From a8f668af294a39e39db62dd2a3dba9cfa0722069 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 14:41:55 +0800 Subject: [PATCH 01/21] modify python version for weekly test Signed-off-by: Yiheng Wang --- .github/workflows/weekly-tests-cpu.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/weekly-tests-cpu.yml b/.github/workflows/weekly-tests-cpu.yml index 1acf24a2..bcff7c7c 100644 --- a/.github/workflows/weekly-tests-cpu.yml +++ b/.github/workflows/weekly-tests-cpu.yml @@ -6,16 +6,19 @@ on: - cron: "0 5 * * 0" # 5:00, every Sunday # Allows you to run this workflow manually from the Actions tab workflow_dispatch: + # Trigger the workflow on pull request activity + pull_request: + branches: [ dev ] jobs: get-list: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: cache weekly timestamp id: pip-cache run: | @@ -47,10 +50,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: cache weekly timestamp id: pip-cache run: | From 9bee070c48b1d240d5ae7dbe7dcd75c069cb7395 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 14:59:03 +0800 Subject: [PATCH 02/21] revert weekly test running change Signed-off-by: Yiheng Wang --- .github/workflows/weekly-tests-cpu.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/weekly-tests-cpu.yml b/.github/workflows/weekly-tests-cpu.yml index bcff7c7c..f85288b5 100644 --- a/.github/workflows/weekly-tests-cpu.yml +++ b/.github/workflows/weekly-tests-cpu.yml @@ -6,9 +6,6 @@ on: - cron: "0 5 * * 0" # 5:00, every Sunday # Allows you to run this workflow manually from the Actions tab workflow_dispatch: - # Trigger the workflow on pull request activity - pull_request: - branches: [ dev ] jobs: get-list: From e527480102a511692f8784f4a58aaae2550d5016 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 15:12:16 +0800 Subject: [PATCH 03/21] use python 3.9 for premerge cpu test as well Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 4bd1215f..4fc94bd6 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -17,10 +17,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python 3.9 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.9 - name: cache weekly timestamp id: pip-cache run: | From 47c6752188ab80e9c8aa0e64e373d8318cad5ad5 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 15:25:41 +0800 Subject: [PATCH 04/21] test get list Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 13 +++++++++++-- models/valve_landmarks/configs/metadata.json | 3 ++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 4fc94bd6..4eae8442 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -13,14 +13,23 @@ concurrency: cancel-in-progress: true jobs: + get-list: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.8 + uses: actions/setup-python@v2 + with: + python-version: 3.8 premerge-cpu: + needs: get-list runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.9 + - name: Set up Python 3.8 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.8 - name: cache weekly timestamp id: pip-cache run: | diff --git a/models/valve_landmarks/configs/metadata.json b/models/valve_landmarks/configs/metadata.json index b5d12539..c7c1ad7a 100644 --- a/models/valve_landmarks/configs/metadata.json +++ b/models/valve_landmarks/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220729.json", - "version": "0.5.0", + "version": "0.5.1", "changelog": { + "0.5.1": "for debug", "0.5.0": "Fix transform usage", "0.4.3": "README.md fix", "0.4.2": "add name tag", From 841d8b170e3b89f2aaee669be8c92589f2d778e9 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 16:20:21 +0800 Subject: [PATCH 05/21] remove unused install of pipenv Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 4eae8442..b7d9bd64 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -13,16 +13,7 @@ concurrency: cancel-in-progress: true jobs: - get-list: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.8 - uses: actions/setup-python@v2 - with: - python-version: 3.8 premerge-cpu: - needs: get-list runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 @@ -43,8 +34,6 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip wheel - python -m pip install -r requirements-dev.txt - python -m pip install cffi && python -m pip install pipenv - name: check run: | # clean up temporary files From f5f80e99fa1d9413fa9ba08838546ecf8a24c6ce Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 16:45:55 +0800 Subject: [PATCH 06/21] revert rm -rf /opt/hostedtoolcache Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 2 ++ ci/run_premerge_cpu.sh | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index b7d9bd64..4bd1215f 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -34,6 +34,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip wheel + python -m pip install -r requirements-dev.txt + python -m pip install cffi && python -m pip install pipenv - name: check run: | # clean up temporary files diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 4950bd7d..32df1893 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -30,7 +30,7 @@ elif [[ $# -gt 1 ]]; then fi verify_bundle() { - rm -rf /opt/hostedtoolcache + # rm -rf /opt/hostedtoolcache echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) From 29bbff9a3e61902d3518ae61c22e611eedde6129 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 17:44:22 +0800 Subject: [PATCH 07/21] revert debug changes Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 32df1893..4950bd7d 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -30,7 +30,7 @@ elif [[ $# -gt 1 ]]; then fi verify_bundle() { - # rm -rf /opt/hostedtoolcache + rm -rf /opt/hostedtoolcache echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) From 700d7599577f31aa647cfbdb741cd3a58790c337 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Thu, 25 Jan 2024 17:45:44 +0800 Subject: [PATCH 08/21] revert bundle change Signed-off-by: Yiheng Wang --- models/valve_landmarks/configs/metadata.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/models/valve_landmarks/configs/metadata.json b/models/valve_landmarks/configs/metadata.json index c7c1ad7a..b5d12539 100644 --- a/models/valve_landmarks/configs/metadata.json +++ b/models/valve_landmarks/configs/metadata.json @@ -1,8 +1,7 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220729.json", - "version": "0.5.1", + "version": "0.5.0", "changelog": { - "0.5.1": "for debug", "0.5.0": "Fix transform usage", "0.4.3": "README.md fix", "0.4.2": "add name tag", From 17a8f785b35057a6d8a167e07edc6a523101715f Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Fri, 26 Jan 2024 18:35:12 +0800 Subject: [PATCH 09/21] test fix Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 12 ++++++------ ci/run_premerge_cpu.sh | 6 ++++++ models/valve_landmarks/configs/metadata.json | 3 ++- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 4bd1215f..1c4f9f55 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -17,10 +17,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 - uses: actions/setup-python@v2 - with: - python-version: 3.8 + - name: Setup Python 3.9 + run: | + sudo apt-get update + sudo apt-get install -y python3.9 + echo "alias python=python3.9" >> ~/.bashrc + source ~/.bashrc - name: cache weekly timestamp id: pip-cache run: | @@ -34,8 +36,6 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip wheel - python -m pip install -r requirements-dev.txt - python -m pip install cffi && python -m pip install pipenv - name: check run: | # clean up temporary files diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 4950bd7d..ce7199fd 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -31,6 +31,12 @@ fi verify_bundle() { rm -rf /opt/hostedtoolcache + # Reinstall Python 3.9 + sudo apt-get update + sudo apt-get install -y python3.9 + + # Create a symbolic link to ensure python points to python3.9 + sudo ln -s /usr/bin/python3.9 /usr/bin/python echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) diff --git a/models/valve_landmarks/configs/metadata.json b/models/valve_landmarks/configs/metadata.json index b5d12539..cfb49151 100644 --- a/models/valve_landmarks/configs/metadata.json +++ b/models/valve_landmarks/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220729.json", - "version": "0.5.0", + "version": "0.5.1", "changelog": { + "0.5.1": "test", "0.5.0": "Fix transform usage", "0.4.3": "README.md fix", "0.4.2": "add name tag", From 4dd3b096622c2d6b68ceb3d124d5e6bc612e183d Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Fri, 26 Jan 2024 18:41:33 +0800 Subject: [PATCH 10/21] show python version Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index ce7199fd..25e3632e 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -30,13 +30,19 @@ elif [[ $# -gt 1 ]]; then fi verify_bundle() { + echo "Python version before deletion:" + python --version rm -rf /opt/hostedtoolcache + echo "Python