another attempt at removing mamba

.github/workflows/build-images.yml

@@ -191,7 +191,7 @@ jobs:
         wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
         bash install-and-set-up-conda.sh
         eval "$(conda shell.bash hook)"
-        mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+        conda create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
         conda activate bioconda
         python setup.py install
 

images/bioconda-utils-build-env-cos7/Dockerfile

@@ -50,14 +50,14 @@ RUN . /opt/conda/etc/profile.d/conda.sh  && conda activate base && \
     sed -nE \
     '/^conda([><!=~ ].+)?$/p' \
     /opt/bioconda-utils/bioconda_utils-requirements.txt \
-    | xargs -r mamba install --yes && \
+    | xargs -r conda install --yes && \
     # FIXME: "remove truststore" only necessary due to python downgrade.
     #        Updating requirements should fix that.
     #        (Also this removal will break in future.)
-    # mamba remove --yes truststore && \
-    mamba install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
+    # conda remove --yes truststore && \
+    conda install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
     pip install --no-deps --find-links /opt/bioconda-utils bioconda_utils && \
-    mamba clean --yes --index --tarballs && \
+    conda clean --yes --index --tarballs && \
     # Find files that are not already in group "lucky" and change their group and mode.
     find /opt/conda \
     \! -group lucky \

images/create-env/Dockerfile.test

@@ -5,7 +5,6 @@ RUN set -x && \
     CONDA_PKGS_DIRS="/tmp/pkgs" \
       /opt/create-env/env-execute \
         create-env \
-          --conda=mamba \
           /usr/local \
           file findutils grep
 RUN set -x && \
@@ -34,7 +33,6 @@ FROM "${base}" as build_bioconda_package
 RUN set -x && \
     /opt/create-env/env-execute \
       create-env \
-        --conda=mamba \
         --strip-files=\* \
         /usr/local \
         python
@@ -58,7 +56,6 @@ FROM "${base}" as build_conda
 RUN set -x && \
     /opt/create-env/env-execute \
       create-env \
-        --conda=mamba \
         --env-activate-args='--prefix-is-base' \
         --strip-files=\* \
         --remove-paths=\*.a \

images/create-env/README.md

@@ -1,6 +1,6 @@
 # bioconda/create-env
 
-The `create-env` container image, available as [`quay.io/bioconda/create-env`](https://quay.io/repository/bioconda/create-env?tab=tags), provides [`conda`](https://github.com/conda/conda/) (and [`mamba`](https://github.com/mamba-org/mamba)) alongside a convenience wrapper `create-env` to create small container images based on Conda packages.
+The `create-env` container image, available as [`quay.io/bioconda/create-env`](https://quay.io/repository/bioconda/create-env?tab=tags), provides [`conda`](https://github.com/conda/conda/) alongside a convenience wrapper `create-env` to create small container images based on Conda packages.
 
 
 ## Options
@@ -37,13 +37,12 @@ Post-processing steps are triggered by arguments to `create-env`:
 ## Usage example:
 ```Dockerfile
 FROM quay.io/bioconda/create-env:2.1.0 as build
-# Create an environment containing python=3.9 at /usr/local using mamba, strip
+# Create an environment containing python=3.9 at /usr/local, strip
 # files and remove some less important files:
 RUN export CONDA_ADD_PIP_AS_PYTHON_DEPENDENCY=0 \
     && \
     /opt/create-env/env-execute \
       create-env \
-        --conda=mamba \
         --strip-files='bin/*' \
         --strip-files='lib/*' \
         --remove-paths='*.a' \
@@ -87,8 +86,6 @@ RUN /usr/local/env-activate.sh && python -c 'import sys; print(sys.version)'
   ```sh
   . /opt/create-env/env-activate.sh
   export CONDA_ALWAYS_COPY=0
-  create-env --conda=mamba /opt/python-3.8 python=3.8
-  create-env --conda=mamba /opt/python-3.9 python=3.9
   create-env --conda=: --strip-files=\* /opt/python-3.8
   create-env --conda=: --strip-files=\* /opt/python-3.9
   ```

images/create-env/install-conda

@@ -22,23 +22,23 @@ miniconda_boostrap_prefix="$( pwd )/miniconda"
   # Install the base Conda installation.
   . "${miniconda_boostrap_prefix}/etc/profile.d/conda.sh"
 
-  # Install conda, mamba and some additional tools:
+  # Install conda and some additional tools:
   #  - tini: init program,
   #  - binutils, findutils: tools to strip down image/environment size,
 
   # Only need `strip` executable from binutils. Other binaries from the package
   # and especially the "sysroot" dependency is only bloat for this container
   # image. (NOTE: The binary needs libgcc-ng which is explicitly added later.)
-  mamba create --yes \
+  conda create --yes \
     --prefix="${conda_install_prefix}" \
     --channel=conda-forge \
     binutils
   cp -aL "${conda_install_prefix}/bin/strip" ./strip
   conda run --prefix="${conda_install_prefix}" strip -- ./strip
-  mamba remove --yes --all \
+  conda remove --yes --all \
     --prefix="${conda_install_prefix}"
 
-  mamba create --yes \
+  conda create --yes \
     --prefix="${conda_install_prefix}" \
     --channel=conda-forge \
     \
@@ -116,8 +116,7 @@ conda config \
 #     This is intentional as it speeds up conda startup time.
 conda list --name=base
 conda info --all
-mamba --version
-# Make sure we have the requested conda, mamba versions installed.
+# Make sure we have the requested conda version installed, and no mamba
 conda list \
   --export '^(conda|mamba)$' \
   | sed -n 's/=[^=]*$//p' \

images/create-env/prepare.sh

@@ -21,16 +21,10 @@ CONDA_VERSION=$(
         podman run -t $REGISTRY/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG} \
         bash -c "/opt/conda/bin/conda list --export '^conda$'| sed -n 's/=[^=]*$//p'"
 )
-MAMBA_VERSION=$(
-        podman run -t $REGISTRY/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG} \
-        bash -c "/opt/conda/bin/conda list --export '^mamba$'| sed -n 's/=[^=]*$//p'"
-)
 # Remove trailing \r with parameter expansion
 export CONDA_VERSION=${CONDA_VERSION%$'\r'}
-export MAMBA_VERSION=${MAMBA_VERSION%$'\r'}
 
 BUILD_ARGS+=("--build-arg=CONDA_VERSION=$CONDA_VERSION")
-BUILD_ARGS+=("--build-arg=MAMBA_VERSION=$MAMBA_VERSION")
 
 # Needs busybox image to copy some items over
 if [ $(tag_exists $BASE_BUSYBOX_IMAGE_NAME $BASE_TAG) ]; then