From 5f862285f3a4577cee36bbae8a951af7bacf410f Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sun, 7 Jan 2024 01:14:01 +0800
Subject: [PATCH 01/13] build(pipfile): add pre-commit and move cpplint to
 dev-packages

---
 Pipfile      |   3 +-
 Pipfile.lock | 965 ++++++++++++++++++++++++++++++---------------------
 2 files changed, 568 insertions(+), 400 deletions(-)

diff --git a/Pipfile b/Pipfile
index 9caa1d6..1d8424e 100644
--- a/Pipfile
+++ b/Pipfile
@@ -7,9 +7,10 @@ name = "pypi"
 numpy = "*"
 scipy = "*"
 matplotlib = "*"
-cpplint = "*"
 
 [dev-packages]
+pre-commit = "*"
+cpplint = "*"
 pytest = "*"
 pytest-cov = "*"
 
diff --git a/Pipfile.lock b/Pipfile.lock
index c2c357d..11d7020 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "2aaa6fc353c82968a8af4a2377351a12ac4df1b6bb221a0ecc518d0b8c36598c"
+            "sha256": "eda8515dd3a1ff709bab9b9e956a7b3f71c9b63d652cbca5e2a637b2b71a9954"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -18,342 +18,385 @@
     "default": {
         "contourpy": {
             "hashes": [
-                "sha256:031154ed61f7328ad7f97662e48660a150ef84ee1bc8876b6472af88bf5a9b98",
-                "sha256:0f9d350b639db6c2c233d92c7f213d94d2e444d8e8fc5ca44c9706cf72193772",
-                "sha256:130230b7e49825c98edf0b428b7aa1125503d91732735ef897786fe5452b1ec2",
-                "sha256:152fd8f730c31fd67fe0ffebe1df38ab6a669403da93df218801a893645c6ccc",
-                "sha256:1c71fdd8f1c0f84ffd58fca37d00ca4ebaa9e502fb49825484da075ac0b0b803",
-                "sha256:24847601071f740837aefb730e01bd169fbcaa610209779a78db7ebb6e6a7051",
-                "sha256:2e9ebb4425fc1b658e13bace354c48a933b842d53c458f02c86f371cecbedecc",
-                "sha256:30676ca45084ee61e9c3da589042c24a57592e375d4b138bd84d8709893a1ba4",
-                "sha256:31a55dccc8426e71817e3fe09b37d6d48ae40aae4ecbc8c7ad59d6893569c436",
-                "sha256:366a0cf0fc079af5204801786ad7a1c007714ee3909e364dbac1729f5b0849e5",
-                "sha256:38e2e577f0f092b8e6774459317c05a69935a1755ecfb621c0a98f0e3c09c9a5",
-                "sha256:3c184ad2433635f216645fdf0493011a4667e8d46b34082f5a3de702b6ec42e3",
-                "sha256:3caea6365b13119626ee996711ab63e0c9d7496f65641f4459c60a009a1f3e80",
-                "sha256:3e927b3868bd1e12acee7cc8f3747d815b4ab3e445a28d2e5373a7f4a6e76ba1",
-                "sha256:4ee3ee247f795a69e53cd91d927146fb16c4e803c7ac86c84104940c7d2cabf0",
-                "sha256:54d43960d809c4c12508a60b66cb936e7ed57d51fb5e30b513934a4a23874fae",
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+            "markers": "python_version >= '3.9'",
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-            "version": "==0.11.0"
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         },
         "fonttools": {
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             ],
             "markers": "python_version >= '3.8'",
-            "version": "==4.39.0"
+            "version": "==4.47.0"
         },
         "kiwisolver": {
             "hashes": [
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@@ -484,37 +555,133 @@
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+                "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9",
+                "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d",
+                "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6",
+                "sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867",
+                "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47",
+                "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486",
+                "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6",
+                "sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3",
+                "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007",
+                "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938",
+                "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0",
+                "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c",
+                "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735",
+                "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d",
+                "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28",
+                "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4",
+                "sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba",
+                "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8",
+                "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5",
+                "sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd",
+                "sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3",
+                "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0",
+                "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515",
+                "sha256:baa90d3f661d43131ca170712d903e6295d1f7a0f595074f151c0aed377c9b9c",
+                "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c",
+                "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924",
+                "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34",
+                "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43",
+                "sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859",
+                "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673",
+                "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54",
+                "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a",
+                "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b",
+                "sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab",
+                "sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa",
+                "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c",
+                "sha256:fca0e3a251908a499833aa292323f32437106001d436eca0e6e7833256674585",
+                "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d",
+                "sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==6.0.1"
+        },
+        "setuptools": {
+            "hashes": [
+                "sha256:385eb4edd9c9d5c17540511303e39a147ce2fc04bc55289c322b9e5904fe2c05",
+                "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==69.0.3"
+        },
+        "virtualenv": {
+            "hashes": [
+                "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3",
+                "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==20.25.0"
         }
     }
 }

From ddeb59d025e28cfd0441073133b7c4199b97314e Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 13 Jan 2024 13:54:56 +0800
Subject: [PATCH 02/13] feat(handler): add maximum failed iteration error
 handler

---
 uc_sgsim/exception.py    | 16 ++++++++++++++++
 uc_sgsim/random_field.py |  4 ++++
 uc_sgsim/sgsim.py        |  7 +++++++
 3 files changed, 27 insertions(+)

diff --git a/uc_sgsim/exception.py b/uc_sgsim/exception.py
index a052209..ac19922 100644
--- a/uc_sgsim/exception.py
+++ b/uc_sgsim/exception.py
@@ -8,3 +8,19 @@ class VariogramDoesNotCompute(Exception):
     def __init__(self, message: str = default_message):
         self.message = message
         super().__init__(self.message)
+
+
+class IterationError(Exception):
+    """
+    Raises when the continous failed reach the limit.
+    """
+
+    default_message = (
+        'Maximum continuous failed iterations reached. '
+        + 'Please change the combination of parameters. Or set '
+        + 'higher iteration_limit in sgsim instance.'
+    )
+
+    def __init__(self, message: str = default_message):
+        self.message = message
+        super().__init__(self.message)
diff --git a/uc_sgsim/random_field.py b/uc_sgsim/random_field.py
index c57af16..6bdcde2 100644
--- a/uc_sgsim/random_field.py
+++ b/uc_sgsim/random_field.py
@@ -21,6 +21,8 @@ class RandomField:
         __x_size (int): size of the x axis for the random field.
         __y_size (int): size of the y axis for the random field.
         __realization_number (int): number of realizations to generate.
+        iteration_limit (int): The maximum number for continuous iteration number of
+                               realization error.
 
     Methods:
         _create_grid: create the grid for the random field.
@@ -28,6 +30,8 @@ class RandomField:
         save_variogram: save the variogram data to files.
     """
 
+    iteration_limit = 10
+
     def __init__(self, grid_size: int | list[int, int], realization_number: int):
         """
         Initialize a random field object.
diff --git a/uc_sgsim/sgsim.py b/uc_sgsim/sgsim.py
index 78096bd..5feb2a7 100644
--- a/uc_sgsim/sgsim.py
+++ b/uc_sgsim/sgsim.py
@@ -10,6 +10,7 @@
 from uc_sgsim.random_field import SgsimField
 from uc_sgsim.cov_model.base import CovModel
 from uc_sgsim.utils import CovModelStructure, SgsimStructure
+from .exception import IterationError
 
 BASE_DIR = Path(__file__).resolve().parent
 
@@ -62,6 +63,7 @@ def _process(self, randomseed: int = 0, parallel: bool = False) -> np.array:
         np.random.seed(self.randomseed)
         self.n_process = 1 if parallel is False else self.n_process
         counts = 0
+        iteration_failed = 0
         start_time = time.time()
 
         # Loop for randomfield generation
@@ -96,7 +98,11 @@ def _process(self, randomseed: int = 0, parallel: bool = False) -> np.array:
                 # If any simulated value over the limit than discard that realization
                 if z[sample] >= self.z_max or z[sample] <= self.z_min:
                     drop = True
+                    iteration_failed += 1
+                    if iteration_failed >= self.iteration_limit:
+                        raise IterationError()
                     break
+
                 temp = np.hstack([sample, z[sample]])
                 grid = np.vstack([grid, temp])
 
@@ -111,6 +117,7 @@ def _process(self, randomseed: int = 0, parallel: bool = False) -> np.array:
             if drop is False:
                 self.random_field[counts, :] = z
                 counts = counts + 1
+                iteration_failed = 0
             print('Progress = %.2f' % (counts / self.realization_number * 100) + '%', end='\r')
 
         print('Progress = %.2f' % 100 + '%\n', end='\r')

From 370f06c5d96de799a0cb4c68dccfece5f74fa97b Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 13 Jan 2024 14:22:51 +0800
Subject: [PATCH 03/13] refactor(c): add iteration_limit for c code and add
 parameter in py c structure

---
 c_example.c                     |  1 +
 uc_sgsim/c_core/include/sgsim.h |  1 +
 uc_sgsim/c_core/src/sgsim.c     | 15 +++++++++++++--
 uc_sgsim/sgsim.py               |  1 +
 uc_sgsim/utils.py               |  1 +
 5 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/c_example.c b/c_example.c
index ee1c67e..b469292 100644
--- a/c_example.c
+++ b/c_example.c
@@ -20,6 +20,7 @@ int main() {
         .randomseed = 12345,
         .kriging_method = 1,
         .if_alloc_memory = 1,
+        .iteration_limit = 10,
     };
 
     // you can also set max_negibor at cov_model_t. Defualt value is 4.
diff --git a/uc_sgsim/c_core/include/sgsim.h b/uc_sgsim/c_core/include/sgsim.h
index fc2c300..063a6ae 100644
--- a/uc_sgsim/c_core/include/sgsim.h
+++ b/uc_sgsim/c_core/include/sgsim.h
@@ -28,6 +28,7 @@ typedef struct {
     int randomseed;
     int kriging_method;
     int if_alloc_memory;  // Flag to indicate memory allocation status
+    int iteration_limit;  // The tolerance of maximum times of iteration error
     double* array;  // Array to store the simulated values.
     double z_min;  // Minimum simulated value.
     double z_max;  // Maximum simulated value.
diff --git a/uc_sgsim/c_core/src/sgsim.c b/uc_sgsim/c_core/src/sgsim.c
index 7a68d8c..d94357e 100644
--- a/uc_sgsim/c_core/src/sgsim.c
+++ b/uc_sgsim/c_core/src/sgsim.c
@@ -39,8 +39,11 @@ static double epsilon = 1e-6;
 void set_sgsim_default(sgsim_t* sgsim, cov_model_t* cov_model) {
     set_cov_model_default(cov_model);
     double boundary_val = pow(cov_model->sill, 0.5) * 4;
-    sgsim->z_min = sgsim->z_min < epsilon ? -(boundary_val) : sgsim->z_min;
-    sgsim->z_max = sgsim->z_max < epsilon ? boundary_val : sgsim->z_max;
+
+    sgsim->z_min = fabs(sgsim->z_min) < epsilon ? -(boundary_val) : sgsim->z_min;
+    sgsim->z_max = fabs(sgsim->z_max) < epsilon ? boundary_val : sgsim->z_max;
+    sgsim->iteration_limit = sgsim->iteration_limit == 0 ? 10 : sgsim->iteration_limit;
+
     if (sgsim->if_alloc_memory == 1) {
         unsigned long size = (long)sgsim->x_len * (long)sgsim->realization_numbers;
         sgsim->array = calloc(size, sizeof(double));
@@ -63,6 +66,7 @@ void sgsim_run(sgsim_t* sgsim, cov_model_t* cov_model, int vario_flag) {
     x_grid.data = arange(sgsim->x_len);
     count = 0;
     int use_cov_cache = 0;
+    int error_times = 0;  // The counts of continuosly error
     while (count < sgsim->realization_numbers) {
         printf("Number = %d\n", count);
         _sampling.currlen = 0;
@@ -113,6 +117,13 @@ void sgsim_run(sgsim_t* sgsim, cov_model_t* cov_model, int vario_flag) {
                             sgsim->realization_numbers, count);
             }
             count++;
+            error_times = 0;
+        } else {
+            error_times++;
+            if (error_times == sgsim->iteration_limit) {
+                fprintf(stderr, "Maximum error occurred. Exiting the program...\n");
+                return;
+            }
         }
     }
     kriging_memory_free();
diff --git a/uc_sgsim/sgsim.py b/uc_sgsim/sgsim.py
index 5feb2a7..3e97c0c 100644
--- a/uc_sgsim/sgsim.py
+++ b/uc_sgsim/sgsim.py
@@ -264,6 +264,7 @@ def _cpdll(self, randomseed: int) -> np.array:
             randomseed=randomseed,
             kirging_method=kriging,
             if_alloc_memory=0,
+            max_iteration=self.iteration_limit,
             array=(c_double * (mlen * realization_number))(),
             z_min=self.z_min,
             z_max=self.z_max,
diff --git a/uc_sgsim/utils.py b/uc_sgsim/utils.py
index f6b0d55..dabbb75 100644
--- a/uc_sgsim/utils.py
+++ b/uc_sgsim/utils.py
@@ -69,6 +69,7 @@ class SgsimStructure(Structure):
         ('randomseed', c_int),
         ('kriging_method', c_int),
         ('if_alloc_memory', c_int),
+        ('max_iteration', c_int),
         ('array', POINTER(c_double)),
         ('z_min', c_double),
         ('z_max', c_double),

