diff --git a/.github/workflows/commit.yml b/.github/workflows/commit.yml
index 8da6d1b1f1..5e5163f5ce 100644
--- a/.github/workflows/commit.yml
+++ b/.github/workflows/commit.yml
@@ -124,27 +124,14 @@ jobs:
         run: |
           pip install --upgrade pip
           pip install .
-          pip install ".[test, optional]"
-
-      - name: Install executables
-        uses: modflowpy/install-modflow-action@v1
-
-      # todo restore below before merging
-      - name: Install MODFLOW 6 PRT build
+          pip install ".[test,optional]"
+      
+      - name: Install Modflow executables
         uses: modflowpy/install-modflow-action@v1
-        with:
-          # repo: modflow6-nightly-build
-          owner: aprovost-usgs
-          repo: modflow6
-
-      - name: Update FloPy packages
-        if: runner.os != 'Windows'
-        # run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)'
-        run: python -c 'import flopy; flopy.mf6.utils.generate_classes(owner="aprovost-usgs", ref="PRT", backup=False)'
-
-      - name: Run smoke tests
-        working-directory: ./autotest
-        run: pytest -v -n=auto --smoke --durations=0 --keep-failed=.failed
+      
+      - name: Smoke test
+        working-directory: autotest
+        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -163,10 +150,7 @@ jobs:
 
   test:
     name: Test
-    needs:
-      - build
-      - lint
-      - smoke
+    needs: smoke
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -221,27 +205,22 @@ jobs:
           pip install xmipy
           pip install .
 
-      - name: Install executables
+      - name: Install Modflow-related executables
         uses: modflowpy/install-modflow-action@v1
 
-      # todo restore below when prt merges to mf6 develop
-      - name: Install MODFLOW 6 PRT build
+      - name: Install Modflow dev build executables
         uses: modflowpy/install-modflow-action@v1
         with:
-          # repo: modflow6-nightly-build
-          owner: aprovost-usgs
-          repo: modflow6
+          repo: modflow6-nightly-build
 
       - name: Update FloPy packages
         if: runner.os != 'Windows'
-        # run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)'
-        run: python -c 'import flopy; flopy.mf6.utils.generate_classes(owner="aprovost-usgs", ref="PRT", backup=False)'
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Update FloPy packages
         if: runner.os == 'Windows'
         shell: bash -l {0}
-        # run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)'
-        run: python -c 'import flopy; flopy.mf6.utils.generate_classes(owner="aprovost-usgs", ref="PRT", backup=False)'
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Run tests
         if: runner.os != 'Windows'
diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 53f3101377..fe9b014b3b 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -53,7 +53,7 @@ jobs:
             bash
             powershell
 
-      - name: Install Python dependencies
+      - name: Install extra Python dependencies
         if: runner.os == 'Windows'
         shell: bash -l {0}
         run: |
diff --git a/.github/workflows/mf6.yml b/.github/workflows/mf6.yml
index ca1508c9c8..e1709ba687 100644
--- a/.github/workflows/mf6.yml
+++ b/.github/workflows/mf6.yml
@@ -42,7 +42,6 @@ jobs:
         pip install https://github.com/modflowpy/pymake/zipball/master
         pip install https://github.com/Deltares/xmipy/zipball/develop
         pip install https://github.com/MODFLOW-USGS/modflowapi/zipball/develop
-        pip install .
         pip install .[test,optional]
 
     - name: Install gfortran
@@ -51,28 +50,32 @@ jobs:
     - name: Checkout MODFLOW 6
       uses: actions/checkout@v4
       with:
-        repository: aprovost-usgs/modflow6
+        repository: MODFLOW-USGS/modflow6
         path: modflow6
-        ref: PRT
 
     - name: Update flopy MODFLOW 6 classes
       working-directory: modflow6/autotest
-      run: python update_flopy.py
+      run: |
+        python update_flopy.py
 
     - name: Install meson
-      run: pip3 install meson ninja
+      run: |
+        pip3 install meson ninja
 
     - name: Setup modflow
       working-directory: modflow6
-      run: meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin
+      run: |
+        meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin
 
     - name: Build modflow
       working-directory: modflow6
-      run: meson compile -C builddir
+      run: |
+        meson compile -C builddir
 
     - name: Install modflow
       working-directory: modflow6
-      run: meson install -C builddir
+      run: |
+        meson install -C builddir
 
     - name: Get executables
       working-directory: modflow6/autotest
@@ -88,10 +91,12 @@ jobs:
 
     - name: Print coverage report before upload
       working-directory: ./modflow6/autotest
-      run: coverage report
+      run: |
+        coverage report
 
     - name: Upload coverage to Codecov
-      if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
+      if:
+        github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
       uses: codecov/codecov-action@v3
       with:
         files: ./modflow6/autotest/coverage.xml
diff --git a/.github/workflows/rtd.yml b/.github/workflows/rtd.yml
index c28206acc8..b092e4b16e 100644
--- a/.github/workflows/rtd.yml
+++ b/.github/workflows/rtd.yml
@@ -49,9 +49,7 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Install flopy and dependencies
-        run: |
-          pip install .
-          pip install ".[test, doc, optional]"
+        run: pip install ".[test, doc, optional]"
       
       - name: Workaround OpenGL issue on Linux
         if: runner.os == 'Linux'
@@ -79,18 +77,6 @@ jobs:
       - name: Install MODFLOW executables
         uses: modflowpy/install-modflow-action@v1
 
-      # todo restore below before merging
-      - name: Install MODFLOW 6 PRT build
-        uses: modflowpy/install-modflow-action@v1
-        with:
-          owner: aprovost-usgs
-          repo: modflow6
-        
-      - name: Update FloPy
-        run: |
-          python -c 'from flopy.mf6.utils import generate_classes; generate_classes(owner="aprovost-usgs", ref="PRT", backup=False)'
-          pip install .
-
       - name: Run tutorial and example notebooks
         working-directory: autotest
         run: pytest -v -n auto test_notebooks.py