Change bec_lib install to bec

Due to some error when testing on the nodes on gitea, the bec_lib package is imported. Now it has been added in the installation as a hack

.gitea/workflows/test.yaml

@@ -20,6 +20,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        python -m pip install bec
         python -m pip install .
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
@@ -32,11 +33,3 @@ jobs:
     - name: Test with pytest
       run: |
         python -m pytest -vv tests
-
-  release-test:
-    needs: [build_test]
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checking that the above worked
-      run: | 
-       echo "🎉 The job was automatically triggered by the success of build_test."

pyproject.toml

@@ -10,7 +10,7 @@ package-dir = {"" = "src"}
 name = "AMBER-ds4ms"
 version = "0.0.4"
 dependencies = [
-  "numpy>=2",
+  "numpy>=1.14",
   "scipy>=1.7",
   "torch>=2",
   "matplotlib>=3.4",

src/AMBER/background.py

@@ -612,11 +612,12 @@ class background():
         Me = self.set_e_design_matrix(mu_)
 
         # Loss function
-        loss = np.zeros(n_epochs, dtype=self.dtype)
+        loss = []#np.zeros(n_epochs, dtype=self.dtype)
-        loss[1] = 1.0
+        old_loss = 2000000
-        k = 1
+        new_loss = 1000000
+        k = 0
 
-        while (np.abs(loss[k] - loss[k-1]) > 1e-3) and (k < n_epochs-1):
+        while (np.abs(old_loss - new_loss) > 1e-3) and (k < n_epochs):
             # Compute A = Y - B by filling the nans with 0s
             A = np.where(np.isnan(Y_r - b_tmp) == True, 0.0, Y_r - b_tmp)
 
@@ -640,17 +641,18 @@ class background():
             b_tmp = self.R_operator(self.b)
 
             # ######################### Compute loss function ##################
-            loss[k] = 0.5 * np.nansum((Y_r - self.X - b_tmp) ** 2) + lambda_ * np.nansum(np.abs(self.X))
+            loss.append(0.5 * np.nansum((Y_r - self.X - b_tmp) ** 2) + lambda_ * np.nansum(np.abs(self.X)))
 
             for e in range(self.E_size):
-                loss[k] += (beta_/2) * np.matmul(self.b[e, :], np.matmul(Lb_lst[e], self.b[e, :].T))
+                loss[-1] += (beta_/2) * np.matmul(self.b[e, :], np.matmul(Lb_lst[e], self.b[e, :].T))
 
-            loss[k] += (mu_ / 2) * np.trace(np.matmul(self.X.T, np.matmul(Le, self.X)))
+            loss[-1] += (mu_ / 2) * np.trace(np.matmul(self.X.T, np.matmul(Le, self.X)))
 
             if verbose:
-                print(" Iteration ", str(k))
+                print(" Iteration ", str(k+1))
-                print(" Loss function: ", loss[k].item())
+                print(" Loss function: ", loss[-1].item())
-
+            old_loss = new_loss
+            new_loss = loss[-1]
             k += 1
 
         # Compute the propagated background