Fix analyze.py to adopt changes in nmrpca code

Author: comcon1

src/fairmd/lipids/analib/analyze_nmrpca.py

@@ -46,14 +46,12 @@
 
 import MDAnalysis as mda
 import numpy as np
-from deprecated import deprecated
 from MDAnalysis.analysis.base import AnalysisFromFunction
 from scipy import signal
 
 from fairmd.lipids import FMDL_SIMU_PATH
 from fairmd.lipids.api import lipids_set
 from fairmd.lipids.core import System
-from fairmd.lipids.databankio import download_resource_from_uri, resolve_file_url
 from fairmd.lipids.molecules import Lipid
 from fairmd.lipids.schema_validation.engines import get_struc_top_traj_fnames
 
@@ -234,7 +232,7 @@ def verify_lipid(lipid: Lipid) -> bool:
                 has_sn1 = True
             if v["FRAGMENT"] in __tailsn2_vars:
                 has_sn2 = True
-        return (has_sn1 and has_sn2)
+        return has_sn1 and has_sn2
 
     def concatenate_traj(self) -> None:
         """Create Concatenator and corresponding concatenated trajectories.

src/fairmd/lipids/analyze.py

@@ -67,33 +67,18 @@ def computeNMRPCA(  # noqa: N802 (API)
     # TODO: 2test|    parser = Parser(FMDL_SIMU_PATH, readme, eq_time_fname, testTraj)
     try:
         parser = nmrpca.Parser(system, "eq_times.json")
-        # Check trajectory
         print(parser._path)
-        vpcode = parser.validate_path()
-        print("ValidatePath code: ", vpcode)
     except Exception:
         logger.exception("Error initializing NMRPCA parser.")
         return RCODE_ERROR
 
-    if vpcode > 0:
-        logger.error("Some errors in analyze_nmrpca.py::Parser constructor.")
-        return RCODE_ERROR
-
     if (
-        (vpcode < 0 and not recompute)
+        (os.path.isfile(os.path.join(FMDL_SIMU_PATH, system["path"], "eq_times.json")) and not recompute)
         or ("WARNINGS" in system and system["WARNINGS"] is not None and "AMBIGUOUS_ATOMNAMES" in system["WARNINGS"])
         or ("WARNINGS" in system and system["WARNINGS"] is not None and "SKIP_EQTIMES" in system["WARNINGS"])
     ):
         return RCODE_SKIPPED
 
-    # Check if TPR is defined and non-null or ""
-    try:
-        __ = system["TPR"][0][0]
-        _ = __[0]
-    except (KeyError, TypeError):
-        logger.exception("TPR is required for NMRPCA analysis (%d})!", system["ID"])
-        return RCODE_ERROR
-
     try:
         # Download md data
         uc = UniverseConstructor(system)