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Change GITHUB_ to GH_ in docker workflow #41

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merged 7 commits into from
Jun 15, 2023
Merged

Change GITHUB_ to GH_ in docker workflow #41

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1ea6a9f
Change GITHUB_ to GH_ in docker workflow
bodom0015 Jun 9, 2023
9dc4b1e
Use/build Python 3.11 only
bodom0015 Jun 9, 2023
0d21c97
Add "conda init" to Dockerfile
bodom0015 Jun 9, 2023
87080f7
Move conda init eariler in the Dockerfile
bodom0015 Jun 9, 2023
aabd400
force docker build to use bash when running conda commands
bodom0015 Jun 9, 2023
d813404
remove bash -c hack, replace with SHELL
bodom0015 Jun 9, 2023
287ccd0
docker container mamba
esalx Jun 15, 2023
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8 changes: 4 additions & 4 deletions .github/workflows/docker.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ name: Docker
# Dockerfile is still valid.
# To be able to push to the GitHub Container Registry, this expects the following
# secrets to be set in the project:
# - GITHUB_USERNAME : username that write push packages to the moleculemaker GitHub org
# - GITHUB_PASSWORD : PAT associated with the username
# - GH_USERNAME : username that write push packages to the moleculemaker GitHub org
# - GH_PASSWORD : PAT associated with the username
on:
push:
branches:
Expand Down Expand Up @@ -59,8 +59,8 @@ jobs:
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ secrets.GITHUB_USERNAME }}
password: ${{ secrets.GITHUB_PASSWORD }}
username: ${{ secrets.GH_USERNAME }}
password: ${{ secrets.GH_PASSWORD }}


- name: Build and push
Expand Down
18 changes: 12 additions & 6 deletions Dockerfile
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@@ -1,5 +1,5 @@
# Start with miniconda3 based on debian:bullseye
FROM continuumio/miniconda3
FROM condaforge/mambaforge
WORKDIR /

# Install essential build tools
Expand All @@ -8,16 +8,22 @@ RUN apt-get -qq update && \
rm -rf /var/cache/apt/archives /var/lib/apt/lists/*

# Configure conda base environment
RUN conda config --add channels conda-forge
RUN conda install conda-build conda-verify -n base
RUN mamba init bash
RUN mamba install boa -n base && mamba clean -afy

# Copy source code into the container image
COPY . /molli/

# Use conda to build provided conda-recipe
RUN conda build molli/
RUN mamba mambabuild --python=3.11 molli/ && mamba clean -afy

# Install the molli executable
RUN conda install molli -c local
# Create + activate a new environment for Python 11
RUN mamba create -y -n molli python=3.11 && mamba clean -afy
RUN echo "mamba activate molli" >> ~/.bashrc
SHELL ["/bin/bash", "--login", "-c"]

# Install the molli package in the new environment
RUN mamba install molli -c local -n molli -y
RUN mamba install --file /molli/optional-deps.txt -y -n molli && mamba clean -afy

ENTRYPOINT ["molli"]
6 changes: 6 additions & 0 deletions optional-deps.txt
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@@ -0,0 +1,6 @@
notebook
py3dmol
openbabel
rdkit
scikit-learn
pandas