From 3b7f0cf3f010bcac133e4bf85b40053277a3f911 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 13 Jan 2024 16:47:00 +0800
Subject: [PATCH 04/13] test(limit): add test for iteration limit

---
 tests/uc_sgsim_test.py             | 15 ++++++++++++++-
 uc_sgsim/c_core/tests/sgsim_test.c | 25 +++++++++++++++++++++++++
 uc_sgsim/sgsim.py                  |  9 ++++++++-
 3 files changed, 47 insertions(+), 2 deletions(-)

diff --git a/tests/uc_sgsim_test.py b/tests/uc_sgsim_test.py
index 7ffc893..33758bb 100644
--- a/tests/uc_sgsim_test.py
+++ b/tests/uc_sgsim_test.py
@@ -3,7 +3,7 @@
 import uc_sgsim as uc
 from uc_sgsim.kriging import SimpleKriging
 from uc_sgsim.cov_model import Gaussian, Spherical, Exponential
-from uc_sgsim.exception import VariogramDoesNotCompute
+from uc_sgsim.exception import VariogramDoesNotCompute, IterationError
 import os
 
 
@@ -251,3 +251,16 @@ def test_sgsim_repr(self, capsys):
             == 'SgsimField(151, 10, SimpleKriging, GaussianModel'
             + '(bandwidth_len=35, bandwidth_step=1, k_range=17.32, sill=1, nugget=0))'
         )
+
+    def test_sgsim_reach_iteration_limit(self):
+        sgsim = uc.UCSgsim(
+            self.X,
+            100,
+            self.gaussian,
+            z_max=1,
+            z_min=-1,
+            iteration_limit=3,
+            max_neighbor=12,
+        )
+        with pytest.raises(IterationError):
+            sgsim.compute(n_process=1, randomseed=12312)
diff --git a/uc_sgsim/c_core/tests/sgsim_test.c b/uc_sgsim/c_core/tests/sgsim_test.c
index 929bd2c..252dd3d 100644
--- a/uc_sgsim/c_core/tests/sgsim_test.c
+++ b/uc_sgsim/c_core/tests/sgsim_test.c
@@ -149,6 +149,31 @@ UTEST(test, sgsim_ordinary_kriging_with_cov_cache) {
     sgsim_t_free(&sgsim_example);
 }
 
+UTEST(test, sgsim_max_iteration) {
+    sgsim_t sgsim_example = {
+        .x_len = 75,
+        .realization_numbers = 50,
+        .randomseed = 15,
+        .kriging_method = 1,
+        .if_alloc_memory = 1,
+        .iteration_limit = 3,
+        .z_min = -1,
+        .z_max = 1
+    };
+    cov_model_t cov_example = {
+        .bw_l = 35,
+        .bw_s = 1,
+        .k_range = 12,
+        .use_cov_cache = 1,
+        .sill = 1,
+        .nugget = 0,
+        .max_neighbor = 6
+    };
+
+    sgsim_run(&sgsim_example, &cov_example, 0);
+    sgsim_t_free(&sgsim_example);
+}
+
 UTEST(test, variance) {
     double** arr;
     arr = malloc(20 * sizeof(double));
diff --git a/uc_sgsim/sgsim.py b/uc_sgsim/sgsim.py
index 3e97c0c..f88eabb 100644
--- a/uc_sgsim/sgsim.py
+++ b/uc_sgsim/sgsim.py
@@ -148,7 +148,14 @@ def compute(self, n_process: int, randomseed: int) -> np.array:
         parallel = [True] * n_process
 
         # Start parallel computing
-        z = pool.starmap(self._process, zip(rand_list, parallel))
+        try:
+            z = pool.starmap(self._process, zip(rand_list, parallel))
+        except IterationError:
+            # We should handle the error like this to measure the coverage of sub process
+            pool.close()
+            pool.join()
+            raise IterationError()
+
         pool.close()
         # Use pool.join() to measure the coverage of sub process
         pool.join()

From 83d97980e272633763497ec80bd7b04df1aba9f4 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 13 Jan 2024 17:39:49 +0800
Subject: [PATCH 05/13] build(c_core): update dynamic library

---
 uc_sgsim/c_core/uc_sgsim.dll | Bin 84600 -> 85624 bytes
 uc_sgsim/c_core/uc_sgsim.so  | Bin 37016 -> 37112 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/uc_sgsim/c_core/uc_sgsim.dll b/uc_sgsim/c_core/uc_sgsim.dll
index f3228119b6d1780482710c47031c1a68bf6c86a8..f6f123e2fb071838270242f3858b7425ff53d8e5 100644
GIT binary patch
delta 9146
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diff --git a/uc_sgsim/c_core/uc_sgsim.so b/uc_sgsim/c_core/uc_sgsim.so
index 91099ad2d50a3ec5f63b23dddd1e60425b5b6a00..38b8039ca51dfcee916ee0e0bb42a8ff1aeec5dc 100755
GIT binary patch
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L(b@zy(jWc5fZi4R


From 1c930bc270307ae88a0d0b131b8b2eb6ec27e67b Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Mon, 22 Jan 2024 21:50:01 +0800
Subject: [PATCH 06/13] fix(sgsim): make cov cache flag set to false only when
 the realization is generated correctly

---
 uc_sgsim/sgsim.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/uc_sgsim/sgsim.py b/uc_sgsim/sgsim.py
index f88eabb..7680a83 100644
--- a/uc_sgsim/sgsim.py
+++ b/uc_sgsim/sgsim.py
@@ -108,9 +108,6 @@ def _process(self, randomseed: int = 0, parallel: bool = False) -> np.array:
 
                 if neighbor < self.max_neighbor:
                     neighbor += 1
-
-            # Set cov_cache flag to False to ensure cov_cache only compute once
-            self.kriging._cov_cache_flag = False
             self.randomseed += 1
 
             # IF drop is False then proceed to next realization generation
@@ -118,6 +115,8 @@ def _process(self, randomseed: int = 0, parallel: bool = False) -> np.array:
                 self.random_field[counts, :] = z
                 counts = counts + 1
                 iteration_failed = 0
+                # Set cov_cache flag to False to ensure cov_cache only compute once
+                self.kriging._cov_cache_flag = False
             print('Progress = %.2f' % (counts / self.realization_number * 100) + '%', end='\r')
 
         print('Progress = %.2f' % 100 + '%\n', end='\r')

From 3c5b1a371a1846806bee8404b5cb918fbf23a278 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Mon, 29 Jan 2024 22:21:31 +0800
Subject: [PATCH 07/13] build: add pytest-xdist

---
 Pipfile          |   1 +
 Pipfile.lock     | 283 ++++++++++++++++++++++++++---------------------
 requirements.txt |  81 +++++++++++---
 3 files changed, 218 insertions(+), 147 deletions(-)

diff --git a/Pipfile b/Pipfile
index 1d8424e..d0e24b3 100644
--- a/Pipfile
+++ b/Pipfile
@@ -13,6 +13,7 @@ pre-commit = "*"
 cpplint = "*"
 pytest = "*"
 pytest-cov = "*"
+pytest-xdist = "*"
 
