Merge pull request #5715 from shaneknapp/hub-wide-python-bumps

[DH-246] bump python to 3.11
berkeley-dsep-infra · May 14, 2024 · 775fce0 · 775fce0
2 parents 17ef348 + 2a315c5
commit 775fce0
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diff --git a/deployments/a11y/image/environment.yml b/deployments/a11y/image/environment.yml
@@ -4,7 +4,7 @@ channels:
 - conda-forge
 
 dependencies:
-- python==3.11.0
+- python==3.11.*
 - git==2.40.0
 - coverage==7.2.2
 - jupyter-archive==3.4.0

diff --git a/deployments/astro/image/environment.yml b/deployments/astro/image/environment.yml
@@ -5,27 +5,29 @@ channels:
 - pytorch
 
 dependencies:
-- python=3.9.*
+- python=3.11.*
 - jupyter-server-proxy==4.1.2
 # A linux desktop environment
 - websockify
 
 - syncthing==1.18.6
 
-- numpy==1.22.*
-- matplotlib==3.5.*
+- numpy==1.26.*
+- matplotlib==3.8.*
 - graphviz>=2.50.0
 - psycopg2==2.9.*
-- pytorch==2.2.2
-- torchvision==0.17.2
+- pytorch==2.3.0
+- torchvision==0.18.*
 - pytorch-lightning==2.2.1
 - pyaudio==0.2.11
 - cython
 - cartopy
 - protobuf
+- mkl
+- mkl-service
 - mpich
 - mpi4py
-- scikit-learn==1.0.*
+- scikit-learn==1.4.*
 - scikit-image==0.19.*
 - scipy==1.11.3
 - pip
@@ -58,8 +60,6 @@ dependencies:
   - pyvo>=1.2
   - joblib==1.2.0
   - aesara>=2.3.4
-  - mkl==2024.0.0
-  - mkl-service
   - pymc3>=3.11.4
   - requests>=2.27.1
   - ipycanvas

diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile
@@ -123,10 +123,6 @@ RUN apt-get update -qq --yes > /dev/null && \
 
 WORKDIR /home/jovyan
 
-COPY install-mambaforge.bash /tmp/install-mambaforge.bash
-RUN chmod 777 /tmp/install-mambaforge.bash
-RUN /tmp/install-mambaforge.bash
-
 # Needed by RStudio
 RUN apt-get update -qq --yes && \
     apt-get install --yes --no-install-recommends -qq \
@@ -164,6 +160,10 @@ RUN apt-get update -qq --yes && \
     apt-get install --yes  -qq \
         libcurl4-openssl-dev > /dev/null
 
+COPY install-mambaforge.bash /tmp/install-mambaforge.bash
+RUN chmod 777 /tmp/install-mambaforge.bash
+RUN /tmp/install-mambaforge.bash
+
 USER ${NB_USER}
 
 COPY environment.yml /tmp/

diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml
@@ -2,7 +2,7 @@ channels:
 - bioconda
 - conda-forge
 dependencies:
-- python=3.9.*
+- python=3.11.*
 - pip=22.2.*
 
 # Package to allow Jupyter Notebook or JupyterLab applications in one conda env to access other kernels (e.g. qiime2)
@@ -34,10 +34,10 @@ dependencies:
 - syncthing==1.18.6
 
 # Packages for IB120/201/CCB210
-- sympy=1.6.2
+- sympy=1.12
 
 # Packages from bioconda for BioE-131, Fall 2020, Issue #1885
-- bowtie2=2.4.2
+# - bowtie2=2.5.3  # commented out by sknapp 2024.05.07 doesn't support py3.11
 - spades=3.14.1
 
 # Packages for MCB280A, Spring 2022
@@ -48,30 +48,30 @@ dependencies:
 - muscle=3.8.*
 - dendropy=4.4.*
 
-
 # pedagogy packages
-- scipy=1.7.1
-- pandas=1.3.2
+- scipy=1.11.
+- pandas=2.2.2
 - seaborn=0.11.2
 
 # compbio BioE c146, Fall 22 and into the future, issue 3785
-- scikit-learn=1.1.2
+- scikit-learn=1.2.2
 
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048
 - traitlets=5.9.*
 
 # For https://github.com/berkeley-dsep-infra/datahub/issues/1846
 # Conda does not have these
 - pip:
+  - -r infra-requirements.txt
 # MCB280A, Spring 2022
-  - pybedtools==0.9.0
+  - pybedtools==0.10.0
 # removed for PR https://github.com/berkeley-dsep-infra/datahub/pull/4406 - macs2==2.2.7.1
-  - geonomics==1.1.9
-  - nlmpy==1.0.1
-  - datascience==0.17.5
-  - -r infra-requirements.txt
+  - geonomics==1.4.1
+  - nlmpy==1.2.0
+  - datascience==0.17.6
+
 # Packages for MCB-160L iss #3942
-  - allensdk==2.13.6
+  - allensdk==2.16.2
   - otter-grader==3.1.4
 # for exporting notebooks to pdf
   - nbconvert==7.6.0

