[pull] main from 2i2c-org:main

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
 
   # Autoformat: Python code, syntax patterns are modernized
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.16.0
     hooks:
       - id: pyupgrade
         args:
@@ -39,7 +39,7 @@ repos:
 
   # Lint: Python code
   - repo: https://github.com/pycqa/flake8
-    rev: "7.0.0"
+    rev: "7.1.0"
     hooks:
       - id: flake8
         # This is a `.py` file but is encrypted with sops

config/clusters/catalystproject-latam/plnc.values.yaml

@@ -27,17 +27,16 @@ jupyterhub:
 
   singleuser:
     profileList:
-      - display_name: Jupyter SciPy Notebook
-        description: Python environment
-        slug: jupyter
+      - display_name: "CPU only"
+        description: "Start a container limited to a chosen share of capacity"
+        slug: cpu
         default: true
         kubespawner_override:
-          image: quay.io/jupyter/scipy-notebook:2024-03-04
           default_url: /lab
-        profile_options: &profile_options
-          resource_allocation: &resource_allocation
+        profile_options:
+          requests:
             display_name: Resource Allocation
-            choices:
+            choices: &resource_choices
               mem_0_7:
                 display_name: Up to 2G of RAM and 1 CPU
                 kubespawner_override:
@@ -59,25 +58,36 @@ jupyterhub:
                   mem_limit: 24G
                   cpu_guarantee: 1.5
                   cpu_limit: 3
+          image:
+            display_name: Image
+            unlisted_choice:
+              enabled: True
+              display_name: "Custom image"
+              validation_regex: "^.+:.+$"
+              validation_message: "Must be a publicly available docker image, of form <image-name>:<tag>"
+              kubespawner_override:
+                image: "{value}"
+            choices:
+              rstudio:
+                display_name: Rocker Geospatial with RStudio
+                default: true
+                slug: "rstudio"
+                kubespawner_override:
+                  image: "rocker/binder:4.3"
+                  image_pull_policy: Always
+                  default_url: /rstudio
+                  working_dir: /home/rstudio # Ensures container working dir is homedir
+              jupyter:
+                display_name: Jupyter SciPy Notebook
+                slug: "jupyter"
+                kubespawner_override:
+                  image: "quay.io/jupyter/scipy-notebook:2024-03-04"
+                  default_url: /lab
 
-      - display_name: Rocker Geospatial with RStudio
-        description: R environment
-        slug: rocker
-        kubespawner_override:
-          image: rocker/binder:4.3
-          image_pull_policy: Always
-          default_url: /rstudio
-          working_dir: /home/rstudio # Ensures container working dir is homedir
-        profile_options: *profile_options
-
-      - display_name: Pangeo Tensorflow ML Notebook
-        description: Dedicated node with a NVIDIA Tesla T4
-        slug: "tensorflow"
-        kubespawner_override:
-          image: "quay.io/pangeo/ml-notebook:2024.05.07"
-          default_url: /lab
-        profile_options: &profile_gpu_options
-          resource_allocation:
+      - display_name: "With GPUs"
+        description: "Start a container on a dedicated node with a NVIDIA Tesla T4"
+        profile_options:
+          requests:
             display_name: Resource Allocation
             choices:
               mem_26_0:
@@ -87,8 +97,6 @@ jupyterhub:
                   mem_guarantee: 21G
                   mem_limit: null
                   cpu_guarantee: 3
-                  environment:
-                    NVIDIA_DRIVER_CAPABILITIES: compute,utility
                   node_selector:
                     node.kubernetes.io/instance-type: n1-highmem-4
                   extra_resource_limits:
@@ -99,25 +107,10 @@ jupyterhub:
                   mem_guarantee: 92G
                   mem_limit: null
                   cpu_guarantee: 15
-                  environment:
-                    NVIDIA_DRIVER_CAPABILITIES: compute,utility
                   node_selector:
                     node.kubernetes.io/instance-type: n1-highmem-16
                   extra_resource_limits:
                     nvidia.com/gpu: "4"
-
-      - display_name: Pangeo PyTorch ML Notebook
-        description: Dedicated node with a NVIDIA Tesla T4
-        slug: "pytorch"
-        kubespawner_override:
-          image: "quay.io/pangeo/pytorch-notebook:2024.05.07"
-          default_url: /lab
-        profile_options: *profile_gpu_options
-
-      - display_name: Bring your own image
-        description: Specify your own docker image (must have python and jupyterhub installed in it)
-        slug: custom
-        profile_options:
           image:
             display_name: Image
             unlisted_choice:
@@ -127,5 +120,19 @@ jupyterhub:
               validation_message: "Must be a publicly available docker image, of form <image-name>:<tag>"
               kubespawner_override:
                 image: "{value}"
-            choices: {}
-          resource_allocation: *resource_allocation
+            choices:
+              tensorflow:
+                display_name: Tensorflow ML Notebook
+                slug: "tensorflow"
+                kubespawner_override:
+                  image: "quay.io/jupyter/tensorflow-notebook:cuda-2024-07-01"
+              pytorch:
+                display_name: PyTorch ML Notebook
+                default: true
+                slug: "pytorch"
+                kubespawner_override:
+                  image: "quay.io/jupyter/pytorch-notebook:cuda12-2024-07-01"
+        kubespawner_override:
+          default_url: /lab
+          environment:
+            NVIDIA_DRIVER_CAPABILITIES: compute,utility

config/clusters/earthscope/common.values.yaml

@@ -165,6 +165,11 @@ basehub:
                   slug: geolab-general
                   kubespawner_override:
                     image: public.ecr.aws/earthscope-dev/geolab:td-dev-dd5851e6
+                mspass-shortcourse:
+                  display_name: MsPASS
+                  slug: mspass-shortcourse
+                  kubespawner_override:
+                    image: public.ecr.aws/earthscope-dev/mspass_image:mspass_img_test-6db62782
                 jupyter-scipy:
                   display_name: Jupyter
                   slug: jupyter-scipy

config/clusters/nasa-esdis/common.values.yaml

@@ -59,7 +59,7 @@ jupyterhub:
         description: Pangeo based notebook with a Python environment
         default: true
         kubespawner_override:
-          image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:2024-04-09
+          image: public.ecr.aws/nasa-veda/pangeo-notebook-veda-image:53b6fd1256f5
           init_containers:
             # Need to explicitly fix ownership here, as otherwise these directories will be owned
             # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid

config/clusters/nasa-ghg/common.values.yaml

@@ -85,7 +85,7 @@ basehub:
             - US-GHG-Center:ghg-trial-access
             - 2i2c-org:hub-access-for-2i2c-staff
           kubespawner_override:
-            image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:2024-04-09
+            image: public.ecr.aws/nasa-veda/pangeo-notebook-veda-image:53b6fd1256f5
             init_containers:
               # Need to explicitly fix ownership here, as otherwise these directories will be owned
               # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid

config/clusters/nasa-veda/common.values.yaml

@@ -115,7 +115,7 @@ basehub:
           description: Pangeo based notebook with a Python environment
           default: true
           kubespawner_override:
-            image: public.ecr.aws/nasa-veda/nasa-veda-singleuser:2024-04-09
+            image: public.ecr.aws/nasa-veda/pangeo-notebook-veda-image:53b6fd1256f5
             init_containers:
               # Need to explicitly fix ownership here, as otherwise these directories will be owned
               # by root on most NFS filesystems - neither EFS nor Google Filestore support anonuid

docs/contributing/code-review.md

@@ -61,22 +61,21 @@ See [the guiding principles](https://compass.2i2c.org/engineering/workflow/1-wee
 document for more guidance on what else you can do.
 
 You should break this rule when it makes sense, but do not do so
-**casually**. This is an important mechanism by which we can build a
-team we can all trust in over
+**casually**.
 
 This may make you uncomfortable, and that is ok. Ultimately our goal is to
-build a **team we can all trust in**, and this is a very important part
-of getting there.
+build a **team we can all trust in** rather than be a group of individuals
+who can trust each other, and this is a very important part of getting there.
 
 ## After making the PR
 
-After you make your PR, ask yourself these three questions:
+After you make your PR, ask yourself these questions:
 
 1. *If* this PR breaks something, do you feel comfortable debugging it **or**
    reverting it to undo the change?
 2. Do you know how to *verify* the effects of merging this PR?
 
-If the answer to all these 2 questions are 'yes', you should go ahead
+If the answer to all these questions are 'yes', you should go ahead
 and self merge.
 
 If it breaks, you can revert your PR, make changes, and try again.

requirements.txt

@@ -28,8 +28,7 @@ escapism==1.*
 
 # Used for GCP billing management
 pandas
-# FIXME: Unpin when https://github.com/unionai-oss/pandera/issues/1656 gets solved
-numpy<2
+numpy==2.*
 pandera
 prometheus_pandas
 pytest-mock