): assert ( pymake.build_apps( @@ -95,18 +96,18 @@ def test_meson_build(function_tmpdir, target: str) -> None: @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: - with set_dir(function_tmpdir): - pm = pymake.Pymake(verbose=True) - pm.target = target - pm.makefile = True - pm.makefiledir = "." - pm.inplace = True - pm.dryrun = True - pm.makeclean = False + pm = pymake.Pymake(verbose=True) + pm.target = target + pm.makefile = True + pm.makefiledir = "." + pm.inplace = True + pm.dryrun = True + pm.makeclean = False + with set_dir(function_tmpdir): pm.download_target(target) assert pm.download, f"could not download {target} distribution" assert pm.build() == 0, f"could not compile {target}" - success, errmsg = build_with_makefile(target) - assert success, errmsg + success, errmsg = build_with_makefile(target, function_tmpdir, pm.fc) + assert success, errmsg diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py index 4e635899..b82aaf44 100644 --- a/autotest/test_cli_cmds.py +++ b/autotest/test_cli_cmds.py @@ -1,13 +1,10 @@ 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, set_env - -from pymake import linker_update_environment +from modflow_devtools.misc import set_dir RERUNS = 3 @@ -46,45 +43,28 @@ def run_cli_cmd(cmd: list) -> None: @pytest.mark.base @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", - ] - 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: - with set_dir(function_tmpdir): - cmd = [ - "make-program", - "mf2005", - "--double", - "--verbose", - "--appdir", - str(function_tmpdir), - ] - run_cli_cmd(cmd) + cmd = [ + "make-program", + target, + "--appdir", + str(function_tmpdir), + "--verbose", + ] + 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", - ] - run_cli_cmd(cmd) + cmd = [ + "make-program", + ":", + "--appdir", + str(module_tmpdir / "all"), + "--verbose", + "--dryrun", + ] + run_cli_cmd(cmd) @flaky(max_runs=RERUNS) @@ -111,15 +91,10 @@ def test_mfpymake(function_tmpdir, meson: bool) -> None: "--verbose", "-fc", ] - fc = "gfortran" if os.environ.get("FC") is None: - cmd.append(fc) + cmd.append("gfortran") else: - fc = os.environ.get("FC") - cmd.append(fc) - - linker_update_environment(fc=fc) - + cmd.append(os.environ.get("FC")) if meson: cmd.append("--meson") run_cli_cmd(cmd) diff --git a/autotest/test_gridgen.py b/autotest/test_gridgen.py index 00a0aece..ef1365c3 100644 --- a/autotest/test_gridgen.py +++ b/autotest/test_gridgen.py @@ -1,18 +1,16 @@ +import os import pathlib as pl import subprocess -from os import environ from platform import system import pytest import pymake -TARGET_NAME = "gridgen" - @pytest.fixture(scope="module") def target(module_tmpdir) -> pl.Path: - name = TARGET_NAME + name = "gridgen" ext = ".exe" if system() == "Windows" else "" return module_tmpdir / f"{name}{ext}" @@ -32,8 +30,8 @@ def pm(module_tmpdir, target) -> pymake.Pymake: pm = pymake.Pymake(verbose=True) pm.target = str(target) pm.appdir = str(module_tmpdir) - pm.cc = environ.get("CXX", "g++") - pm.fc = None + pm.cc = os.environ.get("CXX", "g++") + pm.fc = os.environ.get("FC", "gfortran") pm.inplace = True pm.makeclean = True yield pm @@ -61,22 +59,19 @@ def run_gridgen(cmd, ws, exe): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.dependency(name="test", depends=["build"]) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression @pytest.mark.parametrize( "cmd", diff --git a/autotest/test_gsflow.py b/autotest/test_gsflow.py new file mode 100644 index 00000000..414e59ec --- /dev/null +++ b/autotest/test_gsflow.py @@ -0,0 +1,83 @@ +import os +from pathlib import Path +from platform import system + +import flopy +import pytest + +import pymake + +# set fpth based on current path +if os.path.basename(os.path.normpath(os.getcwd())) == "autotest": + fpth = Path("temp") +else: + fpth = Path("autotest/temp") +fpth = (fpth / "gsflowexamples/gsflowexamples.txt").resolve() +if fpth.is_file(): + with open(fpth) as f: + lines = f.read().splitlines() + sim_dirs = [line for line in lines if len(line) > 0] +else: + sim_dirs = [] + + +@pytest.fixture(scope="module") +def target(module_tmpdir) -> Path: + name = "gsflow" + ext = ".exe" if system() == "Windows" else "" + return module_tmpdir / f"{name}{ext}" + + +@pytest.fixture(scope="module") +def prog_data(target) -> dict: + return pymake.usgs_program_data.get_target(target.name) + + +@pytest.fixture(scope="module") +def workspace(module_tmpdir, prog_data) -> Path: + return module_tmpdir / prog_data.dirname + + +@pytest.fixture(scope="module") +def pm(module_tmpdir, target) -> pymake.Pymake: + pm = pymake.Pymake(verbose=True) + pm.target = str(target) + pm.appdir = module_tmpdir + pm.makefile = True + pm.makeclean = True + pm.makefiledir = module_tmpdir + pm.inplace = True + pm.networkx = True + pm.verbose = True + yield pm + pm.finalize() + + +@pytest.mark.dependency(name="download") +@pytest.mark.base +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 +def test_compile(pm, target): + assert pm.build() == 0, f"could not compile {target}" + + +@pytest.mark.dependency(name="test", depends=["build"]) +@pytest.mark.regression +@pytest.mark.parametrize("ws", sim_dirs) +def test_gsflow(ws, target): + success, _ = flopy.run_model( + target, + "gsflow.control", + model_ws=ws, + silent=False, + normal_msg=[ + "normal termination", + "Normal completion of GSFLOW", + ], + ) + assert success, f"could not run {ws}" diff --git a/autotest/test_mf2005.py b/autotest/test_mf2005.py index fc7bb6b1..dbf361ea 100644 --- a/autotest/test_mf2005.py +++ b/autotest/test_mf2005.py @@ -6,12 +6,10 @@ import pymake -TARGET_NAME = "mf2005" - @pytest.fixture(scope="module") def target(module_tmpdir) -> Path: - target = TARGET_NAME + target = "mf2005" if sys.platform.lower() == "win32": target += ".exe" return module_tmpdir / target @@ -45,22 +43,19 @@ def run_mf2005(namefile, ws, exe): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.dependency(name="test", depends=["build"]) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression @pytest.mark.parametrize( "namefile", diff --git a/autotest/test_mf6.py b/autotest/test_mf6.py index 2f2e9619..b9470f64 100644 --- a/autotest/test_mf6.py +++ b/autotest/test_mf6.py @@ -10,8 +10,6 @@ import pymake -TARGET_NAME = "mf6" - # set fpth based on current path if os.path.basename(os.path.normpath(os.getcwd())) == "autotest": fpth = Path("temp") @@ -28,7 +26,7 @@ @pytest.fixture(scope="module") def target(module_tmpdir) -> Path: - name = TARGET_NAME + name = "mf6" ext = ".exe" if system() == "Windows" else "" return module_tmpdir / f"{name}{ext}" @@ -70,25 +68,89 @@ def pm(module_tmpdir, target) -> pymake.Pymake: pm.finalize() +def build_with_makefile(pm, workspace, exe): + exe_path = Path(exe) + success = False + with set_dir(workspace): + if os.path.isfile("makefile"): + # wait to delete on windows + if sys.platform.lower() == "win32": + time.sleep(6) + + # clean prior to make + print(f"clean {exe} with makefile") + os.system("make clean") + + # build MODFLOW 6 with makefile + print(f"build {exe} with makefile") + return_code = os.system("make") + + # test if running on Windows with ifort, if True the makefile + # should fail + if sys.platform.lower() == "win32" and pm.fc == "ifort": + if return_code != 0: + success = True + else: + success = False + # verify that target was made + else: + success = exe_path.is_file() + + return success + + @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.dependency(name="test", depends=["build"]) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression @pytest.mark.parametrize("ws", sim_dirs) 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_mf6_existing_meson.py