Merge pull request #95 from kirk0830/spillapi-refactor-2

Refactor: moving all import line to the top of files

SIAB/driver/front.py

@@ -1,4 +1,8 @@
-# interface to initialize
+import os
+from SIAB.io.read_input import read, parse
+from SIAB.interface.abacus import run_all
+import SIAB.spillage.pytorch_swat.api as ssps_api  # old version of backend
+import SIAB.spillage.api as ss_api  # new version of backend
 
 def initialize(version: str = "0.1.0",
                fname: str = "./SIAB_INPUT"):
@@ -22,8 +26,6 @@ def initialize(version: str = "0.1.0",
     fname: str
         input filename, default is "./SIAB_INPUT"
     """
-    import os
-    from SIAB.io.read_input import read, parse
 
     fname = fname.strip().replace("\\", "/")
     user_settings = read(fname=fname, version=version)
@@ -104,7 +106,7 @@ def abacus(general: dict,
     test: bool
         whether to run in test mode, default is True
     """
-    from SIAB.interface.abacus import run_all
+
     folders = run_all(general=general,
                       structures=structures,
                       calculation_settings=calculation_settings,
@@ -156,9 +158,6 @@ def spillage(folders: list,
     }
     ```
     """
-    # interface to Spillage optimization
-    import SIAB.spillage.pytorch_swat.api as ssps_api  # old version of backend
-    import SIAB.spillage.api as ss_api  # new version of backend
     # iteratively generate numerical atomic orbitals here
     optimizer = siab_settings.get("optimizer", "none").lower()
     caller_map = {

SIAB/interface/abacus.py

@@ -1,3 +1,11 @@
+import SIAB.interface.env as sienv
+import os
+import numpy as np
+import SIAB.io.read_output as read_output
+import SIAB.data.interface as db
+from scipy.optimize import curve_fit
+import re
+
 BLSCAN_WARNMSG = """
 WARNING: since SIAB version 2.1(2024.6.3), the original functionality invoked by value \"auto\" is replaced by 
         \"scan\", and for dimer the \"auto\" now will directly use in-built dimer database if available, otherwise will 
@@ -355,8 +363,6 @@ def write(suffix, inp, stru):
     else:
         yield write(folder, input_setting, stru_setting)
 
-
-import SIAB.interface.env as sienv
 def archive(footer: str = "", env: str = "local"):
 
     """mkdir and move correspnding input files to folder"""
@@ -432,7 +438,6 @@ def run_all(general: dict,
         folders.append(folders_istructure)
     return folders
 
-import os
 def is_duplicate(folder: str, abacus_setting: dict):
     """check if the abacus calculation can be safely (really?)
     skipped"""
@@ -504,10 +509,6 @@ def is_duplicate(folder: str, abacus_setting: dict):
 # TASK KIND1 - blscan                        #
 # DESCRIPTION: search bond lengths           #
 # -------------------------------------------#
-import numpy as np
-import SIAB.io.read_output as read_output
-import SIAB.data.interface as db
-from scipy.optimize import curve_fit
 def blscan(general: dict,                  # general settings
            calculation_setting: dict,      # calculation setting, for setting up INPUT file
            env_settings: dict,             # calculation environment settings
@@ -773,7 +774,6 @@ def normal(general: dict,
     """wait for all jobs to finish"""
     return folders
 
-import re
 def read_INPUT(folder: str = "") -> dict:
     """parse ABACUS INPUT file, return a dict"""
     if folder.startswith("INPUT_PARAMETERS"):

SIAB/interface/abacustest.py

@@ -20,6 +20,10 @@
     instead of contents of the file
 
 """
+import os
+import json
+import time
+import re
 
 #ABACUS_IMAGE = "registry.dp.tech/deepmodeling/abacus-intel:latest"
 ABACUS_IMAGE = "registry.dp.tech/dptech/abacus:3.6.4" # this is for submit large batch of jobs, but need to always update
@@ -28,16 +32,14 @@
 PYTHON_IMAGE = "python:3.8"
 ABACUS_COMMAND = "OMP_NUM_THREADS=1 mpirun -n 16 abacus | tee out.log"
 