 [requires]
 python_version = "3.11"
diff --git a/Pipfile.lock b/Pipfile.lock
index 11d7020..c84f591 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "eda8515dd3a1ff709bab9b9e956a7b3f71c9b63d652cbca5e2a637b2b71a9954"
+            "sha256": "f0cfe6a62376d2ef7fbb7ba4e0d49c9416742c5a75588cf2f22d85b3f9686486"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -76,51 +76,51 @@
         },
         "fonttools": {
             "hashes": [
-                "sha256:084511482dd265bce6dca24c509894062f0117e4e6869384d853f46c0e6d43be",
-                "sha256:1193fb090061efa2f9e2d8d743ae9850c77b66746a3b32792324cdce65784154",
-                "sha256:174995f7b057e799355b393e97f4f93ef1f2197cbfa945e988d49b2a09ecbce8",
-                "sha256:253bb46bab970e8aae254cebf2ae3db98a4ef6bd034707aa68a239027d2b198d",
-                "sha256:2a78dba8c2a1e9d53a0fb5382979f024200dc86adc46a56cbb668a2249862fda",
-                "sha256:2d2404107626f97a221dc1a65b05396d2bb2ce38e435f64f26ed2369f68675d9",
-                "sha256:40bdbe90b33897d9cc4a39f8e415b0fcdeae4c40a99374b8a4982f127ff5c767",
-                "sha256:495369c660e0c27233e3c572269cbe520f7f4978be675f990f4005937337d391",
-                "sha256:4a9a51745c0439516d947480d4d884fa18bd1458e05b829e482b9269afa655bc",
-                "sha256:511482df31cfea9f697930f61520f6541185fa5eeba2fa760fe72e8eee5af88b",
-                "sha256:52c82df66201f3a90db438d9d7b337c7c98139de598d0728fb99dab9fd0495ca",
-                "sha256:562681188c62c024fe2c611b32e08b8de2afa00c0c4e72bed47c47c318e16d5c",
-                "sha256:59a6c8b71a245800e923cb684a2dc0eac19c56493e2f896218fcf2571ed28984",
-                "sha256:5dde0eab40faaa5476133123f6a622a1cc3ac9b7af45d65690870620323308b4",
-                "sha256:61df4dee5d38ab65b26da8efd62d859a1eef7a34dcbc331299a28e24d04c59a7",
-                "sha256:62d8ddb058b8e87018e5dc26f3258e2c30daad4c87262dfeb0e2617dd84750e6",
-                "sha256:66c92ec7f95fd9732550ebedefcd190a8d81beaa97e89d523a0d17198a8bda4d",
-                "sha256:843509ae9b93db5aaf1a6302085e30bddc1111d31e11d724584818f5b698f500",
-                "sha256:854421e328d47d70aa5abceacbe8eef231961b162c71cbe7ff3f47e235e2e5c5",
-                "sha256:97620c4af36e4c849e52661492e31dc36916df12571cb900d16960ab8e92a980",
-                "sha256:9acfa1cdc479e0dde528b61423855913d949a7f7fe09e276228298fef4589540",
-                "sha256:a77a60315c33393b2bd29d538d1ef026060a63d3a49a9233b779261bad9c3f71",
-                "sha256:b4fabb8cc9422efae1a925160083fdcbab8fdc96a8483441eb7457235df625bd",
-                "sha256:bf1810635c00f7c45d93085611c995fc130009cec5abdc35b327156aa191f982",
-                "sha256:c01f409be619a9a0f5590389e37ccb58b47264939f0e8d58bfa1f3ba07d22671",
-                "sha256:c59227d7ba5b232281c26ae04fac2c73a79ad0e236bca5c44aae904a18f14faf",
-                "sha256:c75e19971209fbbce891ebfd1b10c37320a5a28e8d438861c21d35305aedb81c",
-                "sha256:ce0e2c88c8c985b7b9a7efcd06511fb0a1fe3ddd9a6cd2895ef1dbf9059719d7",
-                "sha256:d6477ba902dd2d7adda7f0fd3bfaeb92885d45993c9e1928c9f28fc3961415f7",
-                "sha256:d986b66ff722ef675b7ee22fbe5947a41f60a61a4da15579d5e276d897fbc7fa",
-                "sha256:dd23848f877c3754f53a4903fb7a593ed100924f9b4bff7d5a4e2e8a7001ae11",
-                "sha256:e3f4d61f3a8195eac784f1d0c16c0a3105382c1b9a74d99ac4ba421da39a8826",
-                "sha256:e6b968543fde4119231c12c2a953dcf83349590ca631ba8216a8edf9cd4d36a9",
-                "sha256:e77bdf52185bdaf63d39f3e1ac3212e6cfa3ab07d509b94557a8902ce9c13c82",
-                "sha256:e79f1a3970d25f692bbb8c8c2637e621a66c0d60c109ab48d4a160f50856deff",
-                "sha256:e7a0a8848726956e9d9fb18c977a279013daadf0cbb6725d2015a6dd57527992",
-                "sha256:e869da810ae35afb3019baa0d0306cdbab4760a54909c89ad8904fa629991812",
-                "sha256:e8acf6dd0434b211b3bd30d572d9e019831aae17a54016629fa8224783b22df8",
-                "sha256:e8fa20748de55d0021f83754b371432dca0439e02847962fc4c42a0e444c2d78",
-                "sha256:ea592e6a09b71cb7a7661dd93ac0b877a6228e2d677ebacbad0a4d118494c86d",
-                "sha256:ec13a10715eef0e031858c1c23bfaee6cba02b97558e4a7bfa089dba4a8c2ebf",
-                "sha256:f4da089f6dfdb822293bde576916492cd708c37c2501c3651adde39804630538"
+                "sha256:0255dbc128fee75fb9be364806b940ed450dd6838672a150d501ee86523ac61e",
+                "sha256:0a00bd0e68e88987dcc047ea31c26d40a3c61185153b03457956a87e39d43c37",
+                "sha256:0a1d313a415eaaba2b35d6cd33536560deeebd2ed758b9bfb89ab5d97dc5deac",
+                "sha256:0f750037e02beb8b3569fbff701a572e62a685d2a0e840d75816592280e5feae",
+                "sha256:13819db8445a0cec8c3ff5f243af6418ab19175072a9a92f6cc8ca7d1452754b",
+                "sha256:254d9a6f7be00212bf0c3159e0a420eb19c63793b2c05e049eb337f3023c5ecc",
+                "sha256:29495d6d109cdbabe73cfb6f419ce67080c3ef9ea1e08d5750240fd4b0c4763b",
+                "sha256:32ab2e9702dff0dd4510c7bb958f265a8d3dd5c0e2547e7b5f7a3df4979abb07",
+                "sha256:3480eeb52770ff75140fe7d9a2ec33fb67b07efea0ab5129c7e0c6a639c40c70",
+                "sha256:3a808f3c1d1df1f5bf39be869b6e0c263570cdafb5bdb2df66087733f566ea71",
+                "sha256:3b629108351d25512d4ea1a8393a2dba325b7b7d7308116b605ea3f8e1be88df",
+                "sha256:3d71606c9321f6701642bd4746f99b6089e53d7e9817fc6b964e90d9c5f0ecc6",
+                "sha256:3e2b95dce2ead58fb12524d0ca7d63a63459dd489e7e5838c3cd53557f8933e1",
+                "sha256:4a5a5318ba5365d992666ac4fe35365f93004109d18858a3e18ae46f67907670",
+                "sha256:4c811d3c73b6abac275babb8aa439206288f56fdb2c6f8835e3d7b70de8937a7",
+                "sha256:4e743935139aa485fe3253fc33fe467eab6ea42583fa681223ea3f1a93dd01e6",
+                "sha256:4ec558c543609e71b2275c4894e93493f65d2f41c15fe1d089080c1d0bb4d635",
+                "sha256:5465df494f20a7d01712b072ae3ee9ad2887004701b95cb2cc6dcb9c2c97a899",
+                "sha256:5b60e3afa9635e3dfd3ace2757039593e3bd3cf128be0ddb7a1ff4ac45fa5a50",
+                "sha256:63fbed184979f09a65aa9c88b395ca539c94287ba3a364517698462e13e457c9",
+                "sha256:69731e8bea0578b3c28fdb43dbf95b9386e2d49a399e9a4ad736b8e479b08085",
+                "sha256:6dd58cc03016b281bd2c74c84cdaa6bd3ce54c5a7f47478b7657b930ac3ed8eb",
+                "sha256:740947906590a878a4bde7dd748e85fefa4d470a268b964748403b3ab2aeed6c",
+                "sha256:7df26dd3650e98ca45f1e29883c96a0b9f5bb6af8d632a6a108bc744fa0bd9b3",
+                "sha256:7eb7ad665258fba68fd22228a09f347469d95a97fb88198e133595947a20a184",
+                "sha256:7ee48bd9d6b7e8f66866c9090807e3a4a56cf43ffad48962725a190e0dd774c8",
+                "sha256:86e0427864c6c91cf77f16d1fb9bf1bbf7453e824589e8fb8461b6ee1144f506",
+                "sha256:8f57ecd742545362a0f7186774b2d1c53423ed9ece67689c93a1055b236f638c",
+                "sha256:90f898cdd67f52f18049250a6474185ef6544c91f27a7bee70d87d77a8daf89c",
+                "sha256:94208ea750e3f96e267f394d5588579bb64cc628e321dbb1d4243ffbc291b18b",
+                "sha256:a1c154bb85dc9a4cf145250c88d112d88eb414bad81d4cb524d06258dea1bdc0",
+                "sha256:a5d77479fb885ef38a16a253a2f4096bc3d14e63a56d6246bfdb56365a12b20c",
+                "sha256:a86a5ab2873ed2575d0fcdf1828143cfc6b977ac448e3dc616bb1e3d20efbafa",
+                "sha256:ac71e2e201df041a2891067dc36256755b1229ae167edbdc419b16da78732c2f",
+                "sha256:b3e1304e5f19ca861d86a72218ecce68f391646d85c851742d265787f55457a4",
+                "sha256:b8be28c036b9f186e8c7eaf8a11b42373e7e4949f9e9f370202b9da4c4c3f56c",
+                "sha256:c19044256c44fe299d9a73456aabee4b4d06c6b930287be93b533b4737d70aa1",
+                "sha256:d49ce3ea7b7173faebc5664872243b40cf88814ca3eb135c4a3cdff66af71946",
+                "sha256:e040f905d542362e07e72e03612a6270c33d38281fd573160e1003e43718d68d",
+                "sha256:eabae77a07c41ae0b35184894202305c3ad211a93b2eb53837c2a1143c8bc952",
+                "sha256:f791446ff297fd5f1e2247c188de53c1bfb9dd7f0549eba55b73a3c2087a2703",
+                "sha256:f83a4daef6d2a202acb9bf572958f91cfde5b10c8ee7fb1d09a4c81e5d851fd8"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==4.47.0"
+            "version": "==4.47.2"
         },
         "kiwisolver": {
             "hashes": [
@@ -408,34 +408,34 @@
         },
         "scipy": {
             "hashes": [
-                "sha256:00150c5eae7b610c32589dda259eacc7c4f1665aedf25d921907f4d08a951b1c",
-                "sha256:028eccd22e654b3ea01ee63705681ee79933652b2d8f873e7949898dda6d11b6",
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@@ -455,66 +455,74 @@
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         "cpplint": {
             "hashes": [
@@ -531,6 +539,14 @@
             ],
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+        "execnet": {
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@@ -581,11 +597,11 @@
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@@ -597,11 +613,11 @@
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@@ -611,6 +627,14 @@
             "index": "pypi",
             "version": "==4.1.0"
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@@ -642,6 +666,7 @@
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+                "sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef",
                 "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5",
                 "sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd",
                 "sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3",
diff --git a/requirements.txt b/requirements.txt
index 336bd2c..9b5f296 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,18 +1,63 @@
-attrs==22.2.0
-contourpy==1.0.7
-coverage==7.2.1
-cycler==0.11.0
-fonttools==4.39.0
-iniconfig==2.0.0
-kiwisolver==1.4.4
-matplotlib==3.7.1
-numpy==1.24.2
-packaging==23.0
-Pillow==9.4.0
-pluggy==1.0.0
-pyparsing==3.0.9
-pytest==7.2.2
-pytest-cov==4.0.0
-python-dateutil==2.8.2
-scipy==1.10.1
-six==1.16.0
+-i https://pypi.org/simple
+
+cfgv==3.4.0 ; python_version >= '3.8'
+
+colorama==0.4.6 ; sys_platform == 'win32'
+
+contourpy==1.2.0 ; python_version >= '3.9'
+
+coverage[toml]==7.4.1 ; python_version >= '3.8'
+
+cpplint==1.6.1
+
+cycler==0.12.1 ; python_version >= '3.8'
+
+distlib==0.3.8
+
+execnet==2.0.2 ; python_version >= '3.7'
+
+filelock==3.13.1 ; python_version >= '3.8'
+
+fonttools==4.47.2 ; python_version >= '3.8'
+
+identify==2.5.33 ; python_version >= '3.8'
+
+iniconfig==2.0.0 ; python_version >= '3.7'
+
+kiwisolver==1.4.5 ; python_version >= '3.7'
+
+matplotlib==3.8.2
+
+nodeenv==1.8.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
+
+numpy==1.26.3
+
+packaging==23.2 ; python_version >= '3.7'
+
+pillow==10.2.0 ; python_version >= '3.8'
+
+platformdirs==4.1.0 ; python_version >= '3.8'
+
+pluggy==1.4.0 ; python_version >= '3.8'
+
+pre-commit==3.6.0
+
+pyparsing==3.1.1 ; python_full_version >= '3.6.8'
+
+pytest==8.0.0
+
+pytest-cov==4.1.0
+
+pytest-xdist==3.5.0
+
+python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+
+pyyaml==6.0.1 ; python_version >= '3.6'
+
+scipy==1.12.0
+
+setuptools==69.0.3 ; python_version >= '3.8'
+
+six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+
+virtualenv==20.25.0 ; python_version >= '3.7'

From 4e496f76b523a180251931bea67775c55cabc075 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Mon, 29 Jan 2024 22:21:54 +0800
Subject: [PATCH 08/13] ci(py): use pytest-xdist to run unittest in parallel

---
 .github/workflows/sonarcloud.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
index 1ed79bc..a9eac46 100644
--- a/.github/workflows/sonarcloud.yml
+++ b/.github/workflows/sonarcloud.yml
@@ -33,7 +33,7 @@ jobs:
           fi
       - name: Run tests to generate coverage statistics
         run: |
-          pytest --cov --cov-report xml:py_coverage.xml
+          pytest -n auto --cov --cov-report xml:py_coverage.xml
       - uses: actions/upload-artifact@v3
         with:
           name: python-coverage
@@ -64,7 +64,7 @@ jobs:
           }
       - name: Run tests to generate coverage statistics
         run: |
-          pytest --cov --cov-report xml:py_coverage.xml
+          pytest -n auto --cov --cov-report xml:py_coverage.xml
 
   c_test:
     name: c-unittest

From 06c8580e613b4bd82478c1752edc00862960f922 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 10 Feb 2024 21:47:23 +0800
Subject: [PATCH 09/13] test(sgsim): refactor and add test cases

---
 tests/uc_sgsim_test.py | 532 +++++++++++++++++++++++++++++------------
 1 file changed, 379 insertions(+), 153 deletions(-)

diff --git a/tests/uc_sgsim_test.py b/tests/uc_sgsim_test.py
index 33758bb..3ed22af 100644
--- a/tests/uc_sgsim_test.py
+++ b/tests/uc_sgsim_test.py
@@ -6,21 +6,19 @@
 from uc_sgsim.exception import VariogramDoesNotCompute, IterationError
 import os
 
+X = 151
+nR = 10
+hs = 35
+a = 17.32
+bw = 1
+C0 = 1
+gaussian = Gaussian(hs, bw, a, C0)
+spherical = Spherical(hs, bw, a, C0)
+exponential = Exponential(hs, bw, a, C0)
+
 
 @pytest.mark.sgsim
 class TestUCSgsim:
-    @classmethod
-    def setup_class(cls) -> None:
-        cls.X = 151
-        cls.nR = 10
-        cls.bw = 1
-        cls.hs = 35
-        cls.a = 17.32
-        cls.C0 = 1
-        cls.gaussian = Gaussian(cls.hs, cls.bw, cls.a, cls.C0)
-        cls.spherical = Spherical(cls.hs, cls.bw, cls.a, cls.C0)
-        cls.exponential = Exponential(cls.hs, cls.bw, cls.a, cls.C0)
-
     def sgsim_plot(self, sgsim: uc.UCSgsim) -> None:
         sgsim.plot()
         sgsim.plot([0, 1, 2])
@@ -41,154 +39,382 @@ def sgsim_save(self, sgsim: uc.UCSgsim) -> None:
         sgsim.save_random_field('randomfield/', save_single=False)
         sgsim.save_variogram('variogram/', save_single=False)
 