diff --git a/deployments/biology/image/install-mambaforge.bash b/deployments/biology/image/install-mambaforge.bash
@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION='23.1.0-1'
+MAMBAFORGE_VERSION='24.3.0-0'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh

diff --git a/deployments/cee/image/environment.yml b/deployments/cee/image/environment.yml
@@ -4,7 +4,7 @@ channels:
 # Almost all libraries should be added in requirements.txt
 # Only libraries *not* available in PyPI should be here
 dependencies:
-- python=3.9.*
+- python=3.11.*
 - jupyter-server-proxy==4.1.2
 #adding math functionality 
 - matplotlib=3.7.*

diff --git a/deployments/data100/image/environment.yml b/deployments/data100/image/environment.yml
@@ -5,7 +5,7 @@ channels:
 - pytorch
 
 dependencies:
-- python==3.11.0
+- python==3.11.*
 - git==2.39.1
 - jupyter-resource-usage==1.0.0
 - jupyterlab==4.0.11

diff --git a/deployments/data101/image/environment.yml b/deployments/data101/image/environment.yml
@@ -4,7 +4,7 @@ channels:
 - conda-forge
 
 dependencies:
-- python==3.11.0
+- python==3.11.*
 - syncthing==1.20.4
 - git==2.39.1
 - altair==5.0.1

diff --git a/deployments/data102/image/environment.yml b/deployments/data102/image/environment.yml
@@ -5,7 +5,7 @@ channels:
 - pytorch
 
 dependencies:
-- python==3.11.3
+- python==3.11.*
 - git==2.39.1
 - bambi==0.12.0
 - graphviz==8.0.3

diff --git a/deployments/data8/image/environment.yml b/deployments/data8/image/environment.yml
@@ -1,7 +1,7 @@
 dependencies:
 #- nodejs==15.*
 - pip==20.2.*
-- python==3.9.*
+- python==3.11.*
 
 # Packages ported from infra-reqs
 - jupyterhub==4.1.5
@@ -15,14 +15,14 @@ dependencies:
 - jupyter-archive==3.4.0
 - jupyterlab==4.0.11
 - jupyter_server==2.7.0
-- matplotlib==3.4.3
+- matplotlib==3.8.*
 - nbclassic==1.0.0
 - notebook==7.0.7
 - otter-grader==4.3.4 # Based on request from ericvd and sean.morris
 - ipympl==0.7.0
-- pandas==1.3.2
+- pandas==2.2.2
 - scipy==1.11.3
-- statsmodels==0.12.2
+- statsmodels==0.14.1
 - seaborn==0.11.2
 # Otter is pulled in via infra-requirements.txt, since it's present in all hubs
 # Spring 2023 https://github.com/berkeley-dsep-infra/datahub/issues/4291
@@ -33,6 +33,7 @@ dependencies:
 
 # Items not in conda forge
 - pip:
+  - attrs==23.2.0
 #- -r infra-requirements.txt
   - jupyter-tree-download==1.0.1
 # Export notebooks as PDFs with Chrome

diff --git a/deployments/datahub/images/default/environment.yml b/deployments/datahub/images/default/environment.yml
@@ -5,7 +5,7 @@ dependencies:
 - nodejs=16.*
 - traitlets=5.9.*
 - pip=22.2.*
-- python=3.9.*
+- python=3.11.*
 - syncthing==1.18.6
 - nbclassic==1.0.0
 
@@ -14,18 +14,18 @@ dependencies:
 
 # Base scientific packages that other conda packages we install depend on
 # We don't want to have conda packages depend on pip packages if possible
-- numpy=1.22.*
+- numpy=1.26.*
 - matplotlib=3.7.*
 - scipy=1.10.0
 - ipympl=0.9.*
-- pandas=1.3.*
+- pandas==2.2.2
 - statsmodels=0.13.5
-- scikit-learn=1.1.1
+- scikit-learn=1.4.*
 - seaborn=0.11.*
 # - bokeh=2.3.*
 - decorator=5.0.*
 - networkx=2.6.*
-- spacy=3.4.1
+- spacy=3.7.3
 - nltk=3.6.*
 
 # 3577, L&S 22, Spring 2023
@@ -37,11 +37,11 @@ dependencies:
 # EPS88, data100
 # https://github.com/berkeley-dsep-infra/datahub/issues/1796
 # https://github.com/berkeley-dsep-infra/datahub/issues/2824
-- shapely==1.8.0
-- cartopy==0.22.0
+- shapely==2.0.4
+- cartopy==0.23.0
 
 # ls 88-3; neuro
-- pillow=8.3.*
+- pillow=10.3.0
 
 # music 30, spring 2022, https://github.com/berkeley-dsep-infra/datahub/issues/3180
 - pysoundfile==0.10.3.post1
@@ -81,7 +81,7 @@ dependencies:
 - beautifulsoup4==4.9.3
 
