merged with master

ATOMScience-org · Oct 2, 2024 · ce1a426 · ce1a426
2 parents 969bc5f + d271984
commit ce1a426
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Showing 5 changed files with 44 additions and 29 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -40,15 +40,14 @@ jobs:
       - name: pytest
         run: |
           # python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/unit
-          python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/modac/test/unit
-          cd atomsci/ddm/test/unit && python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci/ -vv
+          cd atomsci/ddm/test/unit && python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv
         env:
           ENV: test
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pytest-integrative-1:
     runs-on: ubuntu-latest
     strategy:
@@ -86,15 +85,15 @@ jobs:
       - name: pytest
         run: |
           # TODO: Run this test with pytest for paralell testing
-          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/integrative
+          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
           cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 0
         env:
           ENV: test
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pytest-integrative-2:
     runs-on: ubuntu-latest
     strategy:
@@ -132,15 +131,15 @@ jobs:
       - name: pytest
         run: |
           # TODO: Run this test with pytest for paralell testing
-          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/integrative
+          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
           cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 1
         env:
           ENV: test
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pytest-integrative-3:
     runs-on: ubuntu-latest
     strategy:
@@ -178,15 +177,15 @@ jobs:
       - name: pytest
         run: |
           # TODO: Run this test with pytest for paralell testing
-          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/integrative
+          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
           cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 2
         env:
           ENV: test
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   pytest-integrative-4:
     runs-on: ubuntu-latest
     strategy:
@@ -224,12 +223,12 @@ jobs:
       - name: pytest
         run: |
           # TODO: Run this test with pytest for paralell testing
-          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/integrative
+          # python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
           cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 3
         env:
           ENV: test
 
-      # - name: Upload coverage reports to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/Makefile b/Makefile
@@ -123,7 +123,7 @@ pytest-integrative:
 pytest-unit:
 	@echo "Running unit tests"
 	docker run -v $(shell pwd)/$(WORK_DIR):/$(WORK_DIR) $(IMAGE_REPO):$(TAG) \
-			/bin/bash -l -c "cd atomsci/ddm/test/unit && python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv"
+		       /bin/bash -l -c "cd atomsci/ddm/test/unit && python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci -vv"
 
 # Run ruff linter
 ruff:

diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 [![Develop test](https://github.com/ATOMScience-org/AMPL/actions/workflows/pytest.yml/badge.svg)](https://github.com/ATOMScience-org/AMPL/actions/workflows/pytest.yml)  [![Linter](https://github.com/ATOMScience-org/AMPL/actions/workflows/lint.yml/badge.svg)](https://github.com/ATOMScience-org/AMPL/actions/workflows/lint.yml)    [![Documentation Status](https://readthedocs.org/projects/ampl/badge/?version=stable)](https://ampl.readthedocs.io/en/latest/?badge=stable) 
-![GitHub Release](https://img.shields.io/github/v/release/ATOMScience-org/AMPL)   [![License](http://img.shields.io/:license-mit-blue.svg)](https://github.com/ATOMScience-org/AMPL/blob/master/LICENSE)  [![LinkedIn](https://img.shields.io/badge/linkedin-%230077B5.svg?logo=linkedin&logoColor=white)](https://www.linkedin.com/company/atomscience)
+ [![codecov](https://codecov.io/gh/ATOMScience-org/AMPL/graph/badge.svg)](https://codecov.io/gh/ATOMScience-org/AMPL)
+
+![GitHub Release](https://img.shields.io/github/v/release/ATOMScience-org/AMPL)  [![License](http://img.shields.io/:license-mit-blue.svg)](https://github.com/ATOMScience-org/AMPL/blob/master/LICENSE)  [![LinkedIn](https://img.shields.io/badge/linkedin-%230077B5.svg?logo=linkedin&logoColor=white)](https://www.linkedin.com/company/atomscience)
 
 | [Install](#install) | [Docker](#install-with-docker) | [Tutorials](#ampl-tutorials) |  [Features](#ampl-features) | [Pipeline parameters](atomsci/ddm/docs/PARAMETERS.md) | [Docs](https://ampl.readthedocs.io/en/latest/) |
 

diff --git a/atomsci/ddm/test/integrative/integrative_batch_chunk_tests b/atomsci/ddm/test/integrative/integrative_batch_chunk_tests
@@ -41,7 +41,7 @@ for folder in "${folders[@]}"; do
         if [[ -f "$file" && "$folder" != "__pycache__/" ]]; then
             cd "$folder"
             echo "Testing $folder"
-            pytest --capture=sys --capture=fd --cov=atomsci/ -vv
+            pytest --capture=sys --capture=fd --cov=atomsci -vv
             cd ..
         else
           echo "Skipping folder: $folder. Not a test directory."

diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,14 @@
+comment: # this is a top-level key
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false # if true: only post the comment if coverage changes
+  require_base: false # [true :: must have a base report to post]
+  require_head: true # [true :: must have a head report to post]
+
+ignore:
+  - "venv"
+  - ".venv"
+  - "pip"
+
+github_checks:
+  annotations: false