NickAkhmetov/Python 3.10, uv

.python-version

@@ -1 +1 @@
-3.9.12
+3.10.16

.vscode/tasks.json

@@ -4,7 +4,7 @@
     {
       "label": "pip install",
       "type": "shell",
-      "command": "PIP_CONSTRAINT=context/constraints.txt pip install -r context/requirements.txt --use-deprecated=legacy-resolver",
+      "command": "PIP_CONSTRAINT=context/constraints.txt uv pip sync context/requirements.txt",
       "group": {
         "kind": "build",
         "isDefault": false
@@ -48,19 +48,14 @@
         "kind": "build",
         "isDefault": false
       },
-      "dependsOn": [
-        "pip install",
-        "npm install"
-      ],
+      "dependsOn": ["pip install", "npm install"],
       "dependsOrder": "parallel"
     },
     {
       "label": "Flask Server",
       "type": "shell",
       "command": "${command:python.interpreterPath} -m flask run --debug",
-      "dependsOn": [
-        "Copy app configuration"
-      ],
+      "dependsOn": ["Copy app configuration"],
       "options": {
         "cwd": "${workspaceFolder}/context",
         "env": {
@@ -74,7 +69,7 @@
       "isBackground": true,
       "problemMatcher": {
         "pattern": {
-          "regexp": "",
+          "regexp": ""
         },
         "background": {
           "activeOnStart": true,
@@ -85,19 +80,15 @@
     },
     {
       "label": "Flask Server (+ pip install)",
-      "dependsOn": [
-        "pip install",
-        "Flask Server"
-      ],
-      "dependsOrder": "sequence"
+      "dependsOn": ["pip install", "Flask Server"],
+      "dependsOrder": "sequence",
+      "problemMatcher": []
     },
     {
       "label": "npm run lint",
       "type": "npm",
       "script": "lint",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ],
+      "problemMatcher": ["$eslint-stylish"],
       "options": {
         "cwd": "${workspaceFolder}/context"
       },
@@ -133,10 +124,7 @@
     },
     {
       "label": "React Dev Server (+ lint)",
-      "dependsOn": [
-        "npm run lint",
-        "React Dev Server"
-      ],
+      "dependsOn": ["npm run lint", "React Dev Server"],
       "dependsOrder": "sequence"
     },
     {
@@ -163,41 +151,25 @@
     },
     {
       "label": "dev-start (no install)",
-      "dependsOn": [
-        "Flask Server",
-        "React Dev Server (+ lint)",
-        "Storybook"
-      ],
+      "dependsOn": ["Flask Server", "React Dev Server (+ lint)", "Storybook"],
       "dependsOrder": "parallel",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ]
+      "problemMatcher": ["$eslint-stylish"]
     },
     {
       "label": "dev-start",
-      "dependsOn": [
-        "Install dependencies",
-        "dev-start (no install)"
-      ],
+      "dependsOn": ["Install dependencies", "dev-start (no install)"],
       "group": {
         "kind": "build",
         "isDefault": true
       },
       "dependsOrder": "sequence",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ]
+      "problemMatcher": ["$eslint-stylish"]
     },
     {
       "label": "dev-start (no storybook, no install)",
-      "dependsOn": [
-        "Flask Server",
-        "React Dev Server (+ lint)"
-      ],
+      "dependsOn": ["Flask Server", "React Dev Server (+ lint)"],
       "dependsOrder": "parallel",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ]
+      "problemMatcher": ["$eslint-stylish"]
     },
     {
       "label": "dev-start (no storybook)",
@@ -206,20 +178,13 @@
         "dev-start (no storybook, no install)"
       ],
       "dependsOrder": "sequence",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ]
+      "problemMatcher": ["$eslint-stylish"]
     },
     {
       "label": "dev-start (no storybook, no install, no lint)",
-      "dependsOn": [
-        "Flask Server",
-        "React Dev Server"
-      ],
+      "dependsOn": ["Flask Server", "React Dev Server"],
       "dependsOrder": "parallel",
-      "problemMatcher": [
-        "$eslint-stylish"
-      ]
+      "problemMatcher": ["$eslint-stylish"]
     },
     {
       "label": "Kill project ports",
@@ -230,4 +195,4 @@
       "command": "npx --yes kill-port 5000 5001 6006"
     }
   ]
-}
+}

CHANGELOG-python-3.10.md

@@ -0,0 +1,2 @@
+- Upgrade to Python 3.10.
+- Introduce `uv` for python package management.

