Merge branch 'master' into 920-feature-standardize-dependency-install…

…ation-for-github-actions
mlcommons · Sep 24, 2024 · 50abfd0 · 50abfd0
2 parents 7cfb2ac + 2953a5e
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diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml
@@ -59,4 +59,11 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
-          flags: unittests
+          flags: unittests
+
+      - name: Upload coverage to Codacy
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        uses: codacy/[email protected]
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: ./coverage.xml
diff --git a/README.md b/README.md
@@ -5,7 +5,8 @@
   <a href="https://github.com/mlcommons/GaNDLF/actions/workflows/codeql-analysis.yml" alt="Code Analysis"><img src="https://github.com/mlcommons/GaNDLF/workflows/CodeQL/badge.svg" /></a>
   <a href="https://hub.docker.com/repository/docker/cbica/gandlf" alt="Docker CI"><img src="https://github.com/mlcommons/GaNDLF/actions/workflows/docker-image.yml/badge.svg" /></a>
   <a href="https://codecov.io/gh/mlcommons/GaNDLF" alt="Code Coverage"><img src="https://codecov.io/gh/mlcommons/GaNDLF/branch/master/graph/badge.svg?token=4I54XEI3WE" /></a>
-  <a href="https://app.codacy.com/gh/mlcommons/GaNDLF?utm_source=github.com&utm_medium=referral&utm_content=mlcommons/GaNDLF&utm_campaign=Badge_Grade_Settings"><img alt="Codacy" src="https://api.codacy.com/project/badge/Grade/b2cf27ddce1b4907abb47a82931dcbca"></a><br>
+  <a href="https://app.codacy.com/gh/mlcommons/GaNDLF/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage" alt="Codacy Code Coverage"><img src="https://app.codacy.com/project/badge/Coverage/51a47165e3644ec6acdfbac345843b7c" /></a><br>
+  <a href="https://app.codacy.com/gh/mlcommons/GaNDLF/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade"><img alt="Codacy" src="https://app.codacy.com/project/badge/Grade/51a47165e3644ec6acdfbac345843b7c"></a>
   <a href="https://pypi.org/project/GANDLF/" alt="Install"><img src="https://img.shields.io/pypi/v/gandlf?color=blue" /></a>
   <a href="https://anaconda.org/conda-forge/gandlf" alt="Install"><img src="https://img.shields.io/conda/vn/conda-forge/gandlf?color=green" /></a>
   <a href="https://github.com/mlcommons/GaNDLF/discussions" alt="Issues"><img src="https://img.shields.io/badge/Support-Discussion-blue?color=red" /></a>

diff --git 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
@@ -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: 0.1.1-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
@@ -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: 0.1.1-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
@@ -94,6 +94,6 @@ scheduler:
 track_memory_usage: false
 verbose: false
 version:
-  maximum: 0.1.0-dev
+  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
@@ -99,6 +99,6 @@ scheduler:
 track_memory_usage: false
 verbose: false
 version:
-  maximum: 0.1.0-dev
+  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
@@ -59,6 +59,6 @@ scheduler:
 track_memory_usage: false
 verbose: false
 version:
-  maximum: 0.1.0-dev
+  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
@@ -62,6 +62,6 @@ scheduler:
 track_memory_usage: false
 verbose: false
 version:
-  maximum: 0.1.0-dev
+  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
@@ -66,6 +66,6 @@ scheduler:
 track_memory_usage: false
 verbose: true
 version:
-  maximum: 0.1.0-dev
+  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
@@ -89,6 +89,6 @@ scheduler:
 track_memory_usage: false
 verbose: true
 version:
-  maximum: 0.1.0-dev
-  minimum: 0.1.0-dev
+  maximum: 0.1.1-dev
+  minimum: 0.1.1-dev
 weighted_loss: true
diff --git 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: 0.1.1-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
@@ -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: 0.1.1-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
@@ -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: 0.1.1-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
@@ -55,7 +55,7 @@ save_output: false
 scaling_factor: 1
 scheduler: triangle
 version:
-  maximum: 0.1.0-dev
+  maximum: 0.1.1-dev
   minimum: 0.0.14
 weighted_loss: True
 
diff --git 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: 0.1.1-dev
   minimum: 0.0.14
 weighted_loss: false
 
diff --git 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: 0.1.1-dev
   }
 model:
   {

diff --git 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: 0.1.1-dev # this should NOT be made a variable, but should be tested after every tag is created
   }
 # Choose the model parameters here
 model: