Bulk: bioconda-utils v3.3.0

common.sh

@@ -1,3 +1,3 @@
-BIOCONDA_UTILS_TAG=v2.13.2
-MAMBAFORGE_VER=23.1.0-1
+BIOCONDA_UTILS_TAG=v3.3.0
+MAMBAFORGE_VER=24.3.0-0
 MAMBAFORGE_INSTALLATION_DIR="/opt/mambaforge"

configure-conda.sh

@@ -21,11 +21,13 @@ then
 fi
 
 conda config --set always_yes yes
-conda config --add channels defaults
 conda config --add channels bioconda
 conda config --add channels conda-forge
+conda config --remove channels defaults || true
 conda config --set channel_priority strict
+# .conda support is pending https://github.com/conda/infrastructure/issues/950
+# conda config --set conda_build.pkg_format 2
 
 if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then
     conda config --add channels "file://${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
-fi
+fi

install-and-set-up-conda.sh

@@ -5,7 +5,6 @@ set -e
 # - Installs mambaforge to ${HOME}/mambaforge. Version is determined by common.sh,
 #   which is downloaded at runtime.
 # - Sets channel order and sets strict channel priority
-# - Installs mamba into the base env
 # - Installs bioconda-utils into a "bioconda" env (unless
 #   $BIOCONDA_DISABLE_BUILD_PREP=1). Version is determined by common.sh.
 # - Sets up local channel to have highest priority (unless $BIOCONDA_DISABLE_BUILD_PREP=1)
@@ -44,8 +43,6 @@ if [[ $(uname) == "Darwin" ]]; then
     sudo chown -R $USER $(dirname $MAMBAFORGE_INSTALLATION_DIR)
 
     # conda-forge-ci-setup does some additional setup for Mac.
-    # Installing bioconda-utils and conda-forge-ci-setup with conda causes dependency conflicts.
-    # Installing bioconda-utils and conda-forge-ci-setup with mamba works fine.
     BIOCONDA_ADDITIONAL_INSTALL_PKGS="conda-forge-ci-setup"
 else
     mkdir -p $(dirname $MAMBAFORGE_INSTALLATION_DIR)
@@ -67,8 +64,6 @@ export PATH="${MAMBAFORGE_INSTALLATION_DIR}/bin:${PATH}"
 # disable build preparation here because we don't yet have the local channel from conda-build
 BIOCONDA_DISABLE_BUILD_PREP=1 bash configure-conda.sh
 
-mamba install mamba -y
-
 # By default, for building packages, we install bioconda-utils. However when
 # testing bioconda-utils itself, we don't want to install a release, in
 # which case set BIOCONDA_DISABLE_BUILD_PREP to a non-zero value.
@@ -78,17 +73,19 @@ if [ ${BIOCONDA_DISABLE_BUILD_PREP:=0} == 0 ]; then
     source ${MAMBAFORGE_INSTALLATION_DIR}/etc/profile.d/mamba.sh
 
     # set up env with all dependencies
-    mamba create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS
+    conda create -n bioconda -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt $BIOCONDA_ADDITIONAL_INSTALL_PKGS
 
-    mamba activate bioconda
+    conda activate bioconda
 
     # install bioconda-utils itself via pip (this way we don't always have to wait for the conda package to be built before being able to fix things here)
     pip install git+https://github.com/bioconda/bioconda-utils.git@$BIOCONDA_UTILS_TAG
 
     # Set local channel as highest priority (requires conda-build, which is
     # installed as a dependency of bioconda-utils)
     mkdir -p "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld/{noarch,linux-64,osx-64,linux-aarch64,osx-arm64}"
-    conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
+    # The base installation does not include conda-index, so use "command conda" to run bioconda
+    # env's "conda index".
+    command conda index "${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
     conda config --add channels "file://${MAMBAFORGE_INSTALLATION_DIR}/conda-bld"
 fi