b/autotest/test_mf6_existing_meson.py index 4413c80d..a3bfd895 100644 --- a/autotest/test_mf6_existing_meson.py +++ b/autotest/test_mf6_existing_meson.py @@ -1,24 +1,24 @@ import os import sys from pathlib import Path -from platform import system from typing import List import pytest -from modflow_devtools.misc import set_dir -from modflow_devtools.ostags import get_binary_suffixes import pymake -from pymake import linker_update_environment - -TARGET_NAME = "mf6" @pytest.fixture(scope="module") def targets() -> List[Path]: - target = TARGET_NAME - ext, shared_ext = get_binary_suffixes() + target = "mf6" + ext = "" + shared_ext = ".so" 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 @@ -40,7 +40,6 @@ 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) @@ -50,57 +49,52 @@ def pm(workspace, targets) -> pymake.Pymake: @pytest.mark.base -@pytest.mark.xdist_group(TARGET_NAME) def test_build_with_existing_meson(pm, module_tmpdir, workspace, targets): - with set_dir(module_tmpdir): - # set default compilers - fc, cc = "gfortran", "gcc" - - # get the arguments - for idx, arg in enumerate(sys.argv): - if arg == "-fc": - fc = sys.argv[idx + 1] - elif "-fc=" in arg: - fc = arg.split("=")[1] - if arg == "-cc": - cc = sys.argv[idx + 1] - elif "-cc=" in arg: - cc = arg.split("=")[1] - - # check if fc differs from environmental variable - fc_env = os.environ.get("FC") - if fc_env is not None: - if fc != fc_env: - fc = fc_env - - # check if cc differs from environmental variable - cc_env = os.environ.get("CC") - if cc_env is not None: - if cc != cc_env: - cc = cc_env - - # print fortran and c/c++ compilers - print(f"fortran compiler={fc}\n" + f"c/c++ compiler={cc}\n") - - # download modflow 6 - 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, - 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: - exe_pth = os.path.join(pm.appdir, executable) - assert os.path.isfile(exe_pth), f"{exe_pth} does not exist" + # set default compilers + fc, cc = "gfortran", "gcc" + + # get the arguments + for idx, arg in enumerate(sys.argv): + if arg == "-fc": + fc = sys.argv[idx + 1] + elif "-fc=" in arg: + fc = arg.split("=")[1] + if arg == "-cc": + cc = sys.argv[idx + 1] + elif "-cc=" in arg: + cc = arg.split("=")[1] + + # check if fc differs from environmental variable + fc_env = os.environ.get("FC") + if fc_env is not None: + if fc != fc_env: + fc = fc_env + + # check if cc differs from environmental variable + cc_env = os.environ.get("CC") + if cc_env is not None: + if cc != cc_env: + cc = cc_env + + # print fortran and c/c++ compilers + print(f"fortran compiler={fc}\n" + f"c/c++ compiler={cc}\n") + + # download modflow 6 + pm.download_target(targets[0], download_path=module_tmpdir) + assert pm.download, f"could not download {targets[0]} distribution" + + # 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" + + # check that all of the executables exist + for executable in targets: + exe_pth = os.path.join(pm.appdir, executable) + assert os.path.isfile(exe_pth), f"{exe_pth} does not exist" diff --git a/autotest/test_mflgr.py b/autotest/test_mflgr.py new file mode 100644 index 00000000..1de8c968 --- /dev/null +++ b/autotest/test_mflgr.py @@ -0,0 +1,34 @@ +from pathlib import Path + +import pytest + +import pymake + + +@pytest.fixture(scope="module") +def target(module_tmpdir) -> Path: + target = "mflgr" + return module_tmpdir / target + + +@pytest.fixture(scope="module") +def prog_dict(target) -> dict: + return pymake.usgs_program_data.get_target(target) + + +@pytest.fixture(scope="module") +def workspace(module_tmpdir, prog_dict) -> Path: + return module_tmpdir / prog_dict.dirname + + +def compile_code(ws, exe): + return pymake.build_apps( + str(exe), download_dir=ws, appdir=ws, verbose=True + ) + + +@pytest.mark.base +def test_compile(module_tmpdir, target): + assert ( + compile_code(module_tmpdir, target) == 0 + ), f"could not compile {target}" diff --git a/autotest/test_mfnwt.py b/autotest/test_mfnwt.py new file mode 100644 index 00000000..f7cb8013 --- /dev/null +++ b/autotest/test_mfnwt.py @@ -0,0 +1,91 @@ +import os +import sys +import time +from pathlib import Path + +import pytest +from modflow_devtools.misc import set_dir + +import pymake + + +@pytest.fixture(scope="module") +def target(module_tmpdir) -> str: + target = "mfnwt" + return module_tmpdir / target + + +@pytest.fixture(scope="module") +def prog_data(target) -> dict: + return pymake.usgs_program_data.get_target(target.name) + + +@pytest.fixture(scope="module") +def workspace(module_tmpdir, prog_data) -> Path: + return module_tmpdir / prog_data.dirname + + +@pytest.fixture(scope="module") +def pm(module_tmpdir, target) -> pymake.Pymake: + pm = pymake.Pymake(verbose=True) + pm.target = str(target) + pm.appdir = str(module_tmpdir) + pm.makefile = True + pm.makefiledir = str(module_tmpdir) + pm.inplace = True + pm.dryrun = False + pm.verbose = True + yield pm + pm.finalize() + + +def build_with_makefile(ws): + success = True + with set_dir(ws): + if os.path.isfile("makefile"): + # wait to delete on windows + if sys.platform.lower() == "win32": + time.sleep(6) + + # clean prior to make + print(f"clean {target} with makefile") + os.system("make clean") + + # build MODFLOW-NWT with makefile + print(f"build {target} with makefile") + return_code = os.system("make") + + # test if running on Windows with ifort, if True the makefile + # should fail + errmsg = f"{target} created by makefile does not exist." + if sys.platform.lower() == "win32" and pm.fc == "ifort": + if return_code != 0: + success = True + else: + success = False + # verify that MODFLOW-NWT was made + else: + success = os.path.isfile(target) + else: + errmsg = "makefile does not exist" + + assert success, errmsg + + +@pytest.mark.dependency(name="download") +@pytest.mark.base +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 +def test_compile(pm, target): + assert pm.build() == 0, f"could not compile {target}" + + +@pytest.mark.dependency(name="makefile", depends=["build"]) +@pytest.mark.base +def test_makefile(workspace): + build_with_makefile(workspace) diff --git a/autotest/test_mfusg.py b/autotest/test_mfusg.py index 22fc17c0..0f13c3e3 100644 --- a/autotest/test_mfusg.py +++ b/autotest/test_mfusg.py @@ -68,8 +68,7 @@ def run_mfusg(fn, exe): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group("mfusg") -@pytest.mark.regression +@pytest.mark.base 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]}" @@ -79,8 +78,7 @@ def test_download(pm, pm_gsi, module_tmpdir, targets): @pytest.mark.dependency(name="build", depends=["download"]) -@pytest.mark.xdist_group("mfusg") -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, pm_gsi, targets): assert pm.build() == 0, f"could not compile {targets[0]}" assert (targets[0]).is_file() @@ -89,8 +87,7 @@ def test_compile(pm, pm_gsi, targets): assert targets[1].is_file() -@pytest.mark.dependency(name="test", depends=["download", "build"]) -@pytest.mark.xdist_group("mfusg") +@pytest.mark.dependency(name="test", depends=["build"]) @pytest.mark.regression @pytest.mark.parametrize( "namefile", diff --git a/autotest/test_misc_programs.py b/autotest/test_misc_programs.py new file mode 100644 index 00000000..93d4e30a --- /dev/null +++ b/autotest/test_misc_programs.py @@ -0,0 +1,24 @@ +import pytest + +import pymake + +targets = [ + "crt", + "vs2dt", + "zonbud3", +] + + +@pytest.mark.base +@pytest.mark.parametrize("target", targets) +def test_compile(module_tmpdir, target): + bin_dir = module_tmpdir / "bin" + assert ( + pymake.build_apps( + str(bin_dir / target), + download_dir=str(module_tmpdir), + appdir=str(bin_dir), + verbose=True, + ) + == 0 + ), f"could not compile {target}" diff --git a/autotest/test_mp6.py b/autotest/test_mp6.py index abea072d..51c14522 100644 --- a/autotest/test_mp6.py +++ b/autotest/test_mp6.py @@ -8,12 +8,10 @@ import pymake -TARGET_NAME = "mp6" - @pytest.fixture(scope="module") def target(module_tmpdir) -> Path: - name = TARGET_NAME + name = "mp6" ext = ".exe" if system() == "Windows" else "" return module_tmpdir / f"{name}{ext}" @@ -62,22 +60,19 @@ def update_files(fn, workspace): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {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)] diff --git a/autotest/test_mp7.py b/autotest/test_mp7.py index 80b6fa28..24b1c669 100644 --- a/autotest/test_mp7.py +++ b/autotest/test_mp7.py @@ -10,12 +10,10 @@ ext = ".exe" if system() == "Windows" else "" -TARGET_NAME = "mp7" - @pytest.fixture(scope="module") def target(module_tmpdir): - name = TARGET_NAME + name = "mp7" return module_tmpdir / f"{name}{ext}" @@ -145,22 +143,19 @@ def run_modpath7(namefile, mp7_exe, mf2005_exe, mfusg_exe, mf6_exe): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.dependency(name="download_exes") -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression def test_download_exes(module_tmpdir): pymake.getmfexes( @@ -171,7 +166,6 @@ def test_download_exes(module_tmpdir): @pytest.mark.dependency( name="test", depends=["download", "download_exes", "build"] ) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression @pytest.mark.parametrize( "namefile", diff --git a/autotest/test_mt3dusgs.py b/autotest/test_mt3d.py similarity index 84% rename from autotest/test_mt3dusgs.py rename to autotest/test_mt3d.py index eb589ba5..f9c2ea0b 100644 --- a/autotest/test_mt3dusgs.py +++ b/autotest/test_mt3d.py @@ -1,21 +1,16 @@ import os import sys from pathlib import Path -from platform import system import flopy import pytest import pymake -TARGET_NAME = "mt3dusgs" -EXT = ".exe" if system() == "Windows" else "" - @pytest.fixture(scope="module") def target(module_tmpdir) -> Path: - name = TARGET_NAME - return module_tmpdir / f"{TARGET_NAME}{EXT}" + return module_tmpdir / "mt3dusgs" @pytest.fixture(scope="module") @@ -92,9 +87,22 @@ def run_mt3dusgs(workspace, mt3dms_exe, mfnwt_exe, mf6_exe): return success +@pytest.mark.dependency(name="download_mt3dms") +@pytest.mark.base +def test_download_mt3dms(pm, module_tmpdir): + pm.target = "mt3dms" + pm.download_target(pm.target, download_path=module_tmpdir) + assert pm.download, f"could not download {pm.target} distribution" + + +@pytest.mark.dependency(name="build_mt3dms", depends=["download_mt3dms"]) +@pytest.mark.base +def test_compile_mt3dms(pm): + assert pm.build() == 0, f"could not compile {pm.target}" + + @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_download(pm, module_tmpdir, target): pm.reset(str(target)) pm.download_target(target, download_path=module_tmpdir) @@ -102,23 +110,19 @@ def test_download(pm, module_tmpdir, target): @pytest.mark.dependency(name="build", depends=["download"]) -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.regression -# @pytest.mark.skipif(sys.platform == "darwin", reason="do not run on OSX") -@pytest.mark.skipif(sys.platform == "win32", reason="do not run on Windows") -@pytest.mark.xdist_group(TARGET_NAME) +@pytest.mark.skipif(sys.platform == "darwin", reason="do not run on OSX") def test_download_exes(module_tmpdir): pymake.getmfexes(module_tmpdir, exes=("mfnwt", "mf6"), verbose=True) @pytest.mark.regression -@pytest.mark.xdist_group(TARGET_NAME) -# @pytest.mark.skipif(sys.platform == "darwin", reason="do not run on OSX") +@pytest.mark.skipif(sys.platform == "darwin", reason="do not run on OSX") @pytest.mark.skipif(sys.platform == "win32", reason="do not run on Windows") @pytest.mark.parametrize( "ws", diff --git a/autotest/test_seawat.py b/autotest/test_seawat.py index d20183f1..1dfbd431 100644 --- a/autotest/test_seawat.py +++ b/autotest/test_seawat.py @@ -9,12 +9,10 @@ import pymake -TARGET_NAME = "swtv4" - @pytest.fixture(scope="module") def target(module_tmpdir) -> Path: - name = TARGET_NAME + name = "swtv4" ext = ".exe" if system() == "Windows" else "" return module_tmpdir / f"{name}{ext}" @@ -78,22 +76,19 @@ def build_seawat_dependency_graphs(src_path, dep_path): @pytest.mark.dependency(name="download") -@pytest.mark.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base 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.xdist_group(TARGET_NAME) -@pytest.mark.regression +@pytest.mark.base def test_compile(pm, target): assert pm.build() == 0, f"could not compile {target}" @pytest.mark.dependency(name="test", depends=["build"]) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression @pytest.mark.parametrize( "namefile", @@ -127,7 +122,6 @@ def test_seawat(namefile, workspace, target): @pytest.mark.dependency(name="graph", depends=["test"]) -@pytest.mark.xdist_group(TARGET_NAME) @pytest.mark.regression def test_dependency_graphs(workspace, prog_data): src_path = workspace / prog_data.srcdir diff --git a/autotest/test_triangle_makefile.py b/autotest/test_triangle_makefile.py new file mode 100644 index 00000000..45579d87 --- /dev/null +++ b/autotest/test_triangle_makefile.py @@ -0,0 +1,69 @@ +import os +import sys + +import flopy +import pytest + +import pymake + + +@pytest.mark.base +def test_pymake_makefile(module_tmpdir): + target = "triangle" + pm = pymake.Pymake(verbose=True) + pm.makefile = True + pm.makeclean = True + # pm.cc = "gcc" + + if sys.platform.lower() == "win32": + if pm.cc == "icl": + return + target += ".exe" + + # get current directory + cwd = os.getcwd() + + # change to working directory so triangle download directory is + # a subdirectory in the working directory + os.chdir(module_tmpdir) + + # build triangle and makefile + assert ( + pymake.build_apps(target, clean=False, pymake_object=pm) == 0 + ), f"could not build {target}" + + if os.path.isfile(os.path.join(module_tmpdir, "makefile")): + print("cleaning with GNU make") + # clean prior to make + print(f"clean {target} with makefile") + success, _ = flopy.run_model( + "make", + None, + cargs="clean", + model_ws=module_tmpdir, + report=True, + normal_msg="rm -rf ./triangle", + silent=False, + ) + + # build triangle with makefile + if success: + print(f"build {target} with makefile") + success, _ = flopy.run_model( + "make", + None, + model_ws=module_tmpdir, + report=True, + normal_msg="cc -O2 -o triangle ./obj_temp/triangle.o", + silent=False, + ) + + # finalize Pymake object + pm.finalize() + + # return to starting directory + os.chdir(cwd) + + assert os.path.isfile( + os.path.join(module_tmpdir, target) + ), f"could not build {target} with makefile" diff --git a/docs/build_apps.md b/docs/build_apps.md index f5c329ad..12b15b90 100644 --- a/docs/build_apps.md +++ b/docs/build_apps.md @@ -7,34 +7,53 @@ and options can be determined by executing: ```console $ make-program --help -usage: make-program [-h] [-fc {ifort,mpiifort,gfortran,none}] [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}] [-dbl] [-dr] [-ff FFLAGS] [-cf CFLAGS] [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--meson] +usage: make-program [-h] [--release_precision] + [-fc {ifort,mpiifort,gfortran,none}] + [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}] [-dr] + [-ff FFLAGS] [-cf CFLAGS] [-ad APPDIR] [-v] [--keep] + [--zip ZIP] [--meson] targets Download and build USGS MODFLOW and related programs. positional arguments: - targets Program(s) to build. Options: crt, gridgen, libmf6, mf2000, mf2005, mf6, mflgr, mfnwt, mfusg, mfusg_gsi, mp6, mp7, mt3dms, mt3dusgs, sutra, swtv4, triangle, vs2dt, zbud6, zonbud3, - zonbudusg, :. Specifying the target to be ':' will build all of the programs. Multiple