fix: mlflow critical upgrade (#2690)

.github/workflows/compatibility_tests.yml

@@ -7,6 +7,10 @@ on:
     branches:
       - main
 
+  # For debug - uncomment below to run on all PRs
+  # pull_request:
+  #   branches: "*"
+
 env:
   JEST_ENV: prod
 
@@ -14,9 +18,9 @@ jobs:
   docker-build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build docker image
@@ -35,7 +39,7 @@ jobs:
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.10
+          - python-version: 3.11
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future
@@ -43,9 +47,9 @@ jobs:
             # matches this pinned version, to avoid a redundant test
             anndata_version: "==0.10.9"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache env vars
@@ -55,14 +59,14 @@ jobs:
         run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
       # FIXME: Only working for Linux
       - name: Python cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.PIP_CACHE }}
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -70,7 +74,7 @@ jobs:
             ${{ runner.os }}-node-
       - name: Brew cache (MacOS)
         if: startsWith(matrix.os, 'macos')
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.BREW_CACHE }}
           key: ${{ runner.os }}-brew-

.github/workflows/push_tests.yml

@@ -14,15 +14,15 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -45,22 +45,22 @@ jobs:
   unit-test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
-      - name: Set up Python 3.9 (pyenv) # pyenv needed for mlflow in cli annotate tests
+      - name: Set up Python 3.11 (pyenv) # pyenv needed for mlflow in cli annotate tests
         uses: gabrielfalcao/pyenv-action@v9
         with:
-          default: 3.9
+          default: 3.11
           command: pip install -U pip # upgrade pip after installing python
       - run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
       - name: Python cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -78,20 +78,20 @@ jobs:
     runs-on: macos-latest
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Python cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}

client/package.json

@@ -139,7 +139,7 @@
     "rimraf": "^3.0.2",
     "serve-favicon": "^2.5.0",
     "terser-webpack-plugin": "^5.1.1",
-    "webpack": "^5.88.2",
+    "webpack": "^5.94.0",
     "webpack-cli": "^4.6.0",
     "webpack-dev-middleware": "^4.1.0",
     "webpack-merge": "^5.0.9",

server/requirements-annotate.txt

@@ -1,2 +1,2 @@
-mlflow==1.27.0
+mlflow==2.16.0
 scanpy