Add Conda packaging and release workflow for SIST

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.

[harryswift01]

Summary

This PR will add the Conda packaging and release infrastructure required for the first maintained SIST 1.0.0 release.

This updates SIST to use an external Bioconda IRF dependency, makes the installed application independent of the source-tree layout, adds Conda package build and regression testing, and introduces automated GitHub and Conda release workflows.

Changes

Conda packaging:

• Add a Conda recipe for building and installing SIST.
• Build the existing C++ implementations using the Conda toolchain.
• Install the SIST wrapper, Perl scripts, and compiled executables into the Conda prefix.
• Add Perl and IRF 3.08 as runtime dependencies.
• Run the existing 16 scientific regression tests against the installed Conda package.
• Update the test fixtures so normal source testing is retained while conda-build tests the installed sist command.

External IRF integration:

• Remove the bundled irf308.linux.exe executable.
• Update IR_finder.pl to use the irf executable supplied by Bioconda.
• Update master.pl so installed scripts and executables are resolved relative to the SIST installation directory.
• Update the existing Makefiles to support the Conda C++ compiler and linker flags.

Release automation and metadata:

• Add a GitHub Actions workflow for preparing and publishing SIST releases.
• Automate version updates in the Conda recipe and CITATION.cff.
• Automate release tagging and GitHub Release creation.
• Build, test, and publish the Conda package to the CCPBioSim Anaconda channel.
• Add SIST citation metadata in CITATION.cff.

Impact

• SIST can now be distributed and installed as a Conda package with its required runtime dependencies.
• IRF is managed as an external pinned dependency rather than a bundled platform-specific executable.
• Package builds are validated against the maintained scientific regression baselines before publication.
• The release process for SIST is reproducible and automated while preserving the established scientific behaviour.

[jimboid]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

[harryswift01]

Look s like all the bits are there and inline with other conda release flows on other projects. We should add the conda install route to the docs if not already there.

That sounds good, I’m just currently working alongside this PR on updating the documentation for the new 1.0.0 release, including the Conda install route and updated usage guidance Docs Issue.

I didn’t want to make this PR too large, so I’ve kept the documentation work separate, but that should be coming soon.