targets can be specified by separating individual targets by a comma (i.e., mf6,zbud6). + targets Program(s) to build. Options: crt, gridgen, libmf6, + mf2000, mf2005, mf6, mflgr, mfnwt, mfusg, mfusg_gsi, + mp6, mp7, mt3dms, mt3dusgs, sutra, swtv4, triangle, + vs2dt, zbud6, zonbud3, zonbudusg, :. Specifying the + target to be ':' will build all of the programs. -options: +optional arguments: -h, --help show this help message and exit + --release_precision If release_precision is False, then the release + precision version will be compiled along with a double + precision version of the program for programs where + the standard_switch and double_switch in + usgsprograms.txt is True. default is True. -fc {ifort,mpiifort,gfortran,none} Fortran compiler to use. (default is gfortran) -cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none} C/C++ compiler to use. (default is gcc) - -dbl, --double Force double precision. (default is False) - -dr, --dryrun Do not actually compile. Files will be deleted, if --makeclean is used. Does not work yet for ifort. (default is False) + -dr, --dryrun Do not actually compile. Files will be deleted, if + --makeclean is used. Does not work yet for ifort. + (default is False) -ff FFLAGS, --fflags FFLAGS - Additional Fortran compiler flags. Fortran compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-ff or --fflags) with a equal sign - (-ff='-O3'). (default is None) + Additional Fortran compiler flags. Fortran compiler + flags should be enclosed in quotes and start with a + blank space or separated from the name (-ff or + --fflags) with a equal sign (-ff='-O3'). (default is + None) -cf CFLAGS, --cflags CFLAGS - Additional C/C++ compiler flags. C/C++ compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-cf or --cflags) with a equal sign - (-cf='-O3'). (default is None) + Additional C/C++ compiler flags. C/C++ compiler flags + should be enclosed in quotes and start with a blank + space or separated from the name (-cf or --cflags) + with a equal sign (-cf='-O3'). (default is None) -ad APPDIR, --appdir APPDIR - Target path that overides path defined target path (default is None) + Target path that overides path defined target path + (default is None) -v, --verbose Verbose output to terminal. (default is False) --keep Keep existing executable. (default is False) - --zip ZIP Zip built executable. (default is None) + --zip ZIP Zip built executable. (default is False) --meson Use meson to build executable. (default is False) Examples: @@ -45,9 +64,6 @@ Examples: Download and compile triangle in the ./temp subdirectory: $ make-program triangle --appdir temp - Download and compile double precision versions of mf2005 and mfusg - $ make-program mf2005,mfusg --double - Download and compile all programs in the ./temp subdirectory: $ make-program : --appdir temp diff --git a/docs/index.rst b/docs/index.rst index 9fa2d6d8..2e520c87 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,7 +17,7 @@ programs released by the USGS. pymake includes example scripts for building MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, MODFLOW-LGR, MODFLOW-2000, MODPATH 6, MODPATH 7, -VS2DT, MT3DMS, MT3D-USGS, SEAWAT, and SUTRA. Example scripts for +GSFLOW, VS2DT, MT3DMS, MT3D-USGS, SEAWAT, and SUTRA. Example scripts for creating the utility programs CRT, Triangle, and GRIDGEN are also included. The scripts download the distribution file from the USGS (and other organizations) and compile the source into a binary executable. diff --git a/docs/installation.md b/docs/installation.md index 6775b1f8..ad7f101e 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -6,13 +6,13 @@ To install a stable version from PyPI: pip install mfpymake ``` -To install the latest pymake release directly from the git repository type: +To install pymake directly from the git repository type: ``` pip install https://github.com/modflowpy/pymake/zipball/master ``` -To update your version of pymake with the latest development version from the git repository type: +To update your version of pymake with the latest from the git repository type: ``` -pip install https://github.com/modflowpy/pymake/zipball/develop --upgrade +pip install https://github.com/modflowpy/pymake/zipball/master --upgrade diff --git a/pixi.lock b/pixi.lock deleted file mode 100644 index 692465a6..00000000 --- a/pixi.lock +++ /dev/null @@ -1,10491 +0,0 @@ -version: 4 -environments: - 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-[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 ." -check-format = "ruff format . --check" -fix-style = "ruff check . --fix; 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=loadgroup -m='base or regression' --durations 0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } -autotest-base = { cmd = "pytest -v -n auto --dist=loadgroup -m='base' --durations 0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } -autotest-request = { cmd = "pytest -v -n=auto -m='requests' --durations=0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } -autotest-schedule = { cmd = "pytest -v -m='schedule' --durations=0 --cov=pymake --cov-report=xml --keep-failed .failed", cwd = "autotest" } - -# coverage report -coverage-report = { cmd = "coverage report", cwd = "autotest"} - -# release -update-version = { cmd = "python scripts/update_version.py -v"} diff --git a/pymake/__init__.py b/pymake/__init__.py index d9926a62..969ad52b 100644 --- a/pymake/__init__.py +++ b/pymake/__init__.py @@ -21,7 +21,6 @@ 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/cmds/build.py b/pymake/cmds/build.py index 3a8a82ab..7d2a7234 100755 --- a/pymake/cmds/build.py +++ b/pymake/cmds/build.py @@ -4,7 +4,6 @@ This script originates from pymake: https://github.com/modflowpy/pymake It requires Python 3.6 or later, and has no dependencies. """ - import sys from pathlib import Path @@ -18,33 +17,27 @@ "targets", "appdir", "verbose", + "release_precision", "fc", "cc", "fflags", "cflags", - "double", "verbose", "zip", "keep", "dryrun", "meson", ) - -# command arguments (sys.argv) to pop from ARGS COM_ARG_KEYS = ( "fc", "cc", "fflags", "cflags", - "double", "zip", "keep", "dryrun", ) -# ARGS to keep and pass to build_apps() -KEEP_ARG_KEYS = ("double",) - def main() -> None: """Command line interface @@ -67,9 +60,6 @@ def main() -> None: Download and compile triangle in the ./temp subdirectory: $ {prog} triangle --appdir temp - Download and compile double precision versions of mf2005 and mfusg - $ {prog} mf2005,mfusg --double - Download and compile all programs in the ./temp subdirectory: $ {prog} : --appdir temp """ @@ -85,8 +75,16 @@ def main() -> None: "Program(s) to build. Options:\n " + ", ".join(all_targets) + ". Specifying the target to be ':' will " - + "build all of the programs. Multiple targets can be specified " - + "by separating individual targets by a comma (i.e., mf6,zbud6)." + + "build all of the programs." + ) + + release_precision_help = ( + "If release_precision is False, then the " + + "release precision version will be compiled " + + "along with a double precision version of " + + "the program for programs where the standard_" + + "switch and double_switch in " + + "usgsprograms.txt is True. default is True." ) # command line arguments specific to make-program @@ -98,6 +96,13 @@ def main() -> None: "choices": None, "action": None, }, + "release_precision": { + "tag": ("--release_precision",), + "help": release_precision_help, + "default": False, + "choices": None, + "action": "store_true", + }, } # add standard command line arguments to parser dictionary for make-program @@ -133,8 +138,7 @@ def main() -> None: # delete arguments that are used