From 71e0197c1a09ab136bb5a74cd1c04c91e355d66a Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 12:22:01 +0800 Subject: [PATCH 01/11] remove requirement for mlflow Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- docs/requirements.txt | 2 +- requirements-dev.txt | 2 +- setup.cfg | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 5acc437391..e5bedf8552 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -22,7 +22,7 @@ sphinx-autodoc-typehints==1.11.1 pandas einops transformers<4.22; python_version <= '3.10' # https://github.com/Project-MONAI/MONAI/issues/5157 -mlflow>=1.28.0, <=2.11.3 +mlflow>=1.28.0 clearml>=1.10.0rc0 tensorboardX imagecodecs; platform_system == "Linux" or platform_system == "Darwin" diff --git a/requirements-dev.txt b/requirements-dev.txt index b207b56b19..219adb0aff 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -34,7 +34,7 @@ pandas requests einops transformers>=4.36.0 -mlflow>=1.28.0, <=2.11.3 +mlflow>=1.28.0 clearml>=1.10.0rc0 matplotlib!=3.5.0 tensorboardX diff --git a/setup.cfg b/setup.cfg index c8ae1630f7..ecd60af9ee 100644 --- a/setup.cfg +++ b/setup.cfg @@ -66,7 +66,7 @@ all = pandas einops transformers<4.22; python_version <= '3.10' - mlflow>=1.28.0, <=2.11.3 + mlflow>=1.28.0 clearml>=1.10.0rc0 matplotlib tensorboardX @@ -125,7 +125,7 @@ einops = transformers = transformers<4.22; python_version <= '3.10' mlflow = - mlflow>=1.28.0, <=2.11.3 + mlflow>=1.28.0 matplotlib = matplotlib clearml = From 20fed73c779008a9d7bd477f6063fe505d1c3cbf Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 13:34:03 +0800 Subject: [PATCH 02/11] temp test Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index b8b73907d4..b53f659b27 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -105,6 +105,7 @@ jobs: python -m pip install -r requirements-dev.txt python -m pip list python setup.py develop # test no compile installation + python -m pip show mlflow shell: bash - name: Run compiled (${{ runner.os }}) run: | @@ -113,6 +114,7 @@ jobs: shell: bash - name: Run quick tests (CPU ${{ runner.os }}) run: | + python -m pip show mlflow python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" python -m unittest -v From 0c4d0f4e46fff7ad1088bf285a82235a25f92b9c Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 13:47:37 +0800 Subject: [PATCH 03/11] temp test Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index b53f659b27..2cf913020d 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -117,7 +117,7 @@ jobs: python -m pip show mlflow python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" - python -m unittest -v + python -m unittest tests/test_mlflow_hander.py env: QUICKTEST: True PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 From 9fc09e01857d3992008164657f4e0c3394b8b24c Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 13:55:13 +0800 Subject: [PATCH 04/11] fix typo Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 2cf913020d..d8dc840ebe 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -117,7 +117,7 @@ jobs: python -m pip show mlflow python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" - python -m unittest tests/test_mlflow_hander.py + python -m unittest tests/test_hander_mlflow.py env: QUICKTEST: True PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 From 8a5c3fd71314f97e25809d8aaf74e33bc623820b Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 14:01:45 +0800 Subject: [PATCH 05/11] fix typo Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index d8dc840ebe..bf36e45158 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -117,7 +117,7 @@ jobs: python -m pip show mlflow python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" - python -m unittest tests/test_hander_mlflow.py + python -m unittest tests/test_handler_mlflow.py env: QUICKTEST: True PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 From 8336174f1f3a3b535d5d51b9df9cbfb59cc2482d Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 14:07:51 +0800 Subject: [PATCH 06/11] temp test Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index bf36e45158..177d1d9c36 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -120,7 +120,7 @@ jobs: python -m unittest tests/test_handler_mlflow.py env: QUICKTEST: True - PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 + # PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 packaging: runs-on: ubuntu-latest From 5d24dd3859af72f6e5514cb9af86379495980478 