README.md

@@ -104,12 +104,17 @@ All designs are in [Figma](https://www.figma.com/files/team/834568130405102661/H
 ### Prerequisites
 
 - `git`: Suggest [installing Apple XCode](https://developer.apple.com/xcode/).
-- `python 3.9`
+- `python 3.10`
+  - `uv` (Recommended):
+    - [Install `uv`](https://docs.astral.sh/uv/getting-started/installation/) using any supported installation method.
+    - Create a `uv` virtual environment with the appropriate python version via `uv venv --python $(cat .python-version)`.
+    - Activate the environment with `source .venv/bin/activate`.
+    - Install locked requirements with `uv pip sync context/requirements.txt` and `uv pip sync context/requirements-dev.txt`.
   - MiniConda:
     - [installing miniconda](https://docs.conda.io/en/latest/miniconda.html#macosx-installers) and [creating a new conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-with-commands): `conda create -n portal python=$(cat .python-version)`
   - pyenv:
     - `brew install pyenv`
-    - `brew install pyenv-virtualenv` 
+    - `brew install pyenv-virtualenv`
     - cd into portal-ui (or provide full path to /portal-ui/.python-version file)
     - `` pyenv install `cat .python-version`  ``
     - `` pyenv virtualenv `cat .python-version` portal ``

context/requirements-dev.txt

@@ -1,142 +1,78 @@
-#
-# This file is autogenerated by pip-compile with Python 3.9
-# by the following command:
-#
-#    pip-compile --allow-unsafe --generate-hashes --output-file=context/requirements-dev.txt context/requirements-dev.in
-#
-autopep8==1.4.4 \
-    --hash=sha256:4d8eec30cc81bc5617dbf1218201d770dc35629363547f17577c61683ccfb3ee
+# This file was autogenerated by uv via the following command:
+#    uv pip compile context/requirements-dev.in --universal --output-file context/requirements-dev.txt
+autopep8==1.4.4
     # via -r context/requirements-dev.in
-boto3==1.26.154 \
-    --hash=sha256:cf1067d101be538f399b685bbe6beb4bfed01095da8497d0c7fa8b8788a65c6b \
-    --hash=sha256:ee2b3733f40f935da78bf76bc8e82af6e90841406e04605e3b2d765b50cad05e
+boto3==1.26.154
     # via -r context/requirements-dev.in
-botocore==1.29.154 \
-    --hash=sha256:a9c7da497ac5f7d4f3e932b4442e7c32cc2936f3a4658165f1528336fc429c3d \
-    --hash=sha256:b9853f72a3c93f1aa8c9a1636911cdbec3662bca2e04e4ee00437c4f8c9fa2d4
+botocore==1.29.154
     # via
     #   boto3
     #   s3transfer
-build==1.2.1 \
-    --hash=sha256:526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d \
-    --hash=sha256:75e10f767a433d9a86e50d83f418e83efc18ede923ee5ff7df93b6cb0306c5d4
+build==1.2.1
     # via pip-tools
-click==8.1.0 \
-    --hash=sha256:19a4baa64da924c5e0cd889aba8e947f280309f1a2ce0947a3e3a7bcb7cc72d6 \
-    --hash=sha256:977c213473c7665d3aa092b41ff12063227751c41d7b17165013e10069cc5cd2
+click==8.1.0
     # via pip-tools
-entrypoints==0.3 \
-    --hash=sha256:589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19 \
-    --hash=sha256:c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451
+colorama==0.4.6 ; os_name == 'nt' or (platform_system == 'Windows' and sys_platform != 'win32') or sys_platform == 'win32'
+    # via
+    #   build
+    #   click
+    #   pytest
+entrypoints==0.3
     # via flake8
-exceptiongroup==1.2.1 \
-    --hash=sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad \
-    --hash=sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16
+exceptiongroup==1.2.1 ; python_full_version < '3.11'
     # via pytest
-flake8==3.7.8 \
-    --hash=sha256:19241c1cbc971b9962473e4438a2ca19749a7dd002dd1a946eaba171b4114548 \
-    --hash=sha256:8e9dfa3cecb2400b3738a42c54c3043e821682b9c840b0448c0503f781130696
+flake8==3.7.8
     # via -r context/requirements-dev.in
-importlib-metadata==8.0.0 \
-    --hash=sha256:15584cf2b1bf449d98ff8a6ff1abef57bf20f3ac6454f431736cd3e660921b2f \
-    --hash=sha256:188bd24e4c346d3f0a933f275c2fec67050326a856b9a359881d7c2a697e8812
-    # via build
-iniconfig==1.1.1 \
-    --hash=sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3 \
-    --hash=sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32
+iniconfig==1.1.1
     # via pytest
-jmespath==1.0.1 \
-    --hash=sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980 \
-    --hash=sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe
+jmespath==1.0.1
     # via
     #   boto3
     #   botocore
-mccabe==0.6.1 \
-    --hash=sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42 \
-    --hash=sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f
+mccabe==0.6.1
     # via flake8
-packaging==21.3 \
-    --hash=sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb \
-    --hash=sha256:ef103e05f519cdc783ae24ea4e2e0f508a9c99b2d4969652eed6a2e1ea5bd522
+packaging==21.3
     # via
     #   build
     #   pytest
-pip-tools==7.4.1 \
-    --hash=sha256:4c690e5fbae2f21e87843e89c26191f0d9454f362d8acdbd695716493ec8b3a9 \
-    --hash=sha256:864826f5073864450e24dbeeb85ce3920cdfb09848a3d69ebf537b521f14bcc9
+pip==24.1.1
+    # via pip-tools
+pip-tools==7.4.1
     # via -r context/requirements-dev.in
-pluggy==1.5.0 \
-    --hash=sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1 \
-    --hash=sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669
+pluggy==1.5.0
     # via pytest
-pycodestyle==2.5.0 \
-    --hash=sha256:95a2219d12372f05704562a14ec30bc76b05a5b297b21a5dfe3f6fac3491ae56 \
-    --hash=sha256:e40a936c9a450ad81df37f549d676d127b1b66000a6c500caa2b085bc0ca976c
+pycodestyle==2.5.0
     # via
     #   autopep8
     #   flake8
-pyflakes==2.1.1 \
-    --hash=sha256:17dbeb2e3f4d772725c777fabc446d5634d1038f234e77343108ce445ea69ce0 \
-    --hash=sha256:d976835886f8c5b31d47970ed689944a0262b5f3afa00a5a7b4dc81e5449f8a2
+pyflakes==2.1.1
     # via flake8
-pyparsing==3.0.7 \
-    --hash=sha256:18ee9022775d270c55187733956460083db60b37d0d0fb357445f3094eed3eea \
-    --hash=sha256:a6c06a88f252e6c322f65faf8f418b16213b51bdfaece0524c1c1bc30c63c484
+pyparsing==3.0.7
     # via packaging
-pyproject-hooks==1.1.0 \
-    --hash=sha256:4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965 \
-    --hash=sha256:7ceeefe9aec63a1064c18d939bdc3adf2d8aa1988a510afec15151578b232aa2
+pyproject-hooks==1.1.0
     # via
     #   build
     #   pip-tools
-pytest==8.2.2 \
-    --hash=sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343 \
-    --hash=sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977
+pytest==8.2.2
     # via
     #   -r context/requirements-dev.in
     #   pytest-mock
-pytest-mock==3.14.0 \
-    --hash=sha256:0b72c38033392a5f4621342fe11e9219ac11ec9d375f8e2a0c164539e0d70f6f \
-    --hash=sha256:2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0
+pytest-mock==3.14.0
     # via -r context/requirements-dev.in
-python-dateutil==2.8.2 \
-    --hash=sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86 \
-    --hash=sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
+python-dateutil==2.8.2
     # via botocore
-s3transfer==0.6.1 \
-    --hash=sha256:3c0da2d074bf35d6870ef157158641178a4204a6e689e82546083e31e0311346 \
-    --hash=sha256:640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9
+s3transfer==0.6.1
     # via boto3
-six==1.16.0 \
-    --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
-    --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
+setuptools==70.0.0
+    # via pip-tools
+six==1.16.0
     # via python-dateutil
-tomli==2.0.1 \
-    --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \
-    --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f
+tomli==2.0.1 ; python_full_version < '3.11'
     # via
     #   build
     #   pip-tools
     #   pytest
-urllib3==1.26.17 \
-    --hash=sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21 \
-    --hash=sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b
+urllib3==1.26.17
     # via botocore
-wheel==0.38.1 \
-    --hash=sha256:7a95f9a8dc0924ef318bd55b616112c70903192f524d120acc614f59547a9e1f \
-    --hash=sha256:ea041edf63f4ccba53ad6e035427997b3bb10ee88a4cd014ae82aeb9eea77bb9
-    # via pip-tools
-zipp==3.19.2 \
-    --hash=sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19 \
-    --hash=sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c
-    # via importlib-metadata
-
-# The following packages are considered to be unsafe in a requirements file:
-pip==24.1.1 \
-    --hash=sha256:5aa64f65e1952733ee0a9a9b1f52496ebdb3f3077cc46f80a16d983b58d1180a \
-    --hash=sha256:efca15145a95e95c00608afeab66311d40bfb73bb2266a855befd705e6bb15a0
-    # via pip-tools
-setuptools==70.0.0 \
-    --hash=sha256:54faa7f2e8d2d11bcd2c07bed282eef1046b5c080d1c32add737d7b5817b1ad4 \
-    --hash=sha256:f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0
+wheel==0.38.1
     # via pip-tools

context/requirements.in

@@ -1,15 +1,15 @@
 # Update requirements.txt if this file changes:
 # pip install pip-tools
 # pip-compile --allow-unsafe --generate-hashes --output-file=context/requirements.txt context/requirements.in
-Flask>=3.0.3
-Flask[async]>=3.0.3
+Flask>=3.1.0
+Flask[async]>=3.1.0
 globus-sdk>=3.9.0
 requests>=2.32.3
 pyyaml>=6.0.1
 python-datauri>=2.2.0
 python-frontmatter>=1.1.0
 hubmap-api-py-client>=0.0.11
-hubmap-commons>=2.1.15
+hubmap-commons>=2.1.18
 # As of 2023-08-24, this is the version of boto3 which is compatible with both the 
 # portal-visualization->vitessce->ome-zarr dependency on aiobotocore~=2.5
 # and the hubmap-commons dependency on boto3>=1.24.47