diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 49a8001..70c4869 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,19 +27,19 @@ jobs:
       matrix:
         include:
           # test latest gcc and python
-          - {os: ubuntu-latest, FC: gcc, FC_V: 13}
-          - {os: macos-latest, FC: gcc, FC_V: 13}
-          - {os: windows-latest, FC: gcc, FC_V: 13}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: macos-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: windows-latest, FC: gcc, FC_V: 13, shell: pwsh}
           # test latest python and intel-classic
-          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: macos-13, FC: intel-classic, FC_V: 2021.7}
-          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7}
+          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: macos-13, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7, shell: pwsh}
           # test latest python and previous gcc
-          - {os: ubuntu-latest, FC: gcc, FC_V: 12}
-          - {os: ubuntu-latest, FC: gcc, FC_V: 11}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 12, shell: bash}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 11, shell: bash}
     defaults:
       run:
-        shell: bash
+        shell: ${{ matrix.shell }}
 
     steps:
       - name: Checkout repo
@@ -91,7 +91,6 @@ jobs:
 
       - name: test on Windows
         if: runner.os == 'Windows'
-        shell: pwsh
         run: |
           pixi run autotest-base
 
@@ -122,16 +121,16 @@ jobs:
       matrix:
         include:
           # test latest gcc and python
-          - {os: ubuntu-latest, FC: gcc, FC_V: 13}
-          - {os: macos-latest, FC: gcc, FC_V: 13}
-          - {os: windows-latest, FC: gcc, FC_V: 13}
+          - {os: ubuntu-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: macos-latest, FC: gcc, FC_V: 13, shell: bash}
+          - {os: windows-latest, FC: gcc, FC_V: 13, shell: pwsh}
           # test latest python and intel
-          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7}
-          - {os: macos-13, FC: intel-classic, FC_V: 2021.7}
-          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7}
+          - {os: ubuntu-latest, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: macos-13, FC: intel-classic, FC_V: 2021.7, shell: bash}
+          - {os: windows-2019, FC: intel-classic, FC_V: 2021.7, shell: pwsh}
     defaults:
       run:
-        shell: bash
+        shell: ${{ matrix.shell }}
 
     steps:
       - name: Checkout repo
@@ -170,13 +169,13 @@ jobs:
       - name: Run scheduled tests
         run: |
           pixi run autotest-schedule
-
+  
       - name: Upload failed test output
         if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: failed-schedule-${{ matrix.os }}-${{ matrix.FC }}-${{ matrix.FC_V }}
-          path: ./autotest/.failed
+          path: autotest/.failed
 
       - name: Print coverage report before upload
         run: |
diff --git a/autotest/test_cli_cmds.py b/autotest/test_cli_cmds.py
index 4e63589..6465f5d 100644
--- a/autotest/test_cli_cmds.py
+++ b/autotest/test_cli_cmds.py
@@ -51,7 +51,7 @@ def test_make_program(function_tmpdir, target: str) -> None:
             "make-program",
             target,
             "--appdir",
-            str(function_tmpdir),
+            ".",
             "--verbose",
         ]
         run_cli_cmd(cmd)
@@ -68,7 +68,7 @@ def test_make_program_double(function_tmpdir) -> None:
             "--double",
             "--verbose",
             "--appdir",
-            str(function_tmpdir),
+            ".",
         ]
         run_cli_cmd(cmd)
 
@@ -81,7 +81,7 @@ def test_make_program_all(module_tmpdir) -> None:
             "make-program",
             ":",
             "--appdir",
-            str(module_tmpdir / "all"),
+            ".",
             "--verbose",
         ]
         run_cli_cmd(cmd)
diff --git a/pixi.toml b/pixi.toml
index 9b13c7a..d6f43bf 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -52,4 +52,4 @@ coverage-report = { cmd = "coverage report", cwd = "autotest"}
 
 # release 
 update-version = { cmd = "python scripts/update_version.py -v"}
-create-codejson = { cmd = "make-code-json" }
\ No newline at end of file
+create-codejson = { cmd = "make-code-json" }