From 0f5e12af5bd8bd93b4127f8634932be3851cb7f9 Mon Sep 17 00:00:00 2001 From: Sarthak Pati Date: Mon, 23 Sep 2024 12:52:26 -0400 Subject: [PATCH 1/5] added the option to upload coverage to codacy --- .github/workflows/python-test.yml | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml index 78c10901e..e5ce765ed 100644 --- a/.github/workflows/python-test.yml +++ b/.github/workflows/python-test.yml @@ -106,10 +106,17 @@ jobs: run: | pytest --cov=. --cov-report=xml --cov-append -k "update_version" - - name: Upload coverage + - name: Upload coverage to CodeCov if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change uses: codecov/codecov-action@v1 with: token: ${{ secrets.CODECOV_TOKEN }} file: ./coverage.xml - flags: unittests \ No newline at end of file + flags: unittests + + - name: Upload coverage to Codacy + if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change + uses: codacy/codacy-coverage-reporter-action@v1.3.0 + with: + project-token: ${{ secrets.CODACY_PROJECT_TOKEN }} + coverage-reports: ./coverage.xml From 0f2a199a50739626165aef75426a27b366bb2cc6 Mon Sep 17 00:00:00 2001 From: Sarthak Pati Date: Mon, 23 Sep 2024 15:12:13 -0400 Subject: [PATCH 2/5] updated badge --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 136333a22..616e9be91 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,9 @@ - Codacy
+ + + Codacy
From aea7b7a10ef0a29ef5e8cf7c8d114f9c27a6200e Mon Sep 17 00:00:00 2001 From: Sarthak Pati Date: Mon, 23 Sep 2024 15:13:25 -0400 Subject: [PATCH 3/5] Update README.md --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 616e9be91..a267fa424 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,8 @@ - - - Codacy
+
+ Codacy From b61b48dd19745207e4d87f257db8a9915f5fd50d Mon Sep 17 00:00:00 2001 From: scap3yvt <149599669+scap3yvt@users.noreply.github.com> Date: Mon, 23 Sep 2024 20:11:32 -0400 Subject: [PATCH 4/5] version updated for tagging --- GANDLF/version.py | 2 +- samples/config_all_options.yaml | 4 ++-- samples/config_classification.yaml | 4 ++-- samples/config_getting_started_classification_histo2d.yaml | 2 +- samples/config_getting_started_classification_rad3d.yaml | 2 +- samples/config_getting_started_regression_histo2d.yaml | 2 +- samples/config_getting_started_regression_rad3d.yaml | 2 +- samples/config_getting_started_segmentation_histo2d.yaml | 2 +- samples/config_getting_started_segmentation_rad3d.yaml | 4 ++-- samples/config_regression.yaml | 4 ++-- samples/config_segmentation_brats.yaml | 4 ++-- samples/config_segmentation_histology.yaml | 4 ++-- testing/config_classification.yaml | 2 +- testing/config_regression.yaml | 2 +- testing/config_segmentation.yaml | 2 +- tutorials/classification_medmnist_notebook/config.yaml | 2 +- 16 files changed, 22 insertions(+), 22 deletions(-) diff --git a/GANDLF/version.py b/GANDLF/version.py index 9d601767a..f810698fb 100644 --- a/GANDLF/version.py +++ b/GANDLF/version.py @@ -2,4 +2,4 @@ # -*- coding: UTF-8 -*- # check GaNDLF wiki for versioning and release guidelines: https://github.com/mlcommons/GaNDLF/wiki -__version__ = "0.1.0-dev" +__version__ = "0.1.0" diff --git a/samples/config_all_options.yaml b/samples/config_all_options.yaml index f460ac252..0348099fe 100644 --- a/samples/config_all_options.yaml +++ b/samples/config_all_options.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0-dev, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.0, + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } ## Choose the model parameters here model: diff --git a/samples/config_classification.yaml b/samples/config_classification.yaml index 7a8ba7704..fa2f25be4 100644 --- a/samples/config_classification.yaml +++ b/samples/config_classification.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0-dev, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.0, + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_getting_started_classification_histo2d.yaml b/samples/config_getting_started_classification_histo2d.yaml index 34b5d069f..998daa0d6 100644 --- a/samples/config_getting_started_classification_histo2d.yaml +++ b/samples/config_getting_started_classification_histo2d.yaml @@ -94,6 +94,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_classification_rad3d.yaml b/samples/config_getting_started_classification_rad3d.yaml index e374ee82a..30d1bd365 100644 --- a/samples/config_getting_started_classification_rad3d.yaml +++ b/samples/config_getting_started_classification_rad3d.yaml @@ -99,6 +99,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_histo2d.yaml b/samples/config_getting_started_regression_histo2d.yaml index 1b325595d..e2675db98 100644 --- a/samples/config_getting_started_regression_histo2d.yaml +++ b/samples/config_getting_started_regression_histo2d.yaml @@ -59,6 +59,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_rad3d.yaml b/samples/config_getting_started_regression_rad3d.yaml index bb1e3f1e6..40dfd2f87 100644 --- a/samples/config_getting_started_regression_rad3d.yaml +++ b/samples/config_getting_started_regression_rad3d.yaml @@ -62,6 +62,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: false diff --git a/samples/config_getting_started_segmentation_histo2d.yaml b/samples/config_getting_started_segmentation_histo2d.yaml index 6640e5a0b..055f63852 100644 --- a/samples/config_getting_started_segmentation_histo2d.yaml +++ b/samples/config_getting_started_segmentation_histo2d.yaml @@ -66,6 +66,6 @@ scheduler: track_memory_usage: false verbose: true version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_segmentation_rad3d.yaml b/samples/config_getting_started_segmentation_rad3d.yaml index 029b18e7a..5c046b799 100644 --- a/samples/config_getting_started_segmentation_rad3d.yaml +++ b/samples/config_getting_started_segmentation_rad3d.yaml @@ -89,6 +89,6 @@ scheduler: track_memory_usage: false verbose: true version: - maximum: 0.1.0-dev - minimum: 0.1.0-dev + maximum: 0.1.0 + minimum: 0.1.0 weighted_loss: true diff --git a/samples/config_regression.yaml b/samples/config_regression.yaml index d3757afcc..25751aba3 100644 --- a/samples/config_regression.yaml +++ b/samples/config_regression.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0-dev, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.0, + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_brats.yaml b/samples/config_segmentation_brats.yaml index 33ae7378e..19fe2fce9 100644 --- a/samples/config_segmentation_brats.yaml +++ b/samples/config_segmentation_brats.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0-dev, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.0, + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_histology.yaml b/samples/config_segmentation_histology.yaml index cedebe7ce..9a2d213e4 100644 --- a/samples/config_segmentation_histology.yaml +++ b/samples/config_segmentation_histology.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0-dev, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.0, + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/testing/config_classification.yaml b/testing/config_classification.yaml index b23ff66f3..14cafd5f4 100644 --- a/testing/config_classification.yaml +++ b/testing/config_classification.yaml @@ -55,7 +55,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: True diff --git a/testing/config_regression.yaml b/testing/config_regression.yaml index b9c8dd764..3d42efafa 100644 --- a/testing/config_regression.yaml +++ b/testing/config_regression.yaml @@ -38,7 +38,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.0-dev + maximum: 0.1.0 minimum: 0.0.14 weighted_loss: false diff --git a/testing/config_segmentation.yaml b/testing/config_segmentation.yaml index 3a5d48a7e..1f5da8445 100644 --- a/testing/config_segmentation.yaml +++ b/testing/config_segmentation.yaml @@ -3,7 +3,7 @@ version: { minimum: 0.0.14, - maximum: 0.1.0-dev + maximum: 0.1.0 } model: { diff --git a/tutorials/classification_medmnist_notebook/config.yaml b/tutorials/classification_medmnist_notebook/config.yaml index 20d9ef784..08abafc22 100644 --- a/tutorials/classification_medmnist_notebook/config.yaml +++ b/tutorials/classification_medmnist_notebook/config.yaml @@ -2,7 +2,7 @@ version: { minimum: 0.0.14, - maximum: 0.1.0-dev # this should NOT be made a variable, but should