Integration #44
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| name: Integration | |
| on: | |
| workflow_call: | |
| workflow_dispatch: | |
| push: | |
| tags: | |
| - 'v*' | |
| schedule: | |
| - cron: "0 0 * * 0,3" | |
| jobs: | |
| get-nonmem: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Cache NONMEM | |
| id: cache-nonmem | |
| uses: actions/cache@v3 | |
| with: | |
| path: 751.zip | |
| key: nonmem-751 | |
| - name: Download NONMEM | |
| if: steps.cache-nonmem.outputs.cache-hit != 'true' | |
| run: | | |
| sudo apt install lynx | |
| echo 'key /' >>lynxcmds | |
| echo 'key 7' >>lynxcmds | |
| echo 'key 5' >>lynxcmds | |
| echo 'key 1' >>lynxcmds | |
| echo 'key ^J' >>lynxcmds | |
| echo 'key ^J' >>lynxcmds | |
| echo 'key /' >>lynxcmds | |
| echo 'key z' >>lynxcmds | |
| echo 'key i' >>lynxcmds | |
| echo 'key p' >>lynxcmds | |
| echo 'key ^J' >>lynxcmds | |
| echo 'key d' >>lynxcmds | |
| echo 'key ^J' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key <delete>' >>lynxcmds | |
| echo 'key 7' >>lynxcmds | |
| echo 'key 5' >>lynxcmds | |
| echo 'key 1' >>lynxcmds | |
| echo 'key .' >>lynxcmds | |
| echo 'key z' >>lynxcmds | |
| echo 'key i' >>lynxcmds | |
| echo 'key p' >>lynxcmds | |
| echo 'key ^J' >>lynxcmds | |
| echo 'key Q' >>lynxcmds | |
| lynx -accept-all-cookies nonmem.iconplc.com -cmd_script=lynxcmds | |
| - name: Upload cache workaround | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cache-workaround | |
| path: 751.zip | |
| retention-days: 1 | |
| integration-ubuntu: | |
| needs: [get-nonmem] | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout Pharmpy | |
| uses: actions/checkout@v4 | |
| - name: Cache NONMEM | |
| id: cache-nonmem | |
| uses: actions/cache@v3 | |
| with: | |
| path: 751.zip | |
| key: nonmem-751 | |
| - name: Unzip NONMEM | |
| run: unzip -P $ZIP_KEY 751.zip | |
| env: | |
| ZIP_KEY: ${{secrets.ZIP_751_KEY}} | |
| - name: Install gfortran | |
| run: sudo apt install gfortran | |
| - name: Print gfortran and gcc version | |
| run: | | |
| gfortran --version | |
| gcc --version | |
| shell: bash | |
| - name: NONMEM license | |
| run: echo $LICENSE_KEY > nm751CD/nonmem.lic | |
| env: | |
| LICENSE_KEY: ${{secrets.LICENSE_KEY}} | |
| - name: Install NONMEM | |
| run: | | |
| cd nm751CD | |
| /bin/bash SETUP75 $(realpath .) $(realpath ../nm751) gfortran y ar same rec q | |
| - name: Create pharmpy.conf | |
| run: | | |
| export CONFDIR=/home/runner/.config/Pharmpy | |
| mkdir -p $CONFDIR | |
| echo '[pharmpy.plugins.nonmem]' > $CONFDIR/pharmpy.conf | |
| echo 'parameter_names=comment,basic' >> $CONFDIR/pharmpy.conf | |
| echo "default_nonmem_path=$(realpath nm751)" >> $CONFDIR/pharmpy.conf | |
| cat $CONFDIR/pharmpy.conf | |
| ls -l /home/runner/work/pharmpy/pharmpy/nm751 | |
| - uses: ./.github/actions/setup-tox | |
| with: | |
| python-version: 3.11 | |
| - name: Run integration tests | |
| run: tox -e integration | |
| integration-macos: | |
| needs: [get-nonmem] | |
| runs-on: macos-12 | |
| steps: | |
| - name: Checkout Pharmpy | |
| uses: actions/checkout@v4 | |
| - name: Setup gfortran | |
| run: | | |
| sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran | |
| sudo mkdir /usr/local/gfortran | |
| sudo ln -s /usr/local/Cellar/gcc@11/11.3.0_1/lib/gcc/11 /usr/local/gfortran/lib | |
| - name: Install realpath | |
| run: brew install coreutils | |
| - name: Print gfortran and gcc version | |
| run: | | |
| gfortran --version | |
| gcc --version | |
| shell: bash | |
| - name: Get NONMEM | |
| id: cache-nonmem | |
| uses: actions/cache@v3 | |
| with: | |
| path: 751.zip | |
| key: nonmem-751 | |
| - name: Unzip NONMEM | |
| run: unzip -P $ZIP_KEY 751.zip | |
| env: | |
| ZIP_KEY: ${{secrets.ZIP_751_KEY}} | |
| - name: NONMEM license | |
| run: echo $LICENSE_KEY > nm751CD/nonmem.lic | |
| env: | |
| LICENSE_KEY: ${{secrets.LICENSE_KEY}} | |
| - name: Install NONMEM | |
| run: | | |
| cd nm751CD | |
| /bin/bash SETUP75 $(realpath .) $(realpath ../nm751) gfortran y ar same rec q | |
| - name: Create pharmpy.conf | |
| run: | | |
| export CONFDIR=/Users/runner/Library/Application\ Support/Pharmpy | |
| mkdir -p "$CONFDIR" | |
| echo '[pharmpy.plugins.nonmem]' > "$CONFDIR/pharmpy.conf" | |
| echo 'parameter_names=comment,basic' >> "$CONFDIR/pharmpy.conf" | |
| echo "default_nonmem_path=$(realpath nm751)" >> "$CONFDIR/pharmpy.conf" | |
| - uses: ./.github/actions/setup-tox | |
| with: | |
| python-version: 3.11 | |
| - name: Run integration tests | |
| run: tox -e integration | |
| integration-windows: | |
| needs: [get-nonmem] | |
| runs-on: windows-2022 | |
| steps: | |
| - name: Checkout Pharmpy | |
| uses: actions/checkout@v4 | |
| # https://github.com/modflowpy/install-gfortran-action/blob/dfc32754e541304f2e7b7ca001e40dce094a5cd6/action.yml#L22-L30 | |
| - name: Setup gfortran | |
| shell: bash | |
| run: | | |
| FCDIR=/c/ProgramData/Chocolatey/bin | |
| LNDIR=/c/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin | |
| if [ -d "$FCDIR" ] && [ -f "$LNDIR/libgfortran-5.dll" ] && [ ! -f "$FCDIR/libgfortran-5.dll" ]; then | |
| ln -s "$LNDIR/libgfortran-5.dll" "$FCDIR/libgfortran-5.dll" | |
| fi | |
| - name: Print gfortran and gcc version | |
| run: | | |
| gfortran --version | |
| gcc --version | |
| shell: bash | |
| - name: Get NONMEM | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: cache-workaround | |
| - name: Cache NONMEM | |
| id: cache-nonmem | |
| uses: actions/cache@v3 | |
| with: | |
| path: 751.zip | |
| key: nonmem-751 | |
| - name: Unzip NONMEM | |
| run: 7z x 751.zip -p%ZIP_KEY% | |
| env: | |
| ZIP_KEY: ${{secrets.ZIP_751_KEY}} | |
| shell: cmd | |
| - name: NONMEM license | |
| run: echo $LICENSE_KEY > nm751CD/nonmem.lic | |
| env: | |
| LICENSE_KEY: ${{secrets.LICENSE_KEY}} | |
| shell: bash | |
| - name: Install NONMEM | |
| run: | | |
| set INSTALLDIR=%CD%\nm751 | |
| cd nm751CD | |
| SETUP75.bat %CD% %INSTALLDIR% gfortran y ar same rec q | |
| shell: cmd | |
| - name: Create pharmpy.conf | |
| run: | | |
| export CONFDIR=/c/Users/runneradmin/AppData/Local/Pharmpy/Pharmpy | |
| mkdir -p $CONFDIR | |
| echo '[pharmpy.plugins.nonmem]' > $CONFDIR/pharmpy.conf | |
| echo 'parameter_names=comment,basic' >> $CONFDIR/pharmpy.conf | |
| echo 'default_nonmem_path=D:\a\pharmpy\pharmpy\nm751' >> $CONFDIR/pharmpy.conf | |
| shell: bash | |
| - uses: ./.github/actions/setup-tox | |
| with: | |
| python-version: 3.11 | |
| - name: Run integration tests | |
| run: tox -e integration |