PolusAI · sameeul · Oct 2, 2024 · Oct 1, 2024 · Oct 2, 2024 · Oct 2, 2024
diff --git 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/[email protected]
         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/[email protected]
         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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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