-import os
-import json
 def read_apns_inp(fname: str) -> dict:
     assert os.path.exists(fname), f"File not found: {fname}"
     with open(fname, "r") as f:
         inp = json.load(f)
     return inp.get("abacustest", {})
 
 def manual_submit(username, password, project_id, ncores, memory, folders):
-    import time, os
+
     assert all([os.path.exists(f) for f in folders]), "Some folders do not exist."
     jobgroup = f"apns_{time.strftime('%Y-%m-%d_%H-%M-%S', time.localtime())}"
     run_dft = [{"ifrun": True, "job_folders": folders, "command": ABACUS_COMMAND, "ncores": ncores, "memory": memory}]
@@ -47,7 +49,6 @@ def manual_submit(username, password, project_id, ncores, memory, folders):
     result_folder = submit(param)
     return result_folder
 
-
 def bohrium_machine(ncores: int, memory: float, device: str, supplier: str):
     """Configure Bohrium machine information
     
@@ -181,7 +182,7 @@ def write_abacustest_param(jobgroup_name: str, bohrium_login: dict, save_dir: st
     Returns:
         dict: abacustest param.json contents
     """
-    import time
+
     prepare = prepare or {}
     predft = predft or {}
     rundft = rundft or []
@@ -205,7 +206,7 @@ def write_abacustest_param(jobgroup_name: str, bohrium_login: dict, save_dir: st
     return result
 
 def submit(abacustest_param: dict) -> str:
-    import time
+
     fparam = f"param-{time.strftime('%Y-%m-%d_%H-%M-%S', time.localtime())}.json"
     with open(fparam, "w") as f:
         json.dump(abacustest_param, f, indent=4)
@@ -217,7 +218,7 @@ def submit(abacustest_param: dict) -> str:
     return folder
 
 def read_keyvals_frominput(fin, keyword: str = None):
-    import re
+
     kv = r"^([\w_-]+)(\s+)([^#]*)(.*)$"
 
     result = {}
@@ -232,7 +233,7 @@ def read_keyvals_frominput(fin, keyword: str = None):
     return result if keyword is None else result[keyword]
 
 def abacus_default():
-    import os
+
     fthis = os.path.abspath(__file__)
     fabacus = fthis.replace("/abacustest.py", "/abacus_input_example")
     result = read_keyvals_frominput(fabacus).items()
@@ -241,7 +242,6 @@ def abacus_default():
 
 if __name__ == "__main__":
 
-    import os, time
     src = "/root/documents/simulation/orbgen/apns-orbgen-project/nelec_delta_test/lcao-v2.0"
     jobgroup = "u-nspin2_lcao-v2.0"
     fgroup = os.path.join(src, jobgroup)

SIAB/interface/env.py

@@ -1,11 +1,13 @@
 """this module is for converting common Liunx command to the version
 compatible with High Performance Computing (HPC) system or say for
 Supercomputer."""
+import os
+import subprocess
+import sys
 
 ##############################################
 #                                            #
 ##############################################
-import os
 def submit(folder: str = "", 
            module_load_command: str = "",
            mpi_command: str = "",
@@ -34,8 +36,7 @@ def submit(folder: str = "",
 ##############################################
 #        basic wrapped linux commands        #
 ##############################################
-import subprocess
-import sys
+
 def run(command: str,
         env: str = "local",
         additional_args: list = None,

SIAB/interface/old_version.py

@@ -335,7 +335,6 @@ def ov_c_init(orbitals: list, folder: str = None):
     return result
 
 import uuid
-import time
 def convert(calculation_setting: dict,
             siab_settings: dict):
     """

SIAB/io/read_input.py

@@ -1,4 +1,12 @@
 import re
+import os
+import json
+import SIAB.io.pseudopotential.tools.basic as siptb
+from SIAB.data.interface import PERIODIC_TABLE_TOINDEX
+from SIAB.io.pseudopotential.api import ppinfo
+from numpy import ceil
+import unittest
+import uuid
 
 def read_siab_plaintext(fname: str = ""):
     keyvalue_pattern = r"^(\w+)(\s+)([^#]*)(#.*)?"
@@ -21,14 +29,12 @@ def read_siab_plaintext(fname: str = ""):
 
     return result
 
-import json
 def read_siab_json(fname: str = ""):
     """parse SIAB_INPUT file with version 0.2.0 in json format"""
     with open(fname, "r") as f:
         result = json.load(f)
     return result
 