-    def test_uc_sgsim_gaussian_py_single_process(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
-        sgsim.compute(n_process=1, randomseed=454)
-        sgsim.variogram_compute(n_process=1)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_with_params(self):
-        sgsim = uc.UCSgsim(
-            self.X,
-            self.nR,
-            self.gaussian,
-            z_max=3,
-            z_min=-3,
-            max_neigh=6,
-        )
-        sgsim.compute(n_process=1, randomseed=454)
-        sgsim.variogram_compute(n_process=1)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_with_params2(self):
-        sgsim = uc.UCSgsim(
-            self.X,
-            self.nR,
-            self.gaussian,
-            z_max=3,
-            z_min=-3,
-            max_neighbor=12,
-            constant_path=True,
-            cov_cache=True,
-        )
-        sgsim.compute(n_process=1, randomseed=454)
-        sgsim.variogram_compute(n_process=1)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_multi_process(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_nugget_py(self):
-        model = Gaussian(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, self.nR, model)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_o_kriging_single_process(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian, kriging='OrdinaryKriging')
-        sgsim.compute(n_process=1, randomseed=454)
-        sgsim.variogram_compute(n_process=1)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_o_kriging_single_process_with_kwargs(self):
-        sgsim = uc.UCSgsim(
-            self.X,
-            self.nR,
-            self.gaussian,
-            kriging='OrdinaryKriging',
-            constant_path=True,
-            cov_cache=True,
-        )
-        sgsim.compute(n_process=1, randomseed=454)
-        sgsim.variogram_compute(n_process=1)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_py_o_kriging_multi_process(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian, kriging='OrdinaryKriging')
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_o_kriging_nugget_py(self):
-        model = Gaussian(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, self.nR, model, kriging='OrdinaryKriging')
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_spherical_py(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.spherical)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_spherical_nugget_py(self):
-        model = Spherical(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, self.nR, model)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_exponential_py(self):
-        sgsim = uc.UCSgsim(self.X, self.nR, self.exponential)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_exponential_nugget_py(self):
-        model = Exponential(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, self.nR, model)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
-        self.sgsim_plot(sgsim)
-        self.sgsim_save(sgsim)
-
-    def test_uc_sgsim_gaussian_c(self):
-        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian)
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
+    @pytest.mark.parametrize(
+        'kriging, cov_model, n_process, kwargs',
+        [
+            ('SimpleKriging', gaussian, 1, {}),
+            ('SimpleKriging', exponential, 1, {}),
+            ('SimpleKriging', spherical, 1, {}),
+            ('SimpleKriging', gaussian, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', exponential, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', spherical, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'SimpleKriging',
+                gaussian,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                exponential,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                spherical,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('SimpleKriging', gaussian, 2, {}),
+            ('SimpleKriging', exponential, 2, {}),
+            ('SimpleKriging', spherical, 2, {}),
+            ('SimpleKriging', gaussian, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', exponential, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', spherical, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'SimpleKriging',
+                gaussian,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                spherical,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                exponential,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('OrdinaryKriging', gaussian, 1, {}),
+            ('OrdinaryKriging', exponential, 1, {}),
+            ('OrdinaryKriging', spherical, 1, {}),
+            ('OrdinaryKriging', gaussian, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            ('OrdinaryKriging', exponential, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            ('OrdinaryKriging', spherical, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            (
+                'OrdinaryKriging',
+                gaussian,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                exponential,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                spherical,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('OrdinaryKriging', gaussian, 2, {}),
+            ('OrdinaryKriging', exponential, 2, {}),
+            ('OrdinaryKriging', spherical, 2, {}),
+            ('OrdinaryKriging', gaussian, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('OrdinaryKriging', exponential, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('OrdinaryKriging', spherical, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'OrdinaryKriging',
+                gaussian,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                exponential,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                spherical,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+        ],
+    )
+    def test_uc_sgsim_gaussian_py(self, kriging, cov_model, n_process, kwargs):
+        sgsim = uc.UCSgsim(X, nR, cov_model, kriging=kriging, **kwargs)
+        sgsim.compute(n_process=n_process, randomseed=454)
+        sgsim.variogram_compute(n_process=n_process)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
-    def test_uc_sgsim_gaussian_ordinary_kriging_c(self):
-        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian, kriging='OrdinaryKriging')
-        sgsim.compute(n_process=2, randomseed=454)
-        sgsim.variogram_compute(n_process=2)
+    @pytest.mark.parametrize(
+        'kriging, cov_model, n_process, kwargs',
+        [
+            ('SimpleKriging', gaussian, 1, {}),
+            ('SimpleKriging', exponential, 1, {}),
+            ('SimpleKriging', spherical, 1, {}),
+            ('SimpleKriging', gaussian, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', exponential, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', spherical, 1, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'SimpleKriging',
+                gaussian,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                exponential,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                spherical,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('SimpleKriging', gaussian, 2, {}),
+            ('SimpleKriging', exponential, 2, {}),
+            ('SimpleKriging', spherical, 2, {}),
+            ('SimpleKriging', gaussian, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', exponential, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('SimpleKriging', spherical, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'SimpleKriging',
+                gaussian,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                spherical,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'SimpleKriging',
+                exponential,
+                2,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('OrdinaryKriging', gaussian, 1, {}),
+            ('OrdinaryKriging', exponential, 1, {}),
+            ('OrdinaryKriging', spherical, 1, {}),
+            ('OrdinaryKriging', gaussian, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            ('OrdinaryKriging', exponential, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            ('OrdinaryKriging', spherical, 1, {'z_max': 4, 'z_min': -4, 'max_neighbor': 6}),
+            (
+                'OrdinaryKriging',
+                gaussian,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                exponential,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                spherical,
+                1,
+                {
+                    'z_max': 3,
+                    'z_min': -3,
+                    'max_neighbor': 12,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            ('OrdinaryKriging', gaussian, 2, {}),
+            ('OrdinaryKriging', exponential, 2, {}),
+            ('OrdinaryKriging', spherical, 2, {}),
+            ('OrdinaryKriging', gaussian, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('OrdinaryKriging', exponential, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            ('OrdinaryKriging', spherical, 2, {'z_max': 3, 'z_min': -3, 'max_neighbor': 6}),
+            (
+                'OrdinaryKriging',
+                gaussian,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                exponential,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+            (
+                'OrdinaryKriging',
+                spherical,
+                2,
+                {
+                    'z_max': 4,
+                    'z_min': -4,
+                    'max_neighbor': 8,
+                    'constant_path': True,
+                    'cov_cache': True,
+                },
+            ),
+        ],
+    )
+    def test_uc_sgsim_gaussian_c(self, kriging, cov_model, n_process, kwargs):
+        sgsim = uc.UCSgsimDLL(X, nR, gaussian, kriging=kriging, **kwargs)
+        sgsim.compute(n_process=n_process, randomseed=454)
+        sgsim.variogram_compute(n_process=n_process)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_wrong_kriging_method(self):
         with pytest.raises(TypeError):
             sgsim = uc.UCSgsim(  # noqa
-                self.X,
-                self.nR,
-                self.gaussian,
+                X,
+                nR,
+                gaussian,
                 kriging='wrongKriging',
             )
 
     def test_uc_sgsim_variogram_exception(self):
-        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian)
+        sgsim = uc.UCSgsimDLL(X, nR, gaussian)
         sgsim.compute(n_process=1, randomseed=454)
         with pytest.raises(VariogramDoesNotCompute):
             sgsim.variogram_plot()
 
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
+        sgsim = uc.UCSgsim(X, nR, gaussian)
         sgsim.compute(n_process=1, randomseed=454)
         with pytest.raises(VariogramDoesNotCompute):
             sgsim.variogram_plot()
@@ -198,10 +424,10 @@ def test_uc_sgsim_variogram_exception(self):
     def test_sgsim_plot_params(self):
         import numpy as np
 
-        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
-        vbandwidth = np.arange(0, self.hs, self.bw)
+        sgsim = uc.UCSgsim(X, nR, gaussian)
+        vbandwidth = np.arange(0, hs, bw)
         np.testing.assert_allclose(sgsim.vbandwidth, vbandwidth)
-        assert sgsim.vmodel == self.gaussian
+        assert sgsim.vmodel == gaussian
         assert sgsim.vmodel_name == 'Gaussian'
         assert sgsim.vbandwidth_step == 1
         assert sgsim.vsill == 1
@@ -209,9 +435,9 @@ def test_sgsim_plot_params(self):
 
     def test_get_all_attributes(self):
         sgsim = uc.UCSgsim(
-            self.X,
-            self.nR,
-            self.gaussian,
+            X,
+            nR,
+            gaussian,
             z_max=3,
             z_min=-3,
             max_neighbor=12,
@@ -227,10 +453,10 @@ def test_get_all_attributes(self):
         assert attributes['constant_path'] is True
         assert attributes['cov_cache'] is True
         assert isinstance(attributes['kriging'], SimpleKriging)
-        assert attributes['model'] == self.gaussian
+        assert attributes['model'] == gaussian
 
     def test_sgsim_repr(self, capsys):
-        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian)
+        sgsim = uc.UCSgsimDLL(X, nR, gaussian)
         # Call repr() to get the string representation
         repr_output = repr(sgsim)
         # Print the repr output (optional)
@@ -254,9 +480,9 @@ def test_sgsim_repr(self, capsys):
 
     def test_sgsim_reach_iteration_limit(self):
         sgsim = uc.UCSgsim(
-            self.X,
+            X,
             100,
-            self.gaussian,
+            gaussian,
             z_max=1,
             z_min=-1,
             iteration_limit=3,

From 7b145d989d5132236cb88cc961342c88edefe36f Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Tue, 26 Mar 2024 11:47:23 +0800
Subject: [PATCH 10/13] ci: upgrade the version of ci action

---
 .github/workflows/cmake.yml             |  4 +--
 .github/workflows/codeql.yml            | 10 +++----
 .github/workflows/github-pre-commit.yml |  8 +++---
 .github/workflows/pypi.yml              |  8 +++---
 .github/workflows/sonarcloud.yml        | 38 ++++++++++++-------------
 5 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 6aaca41..f84e5cd 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: sudo apt-get update && sudo apt-get install -y valgrind
 
     - name: Configure CMake
@@ -40,7 +40,7 @@ jobs:
     env:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: build and test
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index be0de57..080bb21 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -38,9 +38,9 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
     - name: Install dependencies
@@ -55,7 +55,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         setup-python-dependencies: false
@@ -70,7 +70,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -83,6 +83,6 @@ jobs:
     #     ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/github-pre-commit.yml b/.github/workflows/github-pre-commit.yml
index daa0c4d..0abf5af 100644
--- a/.github/workflows/github-pre-commit.yml
+++ b/.github/workflows/github-pre-commit.yml
@@ -8,9 +8,9 @@ jobs:
     name: pre-commit
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install dependencies
@@ -18,5 +18,5 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install cpplint
       - name: Checkout
-        uses: actions/checkout@v3
-      - uses: pre-commit/action@v3.0.0
+        uses: actions/checkout@v4
+      - uses: pre-commit/action@v3.0.1
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 53e0ff9..ae352f8 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/') && github.event_name != 'release'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install dependencies
@@ -41,9 +41,9 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install dependencies
diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
index a9eac46..2592723 100644
--- a/.github/workflows/sonarcloud.yml
+++ b/.github/workflows/sonarcloud.yml
@@ -17,11 +17,11 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -34,7 +34,7 @@ jobs:
       - name: Run tests to generate coverage statistics
         run: |
           pytest -n auto --cov --cov-report xml:py_coverage.xml
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: python-coverage
           path: ./py_coverage.xml
@@ -49,11 +49,11 @@ jobs:
         python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -72,18 +72,18 @@ jobs:
     env:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up Python 3.8 for gcovr
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: install gcovr 5.0
         run: |
           pip install gcovr==5.0 # 5.1 is not supported
       - name: Install sonar-scanner and build-wrapper
-        uses: SonarSource/sonarcloud-github-c-cpp@v1
+        uses: SonarSource/sonarcloud-github-c-cpp
       - name: Run build-wrapper
         run: |
           mkdir build
@@ -109,12 +109,12 @@ jobs:
         run: |
           gcovr --sonarqube > c_coverage.xml
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: c-coverage
           path: |
             ./c_coverage.xml
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: c-coverage2
           path: |
@@ -126,7 +126,7 @@ jobs:
     env:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: build and test
@@ -139,13 +139,13 @@ jobs:
     needs: [python_test]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Download artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
       - name: Run sonar-scanner
-        uses: SonarSource/sonarcloud-github-action@master
+        uses: SonarSource/sonarcloud-github-action
         with:
           args: >
             -Dsonar.projectKey=zncl2222_Stochastic_UC_SGSIM_py
@@ -159,7 +159,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN_PY }} # Put the name of your token here
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4.0.1
         with:
           token: ${{secrets.CODECOV_TOKEN}}
           file: py_coverage.xml
@@ -171,13 +171,13 @@ jobs:
     env:
       BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Install sonar-scanner and build-wrapper
-        uses: SonarSource/sonarcloud-github-c-cpp@v2
+        uses: SonarSource/sonarcloud-github-c-cpp
       - name: Download artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
       - name: Run build-wrapper
         run: |
           mkdir build
@@ -196,7 +196,7 @@ jobs:
                         --define sonar.cfamily.build-wrapper-output="${{ env.BUILD_WRAPPER_OUT_DIR }}" \
                         --define sonar.coverageReportPaths=c-coverage/c_coverage.xml \
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4.0.1
         with:
           token: ${{secrets.CODECOV_TOKEN}}
           file: c-coverage2/cover.info

