ci: convert from nosetest to pytest

.github/workflows/ci-mf6.yml

@@ -8,6 +8,7 @@ on:
       - master
       - develop
       - 'release*'
+      - 'ci-pytest'
   pull_request:
     branches: [master, develop]
 
@@ -99,6 +100,11 @@ jobs:
       run: |
         pytest -v -n auto -k "test_gw" --durations=0 --cov=flopy --cov-report=xml
 
+    - name: Print coverage report before upload
+      working-directory: ./modflow6/autotest
+      run: |
+        coverage report
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v2.1.0
       with:

.github/workflows/ci.yml

@@ -8,6 +8,7 @@ on:
       - master
       - develop
       - 'release*'
+      - 'ci-pytest'
   pull_request:
     branches: [master, develop]
 
@@ -22,7 +23,6 @@ jobs:
       run:
         shell: bash
 
-    if: github.repository_owner == 'modflowpy'
     steps:
 
     # check out repo
@@ -56,7 +56,7 @@ jobs:
       run:
         shell: bash
 
-    if: github.repository_owner == 'modflowpy' && github.event_name != 'schedule'
+    if: github.event_name != 'schedule'
     steps:
     # check out repo
     - name: Checkout flopy repo
@@ -109,11 +109,11 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.9
             run-type: nb
-            test-path: autotest_notebooks.py
+            test-path: run_notebooks.py
           - os: ubuntu-latest
             python-version: 3.9
             run-type: script
-            test-path: autotest_scripts.py
+            test-path: run_scripts.py
     defaults:
       run:
         shell: bash -l {0}
@@ -166,23 +166,42 @@ jobs:
         pip install xmipy
         pip install . --use-feature=in-tree-build
 
-    - name: Download executables needed for tests
+    - name: Prepare for the autotests
+      working-directory: ./autotest
       run: |
-        cd autotest
-        python get_exes.py
-        cd ..
+        pytest -v ci_prepare.py
 
     - name: Add executables directory to path
       run: |
         echo "$HOME/.local/bin" >> $GITHUB_PATH
 
-    - name: Run nosetests
+    - name: Run pytest on autotest scripts on Linux and MacOS
+      if: matrix.run-type == 'std' && runner.os != 'Windows'
+      working-directory: ./autotest
       run: |
-        coverage run -m nose -v --with-id --with-timer \
-        --with-coverage --cover-package=flopy --cover-xml \
-        --cover-xml-file=../coverage.xml -w ./autotest ${{ matrix.test-path }}
+        pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml
+
+    - name: Run pytest on autotest scripts on Windows
+      if: matrix.run-type == 'std' && runner.os == 'Windows'
+      working-directory: ./autotest
+      run: |
+        pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml
+
+    - name: Run pytest on scripts and notebooks
+      if: matrix.run-type != 'std'
+      working-directory: ./autotest
+      run: |
+        pytest -v -n auto --durations=0 --cov=flopy --cov-report=xml ${{ matrix.test-path }}
+
+    - name: Print coverage report before upload
+      working-directory: ./autotest
+      run: |
+        coverage report
 
     - name: Upload coverage to Codecov
+      if:
+        github.repository_owner == 'modflowpy' && github.event_name == 'push'
       uses: codecov/codecov-action@v2.1.0
       with:
-        file: ./coverage.xml
+        directory: ./autotest
+        file: coverage.xml

.github/workflows/rtd.yml

@@ -6,6 +6,7 @@ on:
       - master
       - develop
       - 'release*'
+      - 'ci-pytest'
   pull_request:
     branches: [master, develop]
 
@@ -20,7 +21,6 @@ jobs:
       run:
         shell: bash -l {0}
 
-    if: github.repository_owner == 'modflowpy'
     steps:
       - name: Checkout flopy repo
         uses: actions/checkout@v2.3.4
@@ -57,19 +57,19 @@ jobs:
           pip install xmipy
           pip install .
 
-      - name: Download executables needed for tests
+      - name: Prepare for the autotests
+        working-directory: ./autotest
         run: |
-          python ./autotest/get_exes.py
+          pytest -v ci_prepare.py
 
       - name: Add executables directory to path
         run: |
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Run jupytext on tutorials
+        working-directory: ./.docs
         run: |
-          cd .docs/
           python create_tutorials.py
-          cd ../
 
       - name: Upload completed jupyter notebooks as an artifact for ReadtheDocs
         if:

autotest/ci_cleanup.py

@@ -0,0 +1,33 @@
+# Remove the temp directory if it exists
+import os
+import shutil
+
+from ci_framework import get_parent_path
+
+
+def cleanup_autotests():
+    parent_path = get_parent_path()
+    if parent_path is None:
+        print("can not clean autotests")
+    else:
+        tempdir = os.path.join(parent_path, "temp")
+        if os.path.isdir(tempdir):
+            shutil.rmtree(tempdir)
+    return
+
+
+def cleanup_stray_files():
+    trashExtensions = (".chk", ".dat")
+    parent_path = get_parent_path()
+
+    files = [f for f in os.listdir(parent_path)]
+    for file in files:
+        if os.path.isfile(file):
+            extension = os.path.splitext(file)[1]
+            if extension in trashExtensions:
+                os.remove(file)
+
+
+if __name__ == "__main__":
+    cleanup_autotests()
+    cleanup_stray_files()