From 2ead4fa8f2d441192d7511e2492170f4023ae665 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 25 Sep 2026 10:12:59 +0100 Subject: [PATCH 1/2] chore: update IRF dependency to version `3.09` --- conda-recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index d54831d..c2b1143 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -25,7 +25,7 @@ requirements: - python >=3.12 - biopython >=1.85,<2.0 - beautifulsoup4 >=4.12,<5.0 - - irf >=3.08,<3.09 + - irf >=3.09,<3.10 test: requires: From 541e04eff95b618745ce0cf00b3864459db55785 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 25 Sep 2026 10:17:13 +0100 Subject: [PATCH 2/2] docs: update documentation to point to IRF as `v3.09` --- docs/source/development.rst | 4 ++-- docs/source/installation.rst | 6 +++--- docs/source/source-usage.rst | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source/development.rst b/docs/source/development.rst index 00d015e..88a495a 100644 --- a/docs/source/development.rst +++ b/docs/source/development.rst @@ -30,7 +30,7 @@ also requires: * GNU Make * a C++ compiler -* IRF 3.08 on ``PATH`` +* IRF 3.09 on ``PATH`` Install the Python testing dependencies: @@ -86,7 +86,7 @@ Runtime requirements ~~~~~~~~~~~~~~~~~~~~ * Python, Biopython, and Beautiful Soup -* IRF ``>=3.08,<3.09`` +* IRF ``>=3.09,<3.10`` * compiler runtime libraries resolved by Conda Package-test requirements diff --git a/docs/source/installation.rst b/docs/source/installation.rst index c013cec..a64614c 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -17,8 +17,8 @@ dependencies required by SIST, including: * Inverted Repeats Finder (IRF) * the required C++ runtime libraries -SIST 1.0.0 is validated with IRF 3.08, and the Conda package constrains the -runtime dependency to ``>=3.08,<3.09``. +SIST 1.0.0 is validated with IRF 3.09, and the Conda package constrains the +runtime dependency to ``>=3.09,<3.10``. pytest is used for testing and is not required in a normal SIST runtime environment. @@ -52,7 +52,7 @@ A source build requires: * a C++ compiler * GNU Make * Python 3.12 or later -* IRF 3.08 available as ``irf`` on ``PATH`` +* IRF 3.09 available as ``irf`` on ``PATH`` Build both C++ components from the repository root: diff --git a/docs/source/source-usage.rst b/docs/source/source-usage.rst index 94e68ad..aef52ef 100644 --- a/docs/source/source-usage.rst +++ b/docs/source/source-usage.rst @@ -71,7 +71,7 @@ IRF Cruciform and competition calculations require Inverted Repeats Finder. ``sist``'s IR-finder component invokes ``irf`` from ``PATH``. For source -builds, install a compatible IRF 3.08 executable and ensure that: +builds, install a compatible IRF 3.09 executable and ensure that: .. code-block:: bash