be tested after every tag is created + maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: From 86c8fab7dd29a9f5550b8e10ddb046e0fe011b99 Mon Sep 17 00:00:00 2001 From: scap3yvt <149599669+scap3yvt@users.noreply.github.com> Date: Tue, 24 Sep 2024 07:46:22 -0400 Subject: [PATCH 5/5] version updated for development --- GANDLF/version.py | 2 +- docs/migration_guide.md | 4 ++-- samples/config_all_options.yaml | 4 ++-- samples/config_classification.yaml | 4 ++-- samples/config_getting_started_classification_histo2d.yaml | 2 +- samples/config_getting_started_classification_rad3d.yaml | 2 +- samples/config_getting_started_regression_histo2d.yaml | 2 +- samples/config_getting_started_regression_rad3d.yaml | 2 +- samples/config_getting_started_segmentation_histo2d.yaml | 2 +- samples/config_getting_started_segmentation_rad3d.yaml | 4 ++-- samples/config_regression.yaml | 4 ++-- samples/config_segmentation_brats.yaml | 4 ++-- samples/config_segmentation_histology.yaml | 4 ++-- testing/config_classification.yaml | 2 +- testing/config_regression.yaml | 2 +- testing/config_segmentation.yaml | 2 +- tutorials/classification_medmnist_notebook/config.yaml | 2 +- 17 files changed, 24 insertions(+), 24 deletions(-) diff --git a/GANDLF/version.py b/GANDLF/version.py index f810698fb..969da2b13 100644 --- a/GANDLF/version.py +++ b/GANDLF/version.py @@ -2,4 +2,4 @@ # -*- coding: UTF-8 -*- # check GaNDLF wiki for versioning and release guidelines: https://github.com/mlcommons/GaNDLF/wiki -__version__ = "0.1.0" +__version__ = "0.1.1-dev" diff --git a/docs/migration_guide.md b/docs/migration_guide.md index b435e30c0..552f6fba4 100644 --- a/docs/migration_guide.md +++ b/docs/migration_guide.md @@ -15,8 +15,8 @@ The [0.0.20 release](https://github.com/mlcommons/GaNDLF/releases/tag/0.0.20) wa - The main change is the use of the [Version package](https://github.com/keleshev/version) for systematic semantic versioning [[ref](https://github.com/mlcommons/GaNDLF/pull/841)]. - No change is needed if you are using a [stable version](https://docs.mlcommons.org/GaNDLF/setup/#install-from-package-managers). - If you have installed GaNDLF [from source](https://docs.mlcommons.org/GaNDLF/setup/#install-from-sources) or using a [nightly build](https://docs.mlcommons.org/GaNDLF/setup/#install-from-package-managers), you will need to ensure that the `maximum` key under `version` in the configuration file contains the correct version number: - - Either **including** the `-dev` identifier of the current version (e.g., if the current version is `0.1.0-dev`, then the `maximum` key should be `0.1.0-dev`). - - Or **excluding** the `-dev` identifier of the current version, but increasing the version number by one on any level (e.g., if the current version is `0.1.0-dev`, then the `maximum` key should be `0.1.1`). + - Either **including** the `-dev` identifier of the current version (e.g., if the current version is `0.X.Y-dev`, then the `maximum` key should be `0.X.Y-dev`). + - Or **excluding** the `-dev` identifier of the current version, but increasing the version number by one on any level (e.g., if the current version is `0.X.Y-dev`, then the `maximum` key should be `0.X.Y`). ### Use in HPC Environments diff --git a/samples/config_all_options.yaml b/samples/config_all_options.yaml index 0348099fe..51edecb01 100644 --- a/samples/config_all_options.yaml +++ b/samples/config_all_options.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.1-dev, + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } ## Choose the model parameters here model: diff --git a/samples/config_classification.yaml b/samples/config_classification.yaml index fa2f25be4..8dbd3a082 100644 --- a/samples/config_classification.yaml +++ b/samples/config_classification.