bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Rebuild MaSuRCA recipe #51662

Closed mencian closed 6 days ago

mencian commented 6 days ago

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes. This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe. If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation). Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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coderabbitai[bot] commented 6 days ago
📝 Walkthrough ## Walkthrough This pull request introduces several changes across three main files related to the Masurca software installation and build process. In the `install.sh` script, the `autoreconf -if` command is added to regenerate configuration files, and the `cp` command is modified to `cp -arf` for improved file copying behavior. The `build.sh` script sees updates to environment variable exports, including the use of double quotes for consistency and changes in optimization flags from `-O2` to `-O3`. The handling of library paths during linking is also adjusted. The `meta.yaml` file is updated with a new version number, the addition of a patch file, and several new build dependencies, including `automake`, `autoconf`, `libtool`, and `pkg-config`. Additionally, the formatting of metadata fields is improved, and new fields for development and documentation URLs are added. Overall, these changes enhance the installation and build processes for the Masurca package. ## Possibly related PRs - **#51221**: The `build.sh` script in this PR includes the addition of the `autoreconf -if` command, similar to the changes made in the main PR's `install.sh` script, which also modifies the build configuration process. - **#51641**: The `build.sh` script updates the `CXXFLAGS` to include optimization flags and changes the C++ standard, which aligns with the main PR's focus on enhancing build configurations through similar modifications. ## Suggested labels `please review & merge`

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