Merge pull request #6389 from berkeley-dsep-infra/staging

merging 6374/6386/6387/6388 to prod

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+# Ignore style and complexity
+# E: style errors
+# W: style warnings
+# C: complexity
+# E402: module level import not at top of file
+# I100: Import statements are in the wrong order
+# I101: Imported names are in the wrong order. Should be
+# F841: local variable ... is assigned to but never used
+ignore = E, C, W, I100, I101, D400, F841

.github/ISSUE_TEMPLATE/featurerequest.md

@@ -30,4 +30,3 @@ assignees:
 # Tasks to complete
 
 <!-- What tasks are needed to make this enhancement? -->
-

.github/ISSUE_TEMPLATE/higher-resources.md

@@ -45,4 +45,3 @@ This will help us with the prioritization of this request.
 This will help us scale down resources when the RAM increase is no longer required
 
 **Any additional information we should know about?**
-

.github/ISSUE_TEMPLATE/performance_issue.yml

@@ -9,7 +9,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        Please refer to the commmon causes for the performance issues by referring to this documentation - https://ds-modules.github.io/curriculum-guide/workflow/performance_issue.html. If the above mentioned reasons are not the cause for the performance issues in the hub then or you lack clarity about the issue then  please do raise a request by filling the details below:
+        Please refer to the common causes for the performance issues by referring to this documentation - https://ds-modules.github.io/curriculum-guide/workflow/performance_issue.html. If the above mentioned reasons are not the cause for the performance issues in the hub then or you lack clarity about the issue then  please do raise a request by filling the details below:
   - type: dropdown
     attributes:
       label: Your Role
@@ -91,7 +91,7 @@ body:
   - type: input
     attributes:
       label: Issue timeline
-      description: Mention the date/time when this issue occured
+      description: Mention the date/time when this issue occurred
     validations:
       required: true
   - type: textarea

.github/ISSUE_TEMPLATE/resourcescheduler.yml

@@ -24,7 +24,7 @@ body:
       label: Detailed Requirements
       description: Rationale for requesting increased compute
       value: |
-        - <!--Eg: Conducting Live Workshops/Exams/Flipped Clasroom(s) or due to Deadline for Compute Intensive Assignment-->
+        - <!--Eg: Conducting Live Workshops/Exams/Flipped Classroom(s) or due to Deadline for Compute Intensive Assignment-->
     validations:
       required: true
   - type: dropdown
@@ -40,7 +40,7 @@ body:
   - type: textarea
     attributes:
       label: Request Deadline
-      description: Sepcify the time duration for which you are expecting this increase in compute
+      description: Specify the time duration for which you are expecting this increase in compute
       value: |
         <!-- Specify the start date/time and end date/time -->
     validations:

.github/labeler.yml

@@ -16,6 +16,7 @@ configuration:
   - '**/apt.txt'
   - '**/infra-requirements.txt'
   - '**/requirements.in'
+  - '**/dev-requirements.txt'
   - '**/requirements.txt'
   - '**/runtime.txt'
   - '**/*.json'

.pre-commit-config.yaml

@@ -0,0 +1,101 @@
+# pre-commit is a tool to perform a predefined set of tasks manually and/or
+# automatically before git commits are made.
+#
+# Config reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+#
+# Common tasks
+#
+# - Run on all files:   pre-commit run --all-files
+# - Register git hooks: pre-commit install --install-hooks
+#
+repos:
+  # yaml linter
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        # TODO: remove --no-warnings eventually
+        args: [--no-warnings, -c=./.yamllint.yaml]
+
+  # Autoformat: Python code
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.9
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi ]
+
+  # Autoformat: Python code, syntax patterns are modernized
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.17.0
+    hooks:
+      - id: pyupgrade
+        args:
+          - --py36-plus
+
+  # Autoformat: Python code
+  - repo: https://github.com/pycqa/isort
+    rev: "5.13.2"
+    hooks:
+      - id: isort
+
+  # Autoformat: Python code
+  - repo: https://github.com/psf/black
+    rev: "24.10.0"
+    hooks:
+      - id: black
+        # This is a `.py` file but is encrypted with sops
+
+  # Lint: Python code
+  - repo: https://github.com/pycqa/flake8
+    rev: "7.1.1"
+    hooks:
+      - id: flake8
+        # In case a `.py` file but is encrypted with sops
+        # exclude:
+
+  # Prevent unencrypted files from being committed
+  - repo: https://github.com/yuvipanda/pre-commit-hook-ensure-sops
+    rev: v1.1
+    hooks:
+      - id: sops-encryption
+        # Add files here if they contain the word 'secret' but should not be encrypted
+        # exclude:
+
+  # Prevent known typos from being committed
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args:
+          # Autofix known typos
+          - --write-changes
+        additional_dependencies:
+          - tomli
+
+  # pre-commit.com provided hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    # ref: https://github.com/pre-commit/pre-commit-hooks#hooks-available
+    hooks:
+      # Autoformat: Makes sure files end in a newline and only a newline.
+      - id: end-of-file-fixer
+
+      # Autoformat: Sorts entries in requirements.txt.
+      - id: requirements-txt-fixer
+
+      # Lint: Check for files with names that would conflict on a
+      # case-insensitive filesystem like MacOS HFS+ or Windows FAT.
+      - id: check-case-conflict
+
+      # Lint: Checks that non-binary executables have a proper shebang.
+      - id: check-executables-have-shebangs
+
+# pre-commit.ci config reference: https://pre-commit.ci/#configuration
+#ci:
+#  autoupdate_schedule: monthly

deployments/a11y/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/astro/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/biology/config/common.yaml

@@ -61,6 +61,10 @@ jupyterhub:
       course::1524699::group::all-admins:
         mem_limit: 4096M
         mem_guarantee: 4096M
+      course::1537301: # MCELLBI 201B, https://github.com/berkeley-dsep-infra/datahub/issues/6385
+        mem_limit: 5120M
+        mem_guarantee: 5120M
+
 
       # BioE C149, Fall 2024, https://github.com/berkeley-dsep-infra/datahub/issues/6205
       course::1537116::enrollment_type::teacher:
@@ -120,9 +124,6 @@ jupyterhub:
         mountPath: /etc/github/github-app-private-key.pem
         # data in secret file
 
-
-
-
     nodeSelector:
       hub.jupyter.org/pool-name: biology-pool
     storage:

deployments/biology/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/cee/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/data100/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/data101/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/data102/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/datahub/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/dev/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/dlab/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/edx/config/common.yaml

@@ -77,5 +77,3 @@ jupyterhub:
     extraEnv:
       # Unset NotebookApp from hub/values. Necessary for recent lab versions.
       JUPYTERHUB_SINGLEUSER_APP: "jupyter_server.serverapp.ServerApp"
-
-

deployments/edx/hubploy.yaml

@@ -9,5 +9,3 @@ cluster:
     service_key: gcloud-service-key.json
     cluster: edx
     zone: us-central1
-
-

deployments/edx/secrets/gcloud-service-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/eecs/config/common.yaml

@@ -103,4 +103,4 @@ jupyterhub:
 
       course::1537177: # ELENG 120, https://github.com/berkeley-dsep-infra/datahub/issues/6015
         mem_limit: 4096M
-        mem_guarantee: 4096M
+        mem_guarantee: 4096M

deployments/eecs/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/gradebook/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/highschool/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/ischool/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/julia/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/logodev/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/nature/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/prob140/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/publichealth/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/r/config/common.yaml

@@ -99,4 +99,3 @@ jupyterhub:
       course::1537932: # Data C131A, https://github.com/berkeley-dsep-infra/datahub/issues/6121
         mem_limit: 2048M
         mem_guarantee: 2048M
-

deployments/r/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/shiny/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/stat159/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}

deployments/stat20/secrets/gke-key.json

@@ -27,4 +27,4 @@
 		"unencrypted_suffix": "_unencrypted",
 		"version": "3.7.0"
 	}
-}
+}