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Cap Cython below 3.3 so the pyOpenMS build works again #98

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Merged
t0mdavid-m merged 1 commit into from
Aug 25, 2026
+8 −2
Merged

Cap Cython below 3.3 so the pyOpenMS build works again #98

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5 changes: 4 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,10 @@ RUN echo "mamba activate streamlit-env" >> ~/.bashrc
SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]

RUN pip install --upgrade pip && python -m pip install -U setuptools nose 'Cython>=3.1' 'autowrap==0.24' pandas 'numpy>=2.0' pytest
# Cython is capped below 3.3: autowrap 0.24 reflects on
# Nodes.CConstTypeNode / Nodes.CConstOrVolatileTypeNode, which Cython 3.3
# removed, breaking the pyOpenMS code generation in 'make pyopenms'.
RUN pip install --upgrade pip && python -m pip install -U setuptools nose 'Cython>=3.1,<3.3' 'autowrap==0.24' pandas 'numpy>=2.0' pytest

# Clone OpenMS branch and the associcated contrib+thirdparties+pyOpenMS-doc submodules.
RUN git clone --recursive --depth=1 -b ${OPENMS_BRANCH} --single-branch ${OPENMS_REPO} && cd /OpenMS
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5 changes: 4 additions & 1 deletion Dockerfile.arm
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,10 @@ RUN echo "mamba activate streamlit-env" >> ~/.bashrc
SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]

RUN pip install --upgrade pip && python -m pip install -U setuptools nose 'Cython>=3.1' 'autowrap==0.24' pandas 'numpy>=2.0' pytest
# Cython is capped below 3.3: autowrap 0.24 reflects on
# Nodes.CConstTypeNode / Nodes.CConstOrVolatileTypeNode, which Cython 3.3
# removed, breaking the pyOpenMS code generation in 'make pyopenms'.
RUN pip install --upgrade pip && python -m pip install -U setuptools nose 'Cython>=3.1,<3.3' 'autowrap==0.24' pandas 'numpy>=2.0' pytest

# Clone OpenMS branch and the associcated contrib+thirdparties+pyOpenMS-doc submodules.
RUN git clone --recursive --depth=1 -b ${OPENMS_BRANCH} --single-branch ${OPENMS_REPO} && cd /OpenMS
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