Merge pull request #83 from mbargull/create-env-fixes-2024-06

create-env: Rebuild with newer Buildah, base, deps and fixes

.github/workflows/create-env.yaml

@@ -14,19 +14,43 @@ on:
 jobs:
  build:
  name: Build & Push
- runs-on: ubuntu-22.04
+ runs-on: ubuntu-24.04
+ container:
+ # travier/podman-action contains newer podman/buildah versions.
+ image: quay.io/travier/podman-action
+ options: --privileged
  env:
  MAJOR_VERSION: 3
- MINOR_VERSION: 0
+ MINOR_VERSION: 1
  IMAGE_NAME: create-env
 
  steps:
  - uses: actions/checkout@v4
 
  - name: Set up QEMU
- uses: docker/setup-qemu-action@v2
- with:
- platforms: arm64
+ run: |
+ podman run --rm --privileged \
+ docker.io/tonistiigi/binfmt --install arm64
+
+ - name: Install Tools
+ run: |
+ set -eu
+ # jq is not installed in travier/podman-action
+ dnf install -qy \
+ jq
+ rpm -q \
+ buildah podman \
+ coreutils findutils sed \
+ curl jq \
+ | (
+ while read -r line ; do
+ printf %s\\n "${line}"
+ case "${line}" in (*' not installed'*)
+ err=1 ;;
+ esac
+ done
+ exit "${err-0}"
+ )
 
  - name: Prepare
  id: prepare

images/create-env/CHANGELOG.md

@@ -1,6 +1,25 @@
 # Changelog
 
 
+## bioconda/create-env 3.1 (2024-06-02)
+
+### Changed
+
+- Rebuild with newer Buildah, `bioconda/base-glibc-busybox-bash:3.1`, `conda`/`mamba` from `bioconda-utils=3.2.0`.
+
+### Fixed
+
+- Fix permissions for license files.
+
+- Fix argument separator `--` handling.
+
+- Ensure env vars don't set defaults.
+
+### Added
+
+- Allow passing PREFIX via `--prefix=...`.
+
+
 ## bioconda/create-env 3.0 (2023-10-17)
 
 ### Changed

images/create-env/Dockerfile.test

@@ -69,7 +69,7 @@ COPY --from=build_conda /opt/conda /opt/conda
 COPY --from=build_conda /opt/conda/env-activate.sh /usr/local/
 RUN set -x && \
  /usr/local/env-execute \
- conda info --all \
+ conda info --verbose \
  && \
  { set -x && . /usr/local/env-activate.sh && set +x ; } \
  && \

images/create-env/create-env

@@ -1,10 +1,22 @@
 #! /bin/sh -eu
 
+unset \
+ prefix \
+ conda_impl \
+ create_command \
+ env_activate_args \
+ env_activate_file \
+ env_execute_file \
+ remove_paths_globs \
+ strip_files_globs \
+ licenses_path \
+ ;
+
 for arg do
  case "${arg}" in
  --help )
  cat <<'end-of-help'
-Usage: create-env [OPTIONS]... [--] PREFIX [CONDA_CREATE_ARGS]...
+Usage: create-env [OPTIONS]... [--] [PREFIX] [CONDA_CREATE_ARGS]...
 Use conda (or mamba via --conda=mamba) to create a Conda environment at PREFIX
 according to specifications given by CONDA_CREATE_ARGS.
 
@@ -19,6 +31,8 @@ according to specifications given by CONDA_CREATE_ARGS.
  script. (default: PREFIX/env-activate.sh)
  --env-execute-script=FILE Destination path of environment execution script.
  (default: PREFIX/env-execute)
+ --prefix=PREFIX Destination path of environment.
+ If omitted, first positional argument is PREFIX.
  --remove-paths=GLOB Glob of paths to remove from PREFIX after its
  creation. Can be passed on multiple times. Will
  be passed on to `find -path PREFIX/GLOB`.
@@ -57,6 +71,9 @@ end-of-help
  "${arg#--remove-paths=}"
  )"
  shift ;;
+ --prefix=* )
+ prefix="${arg#--prefix=}"
+ shift ;;
  --strip-files=* )
  strip_files_globs="$(
  printf '%s\n' \
@@ -68,22 +85,25 @@ end-of-help
  licenses_path="${arg#--licenses-path=}"
  shift ;;
  -- )
+ shift
  break ;;
  -* )
- printf 'unknown option: %s\n' "${arg}"
+ printf 'unknown option: %s\n' "${arg}" 1>&2
  exit 1 ;;
  * )
  break
  esac
 done
 
-if [ $# -eq 0 ] ; then
- printf 'missing argument: environment path\n'
- exit 1
+if [ -z "${prefix+x}" ] ; then
+ if [ $# -eq 0 ] ; then
+ printf 'missing argument: environment path\n' 1>&2
+ exit 1
+ fi
+ prefix="${1}"
+ shift
 fi
-
-prefix="${1%%/}"
-shift
+prefix="${prefix%%/}"
 
 conda_impl="${conda_impl:-conda}"
 create_command="${create_command-create}"
@@ -235,6 +255,16 @@ if [ -n "${licenses_path}" ] ; then
  printf 'failed to copy licenses for %s\n' "${pkg}" 1>&2
  exit 1
  }
+ # Workaround https://github.com/conda/conda-build/issues/5330 :
+ # As of conda-build<=24.5, "info" files like "info/licenses/*" retain their original
+ # permissions which leads to downstream issues if they are too restrictive.
+ # => Fix permissions like conda_build.post.fix_permissions does for package content files.
+ if [ -d "${abs_licenses_path}/${pkg}" ] ; then
+ find "${abs_licenses_path}/${pkg}" \
+ -exec chmod 'u+rw,g+rw,o+r' {} \; \
+ -perm -u=x \
+ -exec chmod 'g+x,o+x' {} \;
+ fi
  done
  )
 fi

images/create-env/install-conda

@@ -29,16 +29,16 @@ miniconda_boostrap_prefix="$( pwd )/miniconda"
  # Only need `strip` executable from binutils. Other binaries from the package
  # and especially the "sysroot" dependency is only bloat for this container
  # image. (NOTE: The binary needs libgcc-ng which is explicitly added later.)
- mamba create --yes \
+ conda create --yes \
  --prefix="${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 \
  \
@@ -115,7 +115,8 @@ conda config \
 # NB: Running conda after the .pyc removal will recreate some .pyc files.
 # This is intentional as it speeds up conda startup time.
 conda list --name=base
-conda info --all
+conda info --verbose
+conda --version
 mamba --version
 # Make sure we have the requested conda, mamba versions installed.
 conda list \