replace mamba & conda with micromamba

repo2docker/buildpacks/conda/__init__.py

@@ -337,9 +337,9 @@ class CondaBuildPack(BaseImage):
                     "${NB_USER}",
                     r"""
                 TIMEFORMAT='time: %3R' \
-                bash -c 'time mamba env update -p {0} -f "{1}" && \
+                bash -c 'time /tmp/bin/micromamba install -p {0} -f "{1}" -c conda-forge && \
-                time mamba clean --all -f -y && \
+                # time /tmp/bin/micromamba clean --all -y && \
-                mamba list -p {0} \
+                /tmp/bin/micromamba list -p {0} \
                 '
                 """.format(
                         env_prefix, environment_yml
@@ -356,9 +356,9 @@ class CondaBuildPack(BaseImage):
                 (
                     "${NB_USER}",
                     r"""
-                mamba install -p {0} r-base{1} r-irkernel=1.2 r-devtools -y && \
+                /tmp/bin/micromamba install -p {0} r-base{1} r-irkernel={2} r-devtools -y -c conda-forge && \
-                mamba clean --all -f -y && \
+                #  /tmp/bin/micromamba clean --all -f -y && \
-                mamba list -p {0}
+                /tmp/bin/micromamba list -p {0}
                 """.format(
                         env_prefix, r_pin
                     ),

repo2docker/buildpacks/conda/activate-conda.sh

@@ -1,11 +1,13 @@
 # enable conda and activate the notebook environment
-CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/conda.sh"
+export MAMBA_EXE="/tmp/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/srv/conda"
+CONDA_PROFILE="${CONDA_DIR}/etc/profile.d/mamba.sh"
 test -f $CONDA_PROFILE && . $CONDA_PROFILE
 if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # if the kernel is a separate env, stack them
     # so both are on PATH, notebook first
-    conda activate ${KERNEL_PYTHON_PREFIX}
+    micromamba activate ${KERNEL_PYTHON_PREFIX}
-    conda activate --stack ${NB_PYTHON_PREFIX}
+    micromamba activate ${NB_PYTHON_PREFIX} --stack
 
     # even though it's second on $PATH
     # make sure CONDA_DEFAULT_ENV is the *kernel* env
@@ -14,5 +16,5 @@ if [[ "${KERNEL_PYTHON_PREFIX}" != "${NB_PYTHON_PREFIX}" ]]; then
     # which only contains UI when the two are different
     export CONDA_DEFAULT_ENV="${KERNEL_PYTHON_PREFIX}"
 else
-    conda activate ${NB_PYTHON_PREFIX}
+    micromamba activate ${NB_PYTHON_PREFIX}
 fi

repo2docker/buildpacks/conda/install-miniforge.bash

@@ -5,50 +5,40 @@ set -ex
 
 
 cd $(dirname $0)
-MINIFORGE_VERSION=4.9.2-2
-MAMBA_VERSION=0.7.4
-# SHA256 for installers can be obtained from https://github.com/conda-forge/miniforge/releases
-SHA256SUM="7a7bfaff87680298304a97ba69bcf92f66c810995a7155a2918b99fafb8ca1dc"
 
-URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/Mambaforge-${MINIFORGE_VERSION}-Linux-x86_64.sh"
+URL="https://micro.mamba.pm/api/micromamba/linux-64/latest"
-INSTALLER_PATH=/tmp/miniforge-installer.sh
 
 # make sure we don't do anything funky with user's $HOME
 # since this is run as root
 unset HOME
 
-time wget --quiet $URL -O ${INSTALLER_PATH}
+mkdir -p ${CONDA_DIR}
-chmod +x ${INSTALLER_PATH}
 
-# check sha256 checksum
+time wget -qO- ${URL} | tar -xvj bin/micromamba
-if ! echo "${SHA256SUM}  ${INSTALLER_PATH}" | sha256sum  --quiet -c -; then
+export MAMBA_ROOT_PREFIX=${CONDA_DIR}
-    echo "sha256 mismatch for ${INSTALLER_PATH}, exiting!"
+eval "$(./bin/micromamba shell hook -p ${CONDA_DIR} -s posix)"
-    exit 1
+./bin/micromamba shell init -s bash -p ${CONDA_DIR}
-fi
+# source ~/.bashrc
 
-time bash ${INSTALLER_PATH} -b -p ${CONDA_DIR}
+micromamba activate
-export PATH="${CONDA_DIR}/bin:$PATH"
+# micromamba install conda -n base -c conda-forge
 
-# Preserve behavior of miniconda - packages come from conda-forge + defaults
+export PATH="${PWD}/bin:$PATH"
-conda config --system --append channels defaults
 
-# Do not attempt to auto update conda or dependencies
+cat <<EOT >> ${CONDA_DIR}/.condarc
-conda config --system --set auto_update_conda false
+channels:
-conda config --system --set show_channel_urls true
+  - defaults
-
+auto_update_conda: false
-# bug in conda 4.3.>15 prevents --set update_dependencies
+show_channel_urls: true
-echo 'update_dependencies: false' >> ${CONDA_DIR}/.condarc
+update_dependencies: false
-
+channel_priority: flexible
-# avoid future changes to default channel_priority behavior
+EOT
-conda config --system --set channel_priority "flexible"
-
-time mamba install -y mamba==${MAMBA_VERSION}
 
 echo "installing notebook env:"
 cat "${NB_ENVIRONMENT_FILE}"
 
 
-time mamba create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
+time micromamba create -p ${NB_PYTHON_PREFIX} -f "${NB_ENVIRONMENT_FILE}"
 
 if [[ ! -z "${NB_REQUIREMENTS_FILE:-}" ]]; then
     echo "installing pip requirements"
@@ -65,7 +55,7 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
     # install kernel env and register kernelspec
     echo "installing kernel env:"
     cat "${KERNEL_ENVIRONMENT_FILE}"
-    time mamba create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
+    time micromamba create -p ${KERNEL_PYTHON_PREFIX} -f "${KERNEL_ENVIRONMENT_FILE}"
 
     if [[ ! -z "${KERNEL_REQUIREMENTS_FILE:-}" ]]; then
         echo "installing pip requirements for kernel"
@@ -75,22 +65,18 @@ if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" ]]; then
 
     ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
     echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
-    mamba list -p ${KERNEL_PYTHON_PREFIX}
+    micromamba list -p ${KERNEL_PYTHON_PREFIX}
 fi
 
 # Clean things out!
-time mamba clean --all -f -y
+time micromamba clean --all -y
-
-# Remove the big installer so we don't increase docker image size too much
-rm ${INSTALLER_PATH}
 
 # Remove the pip cache created as part of installing miniforge
 rm -rf /root/.cache
 
 chown -R $NB_USER:$NB_USER ${CONDA_DIR}
 
-mamba list -n root
+micromamba list -p ${NB_PYTHON_PREFIX}
-mamba list -p ${NB_PYTHON_PREFIX}
 
 # Set NPM config
 ${NB_PYTHON_PREFIX}/bin/npm config --global set prefix ${NPM_DIR}

tests/conda/binder-dir/verify

@@ -4,7 +4,7 @@ from subprocess import check_output
 
 assert sys.version_info[:2] == (3, 5), sys.version
 
-out = check_output(["conda", "--version"]).decode("utf8").strip()
+out = check_output(["/tmp/bin/micromamba", "--version"]).decode("utf8").strip()
-assert out == "conda 4.9.2", out
+assert out == "0.12.0", out
 
 import numpy

tests/conda/default-env/postBuild

@@ -1,5 +1,5 @@
 #!/bin/bash
 # install pytest with conda in the default env (should be $KERNEL_PYTHON_PREFIX)
-conda install -yq pytest
+/tmp/bin/micromamba install -yq pytest -p $KERNEL_PYTHON_PREFIX -c conda-forge
 # install there with pip (should be the same)
 pip install there

tests/conda/simple-py2/verify

@@ -14,13 +14,13 @@ assert sorted(specs) == ["python2", "python3"], specs.keys()
 import json
 from subprocess import check_output
 
-envs = json.loads(check_output(["conda", "env", "list", "--json"]).decode("utf8"))
+envs = json.loads(check_output(["/tmp/bin/micromamba", "env", "list", "--json"]).decode("utf8"))
 assert envs == {
     "envs": ["/srv/conda", "/srv/conda/envs/kernel", "/srv/conda/envs/notebook"]
 }, envs
 
 pkgs = json.loads(
-    check_output(["conda", "list", "-n", "kernel", "--json"]).decode("utf8")
+    check_output(["/tmp/bin/micromamba", "list", "-n", "kernel", "--json"]).decode("utf8")
 )
 pkg_names = [pkg["name"] for pkg in pkgs]
 assert "ipykernel" in pkg_names, pkg_names