AllenCell · pgarrison · Dec 16, 2025 · Dec 15, 2025 · Dec 15, 2025 · Dec 16, 2025
diff --git a/.github/actions/pdm/action.yml b/.github/actions/pdm/action.yml
@@ -3,6 +3,10 @@ description: Install PDM from our version
 runs:
   using: composite
   steps:
+    - name: Install Python for PDM
+      # This action reads the Python version from .python-version
+      # PDM 2.12.2 doesn't install properly on Python 3.14
+      uses: actions/setup-python@v6
     - name: Set up PDM
       uses: pdm-project/setup-pdm@c050bdcb2405837648035b6678c75609d53a749f
       with:

diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml
@@ -18,7 +18,7 @@ jobs:
         os: [ubuntu-latest, macOS-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
+      - uses: actions/checkout@v6
       - uses: ./.github/actions/pdm
 
       - name: Generate requirements.txt
@@ -38,7 +38,7 @@ jobs:
 
           rm -rf requirements/*
           mkdir -p requirements/$PLATFORM
-          pdm requirements requirements/$PLATFORM/requirements.txt
+          pdm requirements requirements/$PLATFORM/requirements.txt -d
 
       - name: Get platform variable
         id: platform
@@ -57,7 +57,7 @@ jobs:
           esac
 
       - name: Upload requirements files
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v6
         with:
           name: ${{ steps.platform.outputs.platform }}-requirements
           path: requirements/${{ steps.platform.outputs.platform }}
@@ -66,21 +66,21 @@ jobs:
     needs: [make-requirements]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - name: Download linux requirements files
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v7
         with:
           name: linux-requirements
           path: requirements/linux
 
       - name: Download windows requirements files
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v7
         with:
           name: windows-requirements
           path: requirements/windows
 
       - name: Download macOS requirements files
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v7
         with:
           name: macos-requirements
           path: requirements/macos
@@ -94,7 +94,7 @@ jobs:
         run: echo "::set-output name=timestamp::$(date +'%Y-%m-%d_%H-%M')"
 
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@98357b18bf14b5342f975ff684046ec3b2a07725 # v8.0.0
         with:
           base: ${{ github.ref_name }}
           title: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }}

diff --git a/docs/INSTALL.md b/docs/INSTALL.md
@@ -38,10 +38,10 @@ python install-pdm.py
 > [!WARNING]
 > With this installation method `pdm` will be tied to the exact python version used to install it. If you installed with Python 3.9.13, for example, and you later transition to Python 3.9.17, do not uninstall Python 3.9.13.
 
-`pdm` will be installed into `$HOME/.local/bin`. Check that your version is at least 2.10.
+`pdm` will be installed into `$HOME/.local/bin`. Check that your version is at least 2.10. We test against version 2.12.2.
 ```bash
 $ pdm --version
-PDM, version 2.10.4
+PDM, version 2.12.2
 ```
 
 ## Install the project dependencies

diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt
@@ -2,7 +2,6 @@
 # Please do not edit it manually.
 
 aicscytoparam==0.1.10
-aicsfiles==5.1.0
 aicsimageio==4.14.0
 aicsshparam==0.1.7
 aiohttp==3.9.3
@@ -17,7 +16,6 @@ asttokens==2.4.1
 async-timeout==4.0.3; python_version < "3.11"
 attrs==23.2.0
 av==12.3.0
-backoff==1.11.1
 beautifulsoup4==4.12.3
 bigtree==0.19.3
 bioio==1.0.3
@@ -69,7 +67,6 @@ jedi==0.19.1
 jinja2==3.1.3
 jmespath==1.0.1
 joblib==1.3.2
-jsonpickle==2.2.0
 jsonschema==4.21.1
 jsonschema-specifications==2023.12.1
 jupyter==1.0.0
@@ -79,9 +76,7 @@ jupyter-core==5.7.1
 jupyterlab-pygments==0.3.0
 jupyterlab-widgets==3.0.11
 kiwisolver==1.4.5
-labkey==1.4.1
 lazy-loader==0.3
-lkaccess==1.4.25
 locket==1.0.0
 lxml==4.9.4
 lxml-stubs==0.5.1
@@ -125,7 +120,6 @@ prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0; sys_platform != "win32" or os_name != "nt"
 pure-eval==0.2.2
-pyaml==20.4.0
 pyarrow==17.0.0
 pycparser==2.21
 pydantic==2.6.0
@@ -143,7 +137,6 @@ pyzmq==25.1.2
 qtconsole==5.5.1
 qtpy==2.4.1
 referencing==0.33.0
-rehash==1.0.1
 requests==2.31.0
 resource-backed-dask-array==0.1.0
 rich==13.7.1
@@ -163,7 +156,6 @@ sortedcontainers==2.4.0
 soupsieve==2.5
 stack-data==0.6.3
 tblib==3.0.0
-tenacity==8.1.0
 termcolor==2.4.0
 terminado==0.18.0
 threadpoolctl==3.2.0

diff --git a/requirements/macos/requirements.txt b/requirements/macos/requirements.txt
@@ -2,7 +2,6 @@
 # Please do not edit it manually.
 