version after deletion:" + python --version # Reinstall Python 3.9 sudo apt-get update sudo apt-get install -y python3.9 # Create a symbolic link to ensure python points to python3.9 - sudo ln -s /usr/bin/python3.9 /usr/bin/python + sudo ln -sf /usr/bin/python3.9 /usr/bin/python + echo "Python version after reinstallation:" + python --version echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) From dff8fe7980fedb39cbeb36fd35834374cb518a76 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Fri, 26 Jan 2024 19:56:45 +0800 Subject: [PATCH 11/21] use old way to setup original py39 Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 1c4f9f55..4fc94bd6 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -17,12 +17,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - name: Setup Python 3.9 - run: | - sudo apt-get update - sudo apt-get install -y python3.9 - echo "alias python=python3.9" >> ~/.bashrc - source ~/.bashrc + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 - name: cache weekly timestamp id: pip-cache run: | @@ -36,6 +34,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip wheel + python -m pip install -r requirements-dev.txt + python -m pip install cffi && python -m pip install pipenv - name: check run: | # clean up temporary files From d8fb014994477287311b736f0dd1231c714e3ffc Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Fri, 26 Jan 2024 20:02:16 +0800 Subject: [PATCH 12/21] remove error echo Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 25e3632e..c00a049e 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -33,8 +33,6 @@ verify_bundle() { echo "Python version before deletion:" python --version rm -rf /opt/hostedtoolcache - echo "Python version after deletion:" - python --version # Reinstall Python 3.9 sudo apt-get update sudo apt-get install -y python3.9 From 8958cc2ab63df7386e2f43dd5a4d611a89c0c302 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 12:41:38 +0800 Subject: [PATCH 13/21] change path Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index c00a049e..5b449dae 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -38,7 +38,7 @@ verify_bundle() { sudo apt-get install -y python3.9 # Create a symbolic link to ensure python points to python3.9 - sudo ln -sf /usr/bin/python3.9 /usr/bin/python + export PATH=/usr/bin:$PATH echo "Python version after reinstallation:" python --version echo 'Run verify bundle...' From 42fc3b4fc2c0a28e7dddbea09a138af95296708b Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 13:00:07 +0800 Subject: [PATCH 14/21] clear shell hash Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 5b449dae..da384752 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -37,8 +37,14 @@ verify_bundle() { sudo apt-get update sudo apt-get install -y python3.9 - # Create a symbolic link to ensure python points to python3.9 + # Forcefully create a symbolic link to ensure python points to python3.9 + sudo ln -sf /usr/bin/python3.9 /usr/bin/python + + # Add /usr/bin to the front of the PATH export PATH=/usr/bin:$PATH + + # Clear shell hash and print Python version after reinstallation + hash -r echo "Python version after reinstallation:" python --version echo 'Run verify bundle...' From ecaaa0b5d2d78f783b6882e5c763743e044106ab Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 13:14:32 +0800 Subject: [PATCH 15/21] specify py3.9 Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index da384752..6a4abadf 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -37,16 +37,8 @@ verify_bundle() { sudo apt-get update sudo apt-get install -y python3.9 - # Forcefully create a symbolic link to ensure python points to python3.9 - sudo ln -sf /usr/bin/python3.9 /usr/bin/python - - # Add /usr/bin to the front of the PATH - export PATH=/usr/bin:$PATH - - # Clear shell hash and print Python version after reinstallation - hash -r echo "Python version after reinstallation:" - python --version + python3.9 --version echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) From eab9e74abc9abae36b58a18d6d49e6019b2f2fbb Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 13:29:36 +0800 Subject: [PATCH 16/21] avoid rm cache python Signed-off-by: Yiheng Wang --- ci/run_premerge_cpu.sh | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 6a4abadf..77c03b0e 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -30,15 +30,12 @@ elif [[ $# -gt 1 ]]; then fi