From 5b6e70ef299fb3fdbba213d9eee619a95f531cb4 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 15 May 2024 11:16:18 +0200 Subject: [PATCH 1/2] chore!: Remove defaults channel dependency Signed-off-by: Marcel Bargull --- Dockerfile | 4 +++- bioconda_utils/bioconda_utils-conda_build_config.yaml | 2 +- bioconda_utils/pkg_test.py | 2 +- bioconda_utils/utils.py | 2 +- test/test-config.yaml | 1 - test/test_bioconductor_skeleton.py | 4 ++-- 6 files changed, 8 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index e1247b19e5..f2cbe13867 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,10 +21,12 @@ RUN yum install -y mesa-libGL-devel \ # This changes root's .condarc which ENTRYPOINT copies to /home/conda/.condarc later. RUN . /opt/conda/etc/profile.d/conda.sh && \ conda config \ - --add channels defaults \ --add channels bioconda \ --add channels conda-forge \ && \ + conda config \ + --remove channels defaults || true \ + && \ { conda config --remove repodata_fns current_repodata.json 2> /dev/null || true ; } && \ conda config --prepend repodata_fns repodata.json && \ conda config --set channel_priority strict && \ diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index fc19ffaba3..e633edaf1f 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -55,7 +55,7 @@ numpy: - 1.21.* channel_sources: - - conda-forge,bioconda,defaults + - conda-forge,bioconda channel_targets: - bioconda main diff --git a/bioconda_utils/pkg_test.py b/bioconda_utils/pkg_test.py index 4db38acef9..97cea7f38b 100644 --- a/bioconda_utils/pkg_test.py +++ b/bioconda_utils/pkg_test.py @@ -95,7 +95,7 @@ def get_image_name(path): def test_package( path, name_override=None, - channels=("conda-forge", "local", "bioconda", "defaults"), + channels=("conda-forge", "local", "bioconda"), mulled_args="", base_image=None, conda_image=MULLED_CONDA_IMAGE, diff --git a/bioconda_utils/utils.py b/bioconda_utils/utils.py index 031b9ef294..dd887595ab 100644 --- a/bioconda_utils/utils.py +++ b/bioconda_utils/utils.py @@ -1195,7 +1195,7 @@ def get_list(key): default_config = { 'blacklists': [], - 'channels': ['conda-forge', 'bioconda', 'defaults'], + 'channels': ['conda-forge', 'bioconda'], 'requirements': None, 'upload_channel': 'bioconda' } diff --git a/test/test-config.yaml b/test/test-config.yaml index 5bab2460e2..1e0625555e 100644 --- a/test/test-config.yaml +++ b/test/test-config.yaml @@ -4,4 +4,3 @@ channels: - conda-forge - bioconda - - defaults diff --git a/test/test_bioconductor_skeleton.py b/test/test_bioconductor_skeleton.py index ef624a8a11..5c3aa9662b 100644 --- a/test/test_bioconductor_skeleton.py +++ b/test/test_bioconductor_skeleton.py @@ -15,7 +15,7 @@ config = { - 'channels': ['conda-forge', 'bioconda', 'defaults'] + 'channels': ['conda-forge', 'bioconda'] } @@ -78,7 +78,7 @@ def test_bioc_write_recipe_no_skipping(tmpdir, bioc_fetch): @pytest.mark.skip(reason="Does not work since new bioconductor release?") def test_meta_contents(tmpdir, bioc_fetch): config = { - 'channels': ['conda-forge', 'bioconda', 'defaults'] + 'channels': ['conda-forge', 'bioconda'] } bioconductor_skeleton.write_recipe( 'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch) From 24027320ec5112c563884259012c1680b9a1ebbb Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 15 May 2024 11:22:06 +0200 Subject: [PATCH 2/2] chore: Remove unused MulledDockerfile Signed-off-by: Marcel Bargull --- MulledDockerfile | 37 ------------------------------------- Mulled_entrypoint | 4 ---- 2 files changed, 41 deletions(-) delete mode 100644 MulledDockerfile delete mode 100755 Mulled_entrypoint diff --git a/MulledDockerfile b/MulledDockerfile deleted file mode 100644 index 6170c4a2c4..0000000000 --- a/MulledDockerfile +++ /dev/null @@ -1,37 +0,0 @@ -FROM debian:10-slim as base - -# $ docker build -f MulledDockerfile -t bioconda/mulled_container:latest -# $ docker run --rm -it bioconda/mulled_container:latest /bin/bash -# $ docker push bioconda/mulled_container:latest -# -ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 -ENV PATH /opt/conda/bin:$PATH - - -FROM base as builder - -RUN apt-get update -qq --fix-missing && \ - apt-get install -qqy --no-install-recommends bzip2 ca-certificates curl && \ - apt-get clean && \ - rm -rf /var/lib/apt/lists/* - -RUN curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh -o ~/miniconda.sh && \ - /bin/bash ~/miniconda.sh -b -p /opt/conda && \ - rm ~/miniconda.sh && \ - CONDA_AGGRESSIVE_UPDATE_PACKAGES= CONDA_AUTO_UPDATE_CONDA=0 \ - conda install -y conda-forge::tini && \ - conda clean -ya - - -FROM base - -COPY --from=builder /opt/conda /opt/conda -RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ - echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \ - echo "conda activate base" >> ~/.bashrc && \ - { conda config --remove repodata_fns current_repodata.json || true ; } && \ - conda config --prepend repodata_fns repodata.json -COPY ./Mulled_entrypoint /opt/container-entrypoint - -ENTRYPOINT [ "/opt/conda/bin/tini", "--", "/opt/container-entrypoint"] -CMD [ "/bin/bash" ] diff --git a/Mulled_entrypoint b/Mulled_entrypoint deleted file mode 100755 index d8490a51d8..0000000000 --- a/Mulled_entrypoint +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -l - -conda activate base -exec "${@}"