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Fix mamba installation. #180

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Merged
fernandohds564 merged 19 commits into from
Dec 9, 2025
Merged

Fix mamba installation. #180

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c925372
MNT: Change installer filename for mamba. Now it's Miniforge3.
fernandohds564 Jun 5, 2025
584c0ae
MNT: file mamba.sh is deprecated. change way of initializing mamba.
fernandohds564 Jun 5, 2025
b90f444
MNT: build package is not being installed with mamba anymore. install…
fernandohds564 Jun 5, 2025
bab42cf
MNT: Update pyepics to 3.5.7 to remove pkg_recources dependency for t…
fernandohds564 Jun 9, 2025
e2878c2
BUG: Deactivate before creating deactivation file.
fernandohds564 Jun 18, 2025
6c5f0b4
MNT: do not use --freeze-installed in first call of mamba packages in…
fernandohds564 Jun 18, 2025
a4f3e2a
ENH: Add seaborn to the list of packages to be installed.
fernandohds564 Jun 18, 2025
2832ba0
BUG: Fix problem with ENV_NAME value substitution in `here files`.
fernandohds564 Jun 30, 2025
9365879
MAMBA.MNT: Remove alias for repos inside repos folder in conda enviro…
fernandohds564 Jul 7, 2025
c321c2f
MAMBA.ENH: use repository insertion-devices from lnls-ids instead of …
fernandohds564 Jul 7, 2025
417baf1
MAMBA.ENH: Change default of script to do not clone repos.
fernandohds564 Jul 7, 2025
f34b586
MAMBA.ENH: Define only one path of root folder to find packages.
fernandohds564 Jul 7, 2025
0e43b2d
MAMBA.ENH: use a more robust way of finding out repositories.
fernandohds564 Jul 7, 2025
0cf83d3
MAMBA.STY: use better syntax for defining functions and define local …
fernandohds564 Jul 7, 2025
480226b
MAMBA.MNT: remove deprecated comment in code.
fernandohds564 Jul 7, 2025
fe56491
MAMBA.MNT: Adapt to new workflow in Radia package, defined in lnls-si…
fernandohds564 Jul 7, 2025
453989d
MAMBA.ENH: Change default folder for cloning repos to ~/repos. Add in…
fernandohds564 Jul 7, 2025
9f5c2e5
MAMBA.FIX: Define variable needed to create activation files.
fernandohds564 Aug 7, 2025
b1efa7e
MAMBA.MNT: Add print at the end of execution.
fernandohds564 Aug 7, 2025
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23 changes: 12 additions & 11 deletions bin/sirius-script-mamba-env-create.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -281,9 +281,10 @@ printf_yellow_clear "Install mamba in path /opt/mamba_files/mamba: "
cd /opt/mamba_files
if ! [ -d mamba ]
then
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
sh Mambaforge-Linux-x86_64.sh -b -p /opt/mamba_files/mamba
rm Mambaforge-Linux-x86_64.sh
fname="Miniforge3-Linux-x86_64.sh"
wget https://github.com/conda-forge/miniforge/releases/latest/download/$fname
sh $fname -b -p /opt/mamba_files/mamba
rm $fname
printf_green "done!\n"
else
printf_blue "there already is a mamba installation. Skipping...\n"
Expand All @@ -296,22 +297,21 @@ sudo chown -R $USER:mamba ~/.conda

printf_yellow_clear "Adding mamba and conda to path\n"
source /opt/mamba_files/mamba/etc/profile.d/conda.sh
source /opt/mamba_files/mamba/etc/profile.d/mamba.sh
export MAMBA_ROOT_PREFIX='/opt/mamba_files/mamba'
eval "$(mamba shell hook --shell bash)"

printf_yellow_clear "Adding mamba and conda paths to .bashrc: "
cd ~/
if ! grep -q "MAMBA_ADD" .bashrc;
if ! grep -q "CONDA_ADD" .bashrc;
then
cat >> ~/.bashrc <<'EOM'
# add conda and mamba to path
MAMBA_ADD=/opt/mamba_files/mamba/etc/profile.d/mamba.sh
if [ -f "$MAMBA_ADD" ] ; then
source "$MAMBA_ADD"
fi
CONDA_ADD=/opt/mamba_files/mamba/etc/profile.d/conda.sh
if [ -f "$CONDA_ADD" ] ; then
source "$CONDA_ADD"
fi
export MAMBA_ROOT_PREFIX='/opt/mamba_files/mamba'
eval "$(mamba shell hook --shell bash)"
EOM
printf_green "done!\n"
else
Expand Down Expand Up @@ -347,7 +347,8 @@ printf_yellow "Install some mamba packages in $ENV_NAME environment.\n"
COMM="mamba install --freeze-installed -y"

printf_yellow_clear "- System and generic python packages:\n"
$COMM gxx make binutils swig=4.2.0 libxcrypt build gsl libblas wmctrl fftw \
pip install build
$COMM gxx make binutils swig=4.2.0 libxcrypt gsl libblas wmctrl fftw \
pyparsing bottleneck aiohttp==3.7.4 numpy=1.23 scipy matplotlib \
pytest mpmath entrypoints requests pyqt=5.12.3 pandas pyqtgraph=0.11.0 \
qtpy=2.3.1 QtAwesome=0.7.2 numexpr tk sh pywavelets scikit-image \
Expand All @@ -358,7 +359,7 @@ printf_yellow_clear "- Install EPICS Base:\n"
$COMM -c conda-forge/label/cf202003 epics-base=3.15.6

printf_yellow_clear "- And some other EPICS packages:\n"
$COMM pyepics=3.5.0 pcaspy==0.7.3 pydm=1.10.3 timechart=1.2.3
$COMM pyepics=3.5.7 pcaspy==0.7.3 pydm=1.10.3 timechart=1.2.3
# remove the activate and deactivate files created by pyepics and pydm:
cd $CONDA_PREFIX/etc/conda/activate.d
if [ -f "pydm.bat" ]
Expand Down