From 072141a888f230cb6a079d14efb6df8a7d08d926 Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Mon, 15 Dec 2025 14:37:08 -0800 Subject: [PATCH 1/7] Don't export internal dependencies --- .github/workflows/make-requirements.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml index cc724093..c3e05d5a 100644 --- a/.github/workflows/make-requirements.yml +++ b/.github/workflows/make-requirements.yml @@ -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 From 9444fea366142004590642b3b8ba644f432540c6 Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Mon, 15 Dec 2025 14:40:25 -0800 Subject: [PATCH 2/7] Upgrade upload-artifact and download-artifact --- .github/workflows/make-requirements.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml index c3e05d5a..6057710e 100644 --- a/.github/workflows/make-requirements.yml +++ b/.github/workflows/make-requirements.yml @@ -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 }} @@ -74,13 +74,13 @@ jobs: 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 From 1c74d9f599c1cadb33620341f489547861e1687b Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Tue, 16 Dec 2025 07:22:03 -0800 Subject: [PATCH 3/7] Use Python 3.9 for PDM installation --- .github/actions/pdm/action.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/actions/pdm/action.yml b/.github/actions/pdm/action.yml index 2bb6cdee..3d63bc5b 100644 --- a/.github/actions/pdm/action.yml +++ b/.github/actions/pdm/action.yml @@ -3,6 +3,9 @@ description: Install PDM from our version runs: using: composite steps: + - name: Install Python for PDM + # This action reads the Python version from .python-version + uses: actions/setup-python@v6 - name: Set up PDM uses: pdm-project/setup-pdm@c050bdcb2405837648035b6678c75609d53a749f with: From 5923745413898f3d696f39af9f738f0bac0a7e2f Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Tue, 16 Dec 2025 07:58:14 -0800 Subject: [PATCH 4/7] Upgrade actions/checkout and download-artifact --- .github/actions/pdm/action.yml | 1 + .github/workflows/make-requirements.yml | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/actions/pdm/action.yml b/.github/actions/pdm/action.yml index 3d63bc5b..7d8ba88e 100644 --- a/.github/actions/pdm/action.yml +++ b/.github/actions/pdm/action.yml @@ -5,6 +5,7 @@ runs: 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 diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml index 6057710e..e881ffed 100644 --- 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 @@ -66,9 +66,9 @@ 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 From 9fcaa7c465e203c5c78db1471a2bc83192d02336 Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Tue, 16 Dec 2025 08:04:12 -0800 Subject: [PATCH 5/7] Upgrade peter-evans/create-pull-request --- .github/workflows/make-requirements.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml index e881ffed..7944ce58 100644 --- a/.github/workflows/make-requirements.yml +++ b/.github/workflows/make-requirements.yml @@ -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 }} From 6bd9c8630a95bab5f4592d5fd182bb1a3aa98264 Mon Sep 17 00:00:00 2001 From: pgarrison <5379348+pgarrison@users.noreply.github.com> Date: Tue, 16 Dec 2025 16:08:07 +0000 Subject: [PATCH 6/7] Updating requirements.txt after change to `pdm.lock` was pushed to `admin/public-requirements` --- requirements/linux/requirements.txt | 8 -------- requirements/macos/requirements.txt | 8 -------- requirements/windows/requirements.txt | 8 -------- 3 files changed, 24 deletions(-) diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt index 1687a9d5..df30961e 100644 --- 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 index 1687a9d5..df30961e 100644 --- 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 index 1687a9d5..df30961e 100644 --- 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 From d09930d93a8946c17019b2ff66cfcc14dd7f527b Mon Sep 17 00:00:00 2001 From: Philip Garrison Date: Tue, 16 Dec 2025 09:38:08 -0800 Subject: [PATCH 7/7] PDM version in docs should match github actions --- docs/INSTALL.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/INSTALL.md b/docs/INSTALL.md index 7114fc27..b0d6f66f 100644 --- 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