-import os
 def read(fname: str = "", version: str = "0.1.0"):
     """default value setting is absent"""
     print(f"""
@@ -186,7 +192,7 @@ def natom_from_shape(shape: str):
     return natom.get(shape, 0)
 
 def nbands_from_str(option: str|float|int, shape: str, z_val: float):
-    import re
+
     if isinstance(option, str):
         assert re.match(r"(auto|occ((\+|-)\d+)?|all)", option), f"option should be auto, occ, occ+/-n or all: {option}"
         if option == "auto":
@@ -274,7 +280,6 @@ def abacus_settings(user_settings: dict, minimal_basis: list = None, z_val: floa
             {"lmaxmax": lmax_monomer, "nbands": nbands_monomer})
     return result
 
-import SIAB.io.pseudopotential.tools.basic as siptb
 def siab_settings(user_settings: dict, minimal_basis: list, z_val: float = 0):
     """convert user_settings to SIAB settings the information needed by spillage optimization
     information is organized as follows:
@@ -375,7 +380,7 @@ def nzetagen(zeta_notation, minimal_basis: list):
     list of int
         the nzeta, like [2, 2, 1]
     """
-    import re
+
     assert isinstance(minimal_basis, list), "minimal_basis should be a list"
 
     # 
@@ -464,7 +469,7 @@ def skip_ppread(user_settings: dict):
     bool
         True if the pseudopotential read-in can be skipped, False otherwise
     """
-    import re
+
     skip = True
     # case 1
     # if nbands is specified as auto, occ, all, it must requires the number of valence
@@ -537,9 +542,7 @@ def parse(user_settings: dict):
     """
     # move the information fetch from pseudopotential from front.py here...
     # get value from the dict returned by function from_pseudopotential
-    from SIAB.data.interface import PERIODIC_TABLE_TOINDEX
-    from SIAB.io.pseudopotential.api import ppinfo
-    import os
+
     if skip_ppread(user_settings):
         """the logic here is, because there are pseudopotential can be parsed automatically,
         but the range of supported are limited. For those pseudopotential that is not with
@@ -568,7 +571,6 @@ def parse(user_settings: dict):
     general = description(symbol, user_settings)
     return structures, abacus, siab, env, general
 
-
 def abacus_params():
     pattern = r"^([\w]+)(\s+)([^#]+)(\s*)(#.*)?"
     keys = []
@@ -596,7 +598,7 @@ def cal_nbands_fill_lmax(zval: int, zcore: int, lmax: int, fill_lmax: bool = Tru
     Returns:
         int: the number of bands to include in the calculation
     """
-    from numpy import ceil
+
     # the first and the last element that fills shell of lmax.
     # S: 1, Hydrogen; P: 5, Boron; D: 21, Scandium; F: 58, Cerium;
     # S: 2, Helium;   P: 10, Neon; D: 30, Zinc;     F: 70, Ytterbium
@@ -995,15 +997,14 @@ def cal_nbands_fill_lmax(zval: int, zcore: int, lmax: int, fill_lmax: bool = Tru
 qo_basis                       hydrogen #type of QO basis function: hydrogen: hydrogen-like basis, pswfc: read basis from pseudopotential
 qo_thr                         1e-06 #accuracy for evaluating cutoff radius of QO basis function"""
 
-import unittest
 class TestReadInput(unittest.TestCase):
 
     """use example input as test material
     ./SIAB/example_Si/SIAB_INPUT
     """
 
     def test_parse(self):
-        import uuid, os
+
         self.maxDiff = None
         example = """
 #--------------------------------------------------------------------------------

SIAB/io/read_output.py

@@ -1,4 +1,6 @@
 import os
+import unittest
+
 def read_energy(folder: str,
                 suffix: str,
                 calculation: str = "scf"):
@@ -35,7 +37,7 @@ def read_natom(folder: str,
                     return natom
     return -1
 
-import unittest
+
 class TestReadOutput(unittest.TestCase):
 
     def test_read_energy(self):