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Update IRF dependency to version 3.9 #57

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harryswift01 merged 2 commits into from
Sep 25, 2026
+7 −7
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Update IRF dependency to version 3.9 #57

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2ead4fa
chore: update IRF dependency to version `3.09`
harryswift01 Sep 25, 2026
541e04e
docs: update documentation to point to IRF as `v3.09`
harryswift01 Sep 25, 2026
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2 changes: 1 addition & 1 deletion conda-recipe/meta.yaml
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Expand Up @@ -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:
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4 changes: 2 additions & 2 deletions docs/source/development.rst
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Expand Up @@ -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:

Expand Down Expand Up @@ -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
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6 changes: 3 additions & 3 deletions docs/source/installation.rst
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Expand Up @@ -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.
Expand Down Expand Up @@ -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:

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2 changes: 1 addition & 1 deletion docs/source/source-usage.rst
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Expand Up @@ -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
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