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Let's try using more Conda #78

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988c2e6
will it conda
xrl Apr 17, 2024
6fa4d68
install conda
xrl Apr 17, 2024
b9d6ebb
packages
xrl Apr 17, 2024
269b81b
packages
xrl Apr 17, 2024
521bf5f
ld library path
xrl Apr 17, 2024
503ce18
how about miniconda
xrl Apr 17, 2024
d89772a
don't install by hand
xrl Apr 17, 2024
18a29bc
don't install by hand
xrl Apr 17, 2024
cb4939c
will the envs folder work
xrl Apr 17, 2024
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14 changes: 11 additions & 3 deletions .github/workflows/test_suite.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ jobs:
test:
env:
ARCH: amd64
CARGO_FEATURE_DYNAMIC_LINKING_FROM_CONDA: yes
runs-on: buildjet-16vcpu-ubuntu-2204
permissions:
contents: read
Expand All @@ -26,11 +27,18 @@ jobs:
shell: bash
run: ${SCCACHE_PATH} --show-stats

- name: Miniconda Setup
uses: conda-incubator/setup-miniconda@v3
with:
channels: conda-forge,defaults
channel-priority: true
activate-environment: cheminee

- name: Install rdkit
run: |
sudo bash -c "echo 'deb [trusted=yes] https://rdkit-rs-debian.s3.amazonaws.com jammy main' > /etc/apt/sources.list.d/rdkit-rs.list"
conda install conda-forge::rdkit
sudo apt-get update
sudo apt-get install -y build-essential librdkit-dev libssl-dev libboost1.74-dev libboost-serialization1.74-dev pkg-config
sudo apt-get install -y build-essential libssl-dev libboost1.74-dev libboost-serialization1.74-dev pkg-config

- name: Install latest stable
uses: actions-rs/toolchain@v1
Expand All @@ -40,4 +48,4 @@ jobs:
components: rustfmt, clippy

- name: Cargo Test
run: RUST_WRAPPER=$SCCACHE_PATH cargo test
run: CONDA_PREFIX=/usr/share/miniconda/envs/cheminee LD_LIBRARY_PATH=/usr/share/miniconda/envs/cheminee/lib RUST_WRAPPER=$SCCACHE_PATH cargo test
11 changes: 8 additions & 3 deletions Dockerfile
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@@ -1,8 +1,13 @@
FROM ubuntu:22.04

RUN apt-get update && apt-get install -y ca-certificates && \
echo 'deb [trusted=yes] https://rdkit-rs-debian.s3.amazonaws.com jammy main' > /etc/apt/sources.list.d/rdkit-rs.list && \
apt-get update && apt-get install -y librdkit1 libssl3 libboost-serialization1.74.0
RUN apt-get update && apt-get install -y ca-certificates wget && \
wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh && \
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 && \
rm -rf ~/miniconda3/miniconda.sh && \
~/miniconda3/bin/conda install conda-forge::rdkit && \
sudo apt-get update && \
sudo apt-get install -y build-essential libssl-dev libboost1.74-dev libboost-serialization1.74-dev pkg-config && \
apt-get update && apt-get install -y libssl3 libboost-serialization1.74.0

COPY target/release/cheminee /usr/local/bin/cheminee

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