small updates, drop aarch64 support for now (#18)

.github/workflows/CI.yml

@@ -18,28 +18,28 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        target: [x86_64, x86, aarch64]
+        target: [x86_64, x86] # do not support aarch64 for now: see issue https://github.com/databio/genimtools/issues/18
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
       - name: Build wheels
         uses: PyO3/maturin-action@v1
-        env:
-          # support for lionux aarch64 - see here: https://github.com/apache/opendal/issues/3673
-          CFLAGS_aarch64_unknown_linux_gnu: "-D__ARM_ARCH=8"
+        # 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 libatomic make
+              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 libatomic1 make
+              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

bindings/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "genimtools-py"
-version = "0.0.15"
+version = "0.0.11"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

genimtools/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "genimtools"
-version = "0.0.15"
+version = "0.0.11"
 edition = "2021"
 description = "Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package."
 license = "MIT"

genimtools/docs/changelog.md

@@ -4,25 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.0.15]
-- fix for github runner issue (again)
-
-## [0.0.14]
-- another fix for github runner issue
-
-## [0.0.13]
-- fix github runner issue
-
-## [0.0.12]
+## [0.0.11]
 - redesigned API for the tokenizers to better emulate the huggingface tokenizers API.
 - implemented new traits for tokenizers to allow for more flexibility when creating new tokenizers.
 - bumped the version `pyo3` to `0.21.0`
 - added `rust-numpy` dependency to the python bindings for exporting tokenized regions as numpy arrays.
 
-## [0.0.11]
-- add support for MASK tokens (chrMASK, 0, 0)
-- tokenizers auto-add MASK tokens to the vocabulary if they are not present
-
 ## [0.0.10]
 - update file format specifications