From 7359113025510d0a01b81b8417f036ee6206f8c7 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sat, 8 Jun 2024 22:56:18 +0800
Subject: [PATCH 11/13] ci: build shared library in workflow

---
 .github/workflows/cmake.yml      |  35 ++++++++++++-----------
 .github/workflows/pypi.yml       |  39 ++++++++++++++++++++++++++
 .github/workflows/sonarcloud.yml |  46 +++++++++++++++++++++++++++----
 cmake_build.bat                  |   4 +--
 cmake_build.sh                   |   8 +++---
 uc_sgsim/c_core/uc_sgsim.dll     | Bin 85624 -> 0 bytes
 uc_sgsim/c_core/uc_sgsim.so      | Bin 37112 -> 0 bytes
 7 files changed, 103 insertions(+), 29 deletions(-)
 delete mode 100644 uc_sgsim/c_core/uc_sgsim.dll
 delete mode 100755 uc_sgsim/c_core/uc_sgsim.so

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index f84e5cd..83b688a 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -14,25 +14,24 @@ jobs:
     # You can convert this to a matrix build if you need cross-platform coverage.
     # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v4
-    - run: sudo apt-get update && sudo apt-get install -y valgrind
-
-    - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
-
-    - name: Build
-      # Build your program with the given configuration
-      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
-
-    - name: Test
-      working-directory: ${{github.workspace}}/build
-      # Execute tests defined by the CMake configuration.
-      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: make test && make memcheck
+      - uses: actions/checkout@v4
+      - run: sudo apt-get update && sudo apt-get install -y valgrind
+
+      - name: Configure CMake
+        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+        run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+      - name: Build
+        # Build your program with the given configuration
+        run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+      - name: Test
+        working-directory: ${{github.workspace}}/build
+        # Execute tests defined by the CMake configuration.
+        # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+        run: make test && make memcheck
 
   build_windows:
     name: c-build-windows
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index ae352f8..6e19dfc 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -16,8 +16,32 @@ on:
     types: [published]
 
 jobs:
+  build_shared_library:
+    strategy:
+      matrix:
+        runs-on: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.runs-on }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build DLL & Set file name windows
+        if: matrix.runs-on == 'windows-latest'
+        shell: pwsh
+        run: |
+          .\cmake_build.bat -s
+          echo "filename=uc_sgsim.dll" >> $env:GITHUB_ENV
+      - name: Build Shared Library & Set file name ubuntu
+        if: matrix.runs-on == 'ubuntu-latest'
+        run: |
+          sh ./cmake_build.sh -s
+          echo "filename=uc_sgsim.so" >> "$GITHUB_ENV"
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.runs-on }}-shared-library
+          path: ./uc_sgsim/c_core/${{ env.filename }}
+
   test-release:
     runs-on: ubuntu-latest
+    needs: [build_shared_library]
     if: startsWith(github.ref, 'refs/tags/') && github.event_name != 'release'
     steps:
       - uses: actions/checkout@v4
@@ -29,6 +53,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install build
+      - name: Download All Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+      - run: |
+          mv ./uc_sgsim.dll ./uc_sgsim/c_core
+          mv ./uc_sgsim.so  ./uc_sgsim/c_core
       - name: Build package
         run: python -m build
       - name: Publish distribution to Test PyPI
@@ -39,6 +70,7 @@ jobs:
 
   release-job:
     runs-on: ubuntu-latest
+    needs: [build_shared_library]
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
       - uses: actions/checkout@v4
@@ -50,6 +82,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install build
+      - name: Download All Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+      - run: |
+          mv ./uc_sgsim.dll ./uc_sgsim/c_core
+          mv ./uc_sgsim.so  ./uc_sgsim/c_core
       - name: Build package
         run: python -m build
       - name: Publish distribution to PyPI
diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
index 2592723..5285ce4 100644
--- a/.github/workflows/sonarcloud.yml
+++ b/.github/workflows/sonarcloud.yml
@@ -7,10 +7,33 @@ on:
     types: [opened, synchronize, reopened]
 
 jobs:
+  build_shared_library:
+    strategy:
+      matrix:
+        runs-on: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.runs-on }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build DLL & Set file name windows
+        if: matrix.runs-on == 'windows-latest'
+        shell: pwsh
+        run: |
+          .\cmake_build.bat -s
+          echo "filename=uc_sgsim.dll" >> $env:GITHUB_ENV
+      - name: Build Shared Library & Set file name ubuntu
+        if: matrix.runs-on == 'ubuntu-latest'
+        run: |
+          sh ./cmake_build.sh -s
+          echo "filename=uc_sgsim.so" >> "$GITHUB_ENV"
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.runs-on }}-shared-library
+          path: ./uc_sgsim/c_core/${{ env.filename }}
+
   python_test:
     name: py-unittest
     runs-on: ubuntu-latest
-
+    needs: build_shared_library
     strategy:
       max-parallel: 5
       matrix:
@@ -31,10 +54,17 @@ jobs:
           if [ -f requirements.txt ];
           then pip install -r requirements.txt;
           fi
+      - name: Download All Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+      - run: |
+          mv ./uc_sgsim.so ./uc_sgsim/c_core
       - name: Run tests to generate coverage statistics
         run: |
           pytest -n auto --cov --cov-report xml:py_coverage.xml
       - uses: actions/upload-artifact@v4
+        if: matrix.python-version  == '3.11'
         with:
           name: python-coverage
           path: ./py_coverage.xml
@@ -42,7 +72,7 @@ jobs:
   python_test_windows:
     name: py-unittest-windows
     runs-on: windows-latest
-
+    needs: build_shared_library
     strategy:
       max-parallel: 5
       matrix:
@@ -62,6 +92,12 @@ jobs:
             pip install --upgrade pip
             pip install -r requirements.txt
           }
+      - name: Download All Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+      - run: |
+          mv ./uc_sgsim.dll ./uc_sgsim/c_core
       - name: Run tests to generate coverage statistics
         run: |
           pytest -n auto --cov --cov-report xml:py_coverage.xml
@@ -83,7 +119,7 @@ jobs:
         run: |
           pip install gcovr==5.0 # 5.1 is not supported
       - name: Install sonar-scanner and build-wrapper
-        uses: SonarSource/sonarcloud-github-c-cpp
+        uses: SonarSource/sonarcloud-github-c-cpp@v2
       - name: Run build-wrapper
         run: |
           mkdir build
@@ -145,7 +181,7 @@ jobs:
       - name: Download artifacts
         uses: actions/download-artifact@v4
       - name: Run sonar-scanner
-        uses: SonarSource/sonarcloud-github-action
+        uses: SonarSource/sonarcloud-github-action@master
         with:
           args: >
             -Dsonar.projectKey=zncl2222_Stochastic_UC_SGSIM_py
@@ -175,7 +211,7 @@ jobs:
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Install sonar-scanner and build-wrapper
-        uses: SonarSource/sonarcloud-github-c-cpp
+        uses: SonarSource/sonarcloud-github-c-cpp@v2
       - name: Download artifacts
         uses: actions/download-artifact@v4
       - name: Run build-wrapper
diff --git a/cmake_build.bat b/cmake_build.bat
index 751ce46..de646a5 100644
--- a/cmake_build.bat
+++ b/cmake_build.bat
@@ -5,12 +5,12 @@ cd cbuild
 
 IF /I "%1"=="-s" (
   cmake -DIS_EXECUTE=OFF -G "MinGW Makefiles" ..
+  make
+  %~dp0cbuild/c_example.exe
 ) ELSE (
   cmake -DIS_EXECUTE=ON -G "MinGW Makefiles" ..
 )
 
-make
-%~dp0cbuild/c_example.exe
 cd ..
 
 exit /b 0
diff --git a/cmake_build.sh b/cmake_build.sh
index f276452..9fd8188 100644
--- a/cmake_build.sh
+++ b/cmake_build.sh
@@ -20,11 +20,11 @@ cd cmake_build
 if [ "$is_execute" = true ]; then
     echo "Compile the code into an executable file !"
     cmake -DIS_EXECUTE=ON ..
+    make
+    make test
+    make memcheck
 else
     echo "Compile the code into a shared library (dynamic library) !"
     cmake -DIS_EXECUTE=OFF ..
+    make
 fi
-
-make
-make test
-make memcheck
diff --git a/uc_sgsim/c_core/uc_sgsim.dll b/uc_sgsim/c_core/uc_sgsim.dll
deleted file mode 100644
index f6f123e2fb071838270242f3858b7425ff53d8e5..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 8bf3e050f5f4e93475c95fb15ceee9e983b14903 Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sun, 9 Jun 2024 15:46:22 +0800
Subject: [PATCH 12/13] refactor: use submodule to manage c_array_tools

---
 .gitignore                             |   2 +
 .gitmodules                            |   4 +
 uc_sgsim/c_core/CMakeLists.txt         |   4 +-
 uc_sgsim/c_core/c_array_tools          |   1 +
 uc_sgsim/c_core/include/kriging.h      |   2 +-
 uc_sgsim/c_core/include/random_tools.h |   2 +-
 uc_sgsim/c_core/include/sgsim.h        |   2 +-
 uc_sgsim/c_core/lib/c_array.c          | 159 -------
 uc_sgsim/c_core/lib/c_array.h          | 624 -------------------------
 uc_sgsim/c_core/lib/c_array_mt.c       | 113 -----
 uc_sgsim/c_core/src/kriging.c          |   8 +-
 uc_sgsim/c_core/src/matrix_tools.c     |   2 +-
 uc_sgsim/c_core/src/random_tools.c     |   2 +-
 uc_sgsim/c_core/src/sgsim.c            |   2 +-
 uc_sgsim/c_core/src/variogram.c        |   2 +-
 15 files changed, 20 insertions(+), 909 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 uc_sgsim/c_core/c_array_tools
 delete mode 100644 uc_sgsim/c_core/lib/c_array.c
 delete mode 100644 uc_sgsim/c_core/lib/c_array.h
 delete mode 100644 uc_sgsim/c_core/lib/c_array_mt.c

diff --git a/.gitignore b/.gitignore
index ea5438b..63c3779 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,5 @@ variogram*
 .coverage
 *.o
 *.exe
+*.so
+*.dll
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..6162ea5
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,4 @@
+[submodule "uc_sgsim/c_core/c_array_tools"]
+	path = uc_sgsim/c_core/c_array_tools
+	url = https://github.com/Zncl2222/c_array_tools.git
+	branch = main
diff --git a/uc_sgsim/c_core/CMakeLists.txt b/uc_sgsim/c_core/CMakeLists.txt
index d68b37c..52c2949 100644
--- a/uc_sgsim/c_core/CMakeLists.txt
+++ b/uc_sgsim/c_core/CMakeLists.txt
@@ -19,8 +19,8 @@ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
 # Link each file
 add_library(
     uc_sgsim ${LIB_TYPE}
-    lib/c_array.c
-    lib/c_array_mt.c
+    c_array_tools/src/c_array.c
+    c_array_tools/src/c_array_mt.c
     src/cov_model.c
     src/kriging.c
     src/matrix_tools.c
diff --git a/uc_sgsim/c_core/c_array_tools b/uc_sgsim/c_core/c_array_tools
new file mode 160000
index 0000000..f9e570c
--- /dev/null
+++ b/uc_sgsim/c_core/c_array_tools
@@ -0,0 +1 @@
+Subproject commit f9e570c8ecf5a41f296adf749d8a413098bec8d0
diff --git a/uc_sgsim/c_core/include/kriging.h b/uc_sgsim/c_core/include/kriging.h
index d6d7f4d..cad36cb 100644
--- a/uc_sgsim/c_core/include/kriging.h
+++ b/uc_sgsim/c_core/include/kriging.h
@@ -12,7 +12,7 @@
 #ifndef UC_SGSIM_C_CORE_INCLUDE_KRIGING_H_
 #define UC_SGSIM_C_CORE_INCLUDE_KRIGING_H_
 
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 # include "../include/cov_model.h"
 
 /**
diff --git a/uc_sgsim/c_core/include/random_tools.h b/uc_sgsim/c_core/include/random_tools.h
index 04fdfa2..ebcbc5d 100644
--- a/uc_sgsim/c_core/include/random_tools.h
+++ b/uc_sgsim/c_core/include/random_tools.h
@@ -13,7 +13,7 @@
 #ifndef UC_SGSIM_C_CORE_INCLUDE_RANDOM_TOOLS_H_
 #define UC_SGSIM_C_CORE_INCLUDE_RANDOM_TOOLS_H_
 
