update phonon compatibility

.github/workflows/main.yml

@@ -1,8 +1,8 @@
 name: Python unit-tests
 
 on:
-  - push
-  - pull_request
+- push
+- pull_request
 
 jobs:
   build:
@@ -29,6 +29,10 @@ jobs:
         export DFLOW_DEBUG=1
         coverage run -m unittest -v -f 
         coverage report
-    - uses: codecov/codecov-action@v5
+    - uses: codecov/codecov-action@v7
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      with:
+        use_oidc: true
+permissions:
+  id-token: write

.github/workflows/publish-docker.yml

@@ -16,17 +16,17 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
-      - uses: docker/setup-buildx-action@v3
+      - uses: docker/setup-buildx-action@v4
 
-      - uses: docker/login-action@v3
+      - uses: docker/login-action@v4
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: docker/build-push-action@v6
+      - uses: docker/build-push-action@v7
         with:
           context: .
           file: docs/Dockerfile.bohrium

.github/workflows/publish-pypi.yml

@@ -10,9 +10,9 @@ jobs:
     name: unit tests
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -33,17 +33,17 @@ jobs:
     needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Build package
         run: |
           python -m pip install --upgrade pip build
           python -m build
       - name: Upload distributions
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: python-package-distributions
           path: dist/
@@ -61,7 +61,7 @@ jobs:
       PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
     steps:
       - name: Download distributions
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: python-package-distributions
           path: dist/

apex/core/property/Gruneisen.py

@@ -963,7 +963,7 @@ def _ensure_abacus_volume_outputs(
                 if not os.path.isfile("FORCE_CONSTANTS"):
                     raise FileNotFoundError(f"FORCE_CONSTANTS was not created in {helper_dir}")
                 if not os.path.isfile("mesh.yaml"):
-                    subprocess.check_call(Phonon.phonopy_command("band.conf"), shell=True)
+                    subprocess.check_call(Phonon.phonopy_command("phonopy_disp.yaml --config band.conf"), shell=True)
                     self._write_band_dat()
             finally:
                 os.chdir(cwd)

apex/core/property/Phonon.py

@@ -622,7 +622,7 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                     if not os.path.exists("FORCE_SETS"):
                         raise FileNotFoundError("FORCE_SETS was not created")
                     print('FORCE_SETS is created')
-                    subprocess.check_call(self.phonopy_command("band.conf"), shell=True)
+                    subprocess.check_call(self.phonopy_command("phonopy_disp.yaml --config band.conf"), shell=True)
                     self.write_band_dat()
 
                 elif self.inter_param["type"] == 'vasp':

tests/test_gruneisen.py

@@ -408,7 +408,7 @@ def fake_check_call(command, shell):
                 Path("FORCE_SETS").write_text("fake force sets\n")
             elif command == Phonon.phonopy_setup_command("phonopy_disp.yaml --writefc"):
                 Path("FORCE_CONSTANTS").write_text("fake force constants\n")
-            elif command == Phonon.phonopy_command("band.conf"):
+            elif command == Phonon.phonopy_command("phonopy_disp.yaml --config band.conf"):
                 strain = loadfn("volume.json")["strain"]
                 if strain < 0:
                     frequencies = [4.2, 8.4]
@@ -459,8 +459,11 @@ def fake_run(command, stdout, stderr, text):
             ]),
             3,
         )
-        self.assertEqual(len([cmd for _, cmd in calls if cmd == Phonon.phonopy_command("band.conf")]), 3)
-        self.assertFalse(any(cmd == "phonopy band.conf --abacus" for _, cmd in calls))
+        self.assertEqual(
+            len([cmd for _, cmd in calls if cmd == Phonon.phonopy_command("phonopy_disp.yaml --config band.conf")]),
+            3,
+        )
+        self.assertFalse(any(cmd == "phonopy phonopy_disp.yaml --config band.conf --abacus" for _, cmd in calls))
         self.assertTrue((work_dir / "volume.000000" / "mesh.yaml").is_file())
         self.assertTrue((work_dir / "volume.000001" / "band.dat").is_file())
         self.assertTrue("Temperature(K)  SumGammaCv  Sign" in ptr)

tests/test_phonon.py

@@ -340,7 +340,7 @@ def fake_check_call(command, shell):
             calls.append(command)
             if command.startswith(Phonon.phonopy_setup_command("-f")):
                 Path("FORCE_SETS").write_text("fake force sets\n")
-            elif command == Phonon.phonopy_command("band.conf"):
+            elif command == Phonon.phonopy_command("phonopy_disp.yaml --config band.conf"):
                 Path("band.yaml").write_text("phonon: []\n")
 
         try:
@@ -349,8 +349,8 @@ def fake_check_call(command, shell):
                     patch.object(Phonon, "write_band_dat", side_effect=self._write_band_dat_for_compute):
                 phonon._compute_lower(str(work_dir / "result.json"), [str(task_dir)], [])
             self.assertEqual(calls[0], Phonon.phonopy_setup_command("-f task.0*/OUT.ABACUS/running_scf.log"))
-            self.assertEqual(calls[1], Phonon.phonopy_command("band.conf"))
-            self.assertFalse(any("--abacus" in command and command.startswith("phonopy band.conf") for command in calls))
+            self.assertEqual(calls[1], Phonon.phonopy_command("phonopy_disp.yaml --config band.conf"))
+            self.assertFalse(any("--abacus" in command and "band.conf" in command for command in calls))
         finally:
             shutil.rmtree(work_dir, ignore_errors=True)