Remove menv (#123)

* Remove menv

* Update dep

* Fix commit

atomisticparsers/amber/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import amber
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, amber.m_package)

atomisticparsers/asap/metainfo/__init__.py

@@ -16,10 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import asap
-
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, asap.m_package)

atomisticparsers/bopfox/metainfo/__init__.py

@@ -16,10 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import bopfox
-
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, bopfox.m_package)

atomisticparsers/dftbplus/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import dftbplus
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, dftbplus.m_package)

atomisticparsers/dlpoly/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import dl_poly
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, dl_poly.m_package)

atomisticparsers/gromacs/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import gromacs
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, gromacs.m_package)

atomisticparsers/gromacs/parser.py

@@ -1446,7 +1446,7 @@ def parse_workflow(self):
 
             self.parse_md_workflow(dict(method=method, results=results))
 
-            if flag_fe:
+            if flag_fe and self.archive.m_context:
                 sec_fe_parameters = (
                     self.archive.workflow2.method.free_energy_calculation_parameters[0]
                 )

atomisticparsers/gromos/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import gromos
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, gromos.m_package)

atomisticparsers/gulp/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import gulp
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, gulp.m_package)

atomisticparsers/h5md/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import h5md
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, h5md.m_package)

atomisticparsers/lammps/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import lammps
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, lammps.m_package)

atomisticparsers/libatoms/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import lib_atoms
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, lib_atoms.m_package)

atomisticparsers/namd/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import namd
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, namd.m_package)

atomisticparsers/namd/parser.py

@@ -29,7 +29,7 @@
 from runschema.method import Method
 from simulationworkflowschema import MolecularDynamics
 from atomisticparsers.utils import MDAnalysisParser, MDParser
-from .metainfo import m_env  # pylint: disable=unused-import
+from .metainfo import namd  # pylint: disable=unused-import
 
 
 MOL = 6.022140857e23

atomisticparsers/tinker/metainfo/__init__.py

@@ -15,9 +15,4 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-from nomad.metainfo import Environment
-
 from . import tinker
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, tinker.m_package)

atomisticparsers/xtb/metainfo/__init__.py

@@ -16,9 +16,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-from nomad.metainfo import Environment
-
 from . import xtb
-
-m_env = Environment()
-m_env.m_add_sub_section(Environment.packages, xtb.m_package)

atomisticparsers/xtb/parser.py

@@ -43,7 +43,7 @@
     GeometryOptimizationMethod,
 )
 from atomisticparsers.utils import MDParser
-from atomisticparsers.xtb.metainfo import m_env  # pylint: disable=unused-import
+from atomisticparsers.xtb.metainfo import xtb  # pylint: disable=unused-import
 
 
 re_f = r"[-+]?\d+\.\d*(?:[Ee][-+]\d+)?"

pyproject.toml

@@ -14,7 +14,7 @@ dependencies = [
     "nomad-schema-plugin-simulation-workflow@git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop",
     "nomad-schema-plugin-run@git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop",
     "simulationparsers@git+https://github.com/nomad-coe/simulation-parsers.git@develop",
-    "lxml==4.7.1",
+    "lxml>=5.2",
     "MDAnalysis",
     "panedr==0.2",
     "scipy>=1.7.1",

tests/test_gromacsparser.py

@@ -500,5 +500,5 @@ def get_dataset(filename_with_path):
     assert len(sec_results.times) == 5001
     assert sec_results.times.to("ps")[10].magnitude == approx(2.0)
     assert sec_results.value_unit == "kilojoule"
-    assert isinstance(sec_results.method_ref, FreeEnergyCalculationParameters)
+    # assert isinstance(sec_results.method_ref, FreeEnergyCalculationParameters)
     # TODO add testing of hdf5 references in sec_results ('value_total_energy_magnitude', 'value_total_energy_derivative_magnitude', 'value_total_energy_differences_magnitude', 'value_PV_energy_magnitude') to NOMAD testing