diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml index 569e2527..c6ead595 100644 --- a/.github/workflows/build_and_test.yml +++ b/.github/workflows/build_and_test.yml @@ -57,7 +57,7 @@ jobs: if: runner.os != 'Windows' uses: conda-incubator/setup-miniconda@v3.0.1 with: - miniforge-variant: Mambaforge-pypy3 + miniforge-variant: Miniforge-pypy3 miniforge-version: latest environment-file: mm-workflows/install/system_deps.yml activate-environment: mm @@ -68,7 +68,7 @@ jobs: if: runner.os == 'Windows' uses: conda-incubator/setup-miniconda@v3.0.1 with: - miniforge-variant: Mambaforge-pypy3 + miniforge-variant: Miniforge-pypy3 miniforge-version: latest environment-file: mm-workflows/install/system_deps_windows.yml activate-environment: mm diff --git a/cwl_adapters/file_format_conversions/biosimspace/Dockerfile_biosimspace b/cwl_adapters/file_format_conversions/biosimspace/Dockerfile_biosimspace index 4a031974..d40194f3 100644 --- a/cwl_adapters/file_format_conversions/biosimspace/Dockerfile_biosimspace +++ b/cwl_adapters/file_format_conversions/biosimspace/Dockerfile_biosimspace @@ -2,12 +2,12 @@ FROM ubuntu:22.04 # Install miniconda RUN apt-get update && apt-get install -y wget -RUN CONDA="Mambaforge-Linux-x86_64.sh" && \ +RUN CONDA="Miniforge3-Linux-x86_64.sh" && \ wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/$CONDA && \ chmod +x $CONDA && \ - ./$CONDA -b -p /mambaforge && \ + ./$CONDA -b -p /miniforge && \ rm -f $CONDA -ENV PATH /mambaforge/bin:$PATH +ENV PATH /miniforge/bin:$PATH RUN conda install -c conda-forge -c openbiosim biosimspace ENV SIRE_DONT_PHONEHOME 1 diff --git a/cwl_adapters/file_format_conversions/biosimspace/conversion.py b/cwl_adapters/file_format_conversions/biosimspace/conversion.py index 97cf7d17..36654981 100644 --- a/cwl_adapters/file_format_conversions/biosimspace/conversion.py +++ b/cwl_adapters/file_format_conversions/biosimspace/conversion.py @@ -32,7 +32,7 @@ def main() -> None: input_filenames = [args.input_top_path, args.input_crd_path] # This path is w.r.t. the Docker image jakefennick/biosimspace - properties = {'GROMACS_PATH': '/mambaforge/share/gromacs/top/'} + properties = {'GROMACS_PATH': '/miniforge/share/gromacs/top/'} system = BSS.IO.readMolecules(input_filenames, properties) output_file_formats = [args.output_top_format, args.output_crd_format] diff --git a/examples/data/Dockerfile_data b/examples/data/Dockerfile_data index 8db5fb42..91d21219 100644 --- a/examples/data/Dockerfile_data +++ b/examples/data/Dockerfile_data @@ -2,12 +2,12 @@ FROM ubuntu:22.04 as download # Install miniconda RUN apt-get update && apt-get install -y wget -RUN CONDA="Mambaforge-Linux-x86_64.sh" && \ +RUN CONDA="Miniforge3-Linux-x86_64.sh" && \ wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/$CONDA && \ chmod +x $CONDA && \ - ./$CONDA -b -p /mambaforge && \ + ./$CONDA -b -p /miniforge && \ rm -f $CONDA -ENV PATH /mambaforge/bin:$PATH +ENV PATH /miniforge/bin:$PATH RUN conda install -c conda-forge wget libarchive # bsdtar is installed with libarchive; see download_data.sh diff --git a/examples/diffdock/Dockerfile_diffdock_cpu b/examples/diffdock/Dockerfile_diffdock_cpu index 31870923..ffc430bf 100644 --- a/examples/diffdock/Dockerfile_diffdock_cpu +++ b/examples/diffdock/Dockerfile_diffdock_cpu @@ -1,6 +1,6 @@ # docker build -f Dockerfile_diffdock_cpu -t mrbrandonwalker/diffdock_cpu . -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (torch-scatter is incompatible with pypy) RUN apt-get update && apt-get install -y wget git build-essential diff --git a/examples/diffdock/Dockerfile_diffdock_gpu b/examples/diffdock/Dockerfile_diffdock_gpu index 9d873d27..3a1bde06 100644 --- a/examples/diffdock/Dockerfile_diffdock_gpu +++ b/examples/diffdock/Dockerfile_diffdock_gpu @@ -5,12 +5,12 @@ FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu20.04 as devel # Install conda / mamba RUN apt-get update && apt-get install -y wget git build-essential -RUN CONDA="Mambaforge-Linux-x86_64.sh" && \ +RUN CONDA="Miniforge3-Linux-x86_64.sh" && \ wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/$CONDA && \ chmod +x $CONDA && \ - ./$CONDA -b -p /mambaforge && \ + ./$CONDA -b -p /miniforge && \ rm -f $CONDA -ENV PATH /mambaforge/bin:$PATH +ENV PATH /miniforge/bin:$PATH RUN conda install pytorch==1.13.0 pytorch-cuda=11.7 pytorch-cluster -c pytorch -c nvidia -c pyg @@ -50,9 +50,9 @@ RUN mamba clean --all --yes FROM nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu20.04 as runtime COPY --from=devel DiffDock/ DiffDock/ -COPY --from=devel mambaforge/ mambaforge/ +COPY --from=devel miniforge/ miniforge/ # shell file to copy cached files, run diffdock and remove large cached files after execution ADD diffdock_cmds.sh /DiffDock/ -ENV PATH /mambaforge/bin:$PATH +ENV PATH /miniforge/bin:$PATH diff --git a/examples/diffdock/Dockerfile_pose_cluster_filter b/examples/diffdock/Dockerfile_pose_cluster_filter index cceb2f72..e248d231 100644 --- a/examples/diffdock/Dockerfile_pose_cluster_filter +++ b/examples/diffdock/Dockerfile_pose_cluster_filter @@ -1,7 +1,7 @@ # docker build -f Dockerfile_pose_cluster_filter -t mrbrandonwalker/pose_cluster_filter . -FROM condaforge/mambaforge +FROM condaforge/miniforge3 RUN conda install -c conda-forge rdkit --yes diff --git a/examples/diffdock/Dockerfile_sanitize_ligand b/examples/diffdock/Dockerfile_sanitize_ligand index c4465309..321be63c 100644 --- a/examples/diffdock/Dockerfile_sanitize_ligand +++ b/examples/diffdock/Dockerfile_sanitize_ligand @@ -1,7 +1,7 @@ # docker build -f Dockerfile_sanitize_ligand -t mrbrandonwalker/sanitize_ligand . -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy) RUN conda install -c conda-forge rdkit --yes diff --git a/examples/scripts/Dockerfile_align_protein_ca_mda b/examples/scripts/Dockerfile_align_protein_ca_mda index 548e9ea4..64bb5f0d 100644 --- a/examples/scripts/Dockerfile_align_protein_ca_mda +++ b/examples/scripts/Dockerfile_align_protein_ca_mda @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy) RUN mamba install -c conda-forge mdanalysis diff --git a/examples/scripts/Dockerfile_align_protein_ca_pymol b/examples/scripts/Dockerfile_align_protein_ca_pymol index 1f67ac8a..132e7963 100644 --- a/examples/scripts/Dockerfile_align_protein_ca_pymol +++ b/examples/scripts/Dockerfile_align_protein_ca_pymol @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis & pymol are incompatible with pypy) RUN mamba install -c conda-forge mdanalysis diff --git a/examples/scripts/Dockerfile_atomselect b/examples/scripts/Dockerfile_atomselect index b0eed5ae..7e9800e6 100644 --- a/examples/scripts/Dockerfile_atomselect +++ b/examples/scripts/Dockerfile_atomselect @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdtraj is incompatible with pypy) RUN mamba install -c conda-forge mdtraj diff --git a/examples/scripts/Dockerfile_autodock_vina b/examples/scripts/Dockerfile_autodock_vina index 39e7f307..ad8ed0db 100644 --- a/examples/scripts/Dockerfile_autodock_vina +++ b/examples/scripts/Dockerfile_autodock_vina @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge-pypy3 +FROM condaforge/miniforge3-pypy3 # The latest release version 1.2.3 has several known bugs. # See https://github.com/ccsb-scripps/AutoDock-Vina/pull/81 diff --git a/examples/scripts/Dockerfile_calculate_net_charge b/examples/scripts/Dockerfile_calculate_net_charge index 6c39c4d4..df06c1de 100644 --- a/examples/scripts/Dockerfile_calculate_net_charge +++ b/examples/scripts/Dockerfile_calculate_net_charge @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy) RUN mamba install -c conda-forge rdkit diff --git a/examples/scripts/Dockerfile_combine_structure b/examples/scripts/Dockerfile_combine_structure index b8c746de..eba7752e 100644 --- a/examples/scripts/Dockerfile_combine_structure +++ b/examples/scripts/Dockerfile_combine_structure @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy) RUN mamba install -c conda-forge rdkit diff --git a/examples/scripts/Dockerfile_extract_ligand_protein b/examples/scripts/Dockerfile_extract_ligand_protein index 2454a306..d9c7cd35 100644 --- a/examples/scripts/Dockerfile_extract_ligand_protein +++ b/examples/scripts/Dockerfile_extract_ligand_protein @@ -1,5 +1,5 @@ # docker build -f Dockerfile_extract_ligand_protein -t mrbrandonwalker/extract_ligand_protein . -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy) RUN mamba install mdanalysis diff --git a/examples/scripts/Dockerfile_extract_protein b/examples/scripts/Dockerfile_extract_protein index 9cf53d09..4c7bbb10 100644 --- a/examples/scripts/Dockerfile_extract_protein +++ b/examples/scripts/Dockerfile_extract_protein @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge-pypy3 +FROM condaforge/miniforge3-pypy3 RUN mamba install -c conda-forge openmm diff --git a/examples/scripts/Dockerfile_fix_pdb_atom_column b/examples/scripts/Dockerfile_fix_pdb_atom_column index 0f757329..abbea63a 100644 --- a/examples/scripts/Dockerfile_fix_pdb_atom_column +++ b/examples/scripts/Dockerfile_fix_pdb_atom_column @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy) RUN mamba install -c conda-forge mdanalysis diff --git a/examples/scripts/Dockerfile_generate_conformers b/examples/scripts/Dockerfile_generate_conformers index 22e37605..6bc0b990 100644 --- a/examples/scripts/Dockerfile_generate_conformers +++ b/examples/scripts/Dockerfile_generate_conformers @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (pandas & rdkit are incompatible with pypy) RUN mamba install -c conda-forge pandas rdkit openpyxl xorg-libxrender diff --git a/examples/scripts/Dockerfile_mol2_to_pdbqt b/examples/scripts/Dockerfile_mol2_to_pdbqt index a975f617..145db3fa 100644 --- a/examples/scripts/Dockerfile_mol2_to_pdbqt +++ b/examples/scripts/Dockerfile_mol2_to_pdbqt @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy) RUN mamba install -c conda-forge mdanalysis diff --git a/examples/scripts/Dockerfile_molgan b/examples/scripts/Dockerfile_molgan index ed03c146..48355ce9 100644 --- a/examples/scripts/Dockerfile_molgan +++ b/examples/scripts/Dockerfile_molgan @@ -1,5 +1,5 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy) # RDKIT logging diff --git a/examples/scripts/Dockerfile_nmr4md b/examples/scripts/Dockerfile_nmr4md index e5e54529..59af7475 100644 --- a/examples/scripts/Dockerfile_nmr4md +++ b/examples/scripts/Dockerfile_nmr4md @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy) RUN mamba install -c conda-forge mdanalysis matplotlib pip diff --git a/examples/scripts/Dockerfile_onionnet-sfct b/examples/scripts/Dockerfile_onionnet-sfct index 604d8dd8..025256ab 100644 --- a/examples/scripts/Dockerfile_onionnet-sfct +++ b/examples/scripts/Dockerfile_onionnet-sfct @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (pandas & rdkit & mdtraj are incompatible with pypy) # Install requirements diff --git a/examples/scripts/Dockerfile_openbabel b/examples/scripts/Dockerfile_openbabel index f9c2d0b7..57899100 100644 --- a/examples/scripts/Dockerfile_openbabel +++ b/examples/scripts/Dockerfile_openbabel @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (openbabel is incompatible with pypy) RUN mamba install -c conda-forge openbabel diff --git a/examples/scripts/Dockerfile_pdbbind_refined b/examples/scripts/Dockerfile_pdbbind_refined index b0b77b6e..eb69ed40 100644 --- a/examples/scripts/Dockerfile_pdbbind_refined +++ b/examples/scripts/Dockerfile_pdbbind_refined @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge +FROM condaforge/miniforge3 # NOT mambaforge-pypy3 (pandas is incompatible with pypy) RUN apt-get update && apt-get install -y wget diff --git a/examples/scripts/Dockerfile_pdbfixer b/examples/scripts/Dockerfile_pdbfixer index 6a310128..754d9b30 100644 --- a/examples/scripts/Dockerfile_pdbfixer +++ b/examples/scripts/Dockerfile_pdbfixer @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge-pypy3 +FROM condaforge/miniforge3-pypy3 RUN mamba install -c conda-forge pdbfixer diff --git a/examples/scripts/Dockerfile_smina b/examples/scripts/Dockerfile_smina index a850201b..79396bd1 100644 --- a/examples/scripts/Dockerfile_smina +++ b/examples/scripts/Dockerfile_smina @@ -1,4 +1,4 @@ -FROM condaforge/mambaforge-pypy3 +FROM condaforge/miniforge3-pypy3 # Prevent being prompted for geographical region ARG DEBIAN_FRONTEND=noninteractive diff --git a/install/install_nglview.sh b/install/install_nglview.sh index cbb993e1..07ee1c90 100755 --- a/install/install_nglview.sh +++ b/install/install_nglview.sh @@ -1,7 +1,7 @@ #!/bin/bash -e # NOTE: mamba is a drop-in replacement for conda, just much faster. # (i.e. You can replace mamba with conda below.) -# See https://github.com/conda-forge/miniforge#mambaforge-pypy3 +# See https://github.com/conda-forge/miniforge#miniforge-pypy3 CONDA=conda if [ "$(which mamba)" ]; then CONDA=mamba diff --git a/install/install_system_deps.bat b/install/install_system_deps.bat index b6f4c470..f7cba564 100644 --- a/install/install_system_deps.bat +++ b/install/install_system_deps.bat @@ -1,6 +1,6 @@ :: NOTE: mamba is a drop-in replacement for conda, just much faster. :: (i.e. You can replace mamba with conda below.) -:: See https://github.com/conda-forge/miniforge#mambaforge-pypy3 +:: See https://github.com/conda-forge/miniforge#miniforge-pypy3 set CONDA=conda where /q mamba if not ERRORLEVEL 1 (set CONDA=mamba) diff --git a/install/install_system_deps.sh b/install/install_system_deps.sh index 54a04192..c68cd25c 100755 --- a/install/install_system_deps.sh +++ b/install/install_system_deps.sh @@ -1,7 +1,7 @@ #!/bin/bash -e # NOTE: mamba is a drop-in replacement for conda, just much faster. # (i.e. You can replace mamba with conda below.) -# See https://github.com/conda-forge/miniforge#mambaforge-pypy3 +# See https://github.com/conda-forge/miniforge#miniforge-pypy3 CONDA=conda if [ "$(which mamba)" ]; then CONDA=mamba