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 14:18:30 +0800 Subject: [PATCH 07/11] temp test Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 177d1d9c36..0528d33b96 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -105,7 +105,6 @@ jobs: python -m pip install -r requirements-dev.txt python -m pip list python setup.py develop # test no compile installation - python -m pip show mlflow shell: bash - name: Run compiled (${{ runner.os }}) run: | @@ -114,10 +113,8 @@ jobs: shell: bash - name: Run quick tests (CPU ${{ runner.os }}) run: | - python -m pip show mlflow python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" - python -m unittest tests/test_handler_mlflow.py env: QUICKTEST: True # PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 From a801b2eb66a6851270262632c2f1730e6b09d8d7 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 14:37:05 +0800 Subject: [PATCH 08/11] test Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index 0528d33b96..afc428d6f8 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -115,6 +115,7 @@ jobs: run: | python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' python -c "import monai; monai.config.print_config()" + python -m unittest -v env: QUICKTEST: True # PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 From f72cf2a95c068779fe41beb4f039dbda13bdfc77 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 15:08:45 +0800 Subject: [PATCH 09/11] remove env Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index afc428d6f8..ea2cc8dc6c 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -203,8 +203,6 @@ jobs: ls -al python -m pip install -r requirements-dev.txt python -m unittest -v - env: - PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 build-docs: runs-on: ubuntu-latest From 6409b76cf35618b703ac04a98ec58fc1244f0460 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Mon, 6 May 2024 16:02:21 +0800 Subject: [PATCH 10/11] upgrade pip Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index ea2cc8dc6c..cdca623eb6 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -100,6 +100,7 @@ jobs: python -m pip install --pre -U itk - name: Install the dependencies run: | + python -m pip install --user --upgrade pip wheel python -m pip install torch==1.13.1 torchvision==0.14.1 cat "requirements-dev.txt" python -m pip install -r requirements-dev.txt From beae94016fac7e9a985e4aaf391604ee583f8eb9 Mon Sep 17 00:00:00 2001 From: YunLiu <55491388+KumoLiu@users.noreply.github.com> Date: Fri, 10 May 2024 11:47:49 +0800 Subject: [PATCH 11/11] update version Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> --- .github/workflows/pythonapp.yml | 4 +++- docs/requirements.txt | 2 +- requirements-dev.txt | 2 +- setup.cfg | 4 ++-- 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml index cdca623eb6..d1e77bb567 100644 --- a/.github/workflows/pythonapp.yml +++ b/.github/workflows/pythonapp.yml @@ -119,7 +119,7 @@ jobs: python -m unittest -v env: QUICKTEST: True - # PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 + PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 packaging: runs-on: ubuntu-latest @@ -204,6 +204,8 @@ jobs: ls -al python -m pip install -r requirements-dev.txt python -m unittest -v + env: + PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 build-docs: runs-on: ubuntu-latest diff --git a/docs/requirements.txt b/docs/requirements.txt index e5bedf8552..468545dc19 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -22,7 +22,7 @@ sphinx-autodoc-typehints==1.11.1 pandas einops transformers<4.22; python_version <= '3.10' # https://github.com/Project-MONAI/MONAI/issues/5157 -mlflow>=1.28.0 +mlflow>=2.12.2 clearml>=1.10.0rc0 tensorboardX imagecodecs; platform_system == "Linux" or platform_system == "Darwin" diff --git a/requirements-dev.txt b/requirements-dev.txt index ea42bb395e..83bdae2a5c 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -34,7 +34,7 @@ pandas requests einops transformers>=4.36.0 -mlflow>=1.28.0 +mlflow>=2.12.2 clearml>=1.10.0rc0 matplotlib!=3.5.0 tensorboardX diff --git a/setup.cfg b/setup.cfg index ecd60af9ee..711d5c5558 100644 --- a/setup.cfg +++ b/setup.cfg @@ -66,7 +66,7 @@ all = pandas einops transformers<4.22; python_version <= '3.10' - mlflow>=1.28.0 + mlflow>=2.12.2 clearml>=1.10.0rc0 matplotlib tensorboardX @@ -125,7 +125,7 @@ einops = transformers = transformers<4.22; python_version <= '3.10' mlflow = - mlflow>=1.28.0 + mlflow>=2.12.2 matplotlib = matplotlib clearml =