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 /**
  * @brief Generate a random path of integers.
diff --git a/uc_sgsim/c_core/include/sgsim.h b/uc_sgsim/c_core/include/sgsim.h
index 063a6ae..61834a5 100644
--- a/uc_sgsim/c_core/include/sgsim.h
+++ b/uc_sgsim/c_core/include/sgsim.h
@@ -13,7 +13,7 @@
 #define UC_SGSIM_C_CORE_INCLUDE_SGSIM_H_
 
 # include "cov_model.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 /**
  * @struct sgsim_t
diff --git a/uc_sgsim/c_core/lib/c_array.c b/uc_sgsim/c_core/lib/c_array.c
deleted file mode 100644
index 72c10cc..0000000
--- a/uc_sgsim/c_core/lib/c_array.c
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
-    Copyright (c) 2022 Jian Yu, Chen
-    License: MIT License
-    Version: v1.3.2
-    file   : c_array.c
-
-    The latest version is avaliable at:
-    https://github.com/Zncl2222/c_array_tools
-*/
-
-# include "c_array.h"
-
-/*            This is an implementation of c_array extension            */
-// -----------------------------------------------------------------------
-/*                          Array Min and Max                           */
-
-int c_array_max_int(int* arr, int size) {
-    c_array_maxmin_process(arr, size, "max")
-}
-
-long long c_array_max_long_long(long long* arr, int size) {
-    c_array_maxmin_process(arr, size, "max")
-}
-
-float c_array_max_float(float* arr, int size) {
-    c_array_maxmin_process(arr, size, "max")
-}
-
-double c_array_max_double(double* arr, int size) {
-    c_array_maxmin_process(arr, size, "max")
-}
-
-int c_array_min_int(int* arr, int size) {
-    c_array_maxmin_process(arr, size, "min")
-}
-
-long long c_array_min_long_long(long long* arr, int size) {
-    c_array_maxmin_process(arr, size, "min")
-}
-
-float c_array_min_float(float* arr, int size) {
-    c_array_maxmin_process(arr, size, "min")
-}
-
-double c_array_min_double(double* arr, int size) {
-    c_array_maxmin_process(arr, size, "min")
-}
-
-// -----------------------------------------------------------------------
-/*                     Array standard deviation                         */
-
-var_t c_array_var_int(int* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return (var / size);
-}
-
-var_t c_array_var_long_long(long long* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return (var / size);
-}
-
-var_t c_array_var_float(float* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return (var / size);
-}
-
-var_t c_array_var_double(double* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return (var / size);
-}
-
-std_t c_array_std_int(int* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return sqrt(var / size);
-}
-
-std_t c_array_std_long_long(long long* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return sqrt(var / size);
-}
-
-std_t c_array_std_float(float* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return sqrt(var / size);
-}
-
-std_t c_array_std_double(double* arr, int size, mean_t mean) {
-    c_array_var_process(arr, size, mean)
-    return sqrt(var / size);
-}
-
-// -----------------------------------------------------------------------
-/*                          Array mean value                            */
-
-mean_t c_array_mean_int(int* arr, int size, int sum) {
-    c_array_mean_process(arr, size, sum)
-}
-
-mean_t c_array_mean_long_long(long long* arr, int size, long long sum) {
-    c_array_mean_process(arr, size, sum)
-}
-
-mean_t c_array_mean_float(float* arr, int size, float sum) {
-    c_array_mean_process(arr, size, sum)
-}
-
-mean_t c_array_mean_double(double* arr, int size, double sum) {
-    c_array_mean_process(arr, size, sum)
-}
-
-// -----------------------------------------------------------------------
-/*                              Array Sum                               */
-
-int c_array_sum_int(int* arr, int size) {
-    c_array_sum_process(arr, size)
-}
-
-long long c_array_sum_long(long long* arr, int size) {
-    c_array_sum_process(arr, size)
-}
-
-float c_array_sum_float(float* arr, int size) {
-    c_array_sum_process(arr, size)
-}
-
-double c_array_sum_double(double* arr, int size) {
-    c_array_sum_process(arr, size)
-}
-
-// -----------------------------------------------------------------------
-/*                           Array qsort                                */
-
-int cmpfunc_int(const void * a, const void * b) {
-   return ( *(int*)a - *(int*)b );
-}
-
-int cmpfunc_long(const void * a, const void * b) {
-   return ( *(long long*)a - *(long long*)b );
-}
-
-int cmpfunc_float(const void * a, const void * b) {
-    float ret = *(float*)a - *(float*)b;
-    if(ret > 0){
-        return 1;
-    } else if (ret < 0) {
-        return -1;
-    }
-    return 0;
-}
-
-int cmpfunc_double(const void * a, const void * b) {
-    double ret = *(double*)a - *(double*)b;
-    if(ret > 0){
-        return 1;
-    } else if (ret < 0) {
-        return -1;
-    }
-    return 0;
-}
diff --git a/uc_sgsim/c_core/lib/c_array.h b/uc_sgsim/c_core/lib/c_array.h
deleted file mode 100644
index 7d232af..0000000
--- a/uc_sgsim/c_core/lib/c_array.h
+++ /dev/null
@@ -1,624 +0,0 @@
-/*
-    Copyright (c) 2022 Jian Yu, Chen
-    License: MIT License
-    Version: v1.3.2
-    file   : c_array.h
-
-    The latest version is avaliable at:
-    https://github.com/Zncl2222/c_array_tools
-*/
-
-
-# ifndef C_ARRAY_H
-# define C_ARRAY_H
-
-# include <stdio.h>
-# include <math.h>
-# include <stdlib.h>
-# include <string.h>
-# include <assert.h>
-
-typedef double mean_t;
-typedef double std_t;
-typedef double var_t;
-
-// -----------------------------------------------------------------------
-/*                     Array structure and initialize                   */
-
-# define c_array(T) struct { T* data; size_t size; size_t capacity; }
-
-# define c_array_init(arr, c)                                       \
-    do {                                                            \
-        typeof(*((arr)->data)) x;                                   \
-        (arr)->size = (c);                                          \
-        (arr)->capacity = (c);                                      \
-        (arr)->data = calloc((c), sizeof(x));                       \
-    } while(0)
-
-# define c_array_copy(arr1, arr2)                                                               \
-    do {                                                                                        \
-        char* dtype_arr1 = c_array_dtype(arr1);                                                 \
-        char* dtype_arr2 = c_array_dtype(arr2);                                                 \
-        char* err_msg = "The dtype of two arrays are different";                                \
-        c_array_assert((dtype_arr1 == dtype_arr2), err_msg);                                    \
-        (arr2)->size = (arr1)->size;                                                            \
-        (arr2)->capacity = (arr1)->capacity;                                                    \
-        (arr2)->data = malloc((arr2)->capacity * sizeof(typeof(*(arr2)->data)));                \
-        memcpy((arr2)->data, (arr1)->data, (arr2)->capacity * sizeof(typeof(*(arr2)->data)));   \
-    } while(0)
-
-/* c_array_mt.c is necessary for c_array_randnormal & c_array_rand_range */
-
-# define c_array_randnormal(arr, c, rng_state)                          \
-    do {                                                                \
-        (arr)->size = (c);                                              \
-        (arr)->capacity = (c);                                          \
-        (arr)->data = malloc(sizeof(typeof(*((arr)->data))) * (c));     \
-        for (int i = 0; i < (arr)->size; i++) {                         \
-            (arr)->data[i] = random_normal(rng_state);                  \
-        }                                                               \
-    } while(0)
-
-# define c_array_rand_range(arr, c, rng_function)                       \
-    do {                                                                \
-        (arr)->size = (c);                                              \
-        (arr)->capacity = (c);                                          \
-        (arr)->data = malloc(sizeof(typeof(*((arr)->data))) * (c));     \
-        for (int i = 0; i < (arr)->size; i++) {                         \
-            (arr)->data[i] = rng_function;                              \
-        }                                                               \
-    } while(0)
-
-typedef c_array(int) c_array_int;
-typedef c_array(long long) c_array_long_long;
-typedef c_array(float) c_array_float;
-typedef c_array(double) c_array_double;
-
-// -----------------------------------------------------------------------
-/*                      Array basic operations                          */
-
-# define c_array_capacity(arr) ((arr) ? (arr)->capacity : 0)
-
-# define c_array_size(arr) ((arr) ? (arr)->size : 0)
-
-# define c_array_assign(arr, idx, val)                                   \
-    do {                                                                 \
-        char* err_msg = "Index out of range (size)";                     \
-        c_array_assert((idx < (arr)->size), err_msg);                    \
-        (arr)->data[(idx)] = (val);                                      \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                  Arrary size and attributes settings                 */
-
-# define c_array_byte(arr) (sizeof((arr)->data[0]))
-
-# define c_array_grow(arr)                                                          \
-    do {                                                                            \
-        if((arr)->capacity == 0) {                                                  \
-            (arr)->capacity = 1;                                                    \
-        }                                                                           \
-        (arr)->capacity *= 2;                                                       \
-        void* ptr = realloc((arr)->data, (arr)->capacity * c_array_byte((arr)));    \
-        char* err_msg = "Realloc Failed";                                           \
-        c_array_assert((ptr != NULL), err_msg);                                     \
-        (arr)->data = ptr;                                                          \
-    } while(0)
-
-# define c_array_resize(arr, c)                                             \
-    do {                                                                    \
-        void* ptr = realloc((arr)->data, (c) * c_array_byte((arr)));        \
-        char* err_msg = "Realloc Failed";                                   \
-        c_array_assert((ptr != NULL), err_msg);                             \
-        (arr)->capacity = (c);                                              \
-        (arr)->data = ptr;                                                  \
-    } while(0)
-
-# define c_array_set_size(arr, l)                                       \
-    do {                                                                \
-        char* err_msg = "Size should less than or equal to capacity";   \
-        c_array_assert((l <= (arr)->capacity), err_msg);                \
-        for (int i = (arr)->size; i < (arr)->capacity; i++) {           \
-            (arr)->data[i] = 0;                                         \
-        }                                                               \
-        (arr)->size = (l);                                              \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                  Arrary push_back and pop_back                       */
-
-# define c_array_push_back(arr, val)                             \
-    do {                                                         \
-        if (c_array_capacity((arr)) <= c_array_size((arr))) {    \
-            c_array_grow((arr));                                 \
-        }                                                        \
-        (arr)->data[(arr)->size] = val;                          \
-        (arr)->size++;                                           \
-    } while(0)
-
-# define c_array_pop_back(arr)                          \
-    do {                                                \
-        char* err_msg = "Size should greater than 0";   \
-        c_array_assert(((arr)->size > 0), err_msg);     \
-        (arr)->data[(arr)->size - 1] = 0;               \
-        (arr)->size--;                                  \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                      Arrary insert and remove                        */
-
-# define c_array_moveright(arr, idx)                  \
-    do {                                              \
-        if ((arr)->capacity <= (arr)->size) {         \
-            c_array_grow(arr);                        \
-        }                                             \
-        for(int i = (arr)->size; i > idx; i--) {      \
-            (arr)->data[i] = (arr)->data[i - 1];      \
-        }                                             \
-    } while(0)
-
-# define c_array_moveleft(arr, idx)                         \
-    do {                                                    \
-        for(int i = idx; i < (arr)->size - 1; i++) {        \
-            (arr)->data[i] = (arr)->data[i + 1];            \
-        }                                                   \
-    } while(0)                                              \
-
-# define c_array_insert(arr, idx, val)                  \
-    do {                                                \
-        if ((idx) < (arr)->size) {                      \
-            c_array_moveright((arr), (idx));            \
-            (arr)->data[(idx)] = (val);                 \
-            (arr)->size++;                              \
-        }                                               \
-    } while(0)
-
-# define c_array_remove(arr, idx)                       \
-    do {                                                \
-        char* err_msg = "Size should greater than 0";   \
-        c_array_assert(((arr)->size > 0), err_msg);     \
-        char* err_msg2 = "Index out of range (size)";   \
-        c_array_assert(((arr)->size > idx), err_msg);   \
-        c_array_moveleft(arr, idx);                     \
-        (arr)->size--;                                  \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                       Arrary concatenation                           */
-
-# define c_array_concat(arr1, arr2)                                                 \
-    do {                                                                            \
-        char* err_msg = "The data type of two arrays should be the same";           \
-        c_array_assert((c_array_dtype((arr1)) == c_array_dtype((arr2))), err_msg);  \
-        size_t new_capacity = (arr1)->capacity + (arr2)->capacity;                  \
-        size_t new_size = (arr1)->size + (arr2)->size;                              \
-        if ((arr1)->capacity < new_size) {                                          \
-            c_array_resize(arr1, new_capacity);                                     \
-        }                                                                           \
-        for (int i = 0; i < (arr2)->size; i++) {                                    \
-            (arr1)->data[i + (arr1)->size] = (arr2)->data[i];                       \
-        }                                                                           \
-        (arr1)->size = new_size;                                                    \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                           Array qsort                                */
-
-# define c_array_qsort(arr)                                                                       \
-    do {                                                                                          \
-        qsort((arr)->data, (arr)->size, sizeof(typeof((*(arr)->data))), c_array_qsort_cmp((arr)));\
-    } while(0)
-
-# define c_array_qsort_cmp(arr)                         \
-    _Generic((arr)->data,                               \
-        int*: cmpfunc_int,                              \
-        long long*: cmpfunc_long,                       \
-        float*: cmpfunc_float,                          \
-        double*: cmpfunc_double                         \
-    )
-
-int cmpfunc_int(const void * a, const void * b);
-
-int cmpfunc_long(const void * a, const void * b);
-
-int cmpfunc_float(const void * a, const void * b);
-
-int cmpfunc_double(const void * a, const void * b);
-
-// -----------------------------------------------------------------------
-/*                           Array msort                                */
-
-# define c_array_msort(arr)                                                 \
-    do {                                                                    \
-        int i, j, k, l1, r1, l2, r2;                                        \
-        int curr_size;                                                      \
-        typeof(*(arr)->data) temp[(arr)->size];                             \
-        for (curr_size = 1; curr_size < (arr)->size; curr_size *= 2) {      \
-            l1 = 0;                                                         \
-            k = 0;                                                          \
-            while (l1 + curr_size < (arr)->size) {                          \
-                r1 = l1 + curr_size - 1;                                    \
-                l2 = r1 + 1;                                                \
-                r2 = l2 + curr_size - 1;                                    \
-                if(r2 >= (arr)->size) {                                     \
-                    r2 = (arr)->size - 1;                                   \
-                }                                                           \
-                i = l1;                                                     \
-                j = l2;                                                     \
-                while (i <= r1 && j <= r2) {                                \
-                    if ((arr)->data[i] <= (arr)->data[j]) {                 \
-                        temp[k++] = (arr)->data[i++];                       \
-                    } else {                                                \
-                        temp[k++] = (arr)->data[j++];                       \
-                    }                                                       \
-                }                                                           \
-                while (i <= r1) {                                           \
-                    temp[k++] = (arr)->data[i++];                           \
-                }                                                           \
-                while (j <= r2) {                                           \
-                    temp[k++] = (arr)->data[j++];                           \
-                }                                                           \
-                l1 = r2 + 1;                                                \
-            }                                                               \
-            for (i = l1; k < (arr)->size; i++) {                            \
-                temp[k++] = (arr)->data[i];                                 \
-            }                                                               \
-            for (i = 0; i < (arr)->size; i++) {                             \
-                (arr)->data[i] = temp[i];                                   \
-            }                                                               \
-        }                                                                   \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                              Array Sum                               */
-
-# define c_array_sum(arr)               \
-    _Generic((arr)->data,               \
-        int*: c_array_sum_int,          \
-        long long*: c_array_sum_long,   \
-        float*: c_array_sum_float,      \
-        double*: c_array_sum_double     \
-    )((arr)->data, (arr)->size)
-
-# define c_array_sum_process(arr, size)     \
-    typeof(*(arr)) sum = 0;                 \
-    for (int i = 0; i < size; i++) {        \
-        sum += arr[i];                      \
-    }                                       \
-    return sum;                             \
-
-int c_array_sum_int(int* arr, int size);
-
-long long c_array_sum_long(long long* arr, int size);
-
-float c_array_sum_float(float* arr, int size);
-
-double c_array_sum_double(double* arr, int size);
-
-// -----------------------------------------------------------------------
-/*                          Array mean value                            */
-
-# define c_array_mean(arr)                             \
-    _Generic((arr)->data,                              \
-        int*: c_array_mean_int,                        \
-        long long*: c_array_mean_long_long,            \
-        float*: c_array_mean_float,                    \
-        double*: c_array_mean_double                   \
-    )((arr)->data, (arr)->size, c_array_sum((arr)))
-
-# define c_array_mean_process(arr, size, sum)   \
-    mean_t mean = (mean_t)(sum) / (size);       \
-    return mean;
-
-mean_t c_array_mean_int(int* arr, int size, int sum);
-
-mean_t c_array_mean_long_long(long long* arr, int size, long long sum);
-
-mean_t c_array_mean_float(float* arr, int size, float sum);
-
-mean_t c_array_mean_double(double* arr, int size, double sum);
-
-// -----------------------------------------------------------------------
-/*                     Array standard deviation                         */
-
-# define c_array_std(arr)                           \
-    _Generic((arr)->data,                           \
-        int*: c_array_std_int,                      \
-        long long*: c_array_std_long_long,          \
-        float*: c_array_std_float,                  \
-        double*: c_array_std_double                 \
-    )((arr)->data, (arr)->size, c_array_mean((arr)))
-
-# define c_array_var(arr)                           \
-    _Generic((arr)->data,                           \
-        int*: c_array_var_int,                      \
-        long long*: c_array_var_long_long,          \
-        float*: c_array_var_float,                  \
-        double*: c_array_var_double                 \
-    )((arr)->data, (arr)->size, c_array_mean((arr)))
-
-# define c_array_var_process(arr, size, mean)  \
-    var_t var = 0;                             \
-    for (int i = 0; i < (size); i++) {         \
-        var += pow((arr)[i] - (mean), 2);      \
-    }                                          \
-
-var_t c_array_var_int(int* arr, int size, mean_t mean);
-
-var_t c_array_var_long_long(long long* arr, int size, mean_t mean);
-
-var_t c_array_var_float(float* arr, int size, mean_t mean);
-
-var_t c_array_var_double(double* arr, int size, mean_t mean);
-
-std_t c_array_std_int(int* arr, int size, mean_t mean);
-
-std_t c_array_std_long_long(long long* arr, int size, mean_t mean);
-
-std_t c_array_std_float(float* arr, int size, mean_t mean);
-
-std_t c_array_std_double(double* arr, int size, mean_t mean);
-
-// -----------------------------------------------------------------------
-/*                          Array Min and Max                           */
-
-# define c_array_max(arr)                       \
-    _Generic((arr)->data,                       \
-        int*: c_array_max_int,                  \
-        long long*: c_array_max_long_long,      \
-        float*: c_array_max_float,              \
-        double*: c_array_max_double             \
-    )((arr)->data, (arr)->size)
-
-# define c_array_min(arr)                       \
-    _Generic((arr)->data,                       \
-        int*: c_array_min_int,                  \
-        long long*: c_array_min_long_long,      \
-        float*: c_array_min_float,              \
-        double*: c_array_min_double             \
-    )((arr)->data, (arr)->size)
-
-# define c_array_maxmin_process(arr, n, mode)                               \
-    int odd = (n) & 1;                                                      \
-    typeof(*(arr)) max = -pow(2, (((sizeof(typeof(*(arr)))-  1) * 8)));     \
-    typeof(*(arr)) min = pow(2, (((sizeof(typeof(*(arr)))-  1) * 8))) - 1;  \
-    if (odd) {                                                              \
-        (n)--;                                                              \
-    }                                                                       \
-    typeof(*(arr)) minimum = arr[0];                                        \
-    typeof(*(arr)) maximum = arr[0];                                        \
-    for (int i = 0; i < n; i = i + 2) {                                     \
-        if (arr[i] > arr[i + 1]) {                                          \
-            minimum = arr[i + 1],                                           \
-            maximum = arr[i];                                               \
-        } else {                                                            \
-            minimum = arr[i],                                               \
-            maximum = arr[i + 1];                                           \
-        }                                                                   \
-        if (maximum > max) {                                                \
-            max = maximum;                                                  \
-        }                                                                   \
-        if (minimum < min) {                                                \
-            min = minimum;                                                  \
-        }                                                                   \
-    }                                                                       \
-    if (odd) {                                                              \
-        if (arr[n] > max) {                                                 \
-            max = arr[n];                                                   \
-        }                                                                   \
-        if (arr[n] < min) {                                                 \
-            min = arr[n];                                                   \
-        }                                                                   \
-    }                                                                       \
-    if (mode == "max") {                                                    \
-        return max;                                                         \
-    } else {                                                                \
-        return min;                                                         \
-    }                                                                       \
-
-int c_array_max_int(int* arr, int size);
-
-long long c_array_max_long_long(long long* arr, int size);
-
-float c_array_max_float(float* arr, int size);
-
-double c_array_max_double(double* arr, int size);
-
-int c_array_min_int(int* arr, int size);
-
-long long c_array_min_long_long(long long* arr, int size);
-
-float c_array_min_float(float* arr, int size);
-
-double c_array_min_double(double* arr, int size);
-
-// -----------------------------------------------------------------------
-/*                            Arrary utils                              */
-
-# define c_array_autoformat(arr)   \
-    _Generic((arr).data,           \
-        int*: "%d",                \
-        long long*: "%lld",        \
-        float*: "%f",              \
-        double*: "%lf"             \
-    )
-
-# define c_array_dtype(arr)        \
-    _Generic((arr)->data,          \
-        int*: "int",               \
-        long long*: "long long",   \
-        float*: "float",           \
-        double*: "double"          \
-    )
-
-# define c_array_print(arr)                                         \
-    do {                                                            \
-        printf(#arr);                                               \
-        printf(" = [");                                             \
-        for (int i = 0; i < (arr).size; i++) {                      \
-            if (i < (arr).size - 1) {                               \
-                printf(c_array_autoformat((arr)), (arr).data[i]);   \
-                printf(", ");                                       \
-            } else {                                                \
-                printf(c_array_autoformat((arr)), (arr).data[i]);   \
-            }                                                       \
-        }                                                           \
-        printf("]\n");                                              \
-    } while(0)
-
-# define c_array_printf(arr, format)                    \
-    do {                                                \
-        printf(#arr);                                   \
-        printf(" = [");                                 \
-        for(int i = 0; i < (arr).size; i++) {           \
-            if (i < (arr).size - 1) {                   \
-                printf((format), arr.data[i]);          \
-                printf(", ");                           \
-            } else {                                    \
-                printf((format), arr.data[i]);          \
-            }                                           \
-        }                                               \
-        printf("]\n");                                  \
-    } while(0)
-
-# define c_array_empty(arr) ((arr)->size == 0)
-
-# define c_array_swap(arr, idx1, idx2)                                              \
-    do {                                                                            \
-        char* err_msg = "Index out of range (size)";                                \
-        c_array_assert(((idx1) < (arr)->size && (idx2) < (arr)->size), err_msg);    \
-        typeof(*((arr)->data)) x;                                                   \
-        x = (arr)->data[idx2];                                                      \
-        (arr)->data[idx2] = (arr)->data[idx1];                                      \
-        (arr)->data[idx1] = x;                                                      \
-    } while(0)                                                                      \
-
-# define c_array_reverse(arr)                                                       \
-    do {                                                                            \
-        typeof(*((arr)->data)) x;                                                   \
-        for (int i = 0; i < ((arr)->size / 2); i++) {                               \
-            x = (arr)->data[i];                                                     \
-            (arr)->data[i] = (arr)->data[(arr)->size - 1 - i];                      \
-            (arr)->data[(arr)->size - 1 - i] = x;                                   \
-        }                                                                           \
-    } while(0)
-
-# define c_array_free(arr) (free((arr)->data))
-
-# define c_array_assert(expr, msg)          \
-    do {                                    \
-        if (!(expr)) {                      \
-            printf("Error: %s\n", (msg));   \
-            assert((expr));                 \
-        }                                   \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                  Matrix structure and initialize                     */
-
-# define c_matrix(T) struct { T** data; size_t rows; size_t cols; }
-
-# define c_matrix_init(mat, r, c)                   \
-    do{                                             \
-        typeof(**((mat)->data)) m;                  \
-        typeof(*((mat)->data)) n;                   \
-        (mat)->rows = (r);                          \
-        (mat)->cols = (c);                          \
-        (mat)->data = malloc(r * sizeof(n));        \
-        for (int i = 0; i < (r); i++) {             \
-            (mat)->data[i] = malloc(c * sizeof(m)); \
-        }\
-    } while(0)
-
-typedef c_matrix(int) c_matrix_int;
-typedef c_matrix(long long) c_matrix_long_long;
-typedef c_matrix(float) c_matrix_float;
-typedef c_matrix(double) c_matrix_double;
-
-// -----------------------------------------------------------------------
-/*                       Matrix basic operations                        */
-
-# define c_matrix_rows(mat) ((mat) ? (mat)->rows : 0)
-
-# define c_matrix_cols(mat) ((mat) ? (mat)->cols : 0)
-
-# define c_matrix_assign(mat, row, col, val)                \
-    do {                                                    \
-        char* err_msg = "Index out of range (row)";         \
-        c_array_assert((row < (mat)->rows), err_msg);       \
-        char* err_msg2 = "Index out of range(col)";         \
-        c_array_assert((col < (mat)->cols), err_msg2);      \
-        (mat)->data[row][col] = val;                        \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                            Matrix utils                               */
-
-# define c_matrix_print(mat, format)                        \
-    do {                                                    \
-        printf(#mat);                                       \
-        printf(" =\n   [ ");                                \
-        for (int i = 0; i < (mat).rows; i++) {              \
-            if (i != 0)                                     \
-                printf("     ");                            \
-            printf("[ ");                                   \
-            for(int j = 0; j < (mat).cols; j++) {           \
-                if (j < (mat).cols) {                       \
-                    printf((format), (mat).data[i][j]);     \
-                    printf(", ");                           \
-                } else {                                    \
-                    printf((format), (mat).data[i][j]);     \
-                }                                           \
-            }                                               \
-            printf("]");                                    \
-            if (i < (mat).rows - 1){                        \
-                printf("\n");                               \
-            }                                               \
-        }                                                   \
-        printf(" ]\n");                                     \
-    } while(0)
-
-# define c_matrix_free(mat)                         \
-    do {                                            \
-        for (int i = 0; i < (mat)->rows; i++) {     \
-            free((mat)->data[i]);                   \
-        }                                           \
-        free((mat)->data);                          \
-    } while(0)
-
-// -----------------------------------------------------------------------
-/*                       Random number generator                        */
-
-/*  mt19937 license is declared in c_array_mt.c  */
-# ifndef M_PI
-# define M_PI 3.1415926
-# endif
-
-# define MT_N 624
-# define MT_M 397
-# define MT_MATRIX_A 0x9908b0df
-# define MT_UPPER_MASK 0x80000000
-# define MT_LOWER_MASK 0x7fffffff
-
-typedef struct {
-    unsigned int state[MT_N];
-    int index;
-} mt19937_state;
-
-void mt19937_init(mt19937_state* state, unsigned int seed);
-
-unsigned long mt19937_generate(mt19937_state* state);
-
-float mt19937_get_float(mt19937_state* state);
-
-float mt19937_get_float_range(mt19937_state* state, float m, float n);
-
-double mt19937_get_double(mt19937_state* state);
-
-double mt19937_get_double_range(mt19937_state* state, double m, double n);
-
-int mt19937_get_int32_range(mt19937_state* state, int m, int n);
-
-double mt19937_random_normal(mt19937_state* state);
-
-# endif
diff --git a/uc_sgsim/c_core/lib/c_array_mt.c b/uc_sgsim/c_core/lib/c_array_mt.c
deleted file mode 100644
index de58edf..0000000
--- a/uc_sgsim/c_core/lib/c_array_mt.c
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * Copyright 1996 - 2002, Makoto Matsumoto and Takuji Nishimura,
- * All rights reserved.
- *
- * Copyright 2022, Jian Yu, Chen
- * All rights reserved.
- *
- * -----------------------------------------------------------------------
- * Version: v1.3.2
- * file   : c_array_mt.c
- *
- * The latest version is avaliable at:
- * https://github.com/Zncl2222/c_array_tools
- *
- * -----------------------------------------------------------------------
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *
- * 1. Redistributions of source code must retain the above copyright
- *    notice, this list of conditions and the following disclaimer.
- *
- * 2. Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the distribution.
- *
- * 3. The names of its contributors may not be used to endorse or promote
- *    products derived from this software without specific prior written
- *    permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- */
-
-# include <stdlib.h>
-# include <math.h>
-# include "c_array.h"
-
-
-void mt19937_init(mt19937_state* state, unsigned int seed) {
-    state->state[0] = seed;
-
-    for (int i = 1; i < MT_N; i++) {
-        state->state[i] = (1812433253 * (state->state[i - 1] ^ (state->state[i - 1] >> 30)) + i);
-    }
-
-    state->index = MT_N;
-}
-
-unsigned long mt19937_generate(mt19937_state* state) {
-    if (state->index >= MT_N) {
-        for (int i = 0; i < MT_N - MT_M; i++) {
-            unsigned long x = (state->state[i] & MT_UPPER_MASK) | (state->state[i + 1] & MT_LOWER_MASK);
-            state->state[i] = state->state[i + MT_M] ^ (x >> 1) ^ ((x & 1) * MT_MATRIX_A);
-        }
-
-        for (int i = MT_N - MT_M; i < MT_N-1; i++) {
-            unsigned long x = (state->state[i] & MT_UPPER_MASK) | (state->state[i + 1] & MT_LOWER_MASK);
-            state->state[i] = state->state[i + (MT_M-MT_N)] ^ (x >> 1) ^ ((x & 1) * MT_MATRIX_A);
-        }
-
-        unsigned long x = (state->state[MT_N - 1] & MT_UPPER_MASK) | (state->state[0] & MT_LOWER_MASK);
-        state->state[MT_N - 1] = state->state[MT_M - 1] ^ (x >> 1) ^ ((x & 1) * MT_MATRIX_A);
-
-        state->index = 0;
-    }
-
-    unsigned long y = state->state[state->index++];
-    y ^= (y >> 11);
-    y ^= (y << 7) & 0x9d2c5680;
-    y ^= (y << 15) & 0xefc60000;
-    y ^= (y >> 18);
-
-    return y;
-}
-
-int mt19937_get_int32_range(mt19937_state* state, int m, int n) {
-    return mt19937_generate(state) % (n - m + 1) + m;
-};
-
-float mt19937_get_float(mt19937_state* state) {
-    return (float)mt19937_generate(state) / (float)4294967296.0;
-}
-
-float mt19937_get_float_range(mt19937_state* state, float m, float n) {
-    return ((float)mt19937_generate(state) / (float)4294967296.0) * (n - m) + m;
-}
-
-double mt19937_get_double(mt19937_state* state) {
-    return (double)mt19937_generate(state) / 4294967296.0;
-}
-
-double mt19937_get_double_range(mt19937_state* state, double m, double n) {
-    return ((double)mt19937_generate(state) / 4294967296.0) * (n - m) + m;
-}
-
-double mt19937_random_normal(mt19937_state* state) {
-    double x = mt19937_get_double(state);
-    double y = mt19937_get_double(state);
-    double z = sqrt(-2 * log(x)) * cos(2 * M_PI * y);
-    return z;
-}
diff --git a/uc_sgsim/c_core/src/kriging.c b/uc_sgsim/c_core/src/kriging.c
index 5fd1d75..273e251 100644
--- a/uc_sgsim/c_core/src/kriging.c
+++ b/uc_sgsim/c_core/src/kriging.c
@@ -18,7 +18,7 @@
 # include "../include/cov_model.h"
 # include "../include/matrix_tools.h"
 # include "../include/sort_tools.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 static cov_model_t* model;
 static double k_range;
@@ -118,7 +118,7 @@ void simple_kriging(
     kriging_var = model->sill - kriging_var;
     if (kriging_var < 0)
         kriging_var = 0;
-    fix = mt19937_random_normal(rng_state) * pow(kriging_var, 0.5);
+    fix = random_normal(rng_state) * pow(kriging_var, 0.5);
 
