Update writing of hdf5 data (#105)

* Update writing of hdf5 data * Fix gh actions * Fix test
nomad-coe · Apr 19, 2024 · 68f0d2b · 68f0d2b
1 parent c6fb75e
commit 68f0d2b
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Showing 2 changed files with 5 additions and 33 deletions.
diff --git a/.github/workflows/python-actions.yaml b/.github/workflows/python-actions.yaml
@@ -12,9 +12,9 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
+        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
         # we need the latest nomad version for testing
         pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
-        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
         pip install coverage coveralls
     - name: mypy
       run: |

diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -55,7 +55,6 @@
 )
 from atomisticparsers.utils import MDAnalysisParser, MDParser
 from nomad.atomutils import get_bond_list_from_model_contributions
-from nomad.parsing.parser import to_hdf5
 
 re_float = r"[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?"
 re_n = r"[\n\r]"
@@ -1448,43 +1447,16 @@ def parse_workflow(self):
             self.parse_md_workflow(dict(method=method, results=results))
 
             if flag_fe:
-                filename = os.path.join(
-                    os.path.dirname(self.mainfile.split("/raw/")[-1]),
-                    f"{os.path.basename(self.mainfile)}.archive.hdf5",
-                )
-                if not os.path.isfile(
-                    os.path.join(os.path.dirname(self.mainfile), filename)
-                ):
-                    if self.archive.m_context:
-                        with self.archive.m_context.raw_file(filename, "wb") as f:
-                            pass
                 sec_fe_parameters = (
                     self.archive.workflow2.method.free_energy_calculation_parameters[0]
                 )
                 sec_fe = self.archive.workflow2.results.free_energy_calculations[0]
                 sec_fe.method_ref = sec_fe_parameters
                 if self.archive.m_context:
-                    with self.archive.m_context.raw_file(filename, "r+b") as f:
-                        sec_fe.value_total_energy_magnitude = to_hdf5(
-                            columns[:, 0],
-                            f,
-                            f"{sec_fe.m_path()}/value_total_energy_magnitude",
-                        )
-                        sec_fe.value_total_energy_derivative_magnitude = to_hdf5(
-                            columns[:, 1],
-                            f,
-                            f"{sec_fe.m_path()}/value_total_energy_derivative_magnitude",
-                        )
-                        sec_fe.value_total_energy_differences_magnitude = to_hdf5(
-                            columns[:, 2:-1],
-                            f,
-                            f"{sec_fe.m_path()}/value_total_energy_differences_magnitude",
-                        )
-                        sec_fe.value_PV_energy_magnitude = to_hdf5(
-                            columns[:, -1],
-                            f,
-                            f"{sec_fe.m_path()}/value_PV_energy_magnitude",
-                        )
+                    sec_fe.value_total_energy_magnitude = columns[:, 0]
+                    sec_fe.value_total_energy_derivative_magnitude = columns[:, 1]
+                    sec_fe.value_total_energy_differences_magnitude = columns[:, 2:-1]
+                    sec_fe.value_PV_energy_magnitude = columns[:, -1]
 
     def parse_input(self):
         sec_run = self.archive.run[-1]