chore: fix conda installs (#54)

* chore: do not use the defaults channel * chore: use mamba everywhere
SwissDataScienceCenter · Oct 27, 2023 · 46a5d58 · 46a5d58
1 parent 58ac753
commit 46a5d58
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Showing 11 changed files with 10 additions and 12 deletions.
diff --git a/Renv/environment.yml b/Renv/environment.yml
@@ -1,6 +1,6 @@
 name: "base"
 channels:
-  - defaults
+  - conda-forge
 # dependencies:
 # - add packages here
 # - one per line

diff --git a/aiida/Dockerfile b/aiida/Dockerfile
@@ -18,7 +18,7 @@ USER ${NB_USER}
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml
+RUN mamba env update -q -f /tmp/environment.yml
 
 # get around pyyaml upgrade error ("Cannot uninstall 'PyYAML'. It is a distutils installed project...")
 RUN /opt/conda/bin/pip install --upgrade --force-reinstall pip==9.0.3 && \

diff --git a/aiida/environment.yml b/aiida/environment.yml
@@ -1,7 +1,6 @@
 name: "base"
 channels:
   - conda-forge
-  - defaults
   - cjs14
 dependencies:
 # - aiida-core

diff --git a/desktop/Dockerfile b/desktop/Dockerfile
@@ -18,7 +18,7 @@ FROM renku/renkulab-vnc:0.20.0
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
+RUN mamba env update -q -f /tmp/environment.yml && \
     /opt/conda/bin/pip install -r /tmp/requirements.txt && \
     conda clean -y --all && \
     conda env export -n "root"

diff --git a/desktop/environment.yml b/desktop/environment.yml
@@ -1,6 +1,6 @@
 name: "base"
 channels:
-  - defaults
+  - conda-forge
 # dependencies:
 # - add packages here
 # - one per line

diff --git a/matlab/Dockerfile b/matlab/Dockerfile
@@ -18,7 +18,7 @@ FROM renku/renkulab-matlab:0.20.0
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
+RUN mamba env update -q -f /tmp/environment.yml && \
     /opt/conda/bin/pip install -r /tmp/requirements.txt && \
     conda clean -y --all && \
     conda env export -n "root"

diff --git a/matlab/environment.yml b/matlab/environment.yml
@@ -1,6 +1,6 @@
 name: "base"
 channels:
-  - defaults
+  - conda-forge
 # dependencies:
 # - add packages here
 # - one per line

diff --git a/python-minimal-streamlit/Dockerfile b/python-minimal-streamlit/Dockerfile
@@ -18,15 +18,15 @@ FROM renku/renkulab-py:3.10-0.20.0
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
+RUN mamba env update -q -f /tmp/environment.yml && \
     /opt/conda/bin/pip install -r /tmp/requirements.txt && \
     conda clean -y --all && \
     conda env export -n "root"
 
 # RENKU_VERSION determines the version of the renku CLI
 # that will be used in this image. To find the latest version,
 # visit https://pypi.org/project/renku/#history.
-ARG RENKU_VERSION={{ __renku_version__ | default("1.2.4") }}
+ARG RENKU_VERSION={{ __renku_version__ | default("2.6.2") }}
 
 # to run streamlit
 COPY jupyter_notebook_config.py ${HOME}/.jupyter/

diff --git a/python-minimal-streamlit/environment.yml b/python-minimal-streamlit/environment.yml
@@ -1,6 +1,5 @@
 name: "base"
 channels:
-  - defaults
   - conda-forge
 dependencies:
   - pip

diff --git a/qgis/Dockerfile b/qgis/Dockerfile
@@ -18,7 +18,7 @@ FROM renku/renkulab-qgis:0.20.0
 
 # install the python dependencies
 COPY requirements.txt environment.yml /tmp/
-RUN conda env update -q -f /tmp/environment.yml && \
+RUN mamba env update -q -f /tmp/environment.yml && \
     /opt/conda/bin/pip install -r /tmp/requirements.txt && \
     conda clean -y --all && \
     conda env export -n "root"

diff --git a/qgis/environment.yml b/qgis/environment.yml
@@ -1,6 +1,6 @@
 name: "base"
 channels:
-  - defaults
+  - conda-forge
 # dependencies:
 # - add packages here
 # - one per line