verify_bundle() { - echo "Python version before deletion:" - python --version - rm -rf /opt/hostedtoolcache - # Reinstall Python 3.9 - sudo apt-get update - sudo apt-get install -y python3.9 - - echo "Python version after reinstallation:" - python3.9 --version + for dir in /opt/hostedtoolcache/*; do + if [[ $dir != "/opt/hostedtoolcache/Python" ]]; then + echo "delete $dir" + rm -rf "$dir" + fi + done echo 'Run verify bundle...' pip install -r requirements.txt head_ref=$(git rev-parse HEAD) From 87b0ffecaf7bc0e98f7b5e3dc6eeb7eced507928 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 13:42:36 +0800 Subject: [PATCH 17/21] remove no need pipenv install Signed-off-by: Yiheng Wang --- .github/workflows/premerge-cpu.yml | 2 -- ci/run_premerge_cpu.sh | 1 - 2 files changed, 3 deletions(-) diff --git a/.github/workflows/premerge-cpu.yml b/.github/workflows/premerge-cpu.yml index 4fc94bd6..e46de1ca 100644 --- a/.github/workflows/premerge-cpu.yml +++ b/.github/workflows/premerge-cpu.yml @@ -34,8 +34,6 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip wheel - python -m pip install -r requirements-dev.txt - python -m pip install cffi && python -m pip install pipenv - name: check run: | # clean up temporary files diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh index 77c03b0e..11a233fe 100755 --- a/ci/run_premerge_cpu.sh +++ b/ci/run_premerge_cpu.sh @@ -32,7 +32,6 @@ fi verify_bundle() { for dir in /opt/hostedtoolcache/*; do if [[ $dir != "/opt/hostedtoolcache/Python" ]]; then - echo "delete $dir" rm -rf "$dir" fi done From 249eaa6e90c04e45efe6563498f3cc14f216a467 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Sat, 27 Jan 2024 13:53:21 +0800 Subject: [PATCH 18/21] fix black error Signed-off-by: Yiheng Wang --- ci/unit_tests/test_spleen_deepedit_annotation.py | 6 +++--- .../configs/metadata.json | 3 ++- .../scripts/networks/nest/utils.py | 8 ++------ models/valve_landmarks/configs/metadata.json | 3 +-- .../configs/metadata.json | 3 ++- .../scripts/networks/nest/utils.py | 8 ++------ 6 files changed, 12 insertions(+), 19 deletions(-) diff --git a/ci/unit_tests/test_spleen_deepedit_annotation.py b/ci/unit_tests/test_spleen_deepedit_annotation.py index fa5da6fa..4210d92b 100644 --- a/ci/unit_tests/test_spleen_deepedit_annotation.py +++ b/ci/unit_tests/test_spleen_deepedit_annotation.py @@ -124,9 +124,9 @@ def test_infer_config(self, override): @parameterized.expand([TEST_CASE_2]) def test_infer_click_config(self, override): override["dataset_dir"] = self.dataset_dir - override[ - "dataset#data" - ] = "$[{'image': i, 'background': [], 'spleen': [[6, 6, 6], [8, 8, 8]]} for i in @datalist]" + override["dataset#data"] = ( + "$[{'image': i, 'background': [], 'spleen': [[6, 6, 6], [8, 8, 8]]} for i in @datalist]" + ) bundle_root = override["bundle_root"] sys.path = [bundle_root] + sys.path diff --git a/models/renalStructures_UNEST_segmentation/configs/metadata.json b/models/renalStructures_UNEST_segmentation/configs/metadata.json index 06c84f20..c2cf410a 100644 --- a/models/renalStructures_UNEST_segmentation/configs/metadata.json +++ b/models/renalStructures_UNEST_segmentation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.2.3", + "version": "0.2.4", "changelog": { + "0.2.4": "fix black 24.1 format error", "0.2.3": "update AddChanneld with EnsureChannelFirstd and remove meta_dict", "0.2.2": "add name tag", "0.2.1": "fix license Copyright error", diff --git a/models/renalStructures_UNEST_segmentation/scripts/networks/nest/utils.py b/models/renalStructures_UNEST_segmentation/scripts/networks/nest/utils.py index 70828c04..211283d3 100755 --- a/models/renalStructures_UNEST_segmentation/scripts/networks/nest/utils.py +++ b/models/renalStructures_UNEST_segmentation/scripts/networks/nest/utils.py @@ -37,9 +37,7 @@ def drop_block_2d( total_size = w * h clipped_block_size = min(block_size, min(w, h)) # seed_drop_rate, the gamma parameter - gamma = ( - gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) - ) + gamma = gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) # Forces the block to be inside the feature map. w_i, h_i = torch.meshgrid(torch.arange(w).to(x.device), torch.arange(h).to(x.device)) @@ -89,9 +87,7 @@ def drop_block_fast_2d( b, c, h, w = x.shape total_size = w * h clipped_block_size = min(block_size, min(w, h)) - gamma = ( - gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) - ) + gamma = gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) block_mask = torch.empty_like(x).bernoulli_(gamma) block_mask = F.max_pool2d( diff --git a/models/valve_landmarks/configs/metadata.json b/models/valve_landmarks/configs/metadata.json index cfb49151..b5d12539 100644 --- a/models/valve_landmarks/configs/metadata.json +++ b/models/valve_landmarks/configs/metadata.json @@ -1,8 +1,7 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220729.json", - "version": "0.5.1", + "version": "0.5.0", "changelog": { - "0.5.1": "test", "0.5.0": "Fix transform usage", "0.4.3": "README.md fix", "0.4.2": "add name tag", diff --git a/models/wholeBrainSeg_Large_UNEST_segmentation/configs/metadata.json b/models/wholeBrainSeg_Large_UNEST_segmentation/configs/metadata.json index 69cb257b..9489b50b 100644 --- a/models/wholeBrainSeg_Large_UNEST_segmentation/configs/metadata.json +++ b/models/wholeBrainSeg_Large_UNEST_segmentation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.2.3", + "version": "0.2.4", "changelog": { + "0.2.4": "fix black 24.1 format error", "0.2.3": "fix PYTHONPATH in readme.md", "0.2.2": "add name tag", "0.2.1": "fix license Copyright error", diff --git a/models/wholeBrainSeg_Large_UNEST_segmentation/scripts/networks/nest/utils.py b/models/wholeBrainSeg_Large_UNEST_segmentation/scripts/networks/nest/utils.py index 70828c04..211283d3 100755 --- a/models/wholeBrainSeg_Large_UNEST_segmentation/scripts/networks/nest/utils.py +++ b/models/wholeBrainSeg_Large_UNEST_segmentation/scripts/networks/nest/utils.py @@ -37,9 +37,7 @@ def drop_block_2d( total_size = w * h clipped_block_size = min(block_size, min(w, h)) # seed_drop_rate, the gamma parameter - gamma = ( - gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) - ) + gamma = gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) # Forces the block to be inside the feature map. w_i, h_i = torch.meshgrid(torch.arange(w).to(x.device), torch.arange(h).to(x.device)) @@ -89,9 +87,7 @@ def drop_block_fast_2d( b, c, h, w = x.shape total_size = w * h clipped_block_size = min(block_size, min(w, h)) - gamma = ( - gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) - ) + gamma = gamma_scale * drop_prob * total_size / clipped_block_size**2 / ((w - block_size + 1) * (h - block_size + 1)) block_mask = torch.empty_like(x).bernoulli_(gamma) block_mask = F.max_pool2d( From 77f8b62e3f426005cbd62835056769bf3214db52 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Mon, 29 Jan 2024 11:02:26 +0800 Subject: [PATCH 19/21] update exclude list to support new bundle check Signed-off-by: Yiheng Wang --- ci/get_bundle_list.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/get_bundle_list.py b/ci/get_bundle_list.py index 3e6d5393..440aeb54 100644 --- a/ci/get_bundle_list.py +++ b/ci/get_bundle_list.py @@ -15,7 +15,7 @@ from utils import get_sub_folders # new added bundles should temporarily be added to this list, and remove until they can be downloaded successfully -EXCLUDE_LIST = ["segmentation_template", "classification_template"] +EXCLUDE_LIST = [] def main(models_path): From 923b72628711cfddd3b0f886795917d64fe1332d Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Mon, 29 Jan 2024 11:11:40 +0800 Subject: [PATCH 20/21] trigger weekly test Signed-off-by: Yiheng Wang --- .github/workflows/weekly-tests-cpu.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/weekly-tests-cpu.yml b/.github/workflows/weekly-tests-cpu.yml index f85288b5..7ae0dcbe 100644 --- a/.github/workflows/weekly-tests-cpu.yml +++ b/.github/workflows/weekly-tests-cpu.yml @@ -6,6 +6,7 @@ on: - cron: "0 5 * * 0" # 5:00, every Sunday # Allows you to run this workflow manually from the Actions tab workflow_dispatch: + pull_request: jobs: get-list: From 4eacb73a4e1805fb70bc02848bfa870d4ff06993 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Mon, 29 Jan 2024 11:23:51 +0800 Subject: [PATCH 21/21] revert weekly test change Signed-off-by: Yiheng Wang --- .github/workflows/weekly-tests-cpu.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/weekly-tests-cpu.yml b/.github/workflows/weekly-tests-cpu.yml index 7ae0dcbe..f85288b5 100644 --- a/.github/workflows/weekly-tests-cpu.yml +++ b/.github/workflows/weekly-tests-cpu.yml @@ -6,7 +6,6 @@ on: - cron: "0 5 * * 0" # 5:00, every Sunday # Allows you to run this workflow manually from the Actions tab workflow_dispatch: - pull_request: jobs: get-list: