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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Update ucsc-pslcdnafilter to 472 #51700

Closed mencian closed 3 days ago

mencian commented 3 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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📥 Commits Files that changed from the base of the PR and between 1b56d3395c3451a60d6e93cfa5476c94a03490fe and b23ff546a6915e6b02b1fbceaa50e6f3bee3f241.
📝 Walkthrough
📝 Walkthrough ## Walkthrough The pull request introduces several changes across three files related to the `ucsc-pslcdnafilter` package. In `build.sh`, the handling of compiler flags is modified by adding the optimization flag `-O3` to the `CXXFLAGS` variable, enhancing the compilation process. The script also alters the final steps for managing the built executable, changing the order of operations for setting permissions and moving the executable to the target directory. The `include.macos.patch` file updates the `common.mk` and `makefile` to include the `${PREFIX}/include` path in the `HG_INC` and `KENT_INC` variables, respectively. Additionally, the shebang line of the `expMatrixToBarchartBed` script is changed to allow compatibility with any Python version. The `meta.yaml` file reflects a version increment from "469" to "472", updates the SHA256 checksum, modifies the patch list to include a macOS-specific patch, and adjusts dependencies by adding `clangdev` and removing `zlib`. Minor updates to URLs in the `about` section are also included. ## Possibly related PRs - **#51654**: The changes in the main PR regarding the `CXXFLAGS` variable and the handling of the `twoBitToFa` binary are directly related to the modifications made in the `build.sh` of the `ucsc-twobittofa` recipe, which also updates `CXXFLAGS` to include the `-O3` optimization flag and alters the process for copying the binary. ## Suggested labels `new version`, `please review & merge` ## Suggested reviewers - mencian

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