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.1-dev, + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_getting_started_classification_histo2d.yaml b/samples/config_getting_started_classification_histo2d.yaml index 998daa0d6..5d59c3c3a 100644 --- a/samples/config_getting_started_classification_histo2d.yaml +++ b/samples/config_getting_started_classification_histo2d.yaml @@ -94,6 +94,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_classification_rad3d.yaml b/samples/config_getting_started_classification_rad3d.yaml index 30d1bd365..83c5ef6b8 100644 --- a/samples/config_getting_started_classification_rad3d.yaml +++ b/samples/config_getting_started_classification_rad3d.yaml @@ -99,6 +99,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_histo2d.yaml b/samples/config_getting_started_regression_histo2d.yaml index e2675db98..0101d2ccc 100644 --- a/samples/config_getting_started_regression_histo2d.yaml +++ b/samples/config_getting_started_regression_histo2d.yaml @@ -59,6 +59,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_rad3d.yaml b/samples/config_getting_started_regression_rad3d.yaml index 40dfd2f87..39db08ad4 100644 --- a/samples/config_getting_started_regression_rad3d.yaml +++ b/samples/config_getting_started_regression_rad3d.yaml @@ -62,6 +62,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: false diff --git a/samples/config_getting_started_segmentation_histo2d.yaml b/samples/config_getting_started_segmentation_histo2d.yaml index 055f63852..67871e07d 100644 --- a/samples/config_getting_started_segmentation_histo2d.yaml +++ b/samples/config_getting_started_segmentation_histo2d.yaml @@ -66,6 +66,6 @@ scheduler: track_memory_usage: false verbose: true version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_segmentation_rad3d.yaml b/samples/config_getting_started_segmentation_rad3d.yaml index 5c046b799..39316b755 100644 --- a/samples/config_getting_started_segmentation_rad3d.yaml +++ b/samples/config_getting_started_segmentation_rad3d.yaml @@ -89,6 +89,6 @@ scheduler: track_memory_usage: false verbose: true version: - maximum: 0.1.0 - minimum: 0.1.0 + maximum: 0.1.1-dev + minimum: 0.1.1-dev weighted_loss: true diff --git a/samples/config_regression.yaml b/samples/config_regression.yaml index 25751aba3..a0c1d65f8 100644 --- a/samples/config_regression.yaml +++ b/samples/config_regression.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.1-dev, + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_brats.yaml b/samples/config_segmentation_brats.yaml index 19fe2fce9..d56a30e2f 100644 --- a/samples/config_segmentation_brats.yaml +++ b/samples/config_segmentation_brats.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.1-dev, + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_histology.yaml b/samples/config_segmentation_histology.yaml index 9a2d213e4..ddc6abd99 100644 --- a/samples/config_segmentation_histology.yaml +++ b/samples/config_segmentation_histology.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.0, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.1-dev, + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/testing/config_classification.yaml b/testing/config_classification.yaml index 14cafd5f4..ea8f0f890 100644 --- a/testing/config_classification.yaml +++ b/testing/config_classification.yaml @@ -55,7 +55,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: True diff --git a/testing/config_regression.yaml b/testing/config_regression.yaml index 3d42efafa..474ac163e 100644 --- a/testing/config_regression.yaml +++ b/testing/config_regression.yaml @@ -38,7 +38,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.0 + maximum: 0.1.1-dev minimum: 0.0.14 weighted_loss: false diff --git a/testing/config_segmentation.yaml b/testing/config_segmentation.yaml index 1f5da8445..e49d4b716 100644 --- a/testing/config_segmentation.yaml +++ b/testing/config_segmentation.yaml @@ -3,7 +3,7 @@ version: { minimum: 0.0.14, - maximum: 0.1.0 + maximum: 0.1.1-dev } model: { diff --git a/tutorials/classification_medmnist_notebook/config.yaml b/tutorials/classification_medmnist_notebook/config.yaml index 08abafc22..5e7e1138c 100644 --- a/tutorials/classification_medmnist_notebook/config.yaml +++ b/tutorials/classification_medmnist_notebook/config.yaml @@ -2,7 +2,7 @@ version: { minimum: 0.0.14, - maximum: 0.1.0 # this should NOT be made a variable, but should be tested after every tag is created + maximum: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: