Update build system to handle environment variables at compilation ti… #1410
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(PIP) Install dependencies & package
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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: julia-actions/setup-julia@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Set up job
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Set test-flags1
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Set test-flags2
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Run actions/checkout@v4
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Get tags required by setuptools_scm to generate version
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Set C installation based on matrix value
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Set MPI installation based on matrix value
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Set SBML installation based on matrix value
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Set R installation based on matrix value
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Set Pytorch installation based on matrix value
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Store an ID string for the job
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(WINDOWS) Patch TEMP/TMPDIR on Windows
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(WINDOWS) Disable interpreted language example on Windows for speed
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(WINDOWS,PIP) Set up MSVC Compiler
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(WINDOWS,PIP) Set up MSMPI
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(LINUX,PIP) Cache pip
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(MACOS,PIP) Cache pip
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(WINDOWS,PIP) Cache pip
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(PIP) Set up Python
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(PIP) Set up Python 3.7
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(PIP) Set up Julia
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Set up Matlab
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(PIP) Set up Virtual Env
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(PIP) Install dependencies & package
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(WINDOWS,PIP) Set the vcpkg root config value
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(WINDOWS,PIP) Update R requirements
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(MACOS,PIP) Set C compiler to llvm clang
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(WINDOWS,CONDA) Prune the PATH variable
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(CONDA) Set up miniconda base environment
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(WINDOWS,CONDA) Set up MSVC Compiler
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(CONDA) Build package in base environment
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(CONDA) Build package in base environment (re-attempt)
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(MACOS,CONDA) Install old MacOSX SDK for compatibility with the conda llvm (7)
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(LINUX) Install ncurses 5 for SBML runs with libroadrunner
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(CONDA) Install dependencies & package from existing build
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(CONDA) Install dependencies & package from existing build (re-attempt)
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(MACOS,CONDA) Set allow_multiple_omp config
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Verify installation
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Compile libraries
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Run cmake test in command prompt (CONDA)
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Run cmake test in command prompt (PIP)
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Run tests (1st)
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Re-run test failures (1st)
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Run generated test script (1st)
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Re-run test script failures (1st)
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Run tests (2nd)
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Re-run test failures (2nd)
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Run generated test script (2nd)
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Re-run test script failures (2nd)
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Combine coverage reports
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(CONDA) Generate XML version of coverage report
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Upload coverage report
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Download the last successful workflow environment log
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Create a log of Python package versions
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Run actions/upload-artifact@v4
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Post (PIP) Set up Python
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Post (WINDOWS,PIP) Cache pip
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Post Run actions/checkout@v4
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Complete job
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