by Pymake() class in build_apps for key in arg_key_pop: - if key not in KEEP_ARG_KEYS: - del args[key] + del args[key] # remove args from command line arguments for key in com_arg_pop: diff --git a/pymake/cmds/createjson.py b/pymake/cmds/createjson.py index 97d13439..e82c9483 100755 --- a/pymake/cmds/createjson.py +++ b/pymake/cmds/createjson.py @@ -4,7 +4,6 @@ This script originates from pymake: https://github.com/modflowpy/pymake It requires Python 3.6 or later, and has no dependencies. """ - import sys from pathlib import Path @@ -56,14 +55,6 @@ def main() -> None: "choices": None, "action": None, }, - "appdir": { - "tag": ("-ad", "--appdir"), - "help": "code.json path that overides FPTH defined path, " - + "Default is None.", - "default": None, - "choices": None, - "action": None, - }, "prog_data": { "tag": ("--prog_data",), "help": "User-specified program database. If prog_data is None, " @@ -105,29 +96,12 @@ def main() -> None: "choices": None, "action": "store_true", }, - "partial_json": { - "tag": ("--partial_json",), - "help": "Create a partial code.json based on targets in the " - + "parent path for the code.json file (FPTH). " - + "Default is False.", - "default": False, - "choices": None, - "action": "store_true", - }, - "zip": { - "tag": ("--zip",), - "help": "Zip code.json into ZIP. (default is None)", - "default": None, - "choices": None, - "action": None, - "type": (str, Path), - }, "verbose": { "tag": ( "-v", "--verbose", ), - "help": "Verbose output to terminal. Default is False.", + "help": "boolean for verbose output to terminal. Default is True.", "default": False, "choices": None, "action": "store_true", @@ -142,10 +116,6 @@ def main() -> None: # define args args = vars(parser_args) - # clean up zip argument in args - args["zip_path"] = args["zip"] - del args["zip"] - # run build_apps try: usgs_program_data.export_json(**args) diff --git a/pymake/cmds/mfpymakecli.py b/pymake/cmds/mfpymakecli.py index bd2150c9..3ec5fd0d 100755 --- a/pymake/cmds/mfpymakecli.py +++ b/pymake/cmds/mfpymakecli.py @@ -4,7 +4,6 @@ This script originates from pymake: https://github.com/modflowpy/pymake It requires Python 3.6 or later, and has no dependencies. """ - import sys from pathlib import Path diff --git a/pymake/config.py b/pymake/config.py index bd41d211..b1f377ab 100644 --- a/pymake/config.py +++ b/pymake/config.py @@ -1,12 +1,6 @@ -# mfpymake version file automatically created using -# update_version.py on June 17, 2024 00:23:05 - -# mfpymake version file automatically created using -# update_version.py on June 16, 2024 18:36:44 - __author__ = "Joseph D. Hughes" -__date__ = "June 17, 2024" -__version__ = "1.2.10" +__date__ = "February 11, 2024" +__version__ = "1.2.9" __maintainer__ = "Joseph D. Hughes" __email__ = "jdhughes@usgs.gov" __status__ = "Production" diff --git a/pymake/pymake.py b/pymake/pymake.py index 31d9829a..ac84737c 100644 --- a/pymake/pymake.py +++ b/pymake/pymake.py @@ -54,11 +54,9 @@ import argparse import os -import pathlib as pl import shutil import sys import time -from zipfile import ZipFile from .config import __description__ from .pymake_base import main @@ -258,57 +256,29 @@ def compress_targets(self): targets.append(target) # add code.json - if pl.Path("code.json").exists(): - if "code.json" not in targets: - targets.append("code.json") + if "code.json" not in targets: + targets.append("code.json") # delete the zip file if it exists if os.path.exists(zip_pth): - if self.keep: - if self.verbose: - print( - "Appending files to existing " - + f"zipfile '{pl.Path(zip_pth).resolve()}'" - ) - with ZipFile( - zip_pth, - mode="r", - ) as zf: - available_file_paths = zf.namelist() - pop_list = [] - for target in targets: - for temp_path in available_file_paths: - if target == temp_path: - pop_list.append(target) - break - for target in pop_list: - targets.remove(target) - else: - if self.verbose: - print( - "Deleting existing zipfile " - + f"'{pl.Path(zip_pth).resolve()}'" - ) - os.remove(zip_pth) + if self.verbose: + msg = f"Deleting existing zipfile '{zip_pth}'" + print(msg) + os.remove(zip_pth) # print a message describing the zip process if self.verbose: - print( + msg = ( f"Compressing files in '{appdir}' " - + f"directory to zip file '{pl.Path(zip_pth).resolve()}'" + + f"directory to zip file '{zip_pth}'" ) + print(msg) for idx, target in enumerate(targets): - print( - f" {idx + 1:>3d}. adding " + f"'{target}' to zipfile" - ) + msg = f" {idx + 1:>3d}. adding " + f"'{target}' to zipfile" + print(msg) # compress the compiled executables - if not zip_all( - zip_pth, - dir_pths=appdir, - patterns=targets, - append=self.keep, - ): + if not zip_all(zip_pth, dir_pths=appdir, patterns=targets): self.returncode = 1 return @@ -503,6 +473,8 @@ def _set_include_subdirs(self): "libmf6", "gridgen", "mf6beta", + "gsflow", + "prms", ): self.include_subdirs = True else: @@ -620,7 +592,6 @@ def _set_extrafiles(self): if extrafiles is None: if self._get_base_target() in ("zbud6",): extrafiles = [ - "../../../src/Utilities/CharString.f90", "../../../src/Utilities/ArrayHandlers.f90", "../../../src/Utilities/ArrayReaders.f90", "../../../src/Utilities/BlockParser.f90", diff --git a/pymake/pymake_base.py b/pymake/pymake_base.py index 08da4817..1a1a282b 100644 --- a/pymake/pymake_base.py +++ b/pymake/pymake_base.py @@ -1192,7 +1192,8 @@ def _create_win_batch( # open the batch file f = open(batchfile, "w") - # only write the command to batchfile if env vars aren't already configured + # only write the compilervars batch command to batchfile if env vars aren't already configured + # https://www.intel.com/content/www/us/en/develop/documentation/oneapi-programming-guide/top/oneapi-development-environment-setup/use-the-setvars-script-with-windows.html if os.environ.get("SETVARS_COMPLETED") != "1": line = "call " + intel_setvars + "\n" f.write(line) diff --git a/pymake/pymake_build_apps.py b/pymake/pymake_build_apps.py index 2feb2312..a76e526f 100644 --- a/pymake/pymake_build_apps.py +++ b/pymake/pymake_build_apps.py @@ -41,7 +41,7 @@ def build_apps( download_dir=None, appdir=None, verbose=None, - double=False, + release_precision=True, meson=False, mesondir=".", clean=True, @@ -52,15 +52,19 @@ def build_apps( ---------- targets : str or list of str targets to build. If targets is None, all current targets will - be built. Default is None + be build. Default is None pymake_object : Pymake() Pymake object created outside of build_apps download_dir : str download directory path appdir : str target path - double : bool - force double precision. (default is False) + release_precision : bool + boolean indicating if only the release precision version should be + build. If release_precision is False, then the release precision + version will be compiled along with a double precision version of + the program for programs where the standard_switch and double_switch + in usgsprograms.txt is True. default is True. meson : bool boolean indicating that the executable should be built using the meson build system. (default is False) @@ -88,7 +92,7 @@ def build_apps( targets = usgs_program_data.get_keys(current=True) else: if isinstance(targets, str): - targets = targets.split(",") + targets = [targets] code_dict = {} @@ -205,6 +209,11 @@ def build_apps( download_verify = True timeout = 30 + # reset meson + if target in ("prms",): + pmobj.meson = True + pmobj.inplace = True + # set target and srcdir pmobj.target = target.replace("dev", "") pmobj.srcdir = os.path.join( @@ -212,19 +221,16 @@ def build_apps( ) # determine if single, double, or both should be built - prog_precision = usgs_program_data.get_precision(target) + precision = usgs_program_data.get_precision(target) # just build the first precision in precision list if - # reset prog_precision if double - if double: - prog_precision = ["double"] + # standard_precision is True + if release_precision: + precision = precision[0:1] - for precision_str in prog_precision: + for double in precision: # set double flag - if precision_str == "double": - pmobj.double = True - else: - pmobj.double = False + pmobj.double = double # determine if the target should be built build_target = pmobj.set_build_target_bool( diff --git a/pymake/pymake_parser.py b/pymake/pymake_parser.py index 33f1b129..a9425ba8 100644 --- a/pymake/pymake_parser.py +++ b/pymake/pymake_parser.py @@ -232,7 +232,7 @@ def _get_standard_arg_dict(): }, "zip": { "tag": ("--zip",), - "help": "Zip built executable. (default is None)", + "help": "Zip built executable. (default is False)", "default": None, "choices": None, "action": None, diff --git a/pymake/utils/_Popen_wrapper.py b/pymake/utils/_Popen_wrapper.py index 18eb8df1..e9d2a151 100644 --- a/pymake/utils/_Popen_wrapper.py +++ b/pymake/utils/_Popen_wrapper.py @@ -1,4 +1,6 @@ -"""Private functions for running pymake commands using Popen""" +"""Private functions for running pymake commands using Popen + +""" import sys from subprocess import PIPE, STDOUT, Popen diff --git a/pymake/utils/_compiler_language_files.py b/pymake/utils/_compiler_language_files.py index c2d3fe26..bc510881 100644 --- a/pymake/utils/_compiler_language_files.py +++ b/pymake/utils/_compiler_language_files.py @@ -1,4 +1,5 @@ -"""Private functions for processing c/c++ and fortran files""" +"""Private functions for processing c/c++ and fortran files +""" import os diff --git a/pymake/utils/_compiler_switches.py b/pymake/utils/_compiler_switches.py index d19eff4c..21c7ad74 100644 --- a/pymake/utils/_compiler_switches.py +++ b/pymake/utils/_compiler_switches.py @@ -1,10 +1,9 @@ -"""Public and private functions for setting c/c++ and fortran compiler -flags and appropriate linker flags for defined targets. +"""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, @@ -18,28 +17,6 @@ ) -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'. @@ -362,6 +339,9 @@ def _get_fortran_flags( "fpe:0", "traceback", "nologo", + "Qdiag-disable:7416", + "Qdiag-disable:7025", + "Qdiag-disable:5268", ] if debug: flags += ["debug:full", "Zi"] @@ -804,6 +784,25 @@ def _set_fflags(target, fc="gfortran", argv=True, osname=None, verbose=False): if target == "mp7": if fc == "gfortran": fflags.append("-ffree-line-length-512") + elif target in ("gsflow", "prms"): + if fc == "ifort": + if osname == "win32": + fflags += [ + "-fp:source", + "-names:lowercase", + "-assume:underscore", + ] + else: + pass + elif fc == "gfortran": + fflags += ["-O1", "-fno-second-underscore"] + opt = "-fallow-argument-mismatch" + if _check_gnu_switch_available( + opt, compiler=fc, verbose=verbose + ): + fflags += [ + opt, + ] elif target in ( "mf2000", "mt3dms", @@ -903,6 +902,17 @@ def _set_cflags(target, cc="gcc", argv=True, osname=None, verbose=False): cflags += ["-lm"] else: cflags += ["-DNO_TIMER"] + elif target in ( + "gsflow", + "prms", + ): + if cc in ["icc", "icpl", "icl"]: + if osname == "win32": + cflags += ["-D_CRT_SECURE_NO_WARNINGS"] + else: + cflags += ["-D_UF"] + elif cc == "gcc": + cflags += ["-O1"] # add additional cflags from the command line if argv: @@ -994,10 +1004,6 @@ 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"): @@ -1010,6 +1016,10 @@ def _set_syslibs( lcc = True if lfc and lcc: syslibs += ["-lm"] + elif target in ("gsflow", "prms"): + if "win32" not in osname: + if "ifort" in fc: + syslibs += ["-nofor_main"] # add additional syslibs from the command line if argv: @@ -1060,46 +1070,3 @@ 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/pymake/utils/_usgs_src_update.py b/pymake/utils/_usgs_src_update.py index fbd1752b..0bca9acc 100644 --- a/pymake/utils/_usgs_src_update.py +++ b/pymake/utils/_usgs_src_update.py @@ -10,8 +10,6 @@ import types from typing import Union -from ..utils.usgsprograms import usgs_program_data - def _get_function_names(module, select_name=None): """Get a dictionary of functions available in a user-specified source file. @@ -65,13 +63,9 @@ def _build_replace(targets): if isinstance(targets, str): targets = [targets] - # remove exe extension from targets, as well as - # d (debug) and dbl (double precision) suffixes + # remove exe extension from targets for idx, target in enumerate(targets): - tgt = pl.Path(target).with_suffix("").name.replace("dbl", "") - if tgt.endswith("d") and tgt[:-1] in usgs_program_data.get_keys(): - tgt = tgt[:-1] - targets[idx] = tgt + targets[idx] = pl.Path(target).with_suffix("").name # get a dictionary of update functions funcs = _get_function_names(sys.modules[__name__], select_name="_update_") @@ -346,14 +340,14 @@ def _update_mfusg_gsi_files(srcdir, fc, cc, arch, double): """ tags = { - "FMTARG = 'BINARY'": "FMTARG = 'UNFORMATTED'\n ACCARG = 'STREAM'", # noqa: E501 + "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'", # noqa: E501 + "FORM='FORMATTED',ACCESS='SEQUENTIAL',": "FORM='FORMATTED',ACCESS='SEQUENTIAL'", } fpth = pl.Path(srcdir) / "glo2basu1.f" @@ -468,6 +462,114 @@ def _update_mfnwt_files(srcdir, fc, cc, arch, double): _update_swi(srcdir, double) +def _update_prms_files(srcdir, fc, cc, arch, double): + """Update PRMS source files + + 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 + ------- + + """ + # remove existing *.mod, *.o, and *.a (if any are left) files + dpths = [ + os.path.join(srcdir, o) + for o in os.listdir(srcdir) + if os.path.isdir(os.path.join(srcdir, o)) + ] + + for dpth in dpths: + for f in os.listdir(dpth): + ext = os.path.splitext(f)[1] + fpth = os.path.join(dpth, f) + if ext in [".mod", ".o", ".a"]: + os.remove(fpth) + + # remove specific files + fpths = ( + os.path.join(srcdir, "prms", "gsflow_module.f90"), + os.path.join(srcdir, "prms", "gsflow_prms.f90"), + ) + for fpth in fpths: + if os.path.isfile(fpth): + os.remove(fpth) + + return + + +def _update_gsflow_files(srcdir, fc, cc, arch, double): + """Update GSFLOW source files + + 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 utl7.f + _update_utl7(srcdir) + + # update gwf2swt7.f + _update_swt(srcdir) + + # update gwf2swi27.f or gwf2swi27.fpp + _update_swi(srcdir, double) + + # remove merge and lib directories + pths = [os.path.join(srcdir, "merge"), os.path.join(srcdir, "lib")] + for pth in pths: + if os.path.isdir(pth): + shutil.rmtree(pth) + + # remove existing *.mod, *.o, and *.a (if any are left) files + dpths = [ + os.path.join(srcdir, o) + for o in os.listdir(srcdir) + if os.path.isdir(os.path.join(srcdir, o)) + ] + + for dpth in dpths: + for f in os.listdir(dpth): + ext = os.path.splitext(f)[1] + fpth = os.path.join(dpth, f) + if ext in [".mod", ".o", ".a"]: + os.remove(fpth) + + # remove specific files + fpths = [ + os.path.join(srcdir, "modflow", "gwf2ag1_NWT_rsr.f"), + ] + for fpth in fpths: + if os.path.isfile(fpth): + os.remove(fpth) + + return + + def _update_mf2000_files(srcdir, fc, cc, arch, double): """Update MODFLOW-2000 source files @@ -785,8 +887,6 @@ def _update_mf6_external_dependencies( "Distributed/MpiRunControl.F90", "Distributed/MpiWorld.f90", "Solution/ParallelSolution.f90", - "Distributed/MpiUnitCache.f90", - "Distributed/MpiMessageCache.f90", ) for file in parallel_files: path = srcdir / file diff --git a/pymake/utils/download.py b/pymake/utils/download.py index ea6d9215..c11df28e 100644 --- a/pymake/utils/download.py +++ b/pymake/utils/download.py @@ -95,13 +95,7 @@ def extractall(self, path=None, members=None, pwd=None): self.extract(zipinfo, path, pwd) @staticmethod - def compressall( - path, - file_pths=None, - dir_pths=None, - patterns=None, - append=False, - ): + def compressall(path, file_pths=None, dir_pths=None, patterns=None): """Compress selected files or files in selected directories. Parameters @@ -114,9 +108,6 @@ def compressall( directory paths to include in the output zip file (default is None) patterns : str or list of str file patterns to include in the output zip file (default is None) - append : bool - boolean indicating if file paths should be appended to an existing - zip file Returns ------- @@ -168,19 +159,21 @@ def compressall( tlist.append(file_pth) file_pths = tlist - if append and pl.Path(path).exists(): - mode = "a" - else: - mode = "w" - + # write the zipfile success = True if len(file_pths) > 0: - with ZipFile(path, mode=mode, compression=ZIP_DEFLATED) as zf: - for file_pth in file_pths: - arcname = os.path.basename(file_pth) - zf.write(file_pth, arcname=arcname) + zf = ZipFile(path, "w", ZIP_DEFLATED) + + # write files to zip file + for file_pth in file_pths: + arcname = os.path.basename(file_pth) + zf.write(file_pth, arcname=arcname) + + # close the zip file + zf.close() else: - print("No files to add to the zip file") + msg = "No files to add to the zip file" + print(msg) success = False return success @@ -478,13 +471,7 @@ def download_and_unzip( return success -def zip_all( - path, - file_pths=None, - dir_pths=None, - patterns=None, - append=False, -): +def zip_all(path, file_pths=None, dir_pths=None, patterns=None): """Compress all files in the user-provided list of file paths and directory paths that match the provided file patterns. @@ -500,20 +487,13 @@ def zip_all( patterns : str or list file pattern or list of file patterns s to match to when creating a list of files that will be compressed - append : bool - boolean indicating if file paths should be appended to an existing - zip file Returns ------- """ return pymakeZipFile.compressall( - path, - file_pths=file_pths, - dir_pths=dir_pths, - patterns=patterns, - append=append, + path, file_pths=file_pths, dir_pths=dir_pths, patterns=patterns ) diff --git a/pymake/utils/usgsprograms.py b/pymake/utils/usgsprograms.py index 9e6f6baf..23bfba62 100644 --- a/pymake/utils/usgsprograms.py +++ b/pymake/utils/usgsprograms.py @@ -25,7 +25,7 @@ import pathlib as pl import sys -from .download import _request_header, zip_all +from .download import _request_header class dotdict(dict): @@ -248,9 +248,9 @@ def get_precision(key): target = usgs_program_data().get_target(key) precision = [] if target.standard_switch: - precision.append("default") + precision.append(False) if target.double_switch: - precision.append("double") + precision.append(True) return precision @staticmethod @@ -298,13 +298,10 @@ def list_targets(current=False): @staticmethod def export_json( fpth="code.json", - appdir=None, prog_data=None, current=False, update=True, write_markdown=False, - partial_json=False, - zip_path=None, verbose=False, ): """Export USGS program data as a json file. @@ -313,9 +310,6 @@ def export_json( ---------- fpth : str Path for the json file to be created. Default is "code.json" - appdir : str - path for code.json. Overides code.json path defined in fpth. - Default is None. prog_data : dict User-specified program database. If prog_data is None, it will be created from the USGS program database @@ -332,11 +326,6 @@ def export_json( If True, write markdown file that includes the target name, version, and the last-modified date of the download asset (url). Default is False. - partial_json : bool - Create a partial code.json based on targets in the parent path - for the code.json file. Default is False. - zip_path : str - Zip code.json into zip_path. (default is None) verbose : bool boolean for verbose output to terminal @@ -361,20 +350,15 @@ def export_json( print(f" {idx + 1:>2d}: {key}") # process the passed file path into appdir and file_name - if appdir is None: - appdir = pl.Path(".") - file_name = pl.Path(fpth) - if file_name.parent != str(appdir): - appdir = file_name.parent - file_name = file_name.name - else: - for idx, argv in enumerate(sys.argv): - if argv in ("--appdir", "-ad"): - appdir = pl.Path(sys.argv[idx + 1]) + appdir = pl.Path(".") + file_name = pl.Path(fpth) + if file_name.parent != str(appdir): + appdir = file_name.parent + file_name = file_name.name else: - if isinstance(appdir, str): - appdir = pl.Path(appdir) - file_name = pl.Path(fpth).name + for idx, argv in enumerate(sys.argv): + if argv in ("--appdir", "-ad"): + appdir = pl.Path(sys.argv[idx + 1]) if str(appdir) != ".": appdir.mkdir(parents=True, exist_ok=True) @@ -416,41 +400,12 @@ def export_json( tzinfo=datetime.timezone.utc ) datetime_str = datetime_obj_utc.strftime("%m/%d/%Y") - prog_data[target]["url_download_asset_date"] = ( - datetime_str - ) + prog_data[target][ + "url_download_asset_date" + ] = datetime_str break - if partial_json: - # find targets in appdir - found_targets = [] - for appdir_file in pl.Path(appdir).iterdir(): - temp_target = appdir_file.stem - if temp_target.endswith("dbl"): - temp_target = temp_target.replace("dbl", "") - if temp_target in prog_data.keys(): - if temp_target not in found_targets: - found_targets.append(temp_target) - - # determine which targets to remove - pop_list = [] - for target in prog_data.keys(): - if target not in found_targets: - pop_list.append(target) - - # remove unused targets - for target in pop_list: - del prog_data[target] - - # update double_switch based on executables in appdir - for appdir_file in pl.Path(appdir).iterdir(): - temp_target = appdir_file.stem - if temp_target.endswith("dbl"): - temp_target = temp_target.replace("dbl", "") - if temp_target in prog_data.keys(): - prog_data[temp_target]["double_switch"] = True - - # write code.json to root directory - used by executables CI + # export file try: with open(file_name, "w") as file_obj: json.dump(prog_data, file_obj, indent=4, sort_keys=True) @@ -458,7 +413,7 @@ def export_json( msg = f'could not export json file "{file_name}"' raise IOError(msg) - # write code.json if appdir is not the root directory + # write code.json if str(appdir) != ".": dst = appdir / file_name with open(dst, "w") as file_obj: @@ -485,20 +440,6 @@ def export_json( line += "\n" file_obj.write(line) - # zip code.json - if prog_data is not None and zip_path is not None: - if verbose: - print( - "Compressing code.json to " - + f"zipfile '{pl.Path(zip_path).resolve()}'" - ) - zip_all( - zip_path, - dir_pths=appdir, - patterns=["code.json"], - append=True, - ) - return @staticmethod diff --git a/pymake/utils/usgsprograms.txt b/pymake/utils/usgsprograms.txt index cef494ab..4af573dc 100644 --- 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 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , src , True , False , False -zbud6 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , utils/zonebudget/src, True , False , False -libmf6 , 6.5.0 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.5.0/mf6.5.0_linux.zip , mf6.5.0_linux , srcbmi , True , False , True +mf6 , 6.4.3 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip , mf6.4.3_linux , src , True , False , False +zbud6 , 6.4.3 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip , mf6.4.3_linux , utils/zonebudget/src, True , False , False +libmf6 , 6.4.3 , True , https://github.com/MODFLOW-USGS/modflow6/releases/download/6.4.3/mf6.4.3_linux.zip , mf6.4.3_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://github.com/MODFLOW-USGS/mt3dms/releases/download/2.0/mt3dms-2.0.zip , mt3dms-2.0 , 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 @@ -16,11 +16,12 @@ mfusg , 1.5 , True , https://water.usgs.gov/water-resources/software zonbudusg , 1.5 , True , https://water.usgs.gov/water-resources/software/MODFLOW-USG/mfusg1_5.zip , mfusg1_5 , src/zonebudusg , True , False , False swtv4 , 4.00.05, True , https://water.usgs.gov/water-resources/software/SEAWAT/swt_v4_00_05.zip , swt_v4_00_05 , source , False , True , False 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 , 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 , False , 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 , False , False -mfusg_gsi , 2.3.0 , True , https://www.gsienv.com/wp-content/uploads/2024/03/USG-Transport_Version-2.3.0.zip , USGT-v2-3-0-Source , . , True , False , False -mf6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , src , True , False , False -zbud6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , utils/zonebudget/src, True , False , False -libmf6dev , 6.6.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , srcbmi , True , False , True \ No newline at end of file +mfusg_gsi , 2.2.2 , True , https://www.gsienv.com/wp-content/uploads/2023/11/USG-Transport_Version-2.2.2.zip , USGT-v2-2-2-Source , . , True , False , False +gsflow , 2.2.1 , True , https://water.usgs.gov/water-resources/software/gsflow/gsflow_2.2.1_linux.zip , gsflow_2.2.1 , src , True , False , False +mf6dev , 6.5.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , src , True , False , False +zbud6dev , 6.5.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , utils/zonebudget/src, True , False , False +libmf6dev , 6.5.0.dev0 , False , https://github.com/MODFLOW-USGS/modflow6/archive/refs/heads/develop.zip , modflow6-develop , srcbmi , True , False , True \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index db989452..5b30fda8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ requires-python = ">=3.8" dependencies = [ "numpy", "requests", - "networkx", + "networkx >= 2.6.3", "meson", "ninja", "pydotplus", @@ -41,15 +41,18 @@ dependencies = [ dynamic = ["version", "readme"] [project.optional-dependencies] lint = [ + "black", "cffconvert", - "ruff", + "flake8", + "isort", + "pylint", ] test = [ "mfpymake[lint]", "coverage", "flaky", "filelock", - "pytest!=8.1.0", + "pytest", "pytest-benchmark", "pytest-cov", "pytest-dependency", @@ -87,30 +90,18 @@ include = ["pymake", "pymake.*"] [tool.setuptools.package-data] "pymake.utils" = ["usgsprograms.txt"] -[tool.setuptools_scm] -fallback_version = "999" +[tool.black] +line-length = 79 +target_version = ["py38"] -[tool.ruff] +[tool.flynt] line-length = 79 -target-version = "py38" -include = [ - "pyproject.toml", - "pymake/**/*.py", - "autotest/**/*.py", - "docs/**/*.py", -] +verbose = true -[tool.ruff.lint] -select = ["F", "E", "I001"] -ignore = [ - "E402", # module level import not at top of file - "E712", # Avoid equality comparisons to `True` - "E722", # do not use bare `except` - "E741", # ambiguous variable name - "F401", # unused import - "F403", # unable to detect undefined names (star imports) - "F524", # `.format` missing argument(s) for placeholder(s) - "F811", # Redefinition of unused variable - "F821", # undefined name TODO FIXME - "F841", # local variable assigned but never used -] +[tool.isort] +profile = "black" +src_paths = ["pymake", "autotest", "examples"] +line_length = 79 + +[tool.setuptools_scm] +fallback_version = "999" diff --git a/scripts/update_version.py b/scripts/update_version.py deleted file mode 100644 index 59bdc8d8..00000000 --- a/scripts/update_version.py +++ /dev/null @@ -1,149 +0,0 @@ -import argparse -import re -import textwrap -from datetime import datetime -from pathlib import Path - -from filelock import FileLock -from packaging.version import Version - -_project_name = "mfpymake" -_project_root_path = Path(__file__).parent.parent -_version_txt_path = _project_root_path / "version.txt" -_version_py_path = _project_root_path / "pymake" / "config.py" - -# file names and the path to the file relative to the repo root directory -file_paths_list = [ - _project_root_path / "README.md", - _project_root_path / "version.txt", - _project_root_path / "pymake" / "config.py", -] -file_paths = {pth.name: pth for pth in file_paths_list} # keys for each file - -def split_nonnumeric(s): - match = re.compile("[^0-9]").search(s) - return [s[: match.start()], s[match.start() :]] if match else s - - -_initial_version = Version("0.0.1") -_current_version = Version(_version_txt_path.read_text().strip()) - - -def update_version_txt(version: Version): - with open(_version_txt_path, "w") as f: - f.write(str(version)) - print(f"Updated {_version_txt_path} to version {version}") - - -def update_version_py(timestamp: datetime, version: Version): - lines = file_paths["config.py"].read_text().rstrip().split("\n") - - with open(_version_py_path, "w") as f: - f.write( - f"# {_project_name} version file automatically created using\n" - f"# {Path(__file__).name} on {timestamp:%B %d, %Y %H:%M:%S}\n\n" - ) - for line in lines: - if "__date__" in line: - line = f'__date__ = "{timestamp:%B %d, %Y}"' - elif "__version__" in line: - line = f'__version__ = "{version}"' - f.write(f"{line}\n") - print(f"Updated {_version_py_path} to version {version}") - - - -def update_readme_markdown( - timestamp: datetime, version: Version, approved: bool = False -): - fpth = file_paths["README.md"] - - # read README.md into memory - lines = fpth.read_text().rstrip().split("\n") - - # rewrite README.md - terminate = False - with open(fpth, "w") as f: - for line in lines: - if "### Version " in line: - line = f"### Version {version}" - f.write(f"{line}\n") - if terminate: - break - - print(f"Updated {fpth} to version {version}") - -def update_version( - timestamp: datetime = datetime.now(), - version: Version = None, - approved: bool = False, -): - lock_path = Path(_version_txt_path.name + ".lock") - try: - lock = FileLock(lock_path) - previous = Version(_version_txt_path.read_text().strip()) - version = ( - version - if version - else Version(previous.major, previous.minor, previous.micro) - ) - - with lock: - update_version_txt(version) - update_version_py(timestamp, version) - update_readme_markdown(timestamp, version, approved) - finally: - try: - lock_path.unlink() - except: - pass - - -if __name__ == "__main__": - parser = argparse.ArgumentParser( - prog=f"Update {_project_name} version", - formatter_class=argparse.RawDescriptionHelpFormatter, - epilog=textwrap.dedent( - """\ - Update version information stored in version.txt in the project root, - as well as several other files in the repository. If --version is not - provided, the version number will not be changed. A file lock is held - to synchronize file access. The version tag must comply with standard - '..' format conventions for semantic versioning. - """ - ), - ) - parser.add_argument( - "-v", - "--version", - required=False, - help="Specify the release version", - ) - parser.add_argument( - "-a", - "--approve", - required=False, - action="store_true", - help="Approve the release (defaults false)", - ) - parser.add_argument( - "-g", - "--get", - required=False, - action="store_true", - help="Just get the current version number, no updates (defaults false)", - ) - args = parser.parse_args() - - if args.get: - print( - Version((_project_root_path / "version.txt").read_text().strip()) - ) - else: - update_version( - timestamp=datetime.now(), - version=( - Version(args.version) if args.version else _current_version - ), - approved=args.approve, - ) diff --git a/version.txt b/version.txt deleted file mode 100644 index 732aa7d7..00000000 --- a/version.txt +++ /dev/null @@ -1 +0,0 @@ -1.2.10 \ No newline at end of file