     array[(int)sampling->unsampled_point] = estimation + fix;
 }
@@ -126,7 +126,7 @@ void simple_kriging(
 int find_neighbor(double* array, sampling_state* sampling,
                   mt19937_state* rng_state) {
     if (sampling->neighbor == 0) {
-        array[(int)sampling->unsampled_point] = mt19937_random_normal(rng_state) * model->sill;
+        array[(int)sampling->unsampled_point] = random_normal(rng_state) * model->sill;
         sampling->sampled.data[sampling->idx] = sampling->unsampled_point;
         return 0;
     }
@@ -140,7 +140,7 @@ int find_neighbor(double* array, sampling_state* sampling,
     }
 
     if (close == 0) {
-        array[(int)sampling->unsampled_point] = mt19937_random_normal(rng_state) * model->sill;
+        array[(int)sampling->unsampled_point] = random_normal(rng_state) * model->sill;
         sampling->sampled.data[sampling->idx] = sampling->unsampled_point;
         return 0;
     }
diff --git a/uc_sgsim/c_core/src/matrix_tools.c b/uc_sgsim/c_core/src/matrix_tools.c
index ddf6661..8f677c9 100644
--- a/uc_sgsim/c_core/src/matrix_tools.c
+++ b/uc_sgsim/c_core/src/matrix_tools.c
@@ -16,7 +16,7 @@
 # include <string.h>
 # include <errno.h>
 # include "../include/matrix_tools.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 # ifdef __WIN32__
 # include <io.h>
 # elif defined(__linux__) || defined(__unix__)
diff --git a/uc_sgsim/c_core/src/random_tools.c b/uc_sgsim/c_core/src/random_tools.c
index c5a78d3..ec08c40 100644
--- a/uc_sgsim/c_core/src/random_tools.c
+++ b/uc_sgsim/c_core/src/random_tools.c
@@ -15,7 +15,7 @@
 # include <math.h>
 
 # include "../include/random_tools.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 # ifndef M_PI
 # define M_PI 3.1415926
diff --git a/uc_sgsim/c_core/src/sgsim.c b/uc_sgsim/c_core/src/sgsim.c
index d94357e..c8fa898 100644
--- a/uc_sgsim/c_core/src/sgsim.c
+++ b/uc_sgsim/c_core/src/sgsim.c
@@ -23,7 +23,7 @@
 # include "../include/matrix_tools.h"
 # include "../include/variogram.h"
 # include "../include/sort_tools.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 static c_array_int x_grid;
 static c_array_double u_array;
diff --git a/uc_sgsim/c_core/src/variogram.c b/uc_sgsim/c_core/src/variogram.c
index d2df5ae..a65f6ab 100644
--- a/uc_sgsim/c_core/src/variogram.c
+++ b/uc_sgsim/c_core/src/variogram.c
@@ -16,7 +16,7 @@
 
 # include "../include/variogram.h"
 # include "../include/matrix_tools.h"
-# include "../lib/c_array.h"
+# include "../c_array_tools/src/c_array.h"
 
 void variogram(const double* array, double* v, int mlen, int bw, int bw_s) {
     double z_temp;

From a8b9862c26a3e33ac8815e8503fb3fdbb7edd6ec Mon Sep 17 00:00:00 2001
From: Zncl2222 <3002shinning@gmail.com>
Date: Sun, 9 Jun 2024 16:16:10 +0800
Subject: [PATCH 13/13] ci: pull submoudules before build

---
 .github/workflows/cmake.yml      | 3 +++
 .github/workflows/codeql.yml     | 2 ++
 .github/workflows/pypi.yml       | 2 ++
 .github/workflows/sonarcloud.yml | 8 ++++++++
 4 files changed, 15 insertions(+)

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index 83b688a..c7808e0 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -17,6 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - run: sudo apt-get update && sudo apt-get install -y valgrind
+      - run: git submodule update --init --recursive
 
       - name: Configure CMake
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
@@ -42,6 +43,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: build and test
         run: |
           .\cmake_build.bat
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index 080bb21..d8e7172 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -39,6 +39,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
+    - name: Pull Submodule
+      run: git submodule update --init --recursive
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 6e19dfc..7d362d9 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -23,6 +23,8 @@ jobs:
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: Build DLL & Set file name windows
         if: matrix.runs-on == 'windows-latest'
         shell: pwsh
diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml
index 5285ce4..aad72d2 100644
--- a/.github/workflows/sonarcloud.yml
+++ b/.github/workflows/sonarcloud.yml
@@ -14,6 +14,8 @@ jobs:
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: Build DLL & Set file name windows
         if: matrix.runs-on == 'windows-latest'
         shell: pwsh
@@ -111,6 +113,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: Set up Python 3.8 for gcovr
         uses: actions/setup-python@v5
         with:
@@ -165,6 +169,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: build and test
         run: |
           .\cmake_build.bat
@@ -212,6 +218,8 @@ jobs:
           fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
       - name: Install sonar-scanner and build-wrapper
         uses: SonarSource/sonarcloud-github-c-cpp@v2
+      - name: Pull Submodule
+        run: git submodule update --init --recursive
       - name: Download artifacts
         uses: actions/download-artifact@v4
       - name: Run build-wrapper