drop bbclient

databio · May 22, 2024 · f088027 · f088027
1 parent ad9e7e3
commit f088027
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Showing 4 changed files with 15 additions and 106 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -29,21 +29,21 @@ jobs:
         # env:
         #   # support for lionux aarch64 - see here: https://github.com/apache/opendal/issues/3673
         #   CFLAGS_aarch64_unknown_linux_gnu: "-D__ARM_ARCH=8"
-        with:
-          before-script-linux: |
-            # Check for yum and use it if available, otherwise use apt-get
-            if command -v yum &> /dev/null; then
-              echo "Detected yum package manager"
-              yum -y install openssl-devel perl-IPC-Cmd perl-core # <--- new package added
-            elif command -v apt-get &> /dev/null; then
-              echo "Detected apt-get package manager"
-              apt-get update
-              echo "Installing libssl-dev pkg-config openssl musl-dev"
-              apt-get install -y libssl-dev pkg-config openssl musl-dev perl # <--- new package added
-            else
-              echo "No supported package manager found (yum or apt-get)"
-              exit 1
-            fi
+        # with:
+        #   before-script-linux: |
+        #     # Check for yum and use it if available, otherwise use apt-get
+        #     if command -v yum &> /dev/null; then
+        #       echo "Detected yum package manager"
+        #       yum -y install openssl-devel perl-IPC-Cmd perl-core # <--- new package added
+        #     elif command -v apt-get &> /dev/null; then
+        #       echo "Detected apt-get package manager"
+        #       apt-get update
+        #       echo "Installing libssl-dev pkg-config openssl musl-dev"
+        #       apt-get install -y libssl-dev pkg-config openssl musl-dev perl # <--- new package added
+        #     else
+        #       echo "No supported package manager found (yum or apt-get)"
+        #       exit 1
+        #     fi
           working-directory: ./bindings
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter

diff --git a/genimtools/src/bbclient/mod.rs b/genimtools/src/bbclient/mod.rs
diff --git a/genimtools/src/lib.rs b/genimtools/src/lib.rs
@@ -5,7 +5,6 @@
 //! However, it can be used as a standalone library for working with genomic intervals as well.
 //!
 pub mod ailist;
-pub mod bbclient;
 pub mod common;
 pub mod io;
 pub mod tokenizers;

diff --git a/genimtools/src/tokenizers/tree_tokenizer.rs b/genimtools/src/tokenizers/tree_tokenizer.rs
@@ -4,7 +4,6 @@ use std::path::Path;
 use anyhow::Result;
 use rust_lapper::{Interval, Lapper};
 
-use crate::bbclient::{Bbclient, BedbaseFileCache};
 use crate::common::consts::special_tokens::*;
 use crate::common::models::{Region, RegionSet, TokenizedRegionSet, Universe};
 use crate::common::utils::extract_regions_from_bed_file;
@@ -275,13 +274,6 @@ impl TreeTokenizer {
 
         Ok(self.tokenize_region_set(&rs))
     }
-
-    pub fn from_bedbase(id: &str) -> Result<Self> {
-        let bedbase = Bbclient::default();
-        let bed_file = bedbase.get_bed_file(id)?;
-
-        TreeTokenizer::try_from(bed_file.as_path())
-    }
 }
 
 // use default implementation