 aicscytoparam==0.1.10
-aicsfiles==5.1.0
 aicsimageio==4.14.0
 aicsshparam==0.1.7
 aiohttp==3.9.3
@@ -17,7 +16,6 @@ asttokens==2.4.1
 async-timeout==4.0.3; python_version < "3.11"
 attrs==23.2.0
 av==12.3.0
-backoff==1.11.1
 beautifulsoup4==4.12.3
 bigtree==0.19.3
 bioio==1.0.3
@@ -69,7 +67,6 @@ jedi==0.19.1
 jinja2==3.1.3
 jmespath==1.0.1
 joblib==1.3.2
-jsonpickle==2.2.0
 jsonschema==4.21.1
 jsonschema-specifications==2023.12.1
 jupyter==1.0.0
@@ -79,9 +76,7 @@ jupyter-core==5.7.1
 jupyterlab-pygments==0.3.0
 jupyterlab-widgets==3.0.11
 kiwisolver==1.4.5
-labkey==1.4.1
 lazy-loader==0.3
-lkaccess==1.4.25
 locket==1.0.0
 lxml==4.9.4
 lxml-stubs==0.5.1
@@ -125,7 +120,6 @@ prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0; sys_platform != "win32" or os_name != "nt"
 pure-eval==0.2.2
-pyaml==20.4.0
 pyarrow==17.0.0
 pycparser==2.21
 pydantic==2.6.0
@@ -143,7 +137,6 @@ pyzmq==25.1.2
 qtconsole==5.5.1
 qtpy==2.4.1
 referencing==0.33.0
-rehash==1.0.1
 requests==2.31.0
 resource-backed-dask-array==0.1.0
 rich==13.7.1
@@ -163,7 +156,6 @@ sortedcontainers==2.4.0
 soupsieve==2.5
 stack-data==0.6.3
 tblib==3.0.0
-tenacity==8.1.0
 termcolor==2.4.0
 terminado==0.18.0
 threadpoolctl==3.2.0

diff --git a/requirements/windows/requirements.txt b/requirements/windows/requirements.txt
@@ -2,7 +2,6 @@
 # Please do not edit it manually.
 
 aicscytoparam==0.1.10
-aicsfiles==5.1.0
 aicsimageio==4.14.0
 aicsshparam==0.1.7
 aiohttp==3.9.3
@@ -17,7 +16,6 @@ asttokens==2.4.1
 async-timeout==4.0.3; python_version < "3.11"
 attrs==23.2.0
 av==12.3.0
-backoff==1.11.1
 beautifulsoup4==4.12.3
 bigtree==0.19.3
 bioio==1.0.3
@@ -69,7 +67,6 @@ jedi==0.19.1
 jinja2==3.1.3
 jmespath==1.0.1
 joblib==1.3.2
-jsonpickle==2.2.0
 jsonschema==4.21.1
 jsonschema-specifications==2023.12.1
 jupyter==1.0.0
@@ -79,9 +76,7 @@ jupyter-core==5.7.1
 jupyterlab-pygments==0.3.0
 jupyterlab-widgets==3.0.11
 kiwisolver==1.4.5
-labkey==1.4.1
 lazy-loader==0.3
-lkaccess==1.4.25
 locket==1.0.0
 lxml==4.9.4
 lxml-stubs==0.5.1
@@ -125,7 +120,6 @@ prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0; sys_platform != "win32" or os_name != "nt"
 pure-eval==0.2.2
-pyaml==20.4.0
 pyarrow==17.0.0
 pycparser==2.21
 pydantic==2.6.0
@@ -143,7 +137,6 @@ pyzmq==25.1.2
 qtconsole==5.5.1
 qtpy==2.4.1
 referencing==0.33.0
-rehash==1.0.1
 requests==2.31.0
 resource-backed-dask-array==0.1.0
 rich==13.7.1
@@ -163,7 +156,6 @@ sortedcontainers==2.4.0
 soupsieve==2.5
 stack-data==0.6.3
 tblib==3.0.0
-tenacity==8.1.0
 termcolor==2.4.0
 terminado==0.18.0
 threadpoolctl==3.2.0