Release 1.2.10 (#186)

* chore: bump version to 1.2.10.dev0 (#155)

* update workflows to include develop branch

* update(mf6): v6.4.4 (#157)

* feat(cli): add --double option to make-program (#156)

* fix(_usgs_src_update.py): fix function lookup in _build_replace() (#158)

* replace functions are keyed by name as appears in usgsprograms.txt
* lookup did not account for 'dbl' or 'd' appended to program name

* feat(zip): allow appending to an existing zip file using --keep (#159)

* readme: update readme and installation.md (#160)

* refactor(pymake): limit zip file targets to new targets with --keep (#161)

* remove ifort switches that issue warnings
* write absolute zip file path if using --zip argument

* feat(double): restore double switch in usgsprograms.txt (#162)

* make direct evaluation of target names

* feat(code.json): add features to control code.json output (#163)

* feat(code.json): add capability to control code.json output

* remove implicit double_switch for mf2005, mfnwt, mflgr, and mfusg
* add capability to limit code.json to executables in appdir (--partial_json)
* add capability to zip generated code.json (--zip ZIP)
* add capability to update double_switch based on executable names in appdir

* feat(export_json): add appdir kwarg (#164)

* add appdir kwarg to be consistent with make-program
* add --appdir option to make-code-json cli to be consistent with make-program

* chore(dependencies): restrict yanked pytest version 8.1.0 (#165)

* also use fortran-lang/setup-fortran@main to get the latest gcc fix

* chore(formatting): switch to ruff (#166)

* replace isort/black/pylint/flake8
* keep settings mostly identical
* run ruff check --select NPY201, no changes needed

* chore(format): update rules, split long comment lines (#167)

* update rules in pyproject.toml, add import sorting rule 
* split or ignore comment lines where needed for E501

* ci(release): add automated release workflow (#168)

* build(deps): bump actions/checkout from 3 to 4 (#169)

* build(deps): bump actions/setup-python from 4 to 5 (#170)

* fix(mac/gcc/g++): use classic linker with gnu compilers on c/c++ files (#173)

* build(deps): bump dawidd6/action-download-artifact from 2 to 5 (#175)

* update(mf6): update mf6 version (#174)

* update zbud6 extra files
* update mf6examples
* merging with failures

* fix(gsflow): remove gsflow as a possible target (#176)

gsflow (and prms) cause continual problems trying to include them as
prebuilt executables. New versions require additional work to filter out
extraneous source files and object files. The build process uses specific
compiler flags. In short, supporting gsflow (and prms) requires more
support each time we are ready to make a executables release or when
a new version is released.

* merge with failure - in process of resolving

* ci: add pixi to CI workflow (#177)

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

* update(mfusg): update gsi mfusg version (#178)

* merge with failing gridgent test on MacOS with intel

* build(deps): bump dawidd6/action-download-artifact from 5 to 6 (#179)

* ci(triggers): add concurrency groups to prevent duplicate runs (#180)

* ci(macos): use xcode clt 14.3.1 for intel c++ compiler compatibility (#181)

* gridgen build fails with newer versions of xcode

* ci: update workflows (#183)

* update request ci to use pixi

* Version 1.2.10 (#185)

* Update release.yml

* ci(release): set version to 1.2.10

---------

Co-authored-by: jdhughes-usgs <jdhughes@usgs.gov>
Co-authored-by: wpbonelli <wbonelli@ucar.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

.github/workflows/ci.yml

@@ -0,0 +1,192 @@
+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
+
+