 # PS88 https://github.com/berkeley-dsep-infra/datahub/issues/2925
-- linearmodels==5.4
+- linearmodels==6.0
 
 # JupyterLab pypi extensions
 - jupyterlab-geojson==3.4.0
@@ -93,7 +93,7 @@ dependencies:
 - contextily==1.1.0
 
 # EPS 256, https://github.com/berkeley-dsep-infra/datahub/issues/1775
-- obspy==1.3.0
+- obspy==1.4.1
 
 - pip:
   # - -r /tmp/infra-requirements.txt
@@ -136,10 +136,10 @@ dependencies:
   - ffmpeg-python==0.2.0
 
   # issue #875, global 150Q/pacs 190 - fall 2019
-  - wordcloud==1.8.1
+  - wordcloud==1.9.3
 
   # issue #929, SW 282 - fall 2019
-  - pyreadstat==1.1.2
+  - pyreadstat==1.2.7
 
   # issue 954, EPS24 - fall 2019
   - xarray==0.19.0

diff --git a/deployments/datahub/images/default/install-mambaforge.bash b/deployments/datahub/images/default/install-mambaforge.bash
@@ -3,7 +3,7 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION='23.1.0-1'
+MAMBAFORGE_VERSION='24.3.0-0'
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh

diff --git a/deployments/dev-r/images/default/environment.yml b/deployments/dev-r/images/default/environment.yml
@@ -1,5 +1,5 @@
 dependencies:
-- python=3.10.*
+- python=3.11.* # mamba installation with py3.11 fails: No module named 'conda.cliconda'
 - pip=23.1.*
 - nodejs=18.*
 # bug w/notebook and traitlets: https://github.com/jupyter/notebook/issues/7048

diff --git a/deployments/dev-r/images/default/install-mambaforge.bash b/deployments/dev-r/images/default/install-mambaforge.bash
@@ -7,7 +7,7 @@
 set -ex
 
 cd $(dirname $0)
-MAMBAFORGE_VERSION=23.1.0-1
+MAMBAFORGE_VERSION=24.3.0-0
 
 URL="https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-x86_64.sh"
 INSTALLER_PATH=/tmp/mambaforge-installer.sh

diff --git a/deployments/dev-r/images/secondary/environment.yml b/deployments/dev-r/images/secondary/environment.yml
@@ -1,5 +1,5 @@
 dependencies:
-- python=3.10
+- python=3.11.*
 - pip=23.2.*
 - jupyter-server-proxy==4.1.2
 - jupyter-rsession-proxy==2.2.0

diff --git a/deployments/eecs/image/environment.yml b/deployments/eecs/image/environment.yml
@@ -4,7 +4,7 @@ channels:
 # Almost all libraries should be added in requirements.txt
 # Only libraries *not* available in PyPI should be here
 dependencies:
-- python=3.9.*
+- python=3.11.*
 - nbclassic==1.0.0
 
 - jupyter-server-proxy==4.1.2
@@ -23,31 +23,31 @@ dependencies:
 - cxx-compiler=1.4.2
 - fortran-compiler=1.4.2
 - gdb=11.2
-- libopenblas=0.3.17
+- libopenblas=0.3.27
 - liblapack=3.9.0
 - armadillo=9.900.5
 - gperf=3.1
 # CS 16A
 # From https://github.com/berkeley-dsep-infra/datahub/issues/1363#issuecomment-598916469
-- numpy=1.21.2
-- matplotlib=3.4.3
-- sympy=1.8
+- numpy=1.26.*
+- matplotlib=3.8.*
+- sympy=1.12
 
 # For EECS127/227a
 # See https://github.com/berkeley-dsep-infra/datahub/issues/1631
-- cvxpy=1.2.1
+- cvxpy=1.4.3
 # See https://github.com/berkeley-dsep-infra/datahub/issues/1936
-- scikit-learn=0.24.2
+- scikit-learn=1.4.*
 
 # For CHEM279
 # See https://github.com/berkeley-dsep-infra/datahub/issues/2717
 - git=2.33.0
 
 # From https://github.com/berkeley-dsep-infra/datahub/issues/1505
-- Pillow=8.3.1
+- Pillow=10.3.0
 
 # For ELENG 120 https://github.com/berkeley-dsep-infra/datahub/issues/3566
-- scipy=1.9.0
+- scipy=1.11.3
 - gcc=10.4.0
 
 # https://github.com/berkeley-dsep-infra/datahub/issues/4460
@@ -60,7 +60,7 @@ dependencies:
 - pip
 - pip:
 # From https://github.com/berkeley-dsep-infra/datahub/issues/1639
-  - opencv-python==4.5.3.56
+  - opencv-python==4.9.0.80
   - PyQt5==5.15.4
 # From https://github.com/berkeley-dsep-infra/datahub/issues/1363#issuecomment-598916469
   - lcapy==0.96

diff --git a/deployments/julia/image/environment.yml b/deployments/julia/image/environment.yml
@@ -2,7 +2,7 @@ dependencies:
 - jupyter-server-proxy==4.1.2
 - nodejs==20.8.1
 - pip==22.3.1
-- python==3.10.13
+- python==3.11.*
 - requests==2.31.0
 
 - syncthing==1.